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Sample records for est derived ssr

  1. Analysis of inheritance mode in chrysanthemum using EST-derived SSR markers

    NARCIS (Netherlands)

    Park, Sang Kun; Arens, Paul; Esselink, Danny; Lim, Jin Hee; Shin, Hak Ki

    2015-01-01

    To study the inheritance mode of hexaploid chrysanthemum (random or preferential chromosome pairing), a segregation analysis was carried out using SSR markers derived from chrysanthemum ESTs in the public domain. A total of 248 EST-SSR primer pairs were screened in chrysanthemum cultivars

  2. EST-SSR

    African Journals Online (AJOL)

    user2

    2013-02-27

    Feb 27, 2013 ... databases in silico approaches. The objectives of the present study are: (1) To analyze the distribution and frequency of EST-SSRs in the expressed portion of the radish genome; (2) to develop a comprehensive set of novel EST-SSR markers for radish;. (3) to assess their polymorphism in a set of 48 radish.

  3. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas

    Directory of Open Access Journals (Sweden)

    Li Yujun

    2011-10-01

    Full Text Available Abstract Background Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas, which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. Results In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9% being the most abundant followed by di- (41.2%, tetra- (9.2%, penta- (3.7% and hexa-nucleotide (3.1% repeat types. The top five motifs included AG/CT (26.9%, AAG/CTT (13.5%, AT/TA (10.6%, CCG/CGG (5.8% and AAT/ATT (4.5%. After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30 and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9% and 342 (41.9% primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. Conclusion This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would

  4. An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Rabbi, Ismail Yusuf; Kulembeka, Heneriko Philbert; Masumba, Esther; Marri, Pradeep Reddy; Ferguson, Morag

    2012-07-01

    Cassava (Manihot esculenta Crantz) is one of the most important food security crops in the tropics and increasingly being adopted for agro-industrial processing. Genetic improvement of cassava can be enhanced through marker-assisted breeding. For this, appropriate genomic tools are required to dissect the genetic architecture of economically important traits. Here, a genome-wide SNP-based genetic map of cassava anchored in SSRs is presented. An outbreeder full-sib (F1) family was genotyped on two independent SNP assay platforms: an array of 1,536 SNPs on Illumina's GoldenGate platform was used to genotype a first batch of 60 F1. Of the 1,358 successfully converted SNPs, 600 which were polymorphic in at least one of the parents and was subsequently converted to KBiosciences' KASPar assay platform for genotyping 70 additional F1. High-precision genotyping of 163 informative SSRs using capillary electrophoresis was also carried out. Linkage analysis resulted in a final linkage map of 1,837 centi-Morgans (cM) containing 568 markers (434 SNPs and 134 SSRs) distributed across 19 linkage groups. The average distance between adjacent markers was 3.4 cM. About 94.2% of the mapped SNPs and SSRs have also been localized on scaffolds of version 4.1 assembly of the cassava draft genome sequence. This more saturated genetic linkage map of cassava that combines SSR and SNP markers should find several applications in the improvement of cassava including aligning scaffolds of the cassava genome sequence, genetic analyses of important agro-morphological traits, studying the linkage disequilibrium landscape and comparative genomics.

  5. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.

    Directory of Open Access Journals (Sweden)

    Studer Bruno

    2010-08-01

    Full Text Available Abstract Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST-derived simple sequence repeat (SSR markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM, ranging for individual chromosomes from 70 cM of linkage group (LG 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.

  6. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Yomi

    2012-01-19

    Jan 19, 2012 ... repeats (EST-SSR) markers characterized by new bioinformatic criteria reveal high genetic similarity in sugarcane (Saccharum spp.) breeding lines. Kittipat Ukoskit1*, Penjun Thipmongkolcharoen1 and Prasert Chatwachirawong2. 1Department of Biotechnology, Faculty of Science and Technology, ...

  7. The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris

    Science.gov (United States)

    2011-01-01

    Background Over recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (Phaseolus vulgaris) to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs) in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats), specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the Phaseolus vulgaris EST database. The diversity, degree of transferability and polymorphism of these markers were tested. Results From 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11%) showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the Phaseolus (63.7%), Vigna (25.9%), Glycine (19.8%), Medicago (10.2%), Dipterix (6%) and Arachis (1.8%) genera. The average PIC (Polymorphism Information Content) varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558) population, 24% (76) were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5%) were mapped to 14 linkage groups, resulting in a map length of 1,157 cM. Conclusions A total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of Phaseolus vulgaris. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity was comparable to

  8. Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series.

    Science.gov (United States)

    Blair, Matthew W; Hurtado, Natalia; Chavarro, Carolina M; Muñoz-Torres, Monica C; Giraldo, Martha C; Pedraza, Fabio; Tomkins, Jeff; Wing, Rod

    2011-03-22

    Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants. A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellites; the majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular). Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs) series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC), which averaged 0.310 for polymorphic markers. The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans) have been understudied in comparison to race Nueva

  9. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland; Muylle, Hilde

    2010-01-01

    and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained...

  10. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.).

    Science.gov (United States)

    Qiu, Lijun; Yang, Chun; Tian, Bo; Yang, Jun-Bo; Liu, Aizhong

    2010-12-16

    The castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers. In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic mapping and population structure

  11. SSR mining in oil palm EST database: application in oil palm ...

    Indian Academy of Sciences (India)

    This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) mark- ers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs ...

  12. SSR mining in oil palm EST database: application in oil palm ...

    Indian Academy of Sciences (India)

    This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs.

  13. Novel expressed sequence tag- simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  14. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.

    Directory of Open Access Journals (Sweden)

    Yang Jun-Bo

    2010-12-01

    Full Text Available Abstract Background The castor bean (Ricinus communis L., a monotypic species in the spurge family (Euphorbiaceae, 2n = 20, is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85% in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs provide valuable resources to develop gene-associated SSR markers. Results In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Conclusion Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly

  15. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense

    Directory of Open Access Journals (Sweden)

    Dorado Gabriel

    2008-09-01

    Full Text Available Abstract Background Hordeum chilense, a native South American diploid wild barley, is a potential source of useful genes for cereal breeding. The use of this wild species to increase genetic variation in cereals will be greatly facilitated by marker-assisted selection. Different economically feasible approaches have been undertaken for this wild species with limited direct agricultural use in a search for suitable and cost-effective markers. The availability of Expressed Sequence Tags (EST derived microsatellites or simple sequence repeat (SSR markers, commonly called as EST-SSRs, for barley (Hordeum vulgare represents a promising source to increase the number of genetic markers available for the H. chilense genome. Results All of the 82 barley EST-derived SSR primer pairs tested for transferability to H. chilense amplified products of correct size from this species. Of these 82 barley EST-SSRs, 21 (26% showed polymorphism among H. chilense lines. Identified polymorphic markers were used to test the transferability and polymorphism in other Poaceae family species with the aim of establishing H. chilense phylogenetic relationships. Triticum aestivum-H. chilense addition lines allowed us to determine the chromosomal localizations of EST-SSR markers and confirm conservation of the linkage group. Conclusion From the present study a set of 21 polymorphic EST-SSR markers have been identified to be useful for diversity analysis of H. chilense, related wild barleys like H. murinum, and for wheat marker-assisted introgression breeding. Across-genera transferability of the barley EST-SSR markers has allowed phylogenetic inference within the Triticeae complex.

  16. Development and annotation of perennial Triticeae ESTs and SSR markers.

    Science.gov (United States)

    Bushman, B Shaun; Larson, Steve R; Mott, Ivan W; Cliften, Paul F; Wang, Richard R-C; Chatterton, N Jerry; Hernandez, Alvaro G; Ali, Shahjahan; Kim, Ryan W; Thimmapuram, Jyothi; Gong, George; Liu, Lei; Mikel, Mark A

    2008-10-01

    Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus x L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database (http://titan.biotec.uiuc.edu/triticeae/).

  17. DEVELOPMENT OF EST-SSR MARKERS TO ASSESS GENETIC DIVERSITY OF BROCCOLI AND ITS RELATED SPECIES

    Directory of Open Access Journals (Sweden)

    Nur Kholilatul Izzah

    2017-01-01

    Full Text Available Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.

  18. ESAP plus: a web-based server for EST-SSR marker development.

    Science.gov (United States)

    Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

    2016-12-22

    Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can

  19. Validation of dbEST-SSRs and transferability of some other solanaceous species SSR in ashwagandha [Withania Somnifera (L.) Dunal].

    Science.gov (United States)

    Parmar, Eva K; Fougat, Ranbir S; Patel, Chandni B; Zala, Harshvardhan N; Patel, Mahesh A; Patel, Swati K; Kumar, Sushil

    2015-12-01

    Cross-species transferability and expressed sequence tags (ESTs) in public databases are cost-effective means for developing simple sequence repeats (SSRs) for less-studied species like medicinal plants. In this study, 11 EST-SSR markers developed from 742 available ESTs of Withania Somnifera EST sequences and 95 SSR primer pairs derived from other solanaceous crops (tomato, eggplant, chili, and tobacco) were utilized for their amplification and validation. Out of 11, 10 EST-SSRs showed good amplification quality and produced 13 loci with a product size ranging between 167 and 291 bp. Similarly, of the 95 cross-genera SSR loci assayed, 20 (21 %) markers showed the transferability of 5, 27, 32, and 14.2 % from eggplant, chili, tomato, and tobacco, respectively, to ashwagandha. In toto, these 30 SSR markers reported here will be valuable resources and may be applicable for the analysis of intra- and inter-specific genetic diversity in ashwagandha for which till date no information about SSR is available.

  20. Development of genomic SSR and potential EST-SSR markers in ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    SSR markers in Bupleurum chinense DC. Chun Sui, Jian-He Wei*, Shi-Lin Chen, Huai-Qiong Chen and Cheng-Min Yang. Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences (CAMS) and ...

  1. Characterization and development of EST-SSR markers in sweet potato (Ipomoea batatas (L.) Lam).

    Science.gov (United States)

    Kim, Jin-Hee; Kim, Jun-Hoi; Jo, Won-Sam; Ham, Jeong-Gwan; Chung, Il Kyung; Kim, Kyung-Min

    2016-12-01

    In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.

  2. Development of genomic SSR and potential EST-SSR markers in ...

    African Journals Online (AJOL)

    Nineteen genomic SSR markers were developed using inter-simple sequence repeat (ISSR)- suppression PCR technique in Bupleurum chinense DC., a widely used Chinese medicinal plant. A total of 126 alleles were detected across 22 individual plants of B. chinense DC. f. octoradiatum (Bunge) Shan et Sheh, with an ...

  3. Construction of an EST-SSR-based interspecific transcriptome ...

    Indian Academy of Sciences (India)

    providing natural fibre used in many facets of daily life. The most extensively cultivated cotton species are the allo- .... C for 2min followed by 30 cycles of denaturation at 94. ◦. C for 1min, annealing at 55. ◦. C for .... the SSR analysis protocol on 6% denaturing polyacry- lamide gels at room temperature (Lin et al. 2005). Next,.

  4. Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers.

    Science.gov (United States)

    Wang, M L; Mosjidis, J A; Morris, J B; Dean, R E; Jenkins, T M; Pederson, G A

    2006-06-01

    The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.

  5. Analysis of B-genome derived simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    A study was conducted to investigate the genetic variability between 40 Musa genotypes maintained at the Musa germplasm collection of the International Institute for Tropical Agriculture, Ibadan using nine B-genome derived simple sequence repeat (SSR) markers. The nine primers produced reproducible and discrete ...

  6. SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus.

    Science.gov (United States)

    Poncet, Valérie; Rondeau, Myriam; Tranchant, Christine; Cayrel, Anne; Hamon, Serge; de Kochko, Alexandre; Hamon, Perla

    2006-11-01

    Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST-SSRs) with a motif length of 1-6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST-SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST-SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies.

  7. Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

    Science.gov (United States)

    Awasthi, Praveen; Singh, Ashish; Sheikh, Gulfam; Mahajan, Vidushi; Gupta, Ajai Prakash; Gupta, Suphla; Bedi, Yashbir S; Gandhi, Sumit G

    2017-10-01

    Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.

  8. Development and Characterization of 37 Novel EST-SSR Markers in Pisum sativum (Fabaceae

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    Xiaofeng Zhuang

    2013-01-01

    Full Text Available Premise of the study: Simple sequence repeat markers were developed based on expressed sequence tags (EST-SSR and screened for polymorphism among 23 Pisum sativum individuals to assist development and refinement of pea linkage maps. In particular, the SSR markers were developed to assist in mapping of white mold disease resistance quantitative trait loci. Methods and Results: Primer pairs were designed for 46 SSRs identified in EST contiguous sequences assembled from a 454 pyrosequenced transcriptome of the pea cultivar, ‘LIFTER’. Thirty-seven SSR markers amplified PCR products, of which 11 (30% SSR markers produced polymorphism in 23 individuals, including parents of recombinant inbred lines, with two to four alleles. The observed and expected heterozygosities ranged from 0 to 0.43 and from 0.31 to 0.83, respectively. Conclusions: These EST-SSR markers for pea will be useful for refinement of pea linkage maps, and will likely be useful for comparative mapping of pea and as tools for marker-based pea breeding.

  9. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis for Crossbreeding

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    Yueting Dai

    2017-11-01

    Full Text Available Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu. However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotus eryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.

  10. Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis.

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    Honglin Chen

    Full Text Available The adzuki bean (Vigna angularis (Ohwi Ohwi and Ohashi is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0% as the most abundant motif class, followed by AG/CT (68.4%, AAG/CTT (30.0%, AAAG/CTTT (26.2%, AAAAG/CTTTT (16.1%, and AACGGG/CCCGTT (6.0%. A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.

  11. [Development of new SSR markers from EST of SSH cDNA libraries on rose fragrance].

    Science.gov (United States)

    Yan, Hui-Jun; Zhang, Hao; Xie, Ji-Rong; Li, Shu-Fa; Jian, Hong-Ying; Qiu, Xian-Qin; Wang, Qi-Gang; Wang, Ji-Hua; Tang, Kai-Xue

    2009-09-01

    The new SSR markers of rose related fragrance were developed based on the SSH cDNA libraries of rose floral scent mutant. In this study, 10 EST-SSRs (2.6%) from 391 ESTs in the libraries were identified. Six EST-SSRs primers were designed to sequence flanking SSRs. The primer pairs designed were screened on the wild-type Jinyindao, which has flowers full of pleasant scent, and the mutant-type Wangriqinghuai without perceivable floral scent. Five primer pairs were amplified effectively in Jinyindao and Wangriqinghuai, and 3 were polymorphic between Jinyindao and Wangriqinghuai. Eighteen rose cultivars including fragrant roses and nonfragrant roses were identified by the five prime pairs. These results proved that EST-SSR markers are effective markers to identify the polymorphism of the rose.

  12. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

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    Joanne R Russell

    Full Text Available The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree, which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.

  13. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

    Science.gov (United States)

    Russell, Joanne R; Hedley, Peter E; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.

  14. Development and Characterization of 25 EST-SSR markers in Pinus sylvestris var. mongolica (Pinaceae

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    Pan Fang

    2014-01-01

    Full Text Available Premise of the study: A set of novel expressed sequence tag (EST microsatellite markers was developed in Pinus sylvestris var. mongolica to promote further genetic studies in this species. Methods and Results: One hundred seventy-five EST–simple sequence repeat (SSR primers were designed and synthesized for 31,653 isotigs based on P. tabuliformis EST sequences. The primer pairs were used to identify 25 polymorphic loci in 48 individuals. The number of alleles ranged from two to eight with observed and expected heterozygosity values of 0.0435 to 0.8125 and 0.0430 to 0.7820, respectively. Conclusions: These new polymorphic EST-SSR markers will be useful for assessing genetic diversity, molecular breeding and genetic improvement, and conservation of P. sylvestris var. mongolica.

  15. Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers.

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    Chunling Chen

    Full Text Available Lycium barbarum, commonly known as goji, is important in Chinese herbal medicine and its fruit is a very important agricultural and biological product. However, the molecular mechanism of formation of its fruit and associated medicinal and nutritional components is unexplored. Moreover, this species lacks SSR markers due to lack of genomic and transcriptomic information. In this study, a total of 139,333 unigenes with average length of 1049 bp and N50 of 1579 bp are obtained by trinity assembly from Illumina sequencing reads. A total of 92,498 (66.38% unigenes showed similarities in at least one database including Nr (46.15%, Nt (56.56%, KO (15.56%, Swiss-prot (33.34%, Pfam (33.43%, GO (33.62% and KOG/COG (17.55%. Genes in flavonoid and taurine biosynthesis pathways were found and validated by RT-qPCR. A total of 50,093 EST-SSRs were identified from 38,922 unigenes, and 22,537 EST-SSR primer pairs were designed. Four hundred pairs of SSR markers were randomly selected to validate assembly quality, of which 352 (88% were successful in PCR amplification of genomic DNA from 11 Lycium accessions and 210 produced polymorphisms. The polymorphic loci showed that the genetic similarity of the 11 Lycium accessions ranged from 0.50 to 0.99 and the accessions could be divided into 4 groups. These results will facilitate investigations of the molecular mechanism of formation of L. barbarum fruit and associated medicinal and nutritional components, and will be of value to novel gene discovery and functional genomic studies. The EST-SSR markers will be useful for genetic diversity evaluation, genetic mapping and marker-assisted breeding.

  16. Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability.

    Science.gov (United States)

    Bushman, B Shaun; Larson, Steve R; Tuna, Metin; West, Mark S; Hernandez, Alvaro G; Vullaganti, Deepika; Gong, George; Robins, Joseph G; Jensen, Kevin B; Thimmapuram, Jyothi

    2011-06-01

    Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

  17. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

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    Natalie L. Dillon

    2014-01-01

    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  18. Genetic diversity in the germplasm of black pepper determined by EST-SSR markers.

    Science.gov (United States)

    Wu, B D; Fan, R; Hu, L S; Wu, H S; Hao, C Y

    2016-03-18

    This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the origin of black pepper. The newly developed EST-SSRs are highly valuable resources for the conservation of black pepper germplasm diversity and for black pepper breeding.

  19. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

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    Cherubini Marcello

    2010-10-01

    Full Text Available Abstract Background Expressed Sequence Tags (ESTs are a source of simple sequence repeats (SSRs that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut. Results A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283 were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion We have generated a bin map for oak

  20. Development and Characterization of EST-SSR Markers for the Solidago virgaurea Complex (Asteraceae in the Japanese Archipelago

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    Shota Sakaguchi

    2014-07-01

    Full Text Available Premise of the study: We developed simple sequence repeat (SSR markers from expressed sequence tags (ESTs for the Solidago virgaurea complex, an ecologically and morphologically diverse species complex in the Japanese archipelago, to elucidate population genetic structure and examine taxonomic boundaries. Methods and Results: Utilizing the RNA sequencing data obtained by next-generation sequencing techniques, 15 polymorphic EST-SSR markers with three to 14 alleles were developed, most of which were transferable to different Solidago species native to Eurasia and North America. Conclusions: The EST-SSR markers developed in this study may be useful for elucidating the population structure and taxonomic delimitation of the species complex, as well as for investigating the population genetics and reproductive ecology of Solidago species.

  1. Development of genomic and EST-SSR markers in radish (Raphanus sativus L.)

    OpenAIRE

    Nakatsuji, Ryoichi; Hashida, Tomoko; Matsumoto, Naoko; Tsuro, Masato; Kubo, Nakao; Hirai, Masashi

    2011-01-01

    Radish (Raphanus sativus L.) belongs to Brassicaceae family and is a close relative of Brassica. This species shows a wide morphological diversity, and is an important vegetable especially in Asia. However, molecular research of radish is behind compared to that of Brassica. For example, reports on SSR (simple sequence repeat) markers are limited. Here, we designed 417 radish SSR markers from SSR-enriched genomic libraries and the cDNA data. Of the 256 SSR markers succeeded in PCR, 130 showed...

  2. EST-SSR marker revealed effective over biochemical and morphological scepticism towards identification of specific turmeric (Curcuma longa L.) cultivars.

    Science.gov (United States)

    Sahoo, Ambika; Jena, Sudipta; Kar, Basudeba; Sahoo, Suprava; Ray, Asit; Singh, Subhashree; Joshi, Raj Kumar; Acharya, Laxmikanta; Nayak, Sanghamitra

    2017-05-01

    Turmeric (Curcuma longa L., family Zingiberaceae) is one of the most economically important plants for its use in food, medicine, and cosmetic industries. Cultivar identification is a major constraint in turmeric, owing to high degree of morphological similarity that in turn, affects its commercialization. The present study addresses this constraint, using EST-SSR marker based, molecular identification of 8 elite cultivars and 88 accessions in turmeric. Fifty EST-SSR primers were screened against eight cultivars of turmeric (Suroma, Roma, Lakadong, Megha, Alleppey Supreme, Kedaram, Pratibha, and Suvarna); out of which 11 primers showed polymorphic banding pattern. The polymorphic information content (PIC) of these primers ranged from 0.13 to 0.48. However, only three SSR loci (CSSR 14, CSSR 15, and CSSR 18) gave reproducible unique banding pattern clearly distinguishing the cultivars 'Lakadong' and 'Suvarna' from other cultivars tested. These three unique SSR markers also proved to be effective in identification of 'Lakadong' cultivars when analysed with 88 accessions of turmeric collected from different agro-climatic regions. Furthermore, two identified cultivars (Lakadong and Suvarna) could also be precisely differentiated when analysed and based on phylogenetic tree, with other 94 genotypes of turmeric. The novel SSR markers can be used for identification and authentication of two commercially important turmeric cultivars 'Lakadong' and 'Suvarna'.

  3. Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.

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    Qi Guo

    2017-07-01

    Full Text Available Black locust (Robinia pseudoacacia L. of the family Fabaceae is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-five primers were verified as polymorphic, with clear bands. The polymorphism information content values were 0.033–0.765, the number of alleles per locus ranged from 2 to 10, and the observed and expected heterozygosities were 0.000–0.931 and 0.035–0.810, respectively, indicating a high level of informativeness. Subsequently, 45 polymorphic EST-SSR loci were tested for amplification efficiency, using the verified primers, in an additional nine species of Leguminosae, 23 loci were amplified in more than three species, of which two loci were amplified successfully in all species. These EST-SSR markers provide a valuable tool for investigating the genetic diversity and population structure of R. pseudoacacia, constructing a DNA fingerprint database, performing quantitative trait locus mapping, and preserving genetic information.

  4. Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers.

    Science.gov (United States)

    Hanai, Luiz Ricardo; Santini, Luciane; Camargo, Luis Eduardo Aranha; Fungaro, Maria Helena Pelegrinelli; Gepts, Paul; Tsai, Siu Mui; Vieira, Maria Lucia Carneiro

    2010-01-01

    Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the 'BAT93' x 'Jalo EEP558' cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.

  5. Development of genomic and EST-SSR markers in radish (Raphanus sativus L.)

    Science.gov (United States)

    Nakatsuji, Ryoichi; Hashida, Tomoko; Matsumoto, Naoko; Tsuro, Masato; Kubo, Nakao; Hirai, Masashi

    2011-01-01

    Radish (Raphanus sativus L.) belongs to Brassicaceae family and is a close relative of Brassica. This species shows a wide morphological diversity, and is an important vegetable especially in Asia. However, molecular research of radish is behind compared to that of Brassica. For example, reports on SSR (simple sequence repeat) markers are limited. Here, we designed 417 radish SSR markers from SSR-enriched genomic libraries and the cDNA data. Of the 256 SSR markers succeeded in PCR, 130 showed clear polymorphisms between two radish lines; a rat-tail radish and a Japanese cultivar, ‘Harufuku’. As a test case for evaluation of the present SSRs, we conducted two studies. First, we selected 16 SSRs to calculate polymorphism information contents (PICs) using 16 radish cultivars and four other Brassicaceae species. These markers detected 3–15 alleles (average = 9.6). PIC values ranged from 0.54 to 0.92 (average = 0.78). Second, part of the present SSRs were tested for mapping using our previously-examined mapping population. The map spanned 672.7 cM with nine linkage groups (LGs). The 21 radish SSR markers were distributed throughout the LGs. The SSR markers developed here would be informative and useful for genetic analysis in radish and its related species. PMID:23136479

  6. Transcriptome sequencing of mung bean (Vigna radiate L. genes and the identification of EST-SSR markers.

    Directory of Open Access Journals (Sweden)

    Honglin Chen

    Full Text Available Mung bean (Vigna radiate (L. Wilczek is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0% and 23,235 (47.7% showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5% could be classified into gene ontology categories, 18,316 (37.6% into Swiss-Prot categories and 10,918 (22.4% into KOG database categories (E-value < 1.0E-5. A total of 6,585 (8.3% were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR, and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST. A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%, GAA/TTC (12.6%, AAAT/ATTT (6.8%, AAAAT/ATTTT (6.2% and AAAAAT/ATTTTT (1.9%. A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association

  7. De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers.

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    Yan Long

    Full Text Available Caragana korshinskii Kom. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in Caragana Fabr. genus. In this study, more than two billion bases of high-quality sequence of C. korshinskii were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp. The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%, suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in Fabraceae. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in Caranaga Fabr. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.

  8. Isolation and characterization of twenty-nine novel EST-SSR ...

    Indian Academy of Sciences (India)

    SSR markers ... for S. undulata because of the lack of genomic resources such as genome or transcriptome sequences. Thus, the develop- ..... Unconventional myosin-X-like. 5E-30. M. zebra. XM_004569454.1 are of good practicability and the ...

  9. A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica

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    Ueno Saneyoshi

    2012-04-01

    Full Text Available Abstract Background Microsatellites or simple sequence repeats (SSRs in expressed sequence tags (ESTs are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial second generation sequencing machines has lead to new strategies for developing EST-SSR markers, necessitating the development of bioinformatic framework that can keep pace with the increasing quality and quantity of sequence data produced. We describe an open scheme for analyzing ESTs and developing EST-SSR markers from reads collected by Sanger sequencing and pyrosequencing of sugi (Cryptomeria japonica. Results We collected 141,097 sequence reads by Sanger sequencing and 1,333,444 by pyrosequencing. After trimming contaminant and low quality sequences, 118,319 Sanger and 1,201,150 pyrosequencing reads were passed to the MIRA assembler, generating 81,284 contigs that were analysed for SSRs. 4,059 SSRs were found in 3,694 (4.54% contigs, giving an SSR frequency lower than that in seven other plant species with gene indices (5.4–21.9%. The average GC content of the SSR-containing contigs was 41.55%, compared to 40.23% for all contigs. Tri-SSRs were the most common SSRs; the most common motif was AT, which was found in 655 (46.3% di-SSRs, followed by the AAG motif, found in 342 (25.9% tri-SSRs. Most (72.8% tri-SSRs were in coding regions, but 55.6% of the di-SSRs were in non-coding regions; the AT motif was most abundant in 3′ untranslated regions. Gene ontology (GO annotations showed that six GO terms were significantly overrepresented within SSR-containing contigs. Forty–four EST-SSR markers were developed from 192 primer pairs using two pipelines: read2Marker and the newly-developed CMiB, which combines several open tools. Markers resulting from both pipelines showed no differences in PCR success rate and polymorphisms, but PCR success and polymorphism were significantly affected by the expected PCR product size

  10. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Hinchliffe, Doug J; Turley, Rickie B; Naoumkina, Marina; Kim, Hee Jin; Tang, Yuhong; Yeater, Kathleen M; Li, Ping; Fang, David D

    2011-09-09

    Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (Gossypium hirsutum L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (Li2) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, Li2 is a model system with which to study fiber elongation. Two near-isogenic lines of Ligon lintless-2 (Li2) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC5). An F2 population was developed from a cross between the two Li2 near-isogenic lines and used to develop a linkage map of the Li2 locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the Li2 locus region with two of the markers flanking the Li2 locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS) homeostasis and cytokinin regulation in the Li2 mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the Li2 locus. In the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the Li2 locus on chromosome 18 and resided in a gene with similarity to a

  11. Exploiting Illumina Sequencing for the Development of 95 Novel Polymorphic EST-SSR Markers in Common Vetch (Vicia sativa subsp. sativa

    Directory of Open Access Journals (Sweden)

    Zhipeng Liu

    2014-05-01

    Full Text Available The common vetch (Vicia sativa subsp. sativa, a self-pollinating and diploid species, is one of the most important annual legumes in the world due to its short growth period, high nutritional value, and multiple usages as hay, grain, silage, and green manure. The available simple sequence repeat (SSR markers for common vetch, however, are insufficient to meet the developing demand for genetic and molecular research on this important species. Here, we aimed to develop and characterise several polymorphic EST-SSR markers from the vetch Illumina transcriptome. A total number of 1,071 potential EST-SSR markers were identified from 1025 unigenes whose lengths were greater than 1,000 bp, and 450 primer pairs were then designed and synthesized. Finally, 95 polymorphic primer pairs were developed for the 10 common vetch accessions, which included 50 individuals. Among the 95 EST-SSR markers, the number of alleles ranged from three to 13, and the polymorphism information content values ranged from 0.09 to 0.98. The observed heterozygosity values ranged from 0.00 to 1.00, and the expected heterozygosity values ranged from 0.11 to 0.98. These 95 EST-SSR markers developed from the vetch Illumina transcriptome could greatly promote the development of genetic and molecular breeding studies pertaining to in this species.

  12. High polymorphism in Est-SSR loci for cellulose synthase and β-amylase of sugarcane varieties (Saccharum spp.) used by the industrial sector for ethanol production.

    Science.gov (United States)

    Augusto, Raphael; Maranho, Rone Charles; Mangolin, Claudete Aparecida; Pires da Silva Machado, Maria de Fátima

    2015-01-01

    High and low polymorphisms in simple sequence repeats of expressed sequence tag (EST-SSR) for specific proteins and enzymes, such as β-amylase, cellulose synthase, xyloglucan endotransglucosylase, fructose 1,6-bisphosphate aldolase, and fructose 1,6-bisphosphatase, were used to illustrate the genetic divergence within and between varieties of sugarcane (Saccharum spp.) and to guide the technological paths to optimize ethanol production from lignocellulose biomass. The varieties RB72454, RB867515, RB92579, and SP813250 on the second stage of cutting, all grown in the state of Paraná (PR), and the varieties RB92579 and SP813250 cultured in the PR state and in Northeastern Brazil, state of Pernambuco (PE), were analyzed using five EST-SSR primers for EstC66, EstC67, EstC68, EstC69, and EstC91 loci. Genetic divergence was evident in the EstC67 and EstC69 loci for β-amylase and cellulose synthase, respectively, among the four sugarcane varieties. An extremely high level of genetic differentiation was also detected in the EstC67 locus from the RB82579 and SP813250 varieties cultured in the PR and PE states. High polymorphism in SSR of the cellulose synthase locus may explain the high variability of substrates used in pretreatment and enzymatic hydrolysis processes, which has been an obstacle to effective industrial adaptations.

  13. Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato.

    Science.gov (United States)

    Ohyama, Akio; Shirasawa, Kenta; Matsunaga, Hiroshi; Negoro, Satomi; Miyatake, Koji; Yamaguchi, Hirotaka; Nunome, Tsukasa; Iwata, Hiroyoshi; Fukuoka, Hiroyuki; Hayashi, Takeshi

    2017-08-01

    Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

  14. (SSR) marker development for tomato

    African Journals Online (AJOL)

    -

    2012-09-18

    Sep 18, 2012 ... semi automated and fully automated robotics for liquid handling and genotyping steps. As several of our developed SSR markers were mapped to informative sequences, they are called EST-. SSR putatives. The set of EST-SSR markers would be informative for phylogenetics analysis and genetic mapping.

  15. Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L.

    Science.gov (United States)

    Chand, Subodh Kumar; Nanda, Satyabrata; Rout, Ellojita; Joshi, Raj Kumar

    2015-01-01

    Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.

  16. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

    KAUST Repository

    Singh, Ram K.

    2013-07-01

    Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5\\'UTR and in the ORF (about 27%) and a low frequency was observed in the 3\\'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in

  17. Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations.

    Science.gov (United States)

    Bradbury, Donna; Smithson, Ann; Krauss, Siegfried L

    2013-10-01

    Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian FST outlier tests and allele-climate association analyses to reveal two Eucalyptus EST-SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS-like gene was an FST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second FST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene-homologous EST-SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity. © 2013 John Wiley & Sons Ltd.

  18. Two EST-derived marker systems for cultivar identification in tree peony.

    Science.gov (United States)

    Zhang, J J; Shu, Q Y; Liu, Z A; Ren, H X; Wang, L S; De Keyser, E

    2012-02-01

    Tree peony (Paeonia suffruticosa Andrews), a woody deciduous shrub, belongs to the section Moutan DC. in the genus of Paeonia of the Paeoniaceae family. To increase the efficiency of breeding, two EST-derived marker systems were developed based on a tree peony expressed sequence tag (EST) database. Using target region amplification polymorphism (TRAP), 19 of 39 primer pairs showed good amplification for 56 accessions with amplicons ranging from 120 to 3,000 bp long, among which 99.3% were polymorphic. In contrast, 7 of 21 primer pairs demonstrated adequate amplification with clear bands for simple sequence repeats (SSRs) developed from ESTs, and a total of 33 alleles were found in 56 accessions. The similarity matrices generated by TRAP and EST-SSR markers were compared, and the Mantel test (r = 0.57778, P = 0.0020) showed a moderate correlation between the two types of molecular markers. TRAP markers were suitable for DNA fingerprinting and EST-SSR markers were more appropriate for discriminating synonyms (the same cultivars with different names due to limited information exchanged among different geographic areas). The two sets of EST-derived markers will be used further for genetic linkage map construction and quantitative trait locus detection in tree peony.

  19. Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee based on de novo transcriptomic assemblies.

    Directory of Open Access Journals (Sweden)

    Jingfang Chen

    Full Text Available Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs. From the unigenes, 8,165 EST-SSR loci were identified and 98.57% of them were 1-3 nucleotide repeats with 14.32%, 41.08% and 43.17% of mono-, di- and tri-nucleotide repeats, respectively. Fifty-eight types of motifs were identified with A/T, AG/CT, AT/AT, AC/GT, AAG/CTT and AGG/CCT the most abundant. The lengths of repeated nucleotide sequences in all SSR loci ranged from 12 to 60 bp, with most (88.51% under 20 bp. Among 170 primer pairs were randomly selected from a total of 4,912 SSR primers we designed, 48 yielded unambiguously polymorphic bands with high reproducibility. Cluster analysis using 48 SSRs classified 34 flowering Chinese cabbage cultivars into three groups. A large number of EST-SSR markers identified in this study will facilitate marker-assisted selection in the breeding programs of flowering Chinese cabbage.

  20. Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.).

    Science.gov (United States)

    Fernandez-Silva, I; Eduardo, I; Blanca, J; Esteras, C; Picó, B; Nuez, F; Arús, P; Garcia-Mas, J; Monforte, Antonio José

    2008-12-01

    We report the development of 158 primer pairs flanking SSR motifs in genomic (gSSR) and EST (EST-SSR) melon sequences, all yielding polymorphic bands in melon germplasm, except one that was polymorphic only in Cucurbita species. A similar polymorphism level was found among EST-SSRs and gSSRs, between dimeric and trimeric EST-SSRs, and between EST-SSRs placed in the open reading frame or any of the 5'- or 3'-untranslated regions. Correlation between SSR length and polymorphism was only found for dinucleotide EST-SSRs located within the untranslated regions, but not for trinucleotide EST-SSRs. Transferability of EST-SSRs to Cucurbita species was assayed and 12.7% of the primer pairs amplified at least in one species, although only 5.4% were polymorphic. A set of 14 double haploid lines from the cross between the cultivar "Piel de Sapo" and the accession PI161375 were selected for the bin mapping approach in melon. One hundred and twenty-one SSR markers were newly mapped. The position of 46 SSR loci was also verified by genotyping the complete population. A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density was 4.2 cM/marker or 5.9 cM/SSR.

  1. Assessment of Functional EST-SSR Markers (Sugarcane in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

    Directory of Open Access Journals (Sweden)

    Shamshad Ul Haq

    2016-01-01

    Full Text Available Expressed sequence tags (ESTs are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74% were the most abundant followed by di- (26.10%, tetra- (4.67%, penta- (1.5%, and hexanucleotide (1.2% repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA. Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

  2. (SSR) markers

    African Journals Online (AJOL)

    Yomi

    2012-04-03

    Apr 3, 2012 ... Oilseed rape (Brassica napus L.) is an important oilseed crop worldwide. The objective of this research was to study the genetic diversity and relationships of B. napus accessions using simple sequence repeat (SSR). A set of 217 genotypes was characterized using 37 SSR markers of mapping on the B.

  3. De novo transcriptomic analysis and development of EST-SSR markers in the Siberian tiger (Panthera tigris altaica).

    Science.gov (United States)

    Lu, Taofeng; Sun, Yujiao; Ma, Qin; Zhu, Minghao; Liu, Dan; Ma, Jianzhang; Ma, Yuehui; Chen, Hongyan; Guan, Weijun

    2016-12-01

    The Siberian tiger, Panthera tigris altaica, is an endangered species, and much more work is needed to protect this species, which is still vulnerable to extinction. Conservation efforts may be supported by the genetic assessment of wild populations, for which highly specific microsatellite markers are required. However, only a limited amount of genetic sequence data is available for this species. To identify the genes involved in the lung transcriptome and to develop additional simple sequence repeat (SSR) markers for the Siberian tiger, we used high-throughput RNA-Seq to characterize the Siberian tiger transcriptome in lung tissue (designated 'PTA-lung') and a pooled tissue sample (designated 'PTA'). Approximately 47.5 % (33,187/69,836) of the lung transcriptome was annotated in four public databases (Nr, Swiss-Prot, KEGG, and COG). The annotated genes formed a potential pool for gene identification in the tiger. An analysis of the genes differentially expressed in the PTA lung, and PTA samples revealed that the tiger may have suffered a series of diseases before death. In total, 1062 non-redundant SSRs were identified in the Siberian tiger transcriptome. Forty-three primer pairs were randomly selected for amplification reactions, and 26 of the 43 pairs were also used to evaluate the levels of genetic polymorphism. Fourteen primer pairs (32.56 %) amplified products that were polymorphic in size in P. tigris altaica. In conclusion, the transcriptome sequences will provide a valuable genomic resource for genetic research, and these new SSR markers comprise a reasonable number of loci for the genetic analysis of wild and captive populations of P. tigris altaica.

  4. (SSR) markers

    African Journals Online (AJOL)

    uwerhiavwe

    Variability was observed for six ... rapid increase in climate change, so there is need to develop high yielding ... the past decade including assessment of genetic diversity in maize ... The SSR gel images and marker data were processed using.

  5. Development and Validation of 697 Novel Polymorphic Genomic and EST-SSR Markers in the American Cranberry (Vaccinium macrocarpon Ait.

    Directory of Open Access Journals (Sweden)

    Brandon Schlautman

    2015-01-01

    Full Text Available The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level, and contained moderate to high levels of polymorphism with a polymorphic information content >0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.

  6. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.

    Directory of Open Access Journals (Sweden)

    Li Dejun

    2012-05-01

    Full Text Available Abstract Background In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at least partially due to lack of bark transcriptomic and genomic information. Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development. Results In this study, more than 30 million sequencing reads were generated using Illumina paired-end sequencing technology. In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly. The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 6,867 and 5,559 unigenes were separately assigned to Gene Ontology (GO and Clusters of Orthologous Group (COG. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG database, 12,097 unigenes were assigned to 5 main categories including 123 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (9,043, 74.75%, suggesting the active metabolic processes in rubber tree bark. In addition, a total of 39,257 EST-SSRs were identified from 22,756 unigenes, and the characterizations of EST-SSRs were further analyzed in rubber tree. 110 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among 13 Hevea germplasms, PCR success rate and polymorphism rate of 110 markers were separately 96.36% and 55.45% in this study. Conclusion By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark. This research

  7. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.).

    Science.gov (United States)

    Li, Dejun; Deng, Zhi; Qin, Bi; Liu, Xianghong; Men, Zhonghua

    2012-05-18

    In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at least partially due to lack of bark transcriptomic and genomic information. Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development. In this study, more than 30 million sequencing reads were generated using Illumina paired-end sequencing technology. In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly. The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 6,867 and 5,559 unigenes were separately assigned to Gene Ontology (GO) and Clusters of Orthologous Group (COG). When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 12,097 unigenes were assigned to 5 main categories including 123 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (9,043, 74.75%), suggesting the active metabolic processes in rubber tree bark. In addition, a total of 39,257 EST-SSRs were identified from 22,756 unigenes, and the characterizations of EST-SSRs were further analyzed in rubber tree. 110 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among 13 Hevea germplasms, PCR success rate and polymorphism rate of 110 markers were separately 96.36% and 55.45% in this study. By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark. This research generated a substantial fraction of rubber tree transcriptome

  8. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

    NARCIS (Netherlands)

    Durand, J.; Bodénès, C.; Chancerel, E.; Frigerio, J.M.; Vendramin, G.; Sebastiani, F.; Buonamici, A.; Gailing, O.; Koelewijn, H.P.; Villani, F.; Mattioni, C.; Cherubini, M.; Goicoechea, P.G.; Herrán, A.; Ikaran, Z.; Cabané, C.; Ueno, S.; Alberto, F.; Dumoulin, P.Y.; Guichoux, E.; Daruvar, de A.; Kremer, A.; Plomion, C.

    2010-01-01

    Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate

  9. De novo sequencing analysis of the Rosa roxburghii fruit transcriptome reveals putative ascorbate biosynthetic genes and EST-SSR markers.

    Science.gov (United States)

    Yan, Xiuqin; Zhang, Xue; Lu, Min; He, Yong; An, Huaming

    2015-04-25

    Rosa roxburghii Tratt. is a well-known ornamental rose species native to China. In addition, the fruits of this species are valued for their nutritional and medicinal characteristics, especially their high ascorbic acid (AsA) levels. Nevertheless, AsA biosynthesis in R. roxburghii fruit has not been explored in detail because of a lack of genomic resources for this species. High-throughput transcriptomic sequencing generating large volumes of transcript sequence data can aid in gene discovery and molecular marker development. In this study, we generated more than 53 million clean reads using Illumina paired-end sequencing technology. De novo assembly yielded 106,590 unigenes, with an average length of 343 bp. On the basis of sequence similarity to known proteins, 9301 and 2393 unigenes were classified into Gene Ontology and Clusters of Orthologous Group categories, respectively. There were 7480 unigenes assigned to 124 pathways in the Kyoto Encyclopedia of Gene and Genome pathway database. BLASTx searches identified 498 unique putative transcripts encoding various transcription factors, some known to regulate fruit development. qRT-PCR validated the expressions of most of the genes encoding the main enzymes involved in ascorbate biosynthesis. In addition, 9131 potential simple sequence repeat (SSR) loci were identified among the unigenes. One hundred and two primer pairs were synthesized and 71 pairs produced an amplification product during initial screening. Among the amplified products, 30 were polymorphic in the 16 R. roxburghii germplasms tested. Our study was the first to produce a large volume of transcriptome data from R. roxburghii. The resulting sequence collection is a valuable resource for gene discovery and marker-assisted selective breeding in this rose species. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information

    Directory of Open Access Journals (Sweden)

    Debjyoti Sen Gupta

    2016-10-01

    Full Text Available Lentil (Lens culinaris Medik., a diploid (2n = 14 with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information (ESTs. In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information (NCBI database to develop unigene-based simple sequence repeat (SSR markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed. Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches (using E-value 1 × 10−5 against the public UniProt (http://www.uniprot.org/ and NCBI (http://www.ncbi.nlh.nih.gov/ databases were performed. Further functional annotation was performed using PLAZA (version 3.0 comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.

  11. Development of EST-derived markers in Dendrobium from EST of related taxa

    OpenAIRE

    Narisa Juejun; Chataporn Chunwongse; Julapark Chunwongse

    2013-01-01

    Public databases are useful for molecular marker development. The major aim of this study was to develop expressedsequence tag (EST)-derived markers in Dendrobium from available ESTs of Phalaenopsis and Dendrobium. A total of 6063sequences were screened for simple sequence repeats (SSRs) and introns. Primers flanking these regions were generated andtested on genomic DNAs of Phalaenopsis and Dendrobium. Twenty-three percent of amplifiable Phalaenopsis EST-derivedmarkers were cross-genera trans...

  12. (SSR) markers

    African Journals Online (AJOL)

    SAM

    2014-07-30

    Jul 30, 2014 ... and attempt crosses for genetic improvement of the crop. Key words: Capsicum, genetic diversity, molecular characterization, simple sequence repeats (SSR) markers. INTRODUCTION. Chilli pepper (Capsicum annuum L.) (Solanaceae) has a chromosome number 2n=2x=24. It is indigenous to South.

  13. De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers.

    Science.gov (United States)

    Xanthopoulou, Aliki; Ganopoulos, Ioannis; Psomopoulos, Fotis; Manioudaki, Maria; Moysiadis, Theodoros; Kapazoglou, Aliki; Osathanunkul, Maslin; Michailidou, Sofia; Kalivas, Apostolos; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

    2017-07-30

    The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits. Copyright © 2017. Published by Elsevier B.V.

  14. Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (creole bean, and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis.

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    Sompong Chankaew

    Full Text Available Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

  15. Assessment of genetic diversity and population structure of mung bean (Vigna radiata) germplasm using EST-based and genomic SSR markers.

    Science.gov (United States)

    Chen, Honglin; Qiao, Ling; Wang, Lixia; Wang, Suhua; Blair, Matthew Wohlgemuth; Cheng, Xuzhen

    2015-07-25

    Mung bean is an important legume crop in tropical and subtropical countries of Asia and has high nutritional and economic value. However the genetic diversity of mung bean is poorly characterized. In this study, our goal was to develop and use microsatellite simple sequence repeat (SSR) markers for germplasm evaluation. In total, 500 novel expression sequence tag EST-based SSRs (eSSRs) and genomic SSRs (gSSRs) were developed from mung bean transcriptome and genome sequences. Of these, only 58 were useful for diversity evaluation in a panel of 157 cultivated and wild mung bean accessions from different collection sites in East Asia. A total of 2.66 alleles were detected on average per locus which shows that polymorphism is generally low for the species. The average polymorphic information content (PIC) of gSSRs was higher than eSSRs and most of the polymorphic gSSRs were composed of di- and tri-nucleotide repeats (52.4% and 38.1% of all loci, respectively). The genotypes were differentiated into nine subgroups by cluster analysis, and the wild mung bean accessions separated well from the cultivated accessions. Analysis of molecular variance indicated that 22% of variance was observed among populations and 78% was due to differences within populations. Clustering, population structure analyses showed that non-Chinese cultivated and wild mung bean accessions were separated from Chinese accessions, but no geographical distinctions existed between genotypes collected in China. Interestingly, the average PIC value of cultivated mung bean (0.36) was higher than that of wild mung bean (0.25) showing that further collecting and wide crosses are necessary for mung bean improvement. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Development of EST-derived markers in Dendrobium from EST of related taxa

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    Narisa Juejun

    2013-04-01

    Full Text Available Public databases are useful for molecular marker development. The major aim of this study was to develop expressedsequence tag (EST-derived markers in Dendrobium from available ESTs of Phalaenopsis and Dendrobium. A total of 6063sequences were screened for simple sequence repeats (SSRs and introns. Primers flanking these regions were generated andtested on genomic DNAs of Phalaenopsis and Dendrobium. Twenty-three percent of amplifiable Phalaenopsis EST-derivedmarkers were cross-genera transferable to Dendrobium. Forty-one markers from both Phalaenopsis and Dendrobium thatamplified in Dendrobium were assessed on six commercial cultivars and six wild accessions. All of them were transferableamong Dendrobium species. High polymorphism and heterozygosity were observed within wild accessions. Sixteen polymorphic markers were evaluated for linkage analysis on an F1 segregating population. Seven markers were mapped into threelinkage groups, two of which showed syntenic relationship between dendrobium and rice. This relationship will facilitatefurther quantitative trait loci (QTL mapping and comparative genomic studies of Dendrobium. Our results indicate thatPhalaenopsis EST-derived markers are valuable tools for genetic research and breeding applications in Dendrobium.

  17. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

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    King Graham J

    2010-10-01

    Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

  18. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    Science.gov (United States)

    2010-01-01

    Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). Results In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species. PMID:20969760

  19. De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis.

    Science.gov (United States)

    Zhou, Xiao-Jun; Wang, Yue-Yue; Xu, Ya-Nan; Yan, Rong-Shan; Zhao, Peng; Liu, Wen-Zhe

    2015-06-05

    Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.

  20. De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis

    Directory of Open Access Journals (Sweden)

    Xiao-Jun Zhou

    2015-06-01

    Full Text Available Tapiscia sinensis Oliv (Tapisciaceae is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27% were annotated. A total of 10,002 (19.17% unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG pathway database. Additionally, 10,371 simple sequence repeats (SSRs were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5% were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.

  1. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae).

    Science.gov (United States)

    Zhao, Yue-Mei; Zhou, Tao; Li, Zhong-Hu; Zhao, Gui-Fang

    2015-11-30

    Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.

  2. New gSSR and EST-SSR markers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L. and can be transferred to other invasive Ambrosia species.

    Science.gov (United States)

    Meyer, Lucie; Causse, Romain; Pernin, Fanny; Scalone, Romain; Bailly, Géraldine; Chauvel, Bruno; Délye, Christophe; Le Corre, Valérie

    2017-01-01

    Ambrosia artemisiifolia L., (common ragweed), is an annual invasive and highly troublesome plant species originating from North America that has become widespread across Europe. New sets of genomic and expressed sequence tag (EST) based simple sequence repeats (SSRs) markers were developed in this species using three approaches. After validation, 13 genomic SSRs and 13 EST-SSRs were retained and used to characterize the genetic diversity and population genetic structure of Ambrosia artemisiifolia populations from the native (North America) and invasive (Europe) ranges of the species. Analysing the mating system based on maternal families did not reveal any departure from complete allogamy and excess homozygosity was mostly due the presence of null alleles. High genetic diversity and patterns of genetic structure in Europe suggest two main introduction events followed by secondary colonization events. Cross-species transferability of the newly developed markers to other invasive species of the Ambrosia genus was assessed. Sixty-five percent and 75% of markers, respectively, were transferable from A. artemisiifolia to Ambrosia psilostachya and Ambrosia tenuifolia. 40% were transferable to Ambrosia trifida, this latter species being seemingly more phylogenetically distantly related to A. artemisiifolia than the former two.

  3. Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl. by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development

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    Zunzheng Wei

    2016-09-01

    Full Text Available Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. ‘Rehmannii’ using an Illumina HiSeq 2000 instrument. More than 59.9 million cDNA sequence reads were obtained and assembled into 39,298 unigenes with an average length of 1,038 bp. Among these, 21,077 unigenes showed significant similarity to protein sequences in the non-redundant protein database (Nr and in the Swiss-Prot, Gene Ontology (GO, Cluster of Orthologous Group (COG and Kyoto Encyclopedia of Genes and Genomes (KEGG databases. Moreover, a total of 117 unique transcripts were then defined that might regulate the flower spathe development of colored calla lily. Additionally, 9,933 simple sequence repeats (SSRs and 7,162 single nucleotide polymorphisms (SNPs were identified as putative molecular markers. High-quality primers for 200 SSR loci were designed and selected, of which 58 amplified reproducible amplicons were polymorphic among 21 accessions of colored calla lily. The sequence information and molecular markers in the present study will provide valuable resources for genetic diversity analysis, germplasm characterization and marker-assisted selection in the genus Zantedeschia.

  4. Sequence Analysis of SSR-Flanking Regions Identifies Genome Affinities between Pasture Grass Fungal Endophyte Taxa

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    Eline van Zijll de Jong

    2011-01-01

    Full Text Available Fungal species of the Neotyphodium and Epichloë genera are endophytes of pasture grasses showing complex differences of life-cycle and genetic architecture. Simple sequence repeat (SSR markers have been developed from endophyte-derived expressed sequence tag (EST collections. Although SSR array size polymorphisms are appropriate for phenetic analysis to distinguish between taxa, the capacity to resolve phylogenetic relationships is limited by both homoplasy and heteroploidy effects. In contrast, nonrepetitive sequence regions that flank SSRs have been effectively implemented in this study to demonstrate a common evolutionary origin of grass fungal endophytes. Consistent patterns of relationships between specific taxa were apparent across multiple target loci, confirming previous studies of genome evolution based on variation of individual genes. Evidence was obtained for the definition of endophyte taxa not only through genomic affinities but also by relative gene content. Results were compatible with the current view that some asexual Neotyphodium species arose following interspecific hybridisation between sexual Epichloë ancestors. Phylogenetic analysis of SSR-flanking regions, in combination with the results of previous studies with other EST-derived SSR markers, further permitted characterisation of Neotyphodium isolates that could not be assigned to known taxa on the basis of morphological characteristics.

  5. Loblolly pine SSR markers for shortleaf pine genetics

    Science.gov (United States)

    C. Dana Nelson; Sedley Josserand; Craig S. Echt; Jeff Koppelman

    2007-01-01

    Simple sequence repeats (SSR) are highly informative DNA-based markers widely used in population genetic and linkage mapping studies. We have been developing PCR primer pairs for amplifying SSR markers for loblolly pine (Pinus taeda L.) using loblolly pine DNA and EST sequence data as starting materials. Fifty primer pairs known to reliably amplify...

  6. Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.)

    DEFF Research Database (Denmark)

    Studer, Bruno; Asp, Torben; Frei, Ursula

    2008-01-01

    An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification...... genotypes included in the original screening and revealed SSR polymorphisms for 143 ESTs. Here, we report on 464 EST-derived SSR primer sequences of perennial ryegrass established in laboratory assays, providing a dedicated tool for marker assisted breeding and comparative mapping within and among forage...

  7. Expressed sequence tag-derived polymorphic SSR markers for Fucus serratus and amplification in other species of Fucus

    NARCIS (Netherlands)

    Coyer, J. A.; Hoarau, G.; Beszteri, B.; Pearson, G.; Olsen, J. L.

    The seaweed genus Fucus is a dominant component of intertidal shores throughout the North Atlantic and North Pacific and has been the focus of considerable developmental, ecological, and evolutionary research for the past century. Here, we present details of 21 expressed sequence tag-derived simple

  8. Development of transcriptome-derived SSR markers for Hoya ledongensis (Apocynaceae) and cross-amplification in a congener.

    Science.gov (United States)

    Chen, Zheng; Deng, Yuncheng; Zhou, Renchao; He, Shaoyun

    2016-09-01

    To examine patterns of genetic diversity and test possible hybridization events, microsatellite markers were identified and characterized in Hoya ledongensis (Apocynaceae), and cross-amplification was tested in a congener, H. jianfenglingensis. Based on the transcriptome data of H. ledongensis, 46 microsatellite primer pairs were randomly selected for initial validation. From these, 28 primer pairs were successfully amplified, 12 of which were polymorphic in 36 individuals across three populations of H. ledongensis. The number of alleles per microsatellite locus ranged from two to 11. The observed and expected heterozygosities for the 12 loci ranged from 0.133 to 0.867 and 0.128 to 0.894, respectively. Cross-species amplification was successful for these 12 loci in the congeneric species H. jianfenglingensis. These polymorphic transcriptome-derived simple sequence repeat markers have the potential to be used as multilocus molecular markers to study the population genetics and natural hybridization in species of Hoya.

  9. Development of transcriptome-derived SSR markers for Hoya ledongensis (Apocynaceae) and cross-amplification in a congener1

    Science.gov (United States)

    Chen, Zheng; Deng, Yuncheng; Zhou, Renchao; He, Shaoyun

    2016-01-01

    Premise of the study: To examine patterns of genetic diversity and test possible hybridization events, microsatellite markers were identified and characterized in Hoya ledongensis (Apocynaceae), and cross-amplification was tested in a congener, H. jianfenglingensis. Methods and Results: Based on the transcriptome data of H. ledongensis, 46 microsatellite primer pairs were randomly selected for initial validation. From these, 28 primer pairs were successfully amplified, 12 of which were polymorphic in 36 individuals across three populations of H. ledongensis. The number of alleles per microsatellite locus ranged from two to 11. The observed and expected heterozygosities for the 12 loci ranged from 0.133 to 0.867 and 0.128 to 0.894, respectively. Cross-species amplification was successful for these 12 loci in the congeneric species H. jianfenglingensis. Conclusions: These polymorphic transcriptome-derived simple sequence repeat markers have the potential to be used as multilocus molecular markers to study the population genetics and natural hybridization in species of Hoya. PMID:27672524

  10. Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness

    Directory of Open Access Journals (Sweden)

    Shaw Kerry L

    2010-07-01

    Full Text Available Abstract Background Simple sequence repeats (SSRs are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that can be mined are bacterial artificial chromosome (BAC libraries and expressed sequence tag (EST libraries. Results 288 SSR loci were screened in the rapidly radiating Hawaiian swordtail cricket genus Laupala. SSRs were more densely distributed and contained longer repeat structures in BAC library-derived sequence than in EST library-derived sequence, although neither repeat density nor length was exceptionally elevated despite the relatively large genome size of Laupala. A non-random distribution favoring AT-rich SSRs was observed. Allelic diversity of SSRs was positively correlated with repeat length and was generally higher in AT-rich repeat motifs. Conclusion The first large-scale survey of Orthopteran SSR allelic diversity is presented. Selection contributes more strongly to the size and density distributions of SSR loci derived from EST library sequence than from BAC library sequence, although all SSRs likely are subject to similar physical and structural constraints, such as slippage of DNA replication machinery, that may generate increased allelic diversity in AT-rich sequence motifs. Although in silico approaches work well for SSR locus identification in both EST and BAC libraries, BAC library sequence and AT-rich repeat motifs are generally superior SSR development resources for most applications.

  11. Assessment of in silico BAC-based simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    As a result, 17 SSR markers were developed and tested on one tomato commercial cultivar and eight local landraces. 12 loci (27 alleles) ... According to tomato expressed sequence tag (EST) analysis, some of these developed SSR markers, such as mono and di-nucleotide are related to some genes. The T(16) motif is ...

  12. Isolation and Characterization of Novel EST-Derived Genic Markers in Pisum sativum (Fabaceae

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    Shalu Jain

    2013-10-01

    Full Text Available Premise of the study: Novel markers were developed for pea (Pisum sativum from pea expressed sequence tags (ESTs having significant homology to Medicago truncatula gene sequences to investigate genetic diversity, linkage mapping, and cross-species transferability. Methods and Results: Seventy-seven EST-derived genic markers were developed through comparative mapping between M. truncatula and P. sativum in which 75 markers produced PCR products and 33 were polymorphic among 16 pea genotypes. Conclusions: The novel markers described here will be useful for future genetic studies of P. sativum; their amplification in lentil (Lens culinaris demonstrates their potential for use in closely related species.

  13. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars.

    Science.gov (United States)

    Feng, Shangguo; He, Renfeng; Lu, Jiangjie; Jiang, Mengying; Shen, Xiaoxia; Jiang, Yan; Wang, Zhi'an; Wang, Huizhong

    2016-01-01

    Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938-0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars.

  14. Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae).

    Science.gov (United States)

    Jain, Neelu; Dikshit, H K; Singh, D; Singh, Akanksha; Kumar, Harish

    2013-07-01

    We developed microsatellite markers in the legume Lens culinaris from publicly available databases to enrich the limited marker resource available for the crop. • Eighty-two primer sets were identified using expressed sequence sets of L. culinaris available in the National Center for Biotechnology Information (NCBI) database and were characterized in six species of Lens. Among them, 20 simple sequence repeat (SSR) primers produced no amplification product, 43 produced monomorphic products, and 19 were polymorphic. The primers amplified mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats with one to four alleles. These SSR loci successfully amplified in five related wild species, with a total of 61 primer pairs in L. nigricans and L. odemensis (98.39%), 59 in L. tomentosus (95.1%), and 60 in L. ervoides and L. orientalis (96.7%), respectively. • The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assisted breeding, and characterization of germplasm.

  15. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera.

    Science.gov (United States)

    Ranade, Sonali Sachin; Lin, Yao-Cheng; Zuccolo, Andrea; Van de Peer, Yves; García-Gil, María del Rosario

    2014-08-21

    Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.

  16. Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis).

    Science.gov (United States)

    Xiao, Yong; Zhou, Lixia; Xia, Wei; Mason, Annaliese S; Yang, Yaodong; Ma, Zilong; Peng, Ming

    2014-12-19

    The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant Elaeis guineensis. In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from Elaeis guineensis transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of Elaeis guineensis varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using in-silico mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16 Elaeis guineensis chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one ICE1 putative ortholog, five CBF putative orthologs, 19 NAC transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers. In the present study, a series of SSR markers were developed based on sequences

  17. Mining, genetic mapping and expression analysis of EST-derived resistance gene homologs (RGHs) in cotton.

    Science.gov (United States)

    Ren, Gaofeng; Li, Ximei; Lin, Zhongxu

    2014-07-27

    Cotton is the dominant textile crop and also serves as an important oil crop. An estimated 15% economic loss associated with cotton production in China has been caused by diseases, and no resistance genes have been cloned in this crop. Molecular markers developed from resistance gene homologues (RGHs) might be tightly linked with target genes and could be used for marker-assisted selection (MAS) or gene cloning. To genetically map expressed RGHs, 100 potential pathogenesis-related proteins (PRPs) and 215 resistance gene analogs (RGAs) were identified in the cotton expressed sequence tag database, and 347 specific primers were developed. Meanwhile, 61 cotton genome-derived RGA markers and 24 resistance gene analog polymorphism (RGAP) markers from published papers were included to view their genomic distribution. As a result, 38 EST-derived and 17 genome-derived RGH markers were added to our interspecific genetic map. These 55 markers were distributed on 18 of the 26 cotton chromosomes, with 34 markers on 6 chromosomes (Chr03, Chr04, Chr11, Chr17, Chr19 and Chr26). Homologous RGHs tended to be clustered; RGH clusters appeared on 9 chromosomes, with larger clusters on Chr03, Chr04 and Chr19, which suggests that RGH clusters are widely distributed in the cotton genome. Expression analysis showed that 19 RGHs were significantly altered after inoculation with the V991 stain of Verticillium dahliae. Comparative mapping showed that four RGH markers were linked with mapped loci for Verticillium wilt resistance. The genetic mapping of RGHs confirmed their clustering in cotton genome. Expression analysis and comparative mapping suggest that EST-derived RGHs participate in cotton resistance. RGH markers are seemed to be useful tools to detected resistance loci and identify candidate resistance genes in cotton.

  18. Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae)1

    Science.gov (United States)

    Jain, Neelu; Dikshit, H. K.; Singh, D.; Singh, Akanksha; Kumar, Harish

    2013-01-01

    • Premise of the study: We developed microsatellite markers in the legume Lens culinaris from publicly available databases to enrich the limited marker resource available for the crop. • Methods and Results: Eighty-two primer sets were identified using expressed sequence sets of L. culinaris available in the National Center for Biotechnology Information (NCBI) database and were characterized in six species of Lens. Among them, 20 simple sequence repeat (SSR) primers produced no amplification product, 43 produced monomorphic products, and 19 were polymorphic. The primers amplified mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats with one to four alleles. These SSR loci successfully amplified in five related wild species, with a total of 61 primer pairs in L. nigricans and L. odemensis (98.39%), 59 in L. tomentosus (95.1%), and 60 in L. ervoides and L. orientalis (96.7%), respectively. • Conclusions: The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assisted breeding, and characterization of germplasm. PMID:25202567

  19. Discovery of EST-Derived Microsatellite Primers in the Legume Lens culinaris (Fabaceae

    Directory of Open Access Journals (Sweden)

    Neelu Jain

    2013-06-01

    Full Text Available Premise of the study: We developed microsatellite markers in the legume Lens culinaris from publicly available databases to enrich the limited marker resource available for the crop. Methods and Results: Eighty-two primer sets were identified using expressed sequence sets of L. culinaris available in the National Center for Biotechnology Information (NCBI database and were characterized in six species of Lens. Among them, 20 simple sequence repeat (SSR primers produced no amplification product, 43 produced monomorphic products, and 19 were polymorphic. The primers amplified mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats with one to four alleles. These SSR loci successfully amplified in five related wild species, with a total of 61 primer pairs in L. nigricans and L. odemensis (98.39%, 59 in L. tomentosus (95.1 %, and 60 in L. ervoides and L. orientalis (96.7%, respectively. Conclusions: The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assisted breeding, and characterization of germplasm.

  20. Transferability of simple sequence repeat (SSR) markers developed in guava (Psidium guajava L.) to four Myrtaceae species.

    Science.gov (United States)

    Rai, Manoj K; Phulwaria, Mahendra; Shekhawat, N S

    2013-08-01

    Present study demonstrated the cross-genera transferability of 23 simple sequence repeat (SSR) primer pairs developed for guava (Psidium guajava L.) to four new targets, two species of eucalypts (Eucalyptus citriodora, Eucalyptus camaldulensis), bottlebrush (Callistemon lanceolatus) and clove (Syzygium aromaticum), belonging to the family Myrtaceae and subfamily Myrtoideae. Off the 23 SSR loci assayed, 18 (78.2%) gave cross-amplification in E. citriodora, 14 (60.8%) in E. camaldulensis and 17-17 (73.9%) in C. lanceolatus and S. aromaticum. Eight primer pairs were found to be transferable to all four species. The number of alleles detected at each locus ranged from one to nine, with an average of 4.8, 2.6, 4.5 and 4.6 alleles in E. citriodora, E. camaldulensis, C. lanceolatus and S. aromaticum, respectively. The high levels of cross-genera transferability of guava SSRs may be applicable for the analysis of intra- and inter specific genetic diversity of target species, especially in E. citriodora, C. lanceolatus and S. aromaticum, for which till date no information about EST-derived as well as genomic SSR is available.

  1. Validation of EST-derived microsatellite markers for two Cerrado-endemic Campomanesia (Myrtaceae) species.

    Science.gov (United States)

    Miranda, E A G C; Boaventura-Novaes, C R D; Braga, R S; Reis, E F; Pinto, J F N; Telles, M P C

    2016-03-04

    We assessed the transferability of 120 EST-derived Eucalyptus microsatellite primers to Campomanesia adamantium and C. pubescens. Both species are berry trees native to the Brazilian Cerrado, and population genetic information is poor. Twelve markers were used to analyze the genetic variability of four sampled populations. Regarding DNA extraction, we sampled leaf tissues from two populations of each species (80 individuals). Of the 120 primers evaluated, 87 did not amplify any PCR products, and 21 rendered nonspecific amplification. Twelve primers were successfully transferred, providing a low combined probability of genetic identity for both species (5.718 x 10(-10) for C. adamantium; 1.182 x 10(-11) for C. pubescens) and a high probability of paternity exclusion (0.99939 for C. adamantium; 0.99982 for C. pubescens). The average number of alleles in the polymorphic loci was 6.8 for C. adamantium and 7.8 for C. pubescens, ranging from 2 to 16 alleles per locus. The observed heterozygosity values for C. adamantium and C. pubescens were 0.504 and 0.503, respectively, and the expected heterozygosity values for C. adamantium and C. pubescens were 0.517 and 0.579, respectively. The populations exhibited structured genetic variability with qP values of 0.105 for C. adamantium and 0.249 for C. pubescens. Thus, we concluded that these 12 microsatellite markers, transferred from Eucalyptus, were efficient for population genetic studies of C. adamantium and C. pubescens.

  2. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

    Science.gov (United States)

    Rauscher, Gilda; Simko, Ivan

    2013-01-22

    Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

  3. DNA Profiles of MTG (Moderat Tahan Gano) Oil Palm Variety Based on SSR Marker

    Science.gov (United States)

    Putri, L. A. P.; Setiado, H.; Hardianti, R.

    2017-03-01

    The oil palm, an economically important tree in Indonesia, has been one of the world’s major sources of edible oil and a significant precursor of biodiesel fuel. The objectives of this study were to know DNA profile of commercial MTG (Moderat Tahan Gano) oil palm variety collections. A total of 10 trees MTG oil palm variety were used for analysis. In this experiment, the DNA profile diversity was assessed using mEgCIR0174 and SSR-1 loci of oil palm’s specific SSR markers. The results of the experiment indicated out of 3 alleles of pcr product of mEgCIR0174 (198, 203 and 208 bp) and SSR-1 (201, 217 and 232 bp). These preliminary results demonstrated SSR marker can be used to evaluate genetic relatedness among trees of MTG (Moderat Tahan Gano) oil palm variety derived from different crossing or difference to desease resistance trait or misslabeled.

  4. SSR

    African Journals Online (AJOL)

    user

    MapDraw: a Microsoft Excel macro for drawing genetic linkage maps based on given genetic linkage data. Hereditas. (Beijing). 25: 317–321. Liu SB, Zhou RH, Dong YC, Li P, Jia JZ (2006). Development utilization of introgression lines using a synthietic wheat as donor. Theor. Appl. Genet. 112: 1360-1373. Lu CM, Yang WY ...

  5. Development of genomic SSR and potential EST-SSR markers in ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... Tel: +86-10-62818841. Var. parvifolia Shan et Y. Li, B. marginatum Wall. ex DC.,. B. bicaule Helm. and B. scorzonerifolium Willd. var. angustissimum (Franch.) Huang (Song, 2002). Many studies have shown the active component, such as saikosaponins, volatile oils and polysaccharides, varied remarkably ...

  6. Development of genic and genomic SSR markers of robusta coffee (Coffea canephora Pierre Ex A. Froehner).

    Science.gov (United States)

    Hendre, Prasad S; Aggarwal, Ramesh K

    2014-01-01

    Coffee breeding and improvement efforts can be greatly facilitated by availability of a large repository of simple sequence repeats (SSRs) based microsatellite markers, which provides efficiency and high-resolution in genetic analyses. This study was aimed to improve SSR availability in coffee by developing new genic-/genomic-SSR markers using in-silico bioinformatics and streptavidin-biotin based enrichment approach, respectively. The expressed sequence tag (EST) based genic microsatellite markers (EST-SSRs) were developed using the publicly available dataset of 13,175 unigene ESTs, which showed a distribution of 1 SSR/3.4 kb of coffee transcriptome. Genomic SSRs, on the other hand, were developed from an SSR-enriched small-insert partial genomic library of robusta coffee. In total, 69 new SSRs (44 EST-SSRs and 25 genomic SSRs) were developed and validated as suitable genetic markers. Diversity analysis of selected coffee genotypes revealed these to be highly informative in terms of allelic diversity and PIC values, and eighteen of these markers (∼ 27%) could be mapped on a robusta linkage map. Notably, the markers described here also revealed a very high cross-species transferability. In addition to the validated markers, we have also designed primer pairs for 270 putative EST-SSRs, which are expected to provide another ca. 200 useful genetic markers considering the high success rate (88%) of marker conversion of similar pairs tested/validated in this study.

  7. Construction of an EST-SSR-based interspecific transcriptome ...

    Indian Academy of Sciences (India)

    Quantitative trait locus (QTL) mapping is an important method in marker-assisted selection breeding. Many studies on the QTLs focus on cotton fibre yield and quality; however, most are conducted at the DNA level, which may reveal null QTLs. Hence, QTL mapping based on transcriptome maps at the cDNA level is often ...

  8. Development of 101 novel EST-derived single nucleotide polymorphism markers for Zhikong scallop ( Chlamys farreri)

    Science.gov (United States)

    Li, Jiqin; Bao, Zhenmin; Li, Ling; Wang, Xiaojian; Wang, Shi; Hu, Xiaoli

    2013-09-01

    Zhikong scallop ( Chlamys farreri) is an important maricultured species in China. Many researches on this species, such as population genetics and QTL fine-mapping, need a large number of molecular markers. In this study, based on the expressed sequence tags (EST), a total of 300 putative single nucleotide polymorphisms (SNPs) were selected and validated using high resolution melting (HRM) technology with unlabeled probe. Of them, 101 (33.7%) were found to be polymorphic in 48 individuals from 4 populations. Further evaluation with 48 individuals from Qingdao population showed that all the polymorphic loci had two alleles with the minor allele frequency ranged from 0.046 to 0.500. The observed and expected heterozygosities ranged from 0.000 to 0.925 and from 0.089 to 0.505, respectively. Fifteen loci deviated significantly from Hardy-Weinberg equilibrium and significant linkage disequilibrate was detected in one pair of markers. BLASTx gave significant hits for 72 of the 101 polymorphic SNP-containing ESTs. Thirty four polymorphic SNP loci were predicted to be non-synonymous substitutions as they caused either the change of codons (33 SNPs) or pretermination of translation (1 SNP). The markers developed can be used for the population studies and genetic improvement on Zhikong scallop.

  9. EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp ( Litopenaeus vannamei)

    Science.gov (United States)

    Liu, Chengzhang; Wang, Xia; Xiang, Jianhai; Li, Fuhua

    2012-09-01

    Pacific white shrimp has become a major aquaculture and fishery species worldwide. Although a large scale EST resource has been publicly available since 2008, the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure. In this study, a set of 155 411 expressed sequence tags (ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms (SNPs) were predicted, including 9 546 transitions, 5 124 transversions and 2 481 indels. Among the 7 298 SNP substitutions located in functionally annotated contigs, 58.4% (4 262) are non-synonymous SNPs capable of introducing amino acid mutations. Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding. Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous, suggesting negative selection. Distribution of non-synonymous to synonymous substitutions (Ka/Ks) ratio ranges from 0 to 4.01, (average 0.42, median 0.26), suggesting that the majority of the affected genes are under purifying selection. Enrichment analysis identified multiple gene ontology categories under positive or negative selection. Categories involved in innate immune response and male gamete generation are rich in positively selected genes, which is similar to reports in Drosophila and primates. This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species. The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.

  10. The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia Formosa

    Science.gov (United States)

    Brandon Schlautman; Vera Pfeiffer; Juan Zalapa; Johanne Brunet

    2014-01-01

    Numerous microsatellite markers were developed for Aquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST...

  11. Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm.

    Science.gov (United States)

    Zhao, Yongli; Keremane, Manjunath; Prakash, Channapatna S; He, Guohao

    2017-01-01

    The paucity of molecular markers limits the application of genetic and genomic research in date palm (Phoenix dactylifera L.). Availability of expressed sequence tag (EST) sequences in date palm may provide a good resource for developing gene-based markers. This study characterizes a substantial fraction of transcriptome sequences containing simple sequence repeats (SSRs) from the EST sequences in date palm. The EST sequences studied are mainly homologous to those of Elaeis guineensis and Musa acuminata. A total of 911 gene-based SSR markers, characterized with functional annotations, have provided a useful basis not only for discovering candidate genes and understanding genetic basis of traits of interest but also for developing genetic and genomic tools for molecular research in date palm, such as diversity study, quantitative trait locus (QTL) mapping, and molecular breeding. The procedures of DNA extraction, polymerase chain reaction (PCR) amplification of these gene-based SSR markers, and gel electrophoresis of PCR products are described in this chapter.

  12. Reimagining SSR in Contexts of Security Pluralism

    Directory of Open Access Journals (Sweden)

    Megan Price

    2017-07-01

    Full Text Available Within the repertoire of international stabilization interventions, security sector reform (SSR and other conventional efforts to strengthen security and governance institutions remain central. There is increasing recognition that the policies and practices operating under the rubric of SSR are blind to the empirical reality of 'security pluralism' in most stabilization contexts. In these contexts, both security providers directly authorized by the state (police, army and a multitude of other coercive actors engage in producing and reproducing order, and enjoy varying degrees of public authority and legitimacy. Recognizing this, research was undertaken in three cities (Beirut, Nairobi, and Tunis to discern the conditions enabling various security providers to forge constructive relations with local populations and governance actors. Drawing on insights generated by these case studies, this article problematizes conventional state-centric approaches and argues for a bold reimagining of SSR. It makes the case for an SSR approach that prioritizes promoting the accountability and responsiveness of all security providers, integrating efforts to strengthen the social determinants of security, and enabling a phased transition from relational to rules-based systems of security provision and governance.

  13. Isolation and characterization of novel EST-SSRs in the showy dendrobium, Dendrobium nobile (Orchidaceae).

    Science.gov (United States)

    Lu, J J; Kang, J Y; Ye, S R; Wang, H Z

    2014-02-19

    Expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers could enrich the current resource of molecular markers. In this study, microsatellite markers were developed for Dendrobium nobile Lindl. by mining the ESTs. Twenty-eight EST-SSRs amplified 2 to 6 nucleotide repeats with a mean number of 2.82 alleles per locus. The observed and expected heterozygosities per locus ranged from 0.158 to 0.579 and 0.422 to 0.752, respectively. These novel EST-SSRs enriched the current resource of molecular markers for the Dendrobium genus and would facilitate further applications in germplasm appraisal, evolution and genetic diversity studies, genetic mapping, and plant breeding of D. nobile and other congeneric species.

  14. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

    Directory of Open Access Journals (Sweden)

    Dipnarayan Saha

    2017-10-01

    Full Text Available Corchorus capsularis (white jute and C. olitorius (dark jute are the two principal cultivated species of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat (SSR loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinucleotide repeats were most frequent (60% followed by dinucleotide repeats (37.6%. Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR (eSSR markers were successfully mapped to the existing single-nucleotide polymorphism (SNP linkage map of jute, providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C. capsularis and C. olitorius, respectively, and seven wild jute species. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identification. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb (http://jutemarkerdb.icar.gov.in/ for the first time in jute. This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute.

  15. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L. A. Rich.

    Directory of Open Access Journals (Sweden)

    Rusama Marubodee

    Full Text Available Vigna vexillata (L. A. Rich. (tuber cowpea is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s source for V. unguiculata (cowpea, since it was reported to have various resistance gene(s for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean, V. unguiculata and Phaseolus vulgaris (common bean. An F2 population of 300 plants derived from a cross between salt resistant (V1 and susceptible (V5 accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits.

  16. LSGermOPA, a custom OPA of 384 EST-derived SNPs for high-throughput lettuce (Lactuca sativa L.) germplasm fingerprinting

    Science.gov (United States)

    We assessed the genetic diversity and population structure among 148 cultivated lettuce (Lactuca sativa L.) accessions using the high-throughput GoldenGate assay and 384 EST (Expressed Sequence Tag)-derived SNP (single nucleotide polymorphism) markers. A custom OPA (Oligo Pool All), LSGermOPA was fo...

  17. Arduino Based RFID Line Switching Using SSR

    Directory of Open Access Journals (Sweden)

    Michael E.

    2017-10-01

    Full Text Available The importance of line switching cannot be overemphasized as they are used to connect and disconnect substations to and from a distribution grid. At the cradle of technology line switching was achieved via the use of manual switches or fuses which could endanger life as a result of electrocution when expose during maintenance. This ill prompted the development of automated line switching using relays and contactors. With time this tends to fail as a result of wearing of the contact which is as a result of arcing and low voltage. To avert all these ills this paper presents Arduino based Radio Frequency Identification RFID line switching using Solid State Relay SSR. This is to ensure the safety of operators or technologist and to also avert the problem associated with relays and contactors using SSR. This was achieved using RFID RC-522 reader ardriuno Uno SSR and other discrete components. The system was tested and worked perfectly reducing the risk of electrocution and eliminating damage wearing of the contacts common with contactors and relays.

  18. Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Jinsu Gil

    2017-09-01

    Full Text Available Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV of A. gigas, derived from next generation sequencing (NGS. From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC was 0.69; the average observed heterozygosity (HO values, and the expected heterozygosity (HE values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.

  19. SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences.

    Science.gov (United States)

    Pickett, B D; Karlinsey, S M; Penrod, C E; Cormier, M J; Ebbert, M T W; Shiozawa, D K; Whipple, C J; Ridge, P G

    2016-09-01

    Simple Sequence Repeats (SSRs) are used to address a variety of research questions in a variety of fields (e.g. population genetics, phylogenetics, forensics, etc.), due to their high mutability within and between species. Here, we present an innovative algorithm, SA-SSR, based on suffix and longest common prefix arrays for efficiently detecting SSRs in large sets of sequences. Existing SSR detection applications are hampered by one or more limitations (i.e. speed, accuracy, ease-of-use, etc.). Our algorithm addresses these challenges while being the most comprehensive and correct SSR detection software available. SA-SSR is 100% accurate and detected >1000 more SSRs than the second best algorithm, while offering greater control to the user than any existing software. SA-SSR is freely available at http://github.com/ridgelab/SA-SSR CONTACT: perry.ridge@byu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  20. Development of specific simple sequence repeat (SSR) markers for ...

    African Journals Online (AJOL)

    The bulk segregant analysis (BSA) using simple sequence repeat (SSR) markers were deployed to identify the location and genetic effect of this gene. We have generated new set of SSR markers to identify progenies carrying TGMS gene in a cross TGMS/PTT1. The TGMS gene was located on chromosome 2 with 0.0 cM ...

  1. An online conserved SSR discovery through cross-species comparison

    Directory of Open Access Journals (Sweden)

    Tun-Wen Pai

    2009-02-01

    Full Text Available Tun-Wen Pai1, Chien-Ming Chen1, Meng-Chang Hsiao1, Ronshan Cheng2, Wen-Shyong Tzou3, Chin-Hua Hu31Department of Computer Science and Engineering; 2Department of Aquaculture, 3Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan, Republic of ChinaAbstract: Simple sequence repeats (SSRs play important roles in gene regulation and genome evolution. Although there exist several online resources for SSR mining, most of them only extract general SSR patterns without providing functional information. Here, an online search tool, CG-SSR (Comparative Genomics SSR discovery, has been developed for discovering potential functional SSRs from vertebrate genomes through cross-species comparison. In addition to revealing SSR candidates in conserved regions among various species, it also combines accurate coordinate and functional genomics information. CG-SSR is the first comprehensive and efficient online tool for conserved SSR discovery.Keywords: microsatellites, genome, comparative genomics, functional SSR, gene ontology, conserved region

  2. SSR markers reveal genetic variation between improved cassava ...

    African Journals Online (AJOL)

    Five SSR primers that have PIC values between 0.50 and 0.67 were selected and further assessed using simple arithmetic progression combination method. The results obtained revealed a combination of these 5 primers from SSR primers collection at IITA that could readily distinguish the 36 cassava genotypes at 0.93 ...

  3. Chromosomal location of genomic SSR markers associated with ...

    Indian Academy of Sciences (India)

    ... we selected 16 SSR markers mapped only in one genome of chromosome group 2 around 1–21 cM distance to these diagnostic markers based on the SSR consensus map of wheat. Out of 16 SSRs, Xwmc658 identified resistant F2 individuals as a diagnostic marker for yellow rust disease and provided the location of ...

  4. Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

    Science.gov (United States)

    Iandolino, Alberto; Nobuta, Kan; da Silva, Francisco Goes; Cook, Douglas R; Meyers, Blake C

    2008-05-12

    Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was approximately 49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not

  5. Comparative expression profiling in grape (Vitis vinifera berries derived from frequency analysis of ESTs and MPSS signatures

    Directory of Open Access Journals (Sweden)

    Cook Douglas R

    2008-05-01

    Full Text Available Abstract Background Vitis vinifera (V. vinifera is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS and combined it with available Expressed Sequence Tag (EST data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. Results The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS. A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was ~49 TPM (Transcripts Per Million. Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. Conclusion The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed

  6. Factors Affecting SSR in Holstein Dairy Cows

    Directory of Open Access Journals (Sweden)

    Alireza Heravi Mosavi

    2016-08-01

    Full Text Available Introduction Secondary sex ratio (SSR is the proportion of males to females at birth. It has been shown in many different mammalian species, many factors are associated with SSR. Changes in secondary sex ratio in dairy cows is considered economically important and the ability to change it could affect the revenues and profitability of a dairy farm. Thus, sperm or embryo sexing techniques in recent years has attracted more attention. Most breed of dairy cattle are more likely to have female calf is born to use them as replacement heifers and in order to maintain their productive herd number. On the contrary, when the goal is the production of meat, bull calves due to higher growth rates and production efficiency, are more convenient and more economically efficient. The aim of present study was to investigate some key factors affecting SSR in Iranian Holstein cows. According to Fisher, the sex ratio in the population under the control of natural selection is not always the same. There is overwhelming evidence to support the theory that shows Fisher Primary and secondary sex ratio sex ratio can deviate from this balance and natural selection caused a change in this ratio can be in certain circumstances. For example, the secondary sex ratio of 52:48 has been reported in dairy cows. Studies on mammalian species suggest that several factors, including latitude of the location, the dominant regional climate model, time and frequency of mating to ovulation, diet, age of parents, physical score, breed and produced eggs from ovarian left or right can have a significant effect on the secondary sex ratio. Weather conditions may modify the internal environment and the effect on physiological mechanisms or through the impact on the frequency and type of foods available to parents, the secondary sex ratio is impressive. The impact on the quantity and quality of parent's access to food sources in many species of mammals, the sex ratio has been fixed. Previous

  7. Comparative evaluation of genetic diversity using RAPD, SSR and ...

    Indian Academy of Sciences (India)

    A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt ...

  8. FullSSR: Microsatellite Finder and Primer Designer

    Directory of Open Access Journals (Sweden)

    Sebastián Metz

    2016-01-01

    Full Text Available Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.

  9. Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system.

    Directory of Open Access Journals (Sweden)

    Ana M Tomljenovic-Berube

    2010-03-01

    Full Text Available Sequence data from the past decade has laid bare the significance of horizontal gene transfer in creating genetic diversity in the bacterial world. Regulatory evolution, in which non-coding DNA is mutated to create new regulatory nodes, also contributes to this diversity to allow niche adaptation and the evolution of pathogenesis. To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment. To better understand the phenomenon of regulatory evolution in S. enterica, we defined the SsrB regulon and asked how this transcription factor interacts with the cis-regulatory region of target genes. Using ChIP-on-chip, cDNA hybridization, and comparative genomics analyses, we describe the SsrB-dependent regulon of ancestral and horizontally acquired genes. Further, we used a genetic screen and computational analyses integrating experimental data from S. enterica and sequence data from an orthologous regulatory system in the insect endosymbiont, Sodalis glossinidius, to identify the conserved yet flexible palindrome sequence that defines DNA recognition by SsrB. Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB. These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.

  10. Characterization of simple sequence repeats (SSRs from Phlebotomus papatasi (Diptera: Psychodidae expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Hamarsheh Omar

    2011-09-01

    Full Text Available Abstract Background Phlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs, or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers. Results Simple sequence repeats (SSRs were characterized in P. papatasi expressed sequence tags (ESTs derived from a public database, National Center for Biotechnology Information (NCBI. A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AXn repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation. Conclusion The first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

  11. An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L. and Development of SSR and KASP Markers

    Directory of Open Access Journals (Sweden)

    Xiaopeng Hao

    2017-10-01

    Full Text Available Grasspea (Lathyrus sativus L., 2n = 14 has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeqTM 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp. The unigenes were of high-quality. For example, the stay-green (SGR gene of grasspea was aligned with the SGR gene of pea with high similarity. Among these unigenes, 3,204 EST-SSR primers were designed, 284 of which were randomly chosen for validation. Of these validated unigenes, 87 (30.6% EST-SSR primers produced polymorphic amplicons among 43 grasspea accessions selected from different geographical locations. Meanwhile, 146,406 SNPs were screened and 50 SNP loci were randomly chosen for the kompetitive allele-specific PCR (KASP validation. Over 80% (42 SNP loci were successfully transformed to KASP markers. Comparison of the dendrograms according to the SSR and KASP markers showed that the different marker systems are partially consistent with the dendrogram constructed in our study.

  12. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis

    Directory of Open Access Journals (Sweden)

    Qian Ding

    2015-01-01

    Full Text Available Simple sequence repeats (SSRs are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%, amplicons were successfully generated with high quality. Seventeen (89.5% showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.

  13. SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

    Directory of Open Access Journals (Sweden)

    Xiaoyan Song

    2016-05-01

    Full Text Available In potato breeding, it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance. A promising alternative is diploid breeding. Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits. In this study, we used SSR markers to evaluate the genetic diversity of diploid potato cultivars. To screen polymorphic SSR markers, 55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships. Among them, 12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars. The primers produced 6 to 18 bands with an average of 8.2 bands per primer. In total, 98 bands were amplified from 192 cultivars, and 97 of them were polymorphic. Cluster analysis using UPGMA showed the genetic relationships of all accessions tested: 186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers, and the 192 diploid cultivars were divided into 11 groups, and 83.3% constituted the first group. Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level. The results can provide molecular basis for diploid potato breeding.

  14. Cross-species amplification of 105 Lolium perenne SSR loci in 23 species within the Poaceae

    DEFF Research Database (Denmark)

    Jensen, Louise Bach; Holm, Preben Bach; Lübberstedt, Thomas

    2007-01-01

    Amplification of 105 Lolium perenne SSR markers was studied in 23 grass species representing seven tribes from three subfamilies of Poaceae. Twelve of the SSR markers are published for the first time. Between 2% and 96% of the SSR markers could be amplified within a given species. A subset of eight...

  15. SSR-CE/FD assessment of Guizhou approved sugarcane cultivars and regional materials

    Science.gov (United States)

    Twelve sugarcane genotypes (three cultivars and nine clones involved in regional tests) from Guizhou Province, China were analyzed using SSR-capillary electrophoresis/fluorescence detection (SSR-CE/FD) technology to construct the SSR fingerprints and assess the genetic diversity. A total of 131 DNA ...

  16. Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae transcriptome permits large-scale unigene assembly and SSR marker discovery.

    Directory of Open Access Journals (Sweden)

    Haibin Wang

    Full Text Available BACKGROUND: Simple sequence repeats (SSRs are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST sequences have been acquired to date, so the number of available EST-SSR markers is very low. METHODOLOGY/PRINCIPAL FINDINGS: Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59% unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all of the assays were transferable across species and that they exposed a significant amount of allelic diversity. CONCLUSIONS/SIGNIFICANCE: SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

  17. SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids.

    Science.gov (United States)

    Thakur, Ajay Kumar; Singh, Kunwar Harendra; Singh, Lal; Nanjundan, Joghee; Khan, Yasin Jeshima; Singh, Dhiraj

    2018-01-01

    Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B. juncea and three subspecies of B. rapa, while lowest cross-transferability (91.93%) was obtained for Eruca sativa. The average % age of cross-transferability across all the seven species was 98.15%. The number of alleles detected at each locus ranged from one to six with an average of 3.41 alleles per primer pair. Neighbor-Joining-based dendrogram divided all the 40 accessions into two main groups composed of B. juncea/B. nigra/B. rapa and B. carinata/B. napus/B. oleracea. C-genome of oilseed Brassica species remained relatively more conserved than A- and B-genome. A- genome present in B. juncea and B. napus seems distinct from each other and hence provides great opportunity for generating diversity through synthesizing amphidiploids from different sources of A- genome. B. juncea had least intra-specific distance indicating narrow genetic base. B. rapa appears to be more primitive species from which other two diploid species might have evolved. The SSR marker set developed in this study will assist in DNA fingerprinting of various Brassica species cultivars, evaluating the genetic diversity in Brassica germplasm, genome mapping and construction of linkage maps, gene tagging and various other genomics-related studies in Brassica species. Further, the evolutionary relationship established among various Brassica species would assist in formulating suitable breeding strategies for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity present in diploid progenitor gene pools.

  18. Comparative evaluation of genetic diversity using RAPD, SSR and ...

    Indian Academy of Sciences (India)

    [Panwar P., Nath M., Yadav V. K. and Kumar A. 2010 Comparative evaluation of genetic diversity using RAPD, SSR and cytochome P450 gene based markers ... sity analysis, the present study aimed to evaluate the relative usefulness of RAPD .... primer ranged from 3 to 15, and size of the products ranged from 300 bp to ...

  19. Validating simple sequence repeat (SSR) markers for introgression ...

    African Journals Online (AJOL)

    Low hybridization efficiency (22.5%) was achieved using the anther dehiscence method. Such low hybridization efficiency requires use of molecular markers to easily identify plants harbouring the required genotypes. Key words: Stay-green, drought tolerance, quantitative trait loci (QTL), simple sequence repeat (SSR) ...

  20. Identification of informative simple sequence repeat (SSR) markers ...

    African Journals Online (AJOL)

    Phi080) to 0.79 (UMC2359), with a mean PIC of 0.53. The analysis also led to identification of informative SSR markers, namely UMC1862 (bin 1.11), UMC1719 (bin 4.10-4.11), UMC1447 (bin 5.03), UMC2359 (bin 9.07) and UMC1432 (bin 10.02), ...

  1. (SSR) marker- assisted genetic diversity among upland Bt- and non ...

    African Journals Online (AJOL)

    Student

    2011-11-02

    Nov 2, 2011 ... new elite cotton cultivars. Key words: Bt-cotton, dissimilarity matrix, DNA polymorphism, genetic diversity, SSR marker. INTRODUCTION. Cotton is the world's most imperative natural textile fiber and a valuable oil seed crop. Cotton is the main cash crop of Pakistan and provides cotton fiber to the national.

  2. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

    Science.gov (United States)

    Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about its inheritance mechanism. To address this problem, a high throughput molecular genotyping experiment was conducted on 964 single pollen grains and a 288-self progeny S1 map...

  3. Genetic relationships revealed by simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    Genetic relationships revealed by simple sequence repeat (SSR) markers among Ghanaian cassava cultivars released by different research groups. ... Genetic diversity was observed within populations (HS = 0.552) and, therefore, suggesting a low rate of inter-population gene flow among the individuals constituting the ...

  4. Association of AFLP and SSR markers with agronomic and fibre ...

    Indian Academy of Sciences (India)

    Molecular markers linked to QTL contributing to agronomic and fibre quality traits would be useful for cotton improvement. We have attempted to tag yield and fibre quality traits with AFLP and SSR markers using F2 and F3 populations of a cross between two Gossypium hirsutum varieties, PS56-4 and RS2013. Out of 50 ...

  5. SSR marker based DNA fingerprinting and diversity study in rice ...

    African Journals Online (AJOL)

    The genetic diversity and DNA fingerprinting of 15 elite rice genotypes using 30 SSR primers on chromosome numbers 7-12 was investigated. The results revealed that all the primers showed distinct polymorphism among the cultivars studied indicating the robust nature of microsatellites in revealing polymorphism. Cluster ...

  6. Study of simple sequence repeat (SSR) polymorphism for biotic ...

    African Journals Online (AJOL)

    ... as recurrent parent was investigated using 128 simple sequence repeat (SSR) primers covered on chromosome number 1-12. The results reveal that 36 HRM primers showed distinct polymorphism among the donor and recurrent parents studied indicating the robust nature of microsatellites in revealing polymorphism.

  7. Genetic diversity studies and identification of SSR markers ...

    Indian Academy of Sciences (India)

    Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan) ... Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanas 221 005, India; Department of Mycology and ...

  8. Physical location of SSR regions and cytogenetic instabilities in ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 2. Physical location of SSR regions and cytogenetic instabilities in Pinus sylvestris chromosomes revealed by ND-FISH. Ivo Pavia Ana Carvalho Luís Rocha Maria João Gaspar José Lima-Brito. Research Note Volume 93 Issue 2 August 2014 pp 567-571 ...

  9. SSR markers reveal genetic variation between improved cassava ...

    African Journals Online (AJOL)

    cassava genotypes at 0.93 similarity coefficient. These five primers clustered the 36 cassavas into 16 groups at 0.70 similarity coefficient. Application of this few SSR primers would ultimately reduce the cost and time of research for genetic diversity and genotype identification studies for the genetic improvement program of ...

  10. Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums.

    Science.gov (United States)

    Li, Xiaobai; Jin, Feng; Jin, Liang; Jackson, Aaron; Huang, Cheng; Li, Kehu; Shu, Xiaoli

    2014-12-05

    Cymbidium is a genus of 68 species in the orchid family, with extremely high ornamental value. Marker-assisted selection has proven to be an effective strategy in accelerating plant breeding for many plant species. Analysis of cymbidiums genetic background by molecular markers can be of great value in assisting parental selection and breeding strategy design, however, in plants such as cymbidiums limited genomic resources exist. In order to obtain efficient markers, we deep sequenced the C. ensifolium transcriptome to identify simple sequence repeats derived from gene regions (genic-SSR). The 7,936 genic-SSR markers were identified. A total of 80 genic-SSRs were selected, and primers were designed according to their flanking sequences. Of the 80 genic-SSR primer sets, 62 were amplified in C. ensifolium successfully, and 55 showed polymorphism when cross-tested among 9 Cymbidium species comprising 59 accessions. Unigenes containing the 62 genic-SSRs were searched against Non-redundant (Nr), Gene Ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The search resulted in 53 matching Nr sequences, of which 39 had GO terms, 18 were assigned to KOGs, and 15 were annotated with KEGG. Genetic diversity and population structure were analyzed based on 55 polymorphic genic-SSR data among 59 accessions. The genetic distance averaged 0.3911, ranging from 0.016 to 0.618. The polymorphic index content (PIC) of 55 polymorphic markers averaged 0.407, ranging from 0.033 to 0.863. A model-based clustering analysis revealed that five genetic groups existed in the collection. Accessions from the same species were typically grouped together; however, C. goeringii accessions did not always form a separate cluster, suggesting that C. goeringii accessions were polyphyletic. The genic-SSR identified in this study constitute a set of markers that can be applied across multiple Cymbidium species and used for the evaluation

  11. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability.

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

  12. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology.

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  13. Genome-Wide Characterization of Simple Sequence Repeat (SSR Loci in Chinese Jujube and Jujube SSR Primer Transferability.

    Directory of Open Access Journals (Sweden)

    Jing Xiao

    Full Text Available Chinese jujube (Ziziphus jujuba, an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

  14. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

  15. Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.).

    Science.gov (United States)

    Zhao, Yongli; Williams, Roxanne; Prakash, C S; He, Guohao

    2012-12-15

    Date palm (Phoenix dactylifera L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding. In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs) and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs). We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7%) were the most common, followed by tetranucleotide (10.4%) and dinucleotide motifs (9.6%). The motif AG (85.7%) was most abundant in dinucleotides, while motifs AGG (26.8%), AAG (19.3%), and AGC (16.1%) were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4%) of such ESTs had homology with known proteins. Date palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.

  16. Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.

    Directory of Open Access Journals (Sweden)

    Zhao Yongli

    2012-12-01

    Full Text Available Abstract Background Date palm (Phoenix dactylifera L. is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding. Results In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs. We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7% were the most common, followed by tetranucleotide (10.4% and dinucleotide motifs (9.6%. The motif AG (85.7% was most abundant in dinucleotides, while motifs AGG (26.8%, AAG (19.3%, and AGC (16.1% were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4% of such ESTs had homology with known proteins. Conclusion Date palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.

  17. SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeis guineensis.

    Science.gov (United States)

    Tranbarger, Timothy John; Kluabmongkol, Wanwisa; Sangsrakru, Duangjai; Morcillo, Fabienne; Tregear, James W; Tragoonrung, Somvong; Billotte, Norbert

    2012-01-03

    The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's number one source of edible vegetable oil, and the richest dietary source of provitamin A. While new elite genotypes from traditional breeding programs provide steady yield increases, the long selection cycle (10-12 years) and the large areas required to cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding programs have the potential to make significant impacts on the rate of genetic improvement but the limited molecular resources, in particular the lack of molecular markers for agronomic traits of interest, restrict the application of molecular breeding schemes for oil palm. In the current study, 6,103 non-redundant ESTs derived from cDNA libraries of developing vegetative and reproductive tissues were annotated and searched for simple sequence repeats (SSRs). Primer pairs from sequences flanking 289 EST-SSRs were tested to detect polymorphisms in elite breeding parents and their crosses. 230 of these amplified PCR products, 88 of which were polymorphic within the breeding material tested. A detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms within the transcripts, and that the main functional category was related to transcription and post-transcriptional regulation. Indeed, SSR polymorphisms were found in sequences encoding AP2-like, bZIP, zinc finger, MADS-box, and NAC-like transcription factors in addition to other transcriptional regulatory proteins and several RNA interacting proteins. The identification of new EST-SSRs that detect polymorphisms in elite breeding material provides tools for molecular breeding strategies. The identification of SSRs within transcripts, in particular those that encode proteins involved in transcriptional and post-transcriptional regulation, will allow insight into the functional roles of these proteins by studying the phenotypic traits

  18. Development and Characterization of EST-SSR Markers in the Chinese Medicinal Plant Callerya speciosa (Fabaceae

    Directory of Open Access Journals (Sweden)

    Li Li

    2013-06-01

    Full Text Available Premise of the study: The first microsatellite primers were developed for Callerya speciosa, an important traditional medicinal plant with island-mainland distributions in China, to further investigate its genetic variability and population structure. Methods and Results: The microsatellite-containing sequences were selected from a cDNA library of C. speciosa. In total, 58 primer pairs were designed, and 25 of the corresponding loci showed clear amplification. Polymorphisms were assessed in two different natural populations. The mean number of alleles per locus ranged from two to nine. Observed and expected heterozygosity per loci ranged from 0.067 to 0.938 and 0.064 to 0.836, respectively. One out of 25 loci showed departure from Hardy–Weinberg equilibrium expectations in both populations, and three pairs of loci showed significant linkage disequilibrium after Bonferroni correction. Conclusions: These microsatellite markers will be useful tools for genetic and conservation studies and to understand the evolutionary processes in Callerya species.

  19. Characterization of EST-based SSR loci in the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae)

    Science.gov (United States)

    B.M.T. Brunet; D. Doucet; B.R. Sturtevant; F.A.H. Sperling

    2013-01-01

    After identifying 114 microsatellite loci from Choristoneura fumiferana expressed sequence tags, 87 loci were assayed in a panel of 11 wild-caught individuals, giving 29 polymorphic loci. Further analysis of 20 of these loci on 31 individuals collected from a single population in northern Minnesota identified 14 in Hardy-Weinberg equilibrium.

  20. Development and characterization of EST-SSR markers forArtocarpus hypargyreus(Moraceae).

    Science.gov (United States)

    Liu, Haijun; Tan, Weizheng; Sun, Hongbin; Liu, Yu; Meng, Kaikai; Liao, Wenbo

    2016-12-01

    Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Based on the transcriptome data of A. hypargyreus , 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus . The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus . Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus , indicating that they will be of great value for genetic study across this genus.

  1. Development and characterization of EST-SSR markers for Artocarpus hypargyreus (Moraceae)1

    Science.gov (United States)

    Liu, Haijun; Tan, Weizheng; Sun, Hongbin; Liu, Yu; Meng, Kaikai; Liao, Wenbo

    2016-01-01

    Premise of the study: Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Methods and Results: Based on the transcriptome data of A. hypargyreus, 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus. The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. Conclusions: These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus. Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus, indicating that they will be of great value for genetic study across this genus. PMID:28101438

  2. Analyses of Thinopyrum bessarabicum, T. elongatum, and T. junceum chromosomes using EST-SSR markers

    National Research Council Canada - National Science Library

    Jensen, Kevin B; Larson, Steven R; Wang, Richard R.-C

    2010-01-01

    Wild Thinopyrum grasses are important gene pools for forage and cereal crops. Knowledge of their chromosome organizations is pivotal for efficient utilization of this important gene pool in germplasm enhancement programs...

  3. Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae).

    Science.gov (United States)

    Tseng, Yu-Hsin; Huang, Han-Yau; Xu, Wei-Bin; Yang, Hsun-An; Liu, Yan; Peng, Ching-I; Chung, Kuo-Fang

    2017-05-01

    Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa. The expressed sequence tag-simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis.

  4. Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae)1

    Science.gov (United States)

    Tseng, Yu-Hsin; Huang, Han-Yau; Xu, Wei-Bin; Yang, Hsun-An; Liu, Yan; Peng, Ching-I; Chung, Kuo-Fang

    2017-01-01

    Premise of the study: Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. Methods and Results: Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa. Conclusions: The expressed sequence tag–simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis. PMID:28529834

  5. Diversity of garlic (Allium sativum L.) using SSR, EST and AFLP markers

    Science.gov (United States)

    Germplasm from the center of origin/diversity is important for the breeding and fingerprinting crop plants. In this study we utilized both dominant and co-dominant markers for the characterization of garlic samples from diverse geographic origins to assess the relative utility of these markers to id...

  6. Development and Identification of SSR Markers Associated with Starch Properties and β-Carotene Content in the Storage Root of Sweet Potato (Ipomoea batatas L.).

    Science.gov (United States)

    Zhang, Kai; Wu, Zhengdan; Tang, Daobin; Lv, Changwen; Luo, Kai; Zhao, Yong; Liu, Xun; Huang, Yuanxin; Wang, Jichun

    2016-01-01

    Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of genome information. Short sequence repeat (SSR) markers are powerful molecular tools for tracking important loci in crops and for molecular-based breeding strategies; however, few SSR markers and marker-trait associations have hitherto been identified in sweet potato. In this study, we identified 1824 SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato, and designed 1476 primer pairs based on SSR-containing sequences. We mapped 214 pairs of primers in a natural population comprised of 239 germplasms, and identified 1278 alleles with an average of 5.972 alleles per locus and a major allele frequency of 0.7702. Population structure analysis revealed two subpopulations in this panel of germplasms, and phenotypic characterization demonstrated that this panel is suitable for association mapping of starch-related traits. We identified 32, 16, and 17 SSR markers associated with starch content, β-carotene content, and starch composition in the storage root, respectively, using association analysis and further evaluation of a subset of sweet potato genotypes with various characteristics. The SSR markers identified here can be used to select varieties with desired traits and to investigate the genetic mechanism underlying starch and carotenoid formation in the starchy roots of sweet potato.

  7. Nuclear and cytoplasmic genome components of Solanum tuberosum + S. chacoense somatic hybrids and three SSR alleles related to bacterial wilt resistance.

    Science.gov (United States)

    Chen, Lin; Guo, Xianpu; Xie, Conghua; He, Li; Cai, Xingkui; Tian, Lingli; Song, Botao; Liu, Jun

    2013-07-01

    The somatic hybrids were derived previously from protoplast fusion between Solanum tuberosum and S. chacoense to gain the bacterial wilt resistance from the wild species. The genome components analysis in the present research was to clarify the nuclear and cytoplasmic composition of the hybrids, to explore the molecular markers associated with the resistance, and provide information for better use of these hybrids in potato breeding. One hundred and eight nuclear SSR markers and five cytoplasmic specific primers polymorphic between the fusion parents were used to detect the genome components of 44 somatic hybrids. The bacterial wilt resistance was assessed thrice by inoculating the in vitro plants with a bacterial suspension of race 1. The disease index, relative disease index, and resistance level were assigned to each hybrid, which were further analyzed in relation to the molecular markers for elucidating the potential genetic base of the resistance. All of the 317 parental unique nuclear SSR alleles appeared in the somatic hybrids with some variations in the number of bands detected. Nearly 80 % of the hybrids randomly showed the chloroplast pattern of one parent, and most of the hybrids exhibited a fused mitochondrial DNA pattern. One hundred and nine specific SSR alleles of S. chacoense were analyzed for their relationship with the disease index of the hybrids, and three alleles were identified to be significantly associated with the resistance. Selection for the resistant SSR alleles of S. chacoense may increase the possibility of producing resistant pedigrees.

  8. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)

    OpenAIRE

    Peng-cheng Fu; Yan-Zhao Zhang; Hui-yuan Ya; Qing-bo Gao

    2016-01-01

    Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assem...

  9. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery.

    Science.gov (United States)

    Kaur, Sukhjiwan; Cogan, Noel O I; Pembleton, Luke W; Shinozuka, Maiko; Savin, Keith W; Materne, Michael; Forster, John W

    2011-05-25

    Lentil (Lens culinaris Medik.) is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs). De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR)-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

  10. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

    Directory of Open Access Journals (Sweden)

    Materne Michael

    2011-05-01

    Full Text Available Abstract Background Lentil (Lens culinaris Medik. is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs. De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

  11. Identification and differentiation of Ricinus communis L. using SSR markers

    Directory of Open Access Journals (Sweden)

    Zdenka Gálová

    2015-12-01

    Full Text Available Normal 0 false false false CS JA X-NONE The castor-oil plant (Ricinus communis L., a member of the spurge family (Euphorbiaceae, is a versatile industrial oil crop that is cultivated in many tropical and subtropical regions of the world. Castor oil is of continuing importance to the global specialty chemical industry because it is the only commercial source of a hydroxylated fatty acid. Castor also has tremendous future potential as an industrial oilseed crop because of its high seed oil content, unique fatty acid composition, potentially high oil yields and ability to be grown under drought and saline conditions. Knowledge of genetic variability is important for breeding programs to provide the basis for developing desirable genotypes. The aim of this study was to assess genetic diversity within the set of 60 ricin genotypes using 10 SSR primers. Ten SSR primers revealed a total of 67 alleles ranging from 4 to 9 alleles per locus with a mean value of 6.70 alleles per locus. The PIC values ranged from 0.719 to 0.860 with an average value of 0.813 and the DI value ranged from 0.745 to 0.862 with an average value of 0.821. Probability of identity (PI was low ranged from 0.004 to 0.018 with an average of 0.008. A dendrogram was constructed from a genetic distance matrix based on profiles of the 10 SSR loci using the unweighted pair-group method with the arithmetic average (UPGMA. According to analysis, the collection of 60 diverse accessions of castor bean was clustered into six clusters. We could not distinguish 2 genotypes grouped in cluster 1, RM-96 and RM-98, which are genetically the closest. Knowledge on the genetic diversity of castor can be used to future breeding programs of castor.

  12. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers.

    Science.gov (United States)

    Gupta, Mamta; Verma, Bhawna; Kumar, Naresh; Chahota, Rakesh K; Rathour, Rajeev; Sharma, Shyam K; Bhatia, Sabhyata; Sharma, Tilak R

    2012-01-01

    Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n = 2x = 14), cool-season legume crop and is consumed worldwide as a rich source of protein (~24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F(2) plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.

  13. SAT, a flexible and optimized Web application for SSR marker development

    Directory of Open Access Journals (Sweden)

    Rami Jean-François

    2007-11-01

    Full Text Available Abstract Background Simple Sequence Repeats (SSRs, or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. Results SAT (SSR Analysis Tool is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries. SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. Conclusion The SAT Web application is available at http://sat.cirad.fr/sat, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator tropgene@cirad.fr to request a login and password.

  14. SAT, a flexible and optimized Web application for SSR marker development.

    Science.gov (United States)

    Dereeper, Alexis; Argout, Xavier; Billot, Claire; Rami, Jean-François; Ruiz, Manuel

    2007-11-29

    Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries.SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. The SAT Web application is available at http://sat.cirad.fr/sat, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator tropgene@cirad.fr to request a login and password.

  15. Development of SSR markers and construction of a linkage map in jute

    Indian Academy of Sciences (India)

    2012-04-13

    Apr 13, 2012 ... to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). ... ties and utility have been widely discussed elsewhere (Hazra et al. 2004). ...... 174–181. Liu S. S., Kowalskey S. P., Lan T. H., Feldmann K. A. and Paterson.

  16. Development and validation of new SSR markers from expressed regions in the garlic genome

    Science.gov (United States)

    Limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) although SSR markers have become one of the most preferred marker systems because they are typically co-dominant, reproducible, cross species transferable and highly polymorphic. In this ...

  17. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    OpenAIRE

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Amon...

  18. SSR markers in characterization of sweet corn inbred lines

    Directory of Open Access Journals (Sweden)

    Srdić Jelena

    2008-01-01

    Full Text Available Sweet corn differs from field corn in many important traits. So its breeding although includes some standard procedures demand application of techniques that are important for determining special traits, all because of the specificity of its usage. Application of molecular markers becomes almost a necessity for the breeding of sweet corn, especially because this is the type of maize in which still no definitive heterotic patterns have been determined. So getting to know genetic divergence of the sweet corn inbred lines is of great importance for its breeding. In this paper we analyzed genetic similarity of six sweet corn inbreds based on SSR markers. 40 SSR primers were used in DNA amplification. Results were compared and correlated with the data on specific combining ability, obtained by the diallel analysis. The results of SCA were in concurrence with genetic similarity. Values of rank correlation coefficient were negative, indicating that more similar inbred lines had smaller estimates of SCA, and lines that were less similar had higher estimates of SCA. Rank correlation coefficient between SCA and GS according to Dice coefficient was between -0,16 and -0,57*.

  19. Molecular Characterization of Wheat Genotypes Using SSR Markers

    Directory of Open Access Journals (Sweden)

    Sheikh Arslan Sehgal

    2012-07-01

    Full Text Available Wheat (Triticum aestivum L. rusts are the most destructive and widespread among all other diseases of wheat because of their wide distribution, and their capacity to form new races that can attack previously resistant cultivars which result in serious yield losses. The molecular characterization and genetic diversity of 20 wheat genotypes was investigated using 34 polymorphic Simple Sequence Repeats (SSR screened primers. About thirty-one loci were found. Lr-19 gene was present in all 20 wheat genotypes that cause resistance against wheat rust. Shalimar-86 and Chakwal-86 showed the highest genetic diversity with SH-02 and Ufaq respectively, giving a 98.94% genetic similarity and a minimum genetic diversity was observed between Chakwal-50 and Bhakar which showed that they are 74% similar. The current research found that SSR makers could distinguish and characterize all of the genotypes, more screened primers could be used for study and for saturation of different regions in further research. The identification of rust resistant genes in Pakistani wheat germplasm will help in accelerating the breeding program in future, including pyramiding of different wheat resistant genes in wheat genotypes and varieties.

  20. Deteksi Kestabilan Genetik Ramet Kelapa Sawit Hasil Kultur In Vitro Menggunakan SSR

    Directory of Open Access Journals (Sweden)

    Yuni Fitri Cahyaningsih

    2016-06-01

    Full Text Available ABSTRACTCommercial production of oil palm ramet requires the guarantee of high genetic stability. The objectives of this research were to determine 1 genetic diversity of ortet as source of explant, and 2 genetic stability of ramet derived from ortet propagated through tissue culture. Genetic stability analysis was done using ramet from five Tenera (D×P oil palm ortets.As many as 20 ramets were randomly chosen from each ortet. A total of 100 ramets were used for genetic stability analysis. Genetic similarity analysis was analyzed using NTSyspc version 2.1 software with method Similarity for Qualitative Data and Unweighted Pair Group Method Aritmatic (UPGMA. The results indicated 20 SSR primer pairs were polymorphic and could form 44 alleles. As many as 80% of ramets from IS 3 ortet showed genetic similarity ranged from 97-100% to the ortet. All ramets derived from IS 10, IS 20 and IS 40 ortet had 90-100% of genetic similarity to its respective ortet. Futhermore, 95% of ramets from IS 39 ortet had 97-100% of genetic similarity to the ortet.Keywords: Elaeis guineensis Jacq., genetic similarity, tissue culture

  1. Genetic variability assessment in the genus Passiflora by SSR markers

    Directory of Open Access Journals (Sweden)

    Claudia Lougon Paiva

    2014-09-01

    Full Text Available The genus Passiflora encompasses many species that are endemic to the Brazilian territory, including some with economic value. Studies on genetic diversity in this genus are fundamental because they allow understanding genetic variability and distance. The present study aimed to determine the genetic variability and distances among 10 species of the genus Passiflora by using microsatellite markers (Simple Sequence Repeat, SSR. Twenty-eight heterologous microsatellite markers were tested, but only 12 were used in the diversity analysis because they amplified in at least 80% of the species. A clear separation was observed among the subgenuses studied, as well as wide variation among the accessions of Passiflora. This knowledge enables breeders to explore diversity and transfer favorable alleles found in wild species.

  2. Efficiency of biparental crossing in sugarcane analyzed by SSR markers

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    João Messias dos Santos

    2014-07-01

    Full Text Available Sugarcane has hermaphrodite flowers, however, selfing and cross pollination may occur, resulting in selfed or hybrid progeny. The aim of this study was to analyze the paternity of progenies from biparental crosses, in order to identify true hybrids or progenies originating from pollen of unknown origin. Seventy-six progenies from four crosses were analyzed using three highly polymorphic microsatellite markers (SSR. Progenies showed moderate genetic similarity and were grouped into four distinct groups, according to the crosses. Transmission of alleles from parents to offspring was clearly observed, in which selfed individuals were not observed, and only true hybrids or progeny resulting from fertilization with pollen uncommon to both parents were. Results showed that there was contamination with pollen from unknown parents in sugarcane crosses, suggesting that errors in the pedigree may occur, and adjustment in the crossing procedure would decrease progenies from pollen of unknown origin.

  3. Specificity of SSR loci for Melampsora species on poplars

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    Galović Vladislava

    2010-01-01

    Full Text Available Two rust fungi, Melampsora larici populina and Melampsora medusae are common in all poplar growing regions worlwide. M. larici populina is native to Eurasia, while M. medusae is endemic to eastern Unated States on Populus deltoides. Poplar leaf rust (Melampsora sp. is widely spread disease in our country, and can cause significant growing problems. Race that prevails in our growing region is M. Larici populina. This work initiated the research of population composition, i.e. qualitative participation of Melampsora races in popoluation of black poplars hybrid progenies using molecular methods. When five SSR markers were used the results showed that M. larici populina was found in three tested clones, while only M. medusae was determined in clone I-214.

  4. Data of 10 SSR markers for genomes of homo sapiens and monkeys.

    Science.gov (United States)

    Reddy, K K V V V S; Raju, S Viswanadha; Someswara Rao, Chinta

    2017-06-01

    In this data, we present 10 Simple Sequence Repeat(SSR) markers TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA which are extracted from the genomes of homo sapiens and monkeys using string matching mechanism [1]. All loci showed 4 Base Pair(bp) in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that maybe useful for the detection of similarity among the genotypes. Collectively, these data show that the SSR extraction is a valuable method to illustrate genetic variation of genomes.

  5. Regulation of transcription from two ssrS promoters in 6S RNA biogenesis.

    Science.gov (United States)

    Lee, Ji Young; Park, Hongmarn; Bak, Geunu; Kim, Kwang-sun; Lee, Younghoon

    2013-09-01

    ssrS-encoded 6S RNA is an abundant noncoding RNA that binds σ(70)-RNA polymerase and regulates expression at a subset of promoters in Escherichia coli. It is transcribed from two tandem promoters, ssrS P1 and ssrS P2. Regulation of transcription from two ssrS promoters in 6S RNA biogenesis was examined. Both P1 and P2 were growth phase-dependently regulated. Depletion of 6S RNA had no effect on growth-phase-dependent transcription from either promoter, whereas overexpression of 6S RNA increased P1 transcription and decreased P2 transcription, suggesting that transcription from P1 and P2 is subject to feedback activation and feedback inhibition, respectively. This feedback regulation disappeared in Δfis strains, supporting involvement of Fis in this process. The differential feedback regulation may provide a means for maintaining appropriate cellular concentrations of 6S RNA.

  6. Impedance characteristics of DFIGs considering the impacts of DFIG numbers and its application on SSR analysis

    Science.gov (United States)

    You, J. J.; Ning, W. Y.; Jiang, H.; Dong, Y. X.; Liu, H.; Li, Y.

    2017-05-01

    Sub-synchronous resonance (SSR) occurred in the power system with both Doubly Fed Induction Generators (DFIGs) and series-compensated lines. There have been several papers focusing on the analysis of such SSR phenomenon. To the authors’ knowledge, the impacts of DFIG numbers are seldom considered in existing papers. In this paper, the impedance characteristics of DFIGs under different numbers are analyzed. Then the relationship between DFIG numbers and SSR characteristics is discussed. The contributions to be included in the paper are as following: 1) the impedance of N DFIGs is roughly equal to 1/N of the impedance of one DFIG. 2) The SSR risk of system is related with both the numbers of DFIGs and the parameters of the series-compensated lines.

  7. Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers

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    Sandra Bibiana Aguilar

    2007-01-01

    Full Text Available The Andean blackberry belongs to the genus Rubus, the largest of the Rosaceae family and one of the mostdiverse of the plant kingdom. In Colombia Rubus glaucus Benth, known as the Andean raspberry or blackberry, is one of thenine edible of the genus out of forty-four reported species. In this study wild and cultivated genotypes, collected in the CentralAndes of Colombia were analyzed by AFLP and SSR markers. Sexual reproduction seems to play an important role inmaintaining the genetic variability in R. glaucus, and the viability of using the SSR of Rubus alceifolius to characterizeColombian Rubus species was clearly demonstrated. All species evaluated produced very specific banding patterns,differentiating them from the others. Both AFLP and SSR produced bands exclusive to each of the following species: R.robustus, R. urticifolius, R. glaucus, and R. rosifolius. The SSR markers differentiated diploid and tetraploid genotypes of R.glaucus.

  8. Molecular characterization of potato cultivars using SSR markers Caracterização molecular de cultivares de batata por marcadores SSR

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    Patrícia Favoretto

    2011-12-01

    Full Text Available The potato crop has a very narrow genetic base, so the use of molecular markers is a very important tool in the characterization of germplasm banks and evaluation of genetic divergence. The objective of this study was to identify, using microsatellite or simple sequence repeat (SSR markers, 38 accessions of potato from two collections of commercial cultivars. For the molecular characterization 10 loci were used, generating a total of 46 alleles, which were analyzed as binary data. A cluster analysis was performed with the Jaccard´s similarity coefficient and the UPGMA method, using the software NTSYSpc. On average, the number of alleles per locus was 4.6, ranging from two alleles for primers STM1049, STM 1053 and STM 1104 to 12 alleles per locus for primer STM0019a. Of the 46 alleles, only five were monomorphic, therefore presenting 89.1% polymorphism. The polymorphism information content (PIC varied from 0.13 to 0.86, with an average of 0.54. The Jaccard´s coefficient varied from 0.41 to 0.93, showing high genetic variability among accessions. Two possible duplicates [Atlantic (Canada and Atlantic (Chile, and Colorado and Ágata (EPAMIG (duplicates with these SSRs, which did not separate them] were identified. High similarity was also shown by cultivars Chipie and Melodie (EPAMIG, Voyager and Gourmandine (EPAMIG, Eole and Caesar (EPAMIG, and Cupido and Santé (Pirassu. The most genetically divergent accessions (Lady Rosetta and HPC-7B were also identified.A batata possui uma base genética estreita, sendo assim a utilização de marcadores moleculares é uma ferramenta muito importante no processo de caracterização de bancos de germoplasma e avaliação de divergência genética. O objetivo deste trabalho foi avaliar por meio de marcadores microssatélites ou Simple Sequence Repeats (SSR, 38 acessos de batata de duas coleções distintas contendo cultivares comerciais. Para a caracterização molecular foram analisados 10 loci, gerando um

  9. Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers.

    Science.gov (United States)

    Soriano, José Miguel; Romero, Carlos; Vilanova, Santiago; Llácer, Gerardo; Badenes, María Luisa

    2005-02-01

    Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus x domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (-0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus x domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.

  10. Genetic similarity among Tunisian cultivated olive estimated through SSR markers

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    Sofiane Abdelhamid

    2013-02-01

    Full Text Available Olive (Olea europaea L. subsp. europaea var. europaea is one of the oldest fruit tree in the Mediterranean basin, and is cultivated for oil and canned fruit. Part of this interest is driven by the economic importance of olive oil which is increasing throughout the world due to its beneficial effect to human health. In Tunisia, olive has great socio-economic importance, with more than 60 millions olive trees cultivated for olive oil production including a wide range of cultivars which are widely extended from the north to the south regions of the country for its high economic value. Here, we applied microsatellites (SSRs molecular markers to assess the genetic variability of the most important Tunisian olive cultivars. In total, the 10 simple sequence repeats (SSR loci revealed 73 alleles with a mean number of 07 alleles per locus were detected. The polymorphism index content (PIC values were high (0.72 ranging from 0.86 at GAPU 103 to 0.56 at EMO 90. The analysis of the dendrogram showed six main separate groups.

  11. STUDY OF GENETIC VARIABILITY OF TRITICALE VARIETIES BY SSR MARKERS

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    Jana Ondroušková

    2013-04-01

    Full Text Available For the detection of genetic variability ten genotypes of winter triticale (×Triticosecale Wittmack, 2n = 6x = 42; BBAARR were selected: nine varieties and one breeding line with good bread-making quality KM 4-09 with the chromosome translocation 1R.1D 5+10-2. 25 microsatellites markers located in the genome A, B, D and R were chosen for analysis. Eighty-four alleles were detected with an average of 3.36 alleles per locus were detected. For each microsatellite statistical values were calculated diversity index (DI, probabilities of identity (PI and polymorphic information content (PIC were calculated and averages statistical values are: DI 0.55, PI 0.27 and 0.5 PIC. Overall dendrogram based on the UPGMA method (Jaccards similarity coefficient significantly distinguished two groups of genotypes and these groups were divided into sub-clusters. A set of 5 SSR markers (Xwms0752, Xbarc128, Xrems1237, Xwms0861 and Xbrac170 which have the calculated PIC value higher than 0.68 that are sufficient for the identification of the analyzed genotypes was described.

  12. SSR Markers Associated with Proline in Drought Tolerant Wheat Germplasm.

    Science.gov (United States)

    Iqbal, Muhammad Javid; Maqsood, Yasir; Abdin, Zain Ul; Manzoor, Atif; Hassan, Muhammad; Jamil, Amer

    2016-03-01

    Water stress causes major agricultural loss throughout the world as survival of the crops remained under stress and loss in yield. Plants respond to drought stress by means of different adaptive mechanisms such as accumulation of osmoprotectants to counteract the water stress. Amino acid proline is known to occur widely in higher plants and normally accumulates in large quantities as an osmolyte in response to environmental stresses. Biochemical estimation of proline was done in the drought-affected wheat genotypes by spectrophotometric method. Proline promoted a positive effect as root/shoot ratio was enhanced in wheat germplasm under drought stress. SSR primer pairs (45) were tested for polymorphism among selected wheat genotypes. The dendrogram results have shown the wheat genotype association with the levels of proline during induced drought stress. The relationship between pattern of drought responsive biochemical attributes and DNA markers in the selected wheat genotypes was recognized to select drought tolerant genotypes for sowing in drought affected areas of the country.

  13. Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.).

    Science.gov (United States)

    Mokhtar, Morad M; Adawy, Sami S; El-Assal, Salah El-Din S; Hussein, Ebtissam H A

    2016-01-01

    The present investigation was carried out aiming to use the bioinformatics tools in order to identify and characterize, simple sequence repeats within the third Version of the date palm genome and develop a new SSR primers database. In addition single nucleotide polymorphisms (SNPs) that are located within the SSR flanking regions were recognized. Moreover, the pathways for the sequences assigned by SSR primers, the biological functions and gene interaction were determined. A total of 172,075 SSR motifs was identified on date palm genome sequence with a frequency of 450.97 SSRs per Mb. Out of these, 130,014 SSRs (75.6%) were located within the intergenic regions with a frequency of 499 SSRs per Mb. While, only 42,061 SSRs (24.4%) were located within the genic regions with a frequency of 347.5 SSRs per Mb. A total of 111,403 of SSR primer pairs were designed, that represents 291.9 SSR primers per Mb. Out of the 111,403, only 31,380 SSR primers were in the genic regions, while 80,023 primers were in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represents 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. Concerning in vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 18 primers detected polymorphic amplicons among the studied date palm cultivars.

  14. An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species

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    Ana Lilia Alzate-Marin

    2009-10-01

    Full Text Available An efficient and rapid DNA minipreparation modified method for frozen samples was developed for five tropical tree species: Copaifera langsdorffii, Hymenaea courbaril, Eugenia uniflora, Tabebuia roseo alba and Cariniana estrellensis. This procedure that dispenses the use of liquid nitrogen, phenol and the addition of proteinase K, is an adaptation of the CTAB-based DNA extraction method. The modifications included the use of PVP to eliminate the polyphenols, only one chloroform-isoamyl alcohol step and the addition of RNase immediately after extraction with chloroform. The yields of the DNA samples ranged from 25.7 to 42.1 µg from 100 mg leaf tissue. The DNA samples extracted by this method were successfully used for PCR (SSR and RAPD analyses in these five and other twelve tropical tree species.Este trabalho teve como objetivo otimizar um protocolo econômico, rápido e eficaz de minipreparação de DNA genômico, para as espécies florestais Copaifera langsdorffii (Óleo de Copaíba, Hymenaea courbaril (Jatobá, Eugenia uniflora (Pitanga, Tabebuia roseo alba (Ipê Branco e Cariniana estrellensis (Jequitibá Branco. Este método é uma adaptação da técnica de extração CTAB de Doyle e Doyle (1990, o qual consiste principalmente na adição de PVP para eliminar polifenoles, somente uma etapa de extração com clorofórmio-álcool isoamílico e a adição da RNase A imediatamente após a extração com clorofórmio. O método também dispensa o uso de nitrogênio líquido, o uso do fenol e a adição de proteinase K. Os DNAs das espécies florestais extraídos apresentaram alto rendimento e boa qualidade, com rendimento de 25.7 a 42.1 µg de DNA a partir de 100 mg de tecido foliar congelado. Com este protocolo, em apenas 1 dia de trabalho, uma pessoa pode completar o isolamento do DNA de aproximadamente 50 amostras de folhas (dependendo da capacidade da centrífuga. O DNA obtido pode ser usado para métodos de análise baseados em PCR (SSR e

  15. Development of simple sequence repeat (SSR) markers that are ...

    African Journals Online (AJOL)

    Simple sequence repeats (SSRs) markers were developed through data mining of 3,803 expressed sequence tags (ESTs) previously published. A total of 144 di- to penta-type SSRs were identified and they were screened for polymorphism between two turnip cultivars, 'Tsuda' and 'Yurugi Akamaru'. Out of 90 EST-SSRs for ...

  16. Genetic diversity and DNA fingerprinting in jute (Corchorus spp. based on SSR markers

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    Liwu Zhang

    2015-10-01

    Full Text Available Genetic diversity analysis and DNA finger printing are very useful in breeding programs, seed conservation and management. Jute (Corchorus spp. is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties (Huangma 179 and Kuanyechangguo from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with CoSSR305-120 and CoSSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  17. Identification of male genotypes in Pistacia vera L. species using SSR markers

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    Najwa Motaeb Alhajjar

    2017-05-01

    Full Text Available Genetic identification among different 15 male genotypes of Pistacia vera L. species in comparison with five main commercial male cultivars accredited by Ministry of Agriculture (Adam, Jamil, Ebrahim, Elyas and Khalifa was achieved using SSR markers. Seventeen primer pairs out of Twenty SSR primers were able to amplify PCR products. SSR segregation produced 44 putative alleles, of which 34 were polymorphic (77.27%. Genetic similarity among all studied genotypes ranged from 0.45 between Jamil cultivar and MAS1 genotype to 1 between Ebrahim cultivar and MA1 genotype which means that they are identical. The UPGMA cluster analysis based on Jaccard’s coefficient grouped all genotypes into three main clusters. The number of alleles revealed by each SSR analysis ranged from 1 to 5, with a high level of expected heterozygosity (He 0.507. Co-dominant SSRs loci were observed in some studied genotypes giving a value 0.235 of observed heterozygosity (Ho. According to the polymorphic allele’s number and the expected heterozygosity; Marker Index (MI was 23.97. Our results concluded that SSR marker is an informative technique, which revealed high ability to differentiate individuals, and played an important role as a genetic marker for identification and evaluation studies within P. vera species.INTERNATIONAL JOURNAL OF ENVIRONMENTVolume-6, Issue-2, Mar-May 2017, Page: 30-42

  18. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.

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    Peng-cheng Fu

    2016-02-01

    Full Text Available Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae], native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb. (A+ T-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.

  19. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.).

    Science.gov (United States)

    Fu, Peng-Cheng; Zhang, Yan-Zhao; Ya, Hui-Yuan; Gao, Qing-Bo

    2016-01-01

    Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1-6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.

  20. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)

    Science.gov (United States)

    Fu, Peng-cheng; Zhang, Yan-Zhao; Ya, Hui-yuan

    2016-01-01

    Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop. PMID:26925343

  1. Selection of high heterozygosity popcorn varieties in Brazil based on SSR markers.

    Science.gov (United States)

    Eloi, I B O; Mangolin, C A; Scapim, C A; Gonçalves, C S; Machado, M F P S

    2012-07-19

    We analyzed genetic structure and diversity among eight populations of popcorn, using SSR loci as genetic markers. Our objectives were to select SSR loci that could be used to estimate genetic diversity within popcorn populations, and to analyze the genetic structure of promising populations with high levels of heterozygosity that could be used in breeding programs. Fifty-seven alleles (3.7 alleles per locus) were detected; the highest effective number of alleles (4.21) and the highest gene diversity (0.763) were found for the Umc2226 locus. A very high level of population differentiation was found (F(ST) = 0.3664), with F(ST) for each locus ranging from 0.1029 (Umc1664) to 0.6010 (Umc2350). This analysis allowed us to identify SSR loci with high levels of heterozygosity and heterozygous varieties, which could be selected for production of inbred lines and for developing new cultivars.

  2. 78 FR 12130 - Social Security Ruling, SSR 13-3p; Appeal of an Initial Medical Disability Cessation...

    Science.gov (United States)

    2013-02-21

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-3p; Appeal of an Initial Medical Disability Cessation Determination or Decision AGENCY: Social Security Administration. ACTION: Notice of Social Security Ruling (SSR...

  3. 77 FR 43640 - Social Security Ruling, SSR 12-2p; Titles II and XVI: Evaluation of Fibromyalgia

    Science.gov (United States)

    2012-07-25

    ... ADMINISTRATION Social Security Ruling, SSR 12-2p; Titles II and XVI: Evaluation of Fibromyalgia AGENCY: Social... determinable impairment of fibromyalgia, and how we evaluate fibromyalgia in disability claims and continuing... Interpretation Ruling Titles II and XVI: Evaluation of Fibromyalgia Purpose: This Social Security Ruling (SSR...

  4. Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan to other Citrus species and their effectiveness for genetic mapping

    Directory of Open Access Journals (Sweden)

    Ollitrault Patrick

    2008-06-01

    Full Text Available Abstract Background During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide or their position in the coding sequences. Results Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides in 1500 unigenes (13.6%. More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50% concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten Citrus species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR. We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45% were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange than for Citrus basic true species (mandarin, pummelo and citron (70% with a significant proportion suitable for synteny analysis. Conclusion Fourty one new EST-SSR markers were produced and were available for

  5. The use of cross species SSR primers to study genetic diversity of ...

    African Journals Online (AJOL)

    Sixteen pairs of primers designed to amplify SSR regions of Medicago truncatula were used to amplify genomic DNA samples of 20 different okra accessions collected from different regions Burkina Faso. These primers amplified a number of fragments that range from 1-16 with the sizes of 396-506 bp. Each accession was ...

  6. APPLICATION OF RYE SSR MARKERS FOR DETECTION OF GENETIC DIVERSITY IN TRITICALE

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    Želmíra Balážová

    2016-06-01

    Full Text Available Present study aims to testify usefulness of particular rye SSR markers for the detection of genetic diversity degree in the set of 20 triticale cultivars coming from different European countries. For this purpose, a set of six rye SSR markers were used. The set of six polymorphic markers provided 22 alleles with an average frequency of 3.67 alleles per locus. The number of alleles ranged between 2 (SCM43 and 5 (SCM28, SCM86. Resulting from the number and frequency of alleles diversity index (DI, polymorphic information content (PIC and probability of identity (PI were calculated. An average value of PIC for 6 SSR markers was 0.505, the highest value was calculated for rye SSR marker SCM86 (0.706. Based on UPGMA algorithm, a dendrogram was constructed. In dendrogram cultivars were divided into two main clusters. The first cluster contained two cultivars, Russian cultivar Greneder and Slovak cultivar Largus, and second included 18 cultivars. Genetically the closest were two Greek cultivars (Niobi and Thisbi and were close to other Greek cultivar Vrodi. It was possible to separate triticale cultivars of spring and winter form in dendrogram. Results showed the utility of rye microsatellite markers for estimation of genetic diversity of European triticale genotypes leading to genotype identification.

  7. Genetic diversity based on SSR markers in maize (Zea mays L ...

    Indian Academy of Sciences (India)

    The landrace numbers, origins and germplasm characteristics are presented in table 1 of electronic supple- mentary material at http://www.ias.ac.in/jgenet/. For 124 landraces, genomic DNA was isolated from a bulk sample of. Keywords. maize landraces; genetic diversity; SSR; Wuling mountain region. Journal of Genetics ...

  8. Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

    Science.gov (United States)

    A mapping population developed from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum), segregating for a number of important phenotypic traits, has been utilized to produce a genetic linkage map. Data on 233 single sequence repeat (SSR) markers and 1794 sing...

  9. Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.

    Directory of Open Access Journals (Sweden)

    Liuyi Yang

    2015-11-01

    Full Text Available Transcriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR, which consisted of 1–5 bp repeat motifs, based on next-generation sequencing (NGS technology and the RNA-Seq approach. The most abundant motif was mononucleotide (52.33%, followed by trinucleotide (31.96%, and dinucleotide (14.57%. A total of 2525 primer pairs were successfully designed, and 91 out of 311 tested primers were polymorphisms. Overall, 38 genic SSR markers were randomly selected to further validate the degree of genetic diversity, and 22 genic SSR markers (57.89% showed high levels of polymorphism. The average polymorphism information content (PIC value and the number of alleles (Na were 0.63 and 5.27, respectively, and the unweighted pair-group method with arithmetic average (UPGMA cluster analysis grouped the 22 Allium accessions into three groups with Nei’s similarity coefficients ranging from 0.37 to 0.99. This result suggested that these genic SSR markers could be used to develop a higher resolution genetic map and/or to analyze the phylogenetic relationships among Allium plants in the near future.

  10. Spanish version of the Sleep Self-Report (SSR): factorial structure and psychometric properties.

    Science.gov (United States)

    Orgilés, M; Owens, J; Espada, J P; Piqueras, J A; Carballo, J L

    2013-03-01

    The Sleep Self-Report (SSR) is a questionnaire initially created for use with a sample from the USA to assess sleep patterns and problems in school-aged children. The objective of this study was to validate the SSR among a Spanish sample. Participants were 1228 Spanish children from 8 to 12 years of age who completed the questionnaires at school anonymously. Internal consistency was good (ω = 0.85). Convergent validity with anxiety (r = 0.54) and perceived welfare (r = -0.53) measures, and divergent validity with a measure of academic performance and positive influence of peers (r = -0.22) were acceptable. Exploratory analysis suggested a factorial structure composed by four subscales: sleep quality, sleep anxiety, bedtime refusal and sleep routines. Confirmatory analysis indicated a good fit for the model (RMSEA = 0.04; GFI = 0.95; AGFI = 0.93; χ(2)/gl = 2.48). The SSR has demonstrated to have good psychometric properties in the Spanish-speaking sample of children. The factorial structure supported by exploratory and confirmatory analysis examines the most relevant areas of sleep in children. The satisfactory psychometric properties support the use of the Spanish version of the SSR by researchers and clinicians. © 2012 Blackwell Publishing Ltd.

  11. Genetic diversity based on SSR markers in maize (Zea mays L ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 87; Issue 3. Genetic diversity based on SSR markers in maize (Zea mays L.) landraces from Wuling mountain region in China. Yao Qi-Lun Fang Ping Kang Ke-Cheng Pan Guang-Tang. Research Note Volume 87 Issue 3 December 2008 pp 287-291 ...

  12. Physical location of SSR regions and cytogenetic instabilities in ...

    Indian Academy of Sciences (India)

    2014-08-18

    Aug 18, 2014 ... Agrária: Systemas y Recursos Florestales 1, 317–335. Muratova E. N. 1994 Cytogenetical study on Scots pine (Pinus sylvestris L.) in the Central Yakuria. In Cytogenetic studies of for- est trees and shrubs: review, present status, and outlook on the future. (ed. H. Guttenberger, Z. Borzan, S.C. Schlarbaum ...

  13. (SSR) markers that are polymorphic between cultivars in Brassica ...

    African Journals Online (AJOL)

    ajl user 1

    2012-02-07

    Feb 7, 2012 ... Simple sequence repeats (SSRs) markers were developed through data mining of 3,803 expressed sequence tags (ESTs) previously published. A total of 144 di- to penta-type SSRs were identified and they were screened for polymorphism between two turnip cultivars, 'Tsuda' and 'Yurugi Akamaru'. Out.

  14. (SSR) markers that are polymorphic between cultivars in Brassica ...

    African Journals Online (AJOL)

    ajl user 1

    2012-02-07

    Feb 7, 2012 ... there are still a limited number of DNA markers that may provide sufficient anchors for mapping inheritable traits ... As a byproduct of massive EST sequencing, it became possible to develop microsatellite-associated markers ..... several grass species. Theor. Appl. Genet. 109: 783-791. Scott KD, Eggler P, ...

  15. Efficiency of RAPD versus SSR markers for determining genetic diversity among popcorn lines.

    Science.gov (United States)

    Leal, A A; Mangolin, C A; do Amaral, A T; Gonçalves, L S A; Scapim, C A; Mott, A S; Eloi, I B O; Cordovés, V; da Silva, M F P

    2010-01-05

    Using only one type of marker to quantify genetic diversity generates results that have been questioned in terms of reliability, when compared to the combined use of different markers. To compare the efficiency of the use of single versus multiple markers, we quantified genetic diversity among 10 S(7) inbred popcorn lines using both RAPD and SSR markers, and we evaluated how well these two types of markers discriminated the popcorn genotypes. These popcorn genotypes: "Yellow Pearl Popcorn" (P1-1 and P1-5), "Zélia" (P1-2 and P1-4), "Curagua" (P1-3), "IAC 112" (P9-1 and P9-2), "Avati Pichinga" (P9-3 and P9-5), and "Pisankalla" (P9-4) have different soil and climate adaptations. Using RAPD marker analysis, each primer yielded bands of variable intensities that were easily detected, as well as non-specific bands, which were discarded from the analysis. The nine primers used yielded 126 bands, of which 104 were classified as polymorphic, giving an average of 11.6 polymorphisms per primer. Using SSR procedures, the number of alleles per locus ranged from two to five, giving a total of 47 alleles for the 14 SSR loci. When comparing the groups formed using SSR and RAPD markers, there were similarities in the combinations of genotypes from the same genealogy. Correlation between genetic distances obtained through RAPD and SSR markers was relatively high (0.5453), indicating that both techniques are efficient for evaluating genetic diversity in the genotypes of popcorn that we evaluated, though RAPDs yielded more polymorphisms.

  16. RAPD and SSR Polymorphisms in Mutant Lines of Transgenic Wheat Mediated by Low Energy Ion Beam

    Science.gov (United States)

    Wang, Tiegu; Huang, Qunce; Feng, Weisen

    2007-10-01

    Two types of markers-random amplified polymorphic DNA (RAPD) and simple sequence repeat DNA (SSR)-have been used to characterize the genetic diversity among nine mutant lines of transgenic wheat intermediated by low energy ion beam and their four receptor cultivars. The objectives of this study were to analyze RAPD-based and SSR-based genetic variance among transgenic wheat lines and with their receptors, and to find specific genetic markers of special traits of transgenic wheat lines. 170 RAPD primers were amplified to 733 fragments in all the experimental materials. There were 121 polymorphic fragments out of the 733 fragments with a ratio of polymorphic fragments of 16.5%. 29 SSR primer pairs were amplified to 83 fragments in all the experiment materials. There were 57 polymorphic fragments out of the 83 fragments with a ratio of polymorphic fragments of 68.7%. The dendrograms were prepared based on a genetic distance matrix using the UPGMA (Unweighted Pair-group Method with Arithmetic averaging) algorithm, which corresponded well to the results of the wheat pedigree analysis and separated the 13 genotypes into four groups. Association analysis between RAPD and SSR markers with the special traits of transgenic wheat mutant lines discovered that three RAPD markers, s1, opt-16, and f14, were significantly associated with the muticate trait, while three SSR markers, Rht8 (Xgwm261), Rht-B1b, and Rht-D1b, highly associated with the dwarf trait. These markers will be useful for marker-assistant breeding and can be used as candidate markers for further gene mapping and cloning.

  17. A simple ssr analysis for genetic diversity estimation of maize landraces

    Directory of Open Access Journals (Sweden)

    Ignjatovic-Micic Dragana

    2015-01-01

    Full Text Available collection of 2217 landraces from western Balkan (former Yugoslavia is maintained at Maize Research Institute Zemun Polje gene bank. Nine flint and nine dent accessions from six agro-ecological groups (races, chosen on the basis of diverse pedigrees, were analyzed for genetic relatedness using phenotypic and simple sequence repeat (SSR markers. One of the aims was to establish a reliable set of SSR markers for a rapid diversity analysis using polyacrilamide gels and ethidium bromide staining. In the principal component analysis (PCA the first three principal components accounted for 80.86% of total variation and separated most of the flint from dent landraces. Ten SSR primers revealed a total of 56 and 63 alleles in flint and dent landraces, respectively, with low stuttering and good allele resolution on the gels. High average PIC value (0.822 also supports informativeness and utility of the markers used in this study. Higher genetic variation was observed among flint genotypes, as genetic distances between flint landraces covered a larger range of values (0.11- 0.38 than between dent (0.22 - 0.33 genotypes. Both phenotypic and SSR analyses distinguished flint and dent landraces, but neither of them could abstract agro-ecological groups. The SSR method used gave clear, easy to read band patterns that could be used for reliable allele frequency determination. Genetic diversity revealed for both markers indicated that the landraces were highly adapted to specific environmental conditions and purposes and could be valuable sources of genetic variability. [Projekat Ministarstva nauke Republike Srbije, br. TR31028: Exploitation of maize diversity to improve grain quality and drought tolerance

  18. The use of multiplexed simple sequence repeat (SSR) markers for ...

    African Journals Online (AJOL)

    ... NaCRRI, national crops resources research institute; RAPD, random amplified polymorphic DNA; AFLP, amplified fragment length polymorphisms; RFLP, restriction fragment length polymorphisms; SNP, single nucleotide polymorphisms; BAC, bacterial artificial chromosome; PAC, P1-derived artificial chromosome; PCR, ...

  19. Identification, evaluation, and application of the genomic-SSR loci in ramie

    Directory of Open Access Journals (Sweden)

    Ming-Bao Luan

    2016-09-01

    Full Text Available To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%. A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including Ibg5-5, Ibg3-210, Ibg1-11, Ibg6-468, and Ibg6-481. The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting

  20. Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers.

    Science.gov (United States)

    Sharafi, Ata Allah; Abkenar, Asad Asadi; Sharafi, Ali; Masaeli, Mohammad

    2016-01-01

    Iran has a long history of acid lime cultivation and propagation. In this study, genetic variation in 28 acid lime accessions from five regions of south of Iran, and their relatedness with other 19 citrus cultivars were analyzed using Simple Sequence Repeat (SSR) and Inter-Simple Sequence Repeat (ISSR) molecular markers. Nine primers for SSR and nine ISSR primers were used for allele scoring. In total, 49 SSR and 131 ISSR polymorphic alleles were detected. Cluster analysis of SSR and ISSR data showed that most of the acid lime accessions (19 genotypes) have hybrid origin and genetically distance with nucellar of Mexican lime (9 genotypes). As nucellar of Mexican lime are susceptible to phytoplasma, these acid lime genotypes can be used to evaluate their tolerance against biotic constricts like lime "witches' broom disease".

  1. Genetic analysis of some Egyptian rice genotypes using RAPD, SSR ...

    African Journals Online (AJOL)

    nformation of genetic similarities and diversity among superior Egyptian rice genotypes is necessary for future rice breeding programs and derivation of plant lines. Genetic variability and relationships among seven Egyptian rice genotypes namely Giza 178, Giza177, Giza 175, Giza171 Giza 172, Sakha 102, and Sakha 101 ...

  2. Documents of the Repressive Institutions of the Latvian SSR as a Source of History 1940 – 1941 ;1944 - 1991

    OpenAIRE

    Bambals, Ainārs

    2012-01-01

    Annotation Documents of the Repressive Institutions of the Latvian SSR as a Source of History 1940 – 1941 ;1944 - 1991 The doctoral thesis studies the documents of the repressive authorities of the Latvian SSR as a source of history. The topic has been little studied in the Latvian historiography because the respective sources had been unaccessible to researchers for many years. The topic falls in the framework of a broader theme: the research into the the Communist total...

  3. Wgssat: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers from Whole Genomes.

    Science.gov (United States)

    Pandey, Manmohan; Kumar, Ravindra; Srivastava, Prachi; Agarwal, Suyash; Srivastava, Shreya; Nagpure, N S; Jena, J K; Kushwaha, Basdeo

    2017-09-16

    Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, ncRNA, core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes and RNAs. The features of WGSSAT were demonstrated using Takifugurubripes data. This yielded a total of 139057 SSR, out of which 113703 SSR primer pairs were uniquely amplified in silico onto a Takifugurubripes (fugu) genome. Out of 1,13,703 mined SSRs, 81,463 were from coding region (including 4,286 exonic and 77,177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 1,05,641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  5. Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus.

    Science.gov (United States)

    Qu, Jibin; Huang, Chenyang; Zhang, Jinxia

    2016-01-10

    Simple sequence repeats (SSRs) play specific roles in many biological activities. In this paper, we focused on SSRs in the genome of Pleurotus ostreatus, which is a widely cultivated edible mushroom. The distribution curves of SSRs and exons are opposite throughout the genome, which means that SSRs are mostly located in non-coding regions. A comparative analysis of nine fungi suggests that Agaricomycotina fungi have similar SSR distributions. Functional enrichment analysis on the SSR-containing gene set uncovers enriched functions about environmental interactions and important cellular functions for life. Trinucleotide SSRs account for an extremely high fraction of all SSRs, and in exonic regions, they are equivalent to inserting repeating amino acids (RAAs) into the protein sequences. The RAA indel could partly explain some enriched functions of the genes they modify. Agaricomycotina fungi have similar distributions of RAAs, indicating that this may be a potential common mechanism for some specific functions. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS Data in Plants

    Directory of Open Access Journals (Sweden)

    Sima Taheri

    2018-02-01

    Full Text Available Microsatellites, or simple sequence repeats (SSRs, are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq and related tools for mining and development of microsatellites in plants.

  7. NOTE-Polymorphic information content of SSR markers for Coffea spp.

    Directory of Open Access Journals (Sweden)

    Robson Fernando Missio

    2010-01-01

    Full Text Available Thirty-three coffee SSR primers from enriched genomic library with (GT15 and (AGG10 repeats were analyzedin 24 coffee tree accessions. Twenty-two primers were polymorphic among accessions; the number of alleles ranged from 2 to13, with the mean number of 5.1 alleles per primer. PIC values ranged from 0.08 to 0.79. The highest mean PIC values werefound for C. canephora (0.46, and the lowest values for C. arabica (0.22 and triploids (0.22 accessions. The polymorphicSSR markers used in this study were useful for genetic fingerprinting in the coffee tree, especially in the C. canephora and theleaf rust resistant arabica cultivars.

  8. Development and validation of genic-SSR markers in sesame by RNA-seq

    Science.gov (United States)

    2012-01-01

    Background Sesame (Sesamum indicum L.) is one of the most important oil crops; however, a lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of samples from different sesame growth and developmental stages, and mining of genic-SSR markers to identify valuable markers for sesame molecular genetics research. Results In this study, 75 bp and 100 bp paired-end RNA-seq was used to sequence 24 cDNA libraries, and 42,566 uni-transcripts were assembled from more than 260 million filtered reads. The total length of uni-transcript sequences was 47.99 Mb, and 7,324 SSRs (SSRs ≥15 bp) and 4,440 SSRs (SSRs ≥18 bp) were identified. On average, there was one genic-SSR per 6.55 kb (SSRs ≥15 bp) or 10.81 kb (SSRs ≥18 bp). Among perfect SSRs (≥18 bp), di-nucleotide motifs (48.01%) were the most abundant, followed by tri- (20.96%), hexa- (25.37%), penta- (2.97%), tetra- (2.12%), and mono-nucleotides (0.57%). The top four motif repeats were (AG/CT)n [1,268 (34.51%)], (CA/TG)n [281 (7.65%)], (AT/AT)n [215 (5.85%)], and (GAA/TTC)n [131 (3.57%)]. A total of 2,164 SSR primer pairs were identified in the 4,440 SSR-containing sequences (≥18 bp), and 300 SSR primer pairs were randomly chosen for validation. These SSR markers were amplified and validated in 25 sesame accessions (24 cultivated accessions, one wild species). 276 (92.0%) primer pairs yielded PCR amplification products in 24 cultivars. Thirty two primer pairs (11.59%) exhibited polymorphisms. Moreover, 203 primer pairs (67.67%) yielded PCR amplicons in the wild accession and 167 (60.51%) were polymorphic between species. A UPGMA dendrogram based on genetic similarity coefficients showed that the correlation between genotype and geographical source was low and that the genetic basis of sesame in China is narrow, as previously reported. The 32 polymorphic primer pairs were validated using an F2 mapping population; 18 primer pairs exhibited

  9. Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplasm.

    Science.gov (United States)

    Kempf, Katharina; Mora-Ortiz, Marina; Smith, Lydia M J; Kölliker, Roland; Skøt, Leif

    2016-08-30

    Sainfoin is a perennial forage legume with beneficial properties for animal husbandry due to the presence of secondary metabolites. However, worldwide cultivation of sainfoin is marginal due to the lack of varieties with good agronomic performance, adapted to a broad range of environmental conditions. Little is known about the genetics of sainfoin and only few genetic markers are available to assist breeding and genetic investigations. The objective of this study was to develop a set of SSR markers useful for genetic studies in sainfoin and their characterization in diverse germplasm. A set of 400 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 32 sainfoin individuals, representing distinct varieties or landraces. Alleles were scored for presence or absence and polymorphism information content of each SSR locus was calculated with an adapted formula taking into account the tetraploid character of sainfoin. Relationships among individuals were visualized using cluster and principle components analysis. Of the 400 primer combinations tested, 101 reliably detected polymorphisms among the 32 sainfoin individuals. Among the 1154 alleles amplified 250 private alleles were observed. The number of alleles per locus ranged from 2 to 24 with an average of 11.4 alleles. The average polymorphism information content reached values of 0.14 to 0.36. The clustering of the 32 individuals suggested a separation into two groups depending on the origin of the accessions. The SSR markers characterized and tested in this study provide a valuable tool to detect polymorphisms in sainfoin for future genetic studies and breeding programs. As a proof of concept, we showed that these markers can be used to separate sainfoin individuals based on their origin.

  10. Genetic variation of european maize genotypes (zea mays l. Detected using ssr markers

    Directory of Open Access Journals (Sweden)

    Martin Vivodík

    2017-01-01

    Full Text Available The SSR molecular markers were used to assess genetic diversity in 40 old European maize genotypes. Ten SSR primers revealed a total of 65 alleles ranging from 4 (UMC1060 to 8 (UMC2002 and UMC1155 alleles per locus with a mean value of 6.50 alleles per locus. The PIC values ranged from 0.713 (UMC1060 to 0.842 (UMC2002 with an average value of 0.810 and the DI value ranged from 0.734 (UMC1060 to 0.848 (UMC2002 with an average value of 0.819. 100% of used SSR markers had PIC and DI values higher than 0.7 that means high polymorphism of chosen markers used for analysis. Probability of identity (PI was low ranged from 0.004 (UMC1072 to 0.022 (UMC1060 with an average of 0.008. A dendrogram was constructed from a genetic distance matrix based on profiles of the 10 maize SSR loci using the unweighted pair-group method with the arithmetic average (UPGMA. According to analysis, the collection of 40 diverse accessions of maize was clustered into four clusters. The first cluster contained nine genotypes of maize, while the second cluster contained the four genotypes of maize. The third cluster contained 5 maize genotypes. Cluster 4 contained five genotypes from Hungary (22.73%, two genotypes from Poland (9.10%, seven genotypes of maize from Union of Soviet Socialist Republics (31.81%, six genotypes from Czechoslovakia (27.27%, one genotype from Slovak Republic (4.55% and one genotype of maize is from Yugoslavia (4.55%. We could not distinguish 4 maize genotypes grouped in cluster 4, (Voroneskaja and Kocovska Skora and 2 Hungarian maize genotypes - Feheres Sarga Filleres and Mindszentpusztai Feher, which are genetically the closest.

  11. Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

    OpenAIRE

    Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

    2017-01-01

    Flax (Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation...

  12. Search for new approaches to farming in the Ukrainian SSR in the period of "developed socialism"

    OpenAIRE

    Malyarchuk, Oleg

    2015-01-01

    National scientists have elaborated the reform's gist, approaches, stages and consequences in the Ukrainian agricultural sector during the XX - XXI centuries. These studies have been conducted by N. Zhulkanych, S. Zhyvora, M. Zyza, M. Lendiel, E. Mazur, O. Malyarchuk, V. Nechytailo and many others.The paper aims to perform the comprehensive study of general trends and peculiar features of the agricultural development of the Ukrainian SSR in 1963-1990 and to define actual advances and drawback...

  13. Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

    Directory of Open Access Journals (Sweden)

    Cardle Linda

    2008-12-01

    Full Text Available Abstract Background Microsatellites or single sequence repeats (SSRs are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of P. infestans, P. sojae and P. ramorum were mined for candidate SSR markers that could be applied to a wide range of Phytophthora species. Results A first approach, aimed at the identification of polymorphic SSR loci common to many Phytophthora species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAGn, (AGGn and (AGCn were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to P. sojae (P. alni, P. cambivora, P. europaea and P. fragariae. This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times. Conclusion Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of Phytophthora species was challenging. That said, many novel SSR loci for species other than the three 'source species' (P. infestans, P. sojae and P. ramorum are reported, offering great potential for the investigation of Phytophthora populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as

  14. EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance.

    Science.gov (United States)

    Kaur, Sukhjiwan; Cogan, Noel O I; Stephens, Amber; Noy, Dianne; Butsch, Mirella; Forster, John W; Materne, Michael

    2014-03-01

    Large-scale SNP discovery and dense genetic mapping in a lentil intraspecific cross permitted identification of a single chromosomal region controlling tolerance to boron toxicity, an important breeding objective. Lentil (Lens culinaris Medik.) is a highly nutritious food legume crop that is cultivated world-wide. Until recently, lentil has been considered a genomic 'orphan' crop, limiting the feasibility of marker-assisted selection strategies in breeding programs. The present study reports on the identification of single-nucleotide polymorphisms (SNPs) from transcriptome sequencing data, utilisation of expressed sequence tag (EST)-derived simple sequence repeat (SSR) and SNP markers for construction of a gene-based genetic linkage map, and identification of markers in close linkage to major QTLs for tolerance to boron (B) toxicity. A total of 2,956 high-quality SNP markers were identified from a lentil EST database. Sub-sets of 546 SSRs and 768 SNPs were further used for genetic mapping of an intraspecific mapping population (Cassab × ILL2024) that exhibits segregation for B tolerance. Comparative analysis of the lentil linkage map with the sequenced genomes of Medicago truncatula Gaertn., soybean (Glycine max [L.] Merr.) and Lotus japonicus L. indicated blocks of conserved macrosynteny, as well as a number of rearrangements. A single genomic region was found to be associated with variation for B tolerance in lentil, based on evaluation performed over 2 years. Comparison of flanking markers to genome sequences of model species (M. truncatula, soybean and Arabidopsis thaliana) identified candidate genes that are functionally associated with B tolerance, and could potentially be used for diagnostic marker development in lentil.

  15. Development of Genomic Simple Sequence Repeats (SSR) by Enrichment Libraries in Date Palm.

    Science.gov (United States)

    Al-Faifi, Sulieman A; Migdadi, Hussein M; Algamdi, Salem S; Khan, Mohammad Altaf; Al-Obeed, Rashid S; Ammar, Megahed H; Jakse, Jerenj

    2017-01-01

    Development of highly informative markers such as simple sequence repeats (SSR) for cultivar identification and germplasm characterization and management is essential for date palms genetic studies. The present study documents the development of SSR markers and assesses genetic relationships of commonly grown date palm (Phoenix dactylifera L.) cultivars in different geographical regions of Saudi Arabia. A total of 93 novel simple sequence repeat (SSR) markers were screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs are dinucleotide, 25% trinucleotide, 3% tetranucleotide, and 1% pentanucleotide motives and show 100% polymorphism. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis illustrates that cultivars trend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) reveals genetic variation among and within cultivars of 27% and 73%, respectively, according to the geographical distribution of the cultivars. Developed microsatellite markers are of additional value to date palm characterization, tools which can be used by researchers in population genetics, cultivar identification, as well as genetic resource exploration and management. The cultivars tested exhibited a significant amount of genetic diversity and could be suitable for successful breeding programs. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).

  16. Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea).

    Science.gov (United States)

    Göl, Şurhan; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, Anne

    2017-08-01

    Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.

  17. Alleviation SSR and Low Frequency Power Oscillations in Series Compensated Transmission Line using SVC Supplementary Controllers

    Science.gov (United States)

    Kumar, Sanjiv; Kumar, Narendra

    2017-06-01

    In this work, supplementary sub-synchronous damping controllers (SSDC) are proposed for damping sub-synchronous oscillations in power systems with series compensated transmission lines. Series compensation have extensively been used as effective means of increasing the power transfer capability of a transmission lines and improving transient stability limits of power systems. Series compensation with transmission lines may cause sub-synchronous resonance (SSR). The eigenvalue investigation tool is used to ascertain the existence of SSR. It is shown that the addition of supplementary controller is able to stabilize all unstable modes for T-network model. Eigenvalue investigation and time domain transient simulation of detailed nonlinear system are considered to investigate the performance of the controllers. The efficacies of the suggested supplementary controllers are compared on the IEEE first benchmark model for computer simulations of SSR by means of time domain simulation in Matlab/Simulink environment. Supplementary SSDC are considered in order to compare effectiveness of SSDC during higher loading in alleviating the small signal stability problem.

  18. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.

    Science.gov (United States)

    Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps.

  19. A set of EST-SNPs for map saturation and cultivar identification in melon

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    Monforte Antonio J

    2009-07-01

    Full Text Available Abstract Background There are few genomic tools available in melon (Cucumis melo L., a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR, restriction fragment length polymorphisms (RFLP and amplified fragment length polymorphisms (AFLP in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP, more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. Results EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC × 'Piel de sapo' (PS genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. Conclusion This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 × 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR. This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty

  20. A set of EST-SNPs for map saturation and cultivar identification in melon.

    Science.gov (United States)

    Deleu, Wim; Esteras, Cristina; Roig, Cristina; González-To, Mireia; Fernández-Silva, Iria; Gonzalez-Ibeas, Daniel; Blanca, José; Aranda, Miguel A; Arús, Pere; Nuez, Fernando; Monforte, Antonio J; Picó, Maria Belén; Garcia-Mas, Jordi

    2009-07-15

    There are few genomic tools available in melon (Cucumis melo L.), a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR), restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP) in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP), more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs) from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC) x 'Piel de sapo' (PS) genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 x 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR). This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty-eight melon accessions as efficiently as with SSR

  1. EST Vocabulary Instruction

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    Célia D.S. Bell

    2012-05-01

    Full Text Available This study aims at contributing to the investigation on the instruction of EST (English for Science and Technology vocabulary, in terms of receptive use of the language. It evaluates the effectiveness of two teaching approaches to the acquisition of vocabulary. The first approach consisted of teaching vocabulary through the use of dictionaries, where the words were merely translated into the learners’ L1 or defined in the target language thus promoting superficial level of word processing. The second approach employed activities promoting deep level of word processing. Data were analysed quantitatively. Results indicated that the two approaches seem to have some equipotentiality, as far as EST vocabulary is concerned.

  2. Genetic structure and distribution of pythium aphanidermatum populations in Pennsylvania greenhouses based on analysis of AFLP and SSR markers.

    Science.gov (United States)

    Lee, Seonghee; Garzón, Carla D; Moorman, Gary W

    2010-01-01

    Pythium aphanidermatum is one of the most aggressive species in the genus and has a wide host range, but little is known about its population genetic structure. We tested 123 P. aphanidermatum isolates with six AFLP primer combinations and four SSR markers. The genetic diversity of P. aphanidermatum was 0.34 with AFLP and 0.55 with SSR markers. SSR genotypes totaled 3-8 for each locus, and a total of 14 SSR genotypes were found among all isolates. Three major genetic groups were identified with the combination of AFLP and SSR marker data. The genetic structure observed among P. aphanidermatum isolates was related to location and mefenoxam fungicide resistance instead of host. Four genotypes (PA1, PA2, PA5 and PA7) were found in the population from a commercial greenhouse, and the genetic diversity of a greenhouse population was similar to that found in the whole sample. The molecular tools for P. aphanidermatum isolates identified the possible gene flow within and among populations in Pennsylvania greenhouses.

  3. Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

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    Ata Allah Sharafi

    2017-12-01

    Full Text Available In this study, genetic diversity in 19 citrus cultivars was analyzed using Simple Sequence Repeat (SSR, Inter-simple Sequence Repeat (ISSR and cleaved amplified polymorphic sequence (CAPS markers. Nine primers for SSR, nine ISSR primers and two primers for CAPS were used for allele scoring. One chloroplast DNA region (rbcL-ORF106 and one mitochondrial DNA region (18S-5S were analyzed using cleaved amplified polymorphic sequence (CAPS marker in 19 citrus accessions grown in Iran. In total, 45 SSR and 131 ISSR polymorphic alleles and tree organelle genome types were detected. Cluster analysis of SSR and ISSR data was performed using UPGMA method and based on Jaccard's coefficient. The result of this investigation showed that the SSR and ISSR primers were highly informative and efficient in detecting genetic variability and relationships of the citrus accessions. And CAPS marker analysis Results showed that Bakraee and one of off type Mexican lime had banding pattern similar to Clementine Mandarin, while Pummelo regarded as maternal parent of other studied genotypes Citron regarded as father parent showed definite banding pattern among 19 studied genotypes which it confirmed Cytoplasmic inheritance from mother cellular organelles.

  4. Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

    Science.gov (United States)

    Zaki, Noorhariza Mohd; Singh, Rajinder; Rosli, Rozana; Ismail, Ismanizan

    2012-01-01

    Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (Ho) (0.164) and highly positive fixation indices (Fis) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family. PMID:22605966

  5. Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

    Directory of Open Access Journals (Sweden)

    Ismanizan Ismail

    2012-03-01

    Full Text Available Species-specific simple sequence repeat (SSR markers are favored for genetic studies and marker-assisted selection (MAS breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR. Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%, followed by tri-nucleotides (24.2%. Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626. Low values of observed heterozygosity (Ho (0.164 and highly positive fixation indices (Fis in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.

  6. Floral Transcriptome Sequencing for SSR Marker Development and Linkage Map Construction in the Tea Plant (Camellia sinensis)

    Science.gov (United States)

    Wei, Kang; Zhang, Cheng-Cai; Wu, Li-Yun; Qi, Gui-Nian; Cheng, Hao; Zhang, Qiang; Cui, Qing-Mei; Liang, Jin-Bo

    2013-01-01

    Despite the worldwide consumption and high economic importance of tea, the plant (Camellia sinensis) is not well studied in molecular biology. Under the few circumstances in which the plant is studied, C. sinensis flowers, which are important for reproduction and cross-breeding, receive less emphasis than investigation of its leaves or roots. Using high-throughput Illumina RNA sequencing, we analyzed a C. sinensis floral transcriptome, and 26.9 million clean reads were assembled into 75,531 unigenes averaging 402 bp. Among them, 50,792 (67.2%) unigenes were annotated with a BLAST search against the NCBI Non-Redundant (NR) database and 10,290 (16.67%) were detected that contained one or more simple sequence repeats (SSRs). From these SSR-containing sequences, 2,439 candidate SSR markers were developed and 720 were experimentally tested, validating 431 (59.9%) novel polymorphic SSR markers for C. sinensis. Then, a consensus SSR-based linkage map was constructed that covered 1,156.9 cM with 237 SSR markers distributed in 15 linkage groups. Both transcriptome information and the genetic map of C. sinensis presented here offer a valuable foundation for molecular biology investigations such as functional gene isolation, quantitative trait loci mapping, and marker-assisted selection breeding in this important species. PMID:24303059

  7. Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.

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    Mohapatra Trilochan

    2009-05-01

    Full Text Available Abstract Background Despite great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in tea (Camellia sinensis L.. The development of microsatellite markers will have a major impact on genetic analysis, gene mapping and marker assisted breeding. Unigene derived microsatellite (UGMS markers identified from publicly available sequence database have the advantage of assaying variation in the expressed component of the genome with unique identity and position. Therefore, they can serve as efficient and cost effective alternative markers in such species. Results Considering the multiple advantages of UGMS markers, 1,223 unigenes were predicted from 2,181 expressed sequence tags (ESTs of tea (Camellia sinensis L.. A total of 109 (8.9% unigenes containing 120 SSRs were identified. SSR abundance was one in every 3.55 kb of EST sequences. The microsatellites mainly comprised of di (50.8%, tri (30.8%, tetra (6.6%, penta (7.5% and few hexa (4.1% nucleotide repeats. Among the dinucleotide repeats, (GAn.(TCn were most abundant (83.6%. Ninety six primer pairs could be designed form 83.5% of SSR containing unigenes. Of these, 61 (63.5% primer pairs were experimentally validated and used to investigate the genetic diversity among the 34 accessions of different Camellia spp. Fifty one primer pairs (83.6% were successfully cross transferred to the related species at various levels. Functional annotation of the unigenes containing SSRs was done through gene ontology (GO characterization. Thirty six (60% of them revealed significant sequence similarity with the known/putative proteins of Arabidopsis thaliana. Polymorphism information content (PIC ranged from 0.018 to 0.972 with a mean value of 0.497. The average heterozygosity expected (HE and observed (Ho obtained was 0.654 and 0.413 respectively, thereby suggesting highly heterogeneous nature of tea. Further, test

  8. Desenho e validação de iniciadores microssatélites SSR para mamoneira

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    Edna Lôbo Machado

    2013-11-01

    Full Text Available O objetivo deste trabalho foi desenhar, validar e otimizar pares de iniciadores microssatélites SSR para mamoneira. O desenho dos pares de iniciadores foi feito por meio do aplicativo Websat, a partir de sequências depositadas no GenBank do National Center for Biotechnology Information (GenBank/NCBI, e a sua qualidade foi aferida com uso do aplicativo web NetPrimer. Foram utilizadas diferentes concentrações de DNA, cloreto de magnésio, pares de iniciadores, dNTPs e temperatura de anelamento para otimização das condições de PCR. Um total de 30 pares de iniciadores SSR foi desenhado, sintetizado e otimizado. O gel de agarose foi utilizado para detecção dos produtos amplificados, e o gel desnaturante de poliacrilamida, na otimização das condições de PCR e na identificação de polimorfismo. Os pares de iniciadores apresentaram percentagem média de guanina/citosina (GC igual a 47,29% e produtos amplificados com tamanhos entre 128 e 381 pb. Vinte e nove pares de iniciadores SSR (96,7% foram validados, dos quais nove foram polimórficos (23,3%. As concentrações otimizadas para amplificação são: DNA, 25 ng; cloreto de magnésio, 1,2 mmol L-1; iniciadores Forward e Reverse, 0,4 mmol L-1; dNTPs, 0,1 mmol L-1; e temperatura de anelamento, 62 a 64ºC. As ferramentas de bioinformática Websat e Net Primer podem ser utilizadas para desenvolver iniciadores microssatélites de qualidade, para a mamoneira, a partir de sequências depositadas no GenBank/NCBI.

  9. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    Science.gov (United States)

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil.

  10. Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp..

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    Shu Tan

    Full Text Available Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154 derived from a cross between BA3 (C. annuum and YNXML (C. frutescens. Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147 in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0, 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

  11. Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: a comparative analysis among populations across the Southern Western Ghats of India.

    Science.gov (United States)

    Jayakumar, K S; Sajan, J S; Aswati Nair, R; Padmesh Pillai, P; Deepu, S; Padmaja, R; Agarwal, A; Pandurangan, A G

    2014-10-01

    Lagerstroemia speciosa commonly known as 'Banaba' is native of south-east Asia which exhibits both horticultural and therapeutic value. The anti-diabetic and anti-obese property of the tree is attributed to corosolic acid (CRA)-a pentacyclic triterpene seen predominantly in the mature leaves. Although there are studies on either chemical or genetic variation in L. speciosa from different regions, none have dealt with their association to discuss the formation of chemical diversity. For the first time, we have analyzed CRA content in 12 natural populations corresponding to 42 samples seen in the Southern Western Ghats (SWG) using chromatography techniques and genetic variation estimated using SSR markers. Significant variation in percentage distribution of CRA ranging from 0.005% to 0.868% dr.wt. was recorded wherein populations from the north SWG contain relatively more active principle (mean=0.321%) than their counterparts in the south (mean=0.064%). Similarly, SSR data showing relatively high rate of gene flow (Nm=2.72) and low genetic differentiation (FST=0.14) is indicative that populations from north are genetically more diverse than those in the south (Nm=0.48; FST=0.38). The scatter plot derived by Principle Component Analysis (PCA) of chemical and genetic data shows similar pattern of clustering that reveals strong association between the two sets of data. It is concluded that the observed variation in CRA content in natural populations of the species depends more on the genetic background and less on edaphic factors. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. PROBLEMS OF THE EFFICIENCY INCREASING OF TRANSPORTATION BY AIR OF UKRAINIAN SSR (1960-1980

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    Anatoliy Gorban

    2015-11-01

    Full Text Available The article is devoted to the problems of the efficiency increasing of the air transportation. The difficulties of increasing the efficiency of transportation by air in Ukrainian SSR in 1960-1980 were researched, factors that adversely affected the organization of the transport sector were determined and depicted. The article analyzes what caused such difficulties and it was found out that the causes of these difficulties are connected with the organizational problems of air transport of Ukrainian SSR, which negatively affected the operation of the industry. The central aim of the research is to focus on the main problems of air transport of Ukrainian SSR. So, we should say that the transport operation of those years was distributed too unevenly and was dependent on the population density of the territory of the republic. Purpose of the article is to determine, compile and analyze the factors that negatively affected the organization of air transportation of the Ukrainian republic and reduced the efficiency of its operation. Results of the research shows technical, organization and economical deficiency of air transport of Ukrainian SSR which caused the ineffectiveness of this type of transport and determines the nature of such difficulties. Statement of the problem. During the specified period (1960–1980 the air transport had undergone rapid development. Many new airlines were opened, airports were being built and reconstructed, the terms of exploiting of turbojet aircrafts were increased, the speed of planes was increasing. All these facts ensured safe and reliable air connection of all district centers, connected Ukraine with the other Soviet republics and foreign countries by air corridors. Ukrainian Department of Civil Aviation became the biggest regional Department of the Ministry of Civil Aviation of the USSR. But, at the same time the intensity of the increase of cargo and passenger transportation since 1970s led to accumulation of

  13. Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

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    Moradkhani Hoda

    2015-12-01

    Full Text Available The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions of Aegilops and Triticum species with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA revealed that 81% (ISSR and 84% (SSR of variability was partitioned among individuals within populations. Comparing the genetic diversity of Aegilops and Triticum accessions, based on genetic parameters, shows that genetic variation of Ae. crassa and Ae. tauschii species are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA, also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

  14. Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica

    Science.gov (United States)

    Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

    2015-01-01

    Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the “candidate genes” and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

  15. Construction of a SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis).

    Science.gov (United States)

    Ma, Jian-Qiang; Yao, Ming-Zhe; Ma, Chun-Lei; Wang, Xin-Chao; Jin, Ji-Qiang; Wang, Xue-Min; Chen, Liang

    2014-01-01

    Catechins are the most important bioactive compounds in tea, and have been demonstrated to possess a wide variety of pharmacological activities. To characterize quantitative trait loci (QTLs) for catechins content in the tender shoots of tea plant, we constructed a moderately saturated genetic map using 406 simple sequence repeat (SSR) markers, based on a pseudo-testcross population of 183 individuals derived from an intraspecific cross of two Camellia sinensis varieties with diverse catechins composition. The map consisted of fifteen linkage groups (LGs), corresponding to the haploid chromosome number of tea plant (2n = 2x = 30). The total map length was 1,143.5 cM, with an average locus spacing of 2.9 cM. A total of 25 QTLs associated with catechins content were identified over two measurement years. Of these, nine stable QTLs were validated across years, and clustered into four main chromosome regions on LG03, LG11, LG12 and LG15. The population variability explained by each QTL was predominantly at moderate-to-high levels and ranged from 2.4% to 71.0%, with an average of 17.7%. The total number of QTL for each trait varied from four to eight, while the total population variability explained by all QTLs for a trait ranged between 38.4% and 79.7%. This is the first report on the identification of QTL for catechins content in tea plant. The results of this study provide a foundation for further cloning and functional characterization of catechin QTLs for utilization in improvement of tea plant.

  16. Novel STATCOM Controller for Mitigating SSR and Damping Power System Oscillations in a Series Compensated Wind Parks

    DEFF Research Database (Denmark)

    Bak-Jensen, Birgitte; El-Moursi, M. S.; Abdel-Rahman, Mansour Hassan

    2010-01-01

    This paper addresses implementation issues associated with a novel damping control algorithm for a STATCOM in a series compensated wind park for mitigating SSR (subsynchronous resonance) and damping power system oscillations. The IEEE first benchmark model on subsynchronous resonance is adopted...... damping control loop for the STATCOM based on a novel design procedure of nonlinear optimization are developed to meet the damping torque in the range of critical torsional frequencies. The Intelligent Shaft Monitor (ISM) scheme with Synthesized Special Indicator Signals are developed and examined...... the SSR, damping the power system oscillation and enhancing the transient stability margin in response to different SCRs....

  17. Genetic Characterization of Green Bean (Phaseolus vulgaris L.) Accessions from Turkey with SCAR and SSR Markers.

    Science.gov (United States)

    Madakbaş, Seher Yıldız; Sarıkamış, Gölge; Başak, Hakan; Karadavut, Ufuk; Özmen, Canan Yüksel; Daşçı, Mete Gürhan; Çayan, Selin

    2016-08-01

    Characterization, conservation, and utilization of genetic resources is essential for the sustainability in agriculture. Plant genetic resources are important for breeding efforts designed for the generation of new cultivars or for the improvement of existing ones. Green bean has been cultivated extensively in Turkey giving rise to local accessions through selection over time and adaptation to various environmental conditions. The objective of the present study was to determine the genetic relationships of green bean accessions collected from Kırşehir Province of Turkey, located at the central Anatolia. Within a population of 275 green bean accessions, 50 accessions were selected on the basis of morphological observations for further evaluation with SSR and STS/SCAR markers together with 4 reference cultivars of Andean and Mesoamerican origin. SSR markers selected on the basis of high polymorphism information content revealed the genetic relatedness of selected green bean accessions. STS/SCAR markers associated with bean anthracnose, common bacterial blight, white mold, halo blight, and phaseolin protein demonstrated the inheritance of resistance traits of local accessions at the selected loci. These findings may help better utilize genetic resources and furthermore are expected to facilitate forthcoming breeding studies for the generation of novel cultivars well adapted to the region.

  18. SSR Analysis on Diversity of AA Genome Oryza Species in the Southeast and South Asia

    Directory of Open Access Journals (Sweden)

    Jian-zhen LU

    2008-12-01

    Full Text Available To investigate genetic diversities among the AA genome Oryza species in the Southeast and South Asia, a total of 428 accessions of the AA genome Oryza species were genotyped using 36 simple sequence repeats (SSR markers distributed throughout the rice genome. All of the 36 SSR markers generated polymorphic bands, revealing 100% polymorphism. The number of alleles per locus ranged from 3 to 17 with the mean of 8.6. The Nei's genetic diversity index (He ranged from 0.337 at RM455 to 0.865 at RM169 with an average value of 0.650. The genetic diversity of the AA genome Oryza species in the Southeast Asia was obviously higher than that in the South Asia. Among the detected Oryza species in the South and Southeast Asia, O. rufipogon showed the highest genetic diversity. Meanwhile, a higher genetic differentiation (Fst was found among the detected Oryza species in the Southeast Asia than in the South Asia. The Fst value between O. nivara and O. sativa was the highest. The results from the number of specific alleles, specific loci, and allele frequency confirmed the greater genetic variation among the detected species. In addition, the specific allele in RM161 displayed higher frequency (0.193, suggesting its important function in identifying Oryza species of AA genome.

  19. Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

    Science.gov (United States)

    Lee, Hwa-Yong; Moon, Suyun; Shim, Donghwan; Hong, Chang Pyo; Lee, Yi; Koo, Chang-Duck; Chung, Jong-Wook; Ryu, Hojin

    2017-01-01

    The shiitake mushroom (Lentinula edodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2–11; the observed and expected heterozygosity were 0.00–1.00 and 0.10–0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications. PMID:28338645

  20. Development of Simple Sequence Repeat (SSR Markers of Sesame (Sesamum indicum from a Genome Survey

    Directory of Open Access Journals (Sweden)

    Xin Wei

    2014-04-01

    Full Text Available Sesame (Sesamum indicum, an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.

  1. Genetic diversity of different apricot geographical groups determined by SSR markers.

    Science.gov (United States)

    Romero, Carlos; Pedryc, Andrzej; Muñoz, Verónica; Llácer, Gerardo; Badenes, Maria Luisa

    2003-04-01

    Forty apricot cultivars with different geographic origins belonging to the germplasm collections of St. Istvan University (Budapest, Hungary) and the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were studied by means of SSR markers. The aim of the study was to determine the genetic relationships among genotypes from different eco-geographical groups. Sixteen primer pairs flanking microsatellite sequences in the peach genome were assayed. Eleven of them were polymorphic in the set of cultivars studied and allowed every genotype to be unambiguously distinguished. Genetic diversity in the population studied was analyzed using several variability parameters. A total of 34 alleles were detected with a mean value of 3.1 alleles/locus. The expected heterozygosity mean was 0.46 and the observed heterozygosity was 32% on an average leading to a high value of the Wright's fixation index (0.32). Additionally, UPGMA cluster analysis based on Nei's genetic distance grouped genotypes according to their geographic origins and pedigrees. SSR markers have proved to be an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in apricot.

  2. Genomic validation of PB 260 clone of rubber (Hevea brasiliensis) at Cikumpay Plantation by SSR marker

    Science.gov (United States)

    Royani, J. I.; Safarrida, A.; Rachmawati, I.; Khairiyah, H.; Mustika, I. P.; Suyono, A.; Rudiyana, Y.; Kubil; Nurjaya; Arianto, A.

    2017-05-01

    Rubber from Hevea brasiliensis is the only commercial natural rubber in the world. Propagation of rubber trees usually done by grafting and seed germination. BPPT had been producing rubber tree by in vitro technique with embryo somatic methods. Validation of mother plant for in vitro propagation is important to compare between mother plant and propagated plants. The aim for this research was to validation of PB 260 clone that planted at Cikumpay Plantation by SSR marker. Sampling of 10 rubber leaves were done at Cikumpay Plantation based on GPS position from the area of PB 260 clone. Rubber leaves were isolated with CTAB modification method to obtained DNA. Four of SSR primers from rubber, i.e.: hmac 4, hmac 5, hmct 1, and hmct 5, were used as primers to amplification of rubber DNA. The result showed that no band that different from 10 rubber of PB 260 clone at Cikumpay Plantation. This research will continue to compare genomic validation between mother plant and propagated plants that had been produced from BPPT.

  3. Molecular characterization of arabica and Conilon coffee plants genotypes by SSR and ISSR markers

    Directory of Open Access Journals (Sweden)

    Ludymila Brandão Motta

    2014-10-01

    Full Text Available The molecular characterization of ten genotypes of the Coffea arabica plants and of seven genotypes of C. canephora having interesting features for coffee breeding programs was carried to select the parents for breeding. A total of 40 SSR and 29 ISSR primers were used. The primers generated a total of 331 (307 polymorphic and 24 monomorphic bands. Analysis of genetic diversity presented dissimilarity intervals ranging from 0.22 to 0.44 between the Conilon genotypes, from 0.02 to 0.28 between the Arabica genotypes, and from 0.49 to 0.60 between the genotypes of the two species in the joint analysis. Four groups were formed: I = genotypes of C. arabica, II = four progenies of C. canephora, Conilon group, and one non defined C. canephora (Conilon or Robusta, III = one progeny of un-defined C. canephora (Conilon or Robusta and IV = one progeny of C. canephora of Robusta group. The grouping formed was consistent with the origins of each group. High stabilities of the bifurcations were found by bootstrap analysis. The use of molecular markers of the SSR and ISSR types in the diversity study was efficient in distinguishing genotypes between and within C. arabica and C. canephora.

  4. Analysis of genetic structure and interrelationships in lentil species using morphological and SSR markers.

    Science.gov (United States)

    Koul, Priyanka Mohan; Sharma, Vikas; Rana, Maneet; Chahota, Rakesh K; Kumar, Shiv; Sharma, Tilak R

    2017-05-01

    Genetic structure and relationships of 130 lentil accessions belonging to six taxa were analysed. For this purpose, seven morphological traits and 31 polymorphic simple sequence repeat (SSR) primers were used for this purpose. Morphological traits grouped lentil accessions into five main clusters. SSR primers collectively amplified 139 polymorphic alleles in a range of 2-10 with an average of 4.48 alleles. The size of amplified alleles varied from 50 to 650 bp. Polymorphism information content (PIC) ranged from 0.02 to 0.85 with an average of 0.46. Neighbour-joining tree grouped accessions broadly according to their taxonomic ranks, except L. culinaris ssp. odemensis. Analysis of molecular variance (AMOVA) revealed that a major portion (82.0%) of genetic variance resided within species, while only 18% resided among species. Bayesian model-based STRUCTURE analysis assigned all accessions into five clusters and showed some admixture within individuals. Cluster analysis showed that cultivated Lens accessions of Ethiopian origin clustered separately, from other cultivated accessions indicating its distinct lineage. Among the analysed lentil species, L. culinaris ssp. odemensis seemed to have conserved genetic background and needs revision of its taxonomic status. Results of present study provide important information on genetic diversity and relationships among different wild and cultivated taxa of lentil. Thus, these results can be useful in designing breeding strategies for future improvement and taxonomic implications in lentil.

  5. Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars.

    Science.gov (United States)

    Lee, Hwa-Yong; Moon, Suyun; Shim, Donghwan; Hong, Chang Pyo; Lee, Yi; Koo, Chang-Duck; Chung, Jong-Wook; Ryu, Hojin

    2017-03-24

    The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2-11; the observed and expected heterozygosity were 0.00-1.00 and 0.10-0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.

  6. Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes Cultivars

    Directory of Open Access Journals (Sweden)

    Hwa-Yong Lee

    2017-03-01

    Full Text Available The shiitake mushroom (Lentinula edodes is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2–11; the observed and expected heterozygosity were 0.00–1.00 and 0.10–0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.

  7. Applicability of SSR markers to the traceability of monovarietal olive oils.

    Science.gov (United States)

    Vietina, Michelangelo; Agrimonti, Caterina; Marmiroli, Marta; Bonas, Urbana; Marmiroli, Nelson

    2011-06-01

    To protect the features and authenticity of food products, the European Commission enforces two certification labels: Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI). EEC Regulation No. 510/2006 imposes criteria for labelling, production and commercialisation of olive oil. Since plant genotype is a major determinant in establishing the PDO and PGI labels, methods to ascertain the varieties present in a batch of olive oil are essential in validating product conformity. The traceability of olive oil can be assessed through simple sequence repeat (SSR) co-dominant markers targeted to specific regions of DNA from olive cultivars. Twenty-one monovarietal olive oils were analysed with nine nuclear and two shortened SSRs. For each marker the correspondence of allelic profile with the reference cultivar, the reproducibility of profiles in different DNA extractions and the polymorphism information content were determined. The results showed that using a panel of SSR markers such as those described in this paper allows one to make a reliable attribution of an olive oil to a specific cultivar. Copyright © 2011 Society of Chemical Industry.

  8. SSR-based genetic diversity and structure of garlic accessions from Brazil.

    Science.gov (United States)

    da Cunha, Camila Pinto; Resende, Francisco Vilela; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2014-10-01

    Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

  9. Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey.

    Science.gov (United States)

    Wei, Xin; Wang, Linhai; Zhang, Yanxin; Qi, Xiaoqiong; Wang, Xiaoling; Ding, Xia; Zhang, Jing; Zhang, Xiurong

    2014-04-22

    Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.

  10. CitEST libraries

    Directory of Open Access Journals (Sweden)

    Maria Luísa P. Natividade Targon

    2007-01-01

    Full Text Available In order to obtain a better understanding of what is citrus, 33 cDNA libraries were constructed from different citrus species and genera. Total RNA was extracted from fruits, leaves, flowers, bark, seeds and roots, and subjected or not to different biotic and abiotic stresses (pathogens and drought and at several developmental stages. To identify putative promoter sequences, as well as molecular markers that could be useful for breeding programs, one shotgun library was prepared from sweet orange (Citrus sinensis var. Olimpia. In addition, EST libraries were also constructed for a citrus pathogen, the oomycete Phythophthora parasitica in either virulent or avirulent form. A total of 286,559 cDNA clones from citrus were sequenced from their 5’ end, generating 242,790 valid reads of citrus. A total of 9,504 sequences were produced in the shotgun library and the valid reads were assembled using CAP3. In this procedure, we obtained 1,131 contigs and 4,083 singletons. A total of 19,200 cDNA clones from P. parasitica were sequenced, resulting in 16,400 valid reads. The number of ESTs generated in this project is, to our knowledge, the largest citrus sequence database in the world.

  11. (SSR) markers

    African Journals Online (AJOL)

    HP-PROBOOK

    2016-10-05

    Oct 5, 2016 ... Cluster analysis was constructed using DARwin program version 6.0. Forty eight (48) coconut individuals were clustered into three groups. Key words: Coconut palm (Cocos nucifera ... markers, cluster analysis, diversity. INTRODUCTION ... industry in Kenya (Muhammed et al., 2013). Furthermore, the slow ...

  12. (SSR) markers

    African Journals Online (AJOL)

    aghomotsegin

    Unknown. V. vinifera L. 1980s. Russia. Cabernet Franc. Ancient variety of France. V. vinifera L. 1890s. France. Malvasia Istriana. Ancient variety of Greece. V. vinifera L. 2000s. Italy. BиHTA. Unknown. V. vinifera L. 1980s. Bulgaria. Yan Tai No: 73. Muscat hamburg × alicante bouschet. V. vinifera L. ----. China. Beta. Unknown.

  13. Assessment of Genetic Variation within Commercial Iranian Pomegranate (Punica granatum L. Cultivars, Using ISSR and SSR Markers

    Directory of Open Access Journals (Sweden)

    Meysam Madadi

    2017-07-01

    Full Text Available Pomegranate is one of the most important horticultural crops in Iran, and has been cultivated for thousands of years in this country. At this period due to selection of superior cultivars from nature or mutation emerged in these cultivars, and their vegetative propagation, substantial genetic variation has occurred within and among the cultivars. Thus, each cultivar may consist of different clones. According to this issue, diversity within four commercial cultivars of pomegranate was analyzed. Two molecular marker systems including ISSR and SSR were used to evaluate variability between 36 samples of four commercial cultivars. ISSR markers produced 114 amplification products, out of which 97 were polymorphic (83.23%. Mean resolving power was 2.96 for ISSR markers. 19 SSR molecular markers were used, 15 of which amplified polymorphic products, while the remaining ones monomorphic., The number of polymorphic alleles per locus ranged from two to four (average 3.6. The observed and expected heterozygosities ranged from 0.04 to 0.92 and 0.14 to 0.62, respectively. In addition, mean polymorphic information content was 0.45 for SSR loci. Our results showed that commercial Iranian pomegranate have different clones. Therefore, ISSR and SSR markers can be a useful tools for detecting clones of each cultivar.

  14. 78 FR 11939 - Social Security Ruling, SSR 13-2p.; Titles II and XVI: Evaluating Cases Involving Drug Addiction...

    Science.gov (United States)

    2013-02-20

    ... impairment(s). At the hearing and appeals levels, Administrative Law Judges (ALJs) and the Appeals Council....\\1\\ \\1\\ For simplicity, we refer in this SSR only to initial adult claims for disability benefits... benefits under title XVI when they attained age 18, and continuing disability reviews of adults and...

  15. SSR analysis demonstrates that olive production in the southern Marmara region in Turkey uses a single genotype.

    Science.gov (United States)

    Ipek, A; Barut, E; Gulen, H; Oz, A T; Tangu, N A; Ipek, M

    2009-10-20

    The southern Marmara region in Turkey was surveyed to determine the olive cultivars that are used for olive production. Genetic diversity analysis using simple sequence repeat (SSR) markers indicated that the cultivar Gemlik is the major olive cultivar grown in this region, while other olive cultivars are grown only for use as pollinators of Gemlik or for growers' own exotic consumption. Although the quality of Gemlik is widely accepted in Turkey, its tendency toward alternate bearing is a major drawback. Twenty-four genotypes were selected within the cultivar Gemlik because of their tolerance to alternate bearing. These selected genotypes have the same SSR alleles as Gemlik, making them good candidates for developing a Gemlik olive with reduced alternate bearing. About 8% of samples did not share the same SSR alleles with Gemlik, though these genotypes were identified as Gemlik by the growers. Some other standard cultivars that are grown in other regions of Turkey were mistakenly called Gemlik in this region, probably due to the popularity of this cultivar in the southern Marmara region. In conclusion, as indicated by SSR analysis, Gemlik has become the standard cultivar in this region; future research should be focused on techniques to improve the production and quality of table olives and olive oil from this cultivar.

  16. 77 FR 58604 - Social Security Ruling (SSR), 12-1p; Title II: Determining Whether Work Performed in Self...

    Science.gov (United States)

    2012-09-21

    ... ADMINISTRATION Social Security Ruling (SSR), 12-1p; Title II: Determining Whether Work Performed in Self..., Commissioner of Social Security. Policy Interpretation Ruling Title II: Determining whether work performed in... social programs to be SGA. See 20 CFR 404.1572. Policy Interpretation: For work activity performed by...

  17. Development of 15 genic-ssr markers in oil-tea tree (Camellia oleifera based on transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Jia Baoguang

    2014-01-01

    Full Text Available Oil-tea tree is one of the most important woody edible oil plants; however, lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of developing seeds and characterized microsatellites from transcriptome sequences to identify valuable markers for C. oleifera molecular genetics research. A total of 69,798 unigenes were identified, in which 6,949 putative SSR motifs from 6,042 SSR-containing unique putative transcripts were discovered. Twenty-nine primer pairs corresponding to 29 unigene loci were designed, of which 15 polymorphic genic-SSR markers were developed in 18 varieties and characterized by capillary electrophoresis. The number of alleles per locus (Na ranged from 2 to 14, the expected heterozygosity (He ranged from 0.374 to 0.876, and the polymorphism information content (PIC values ranged from 0.498 to 0.887, respectively. Cross-species amplification was also conducted in 15 varieties of C. japonica. All 15 markers successfully amplified PCR products with expected size in C. japonica and exhibited polymorphisms. The 15 polymorphic genic- SSR markers will have potential for applications in genetic diversity evaluation, molecular fingerprinting identification, comparative genome analysis, and genetic mapping in the C. oleifera and C. japonica.

  18. 78 FR 17744 - Social Security Ruling, SSR 13-2p; Titles II and XVI: Evaluating Cases Involving Drug Addiction...

    Science.gov (United States)

    2013-03-22

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-2p; Titles II and XVI: Evaluating Cases Involving Drug Addiction and Alcoholism (DAA); Correction AGENCY: Social Security Administration. ACTION: Notice of Social...

  19. Analysis of simple sequence repeats in rice bean (Vigna umbellata using an SSR-enriched library

    Directory of Open Access Journals (Sweden)

    Lixia Wang

    2016-02-01

    Full Text Available Rice bean (Vigna umbellata Thunb., a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%. Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%, and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker

  20. Genetic diversity trend in Indian rice varieties: an analysis using SSR markers.

    Science.gov (United States)

    Singh, Nivedita; Choudhury, Debjani Roy; Tiwari, Gunjan; Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R K; Sharma, A D; Singh, N K; Singh, Rakesh

    2016-09-05

    The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940-2013), conserved in the National Gene Bank of India using SSR markers. A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend. Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which

  1. Evaluation of Mungbean Mutant Lines to Drought Stress and Their Genetic Relationships Using SSR Markers

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    Yuliasti

    2015-12-01

    Full Text Available Development of mungbean cultivarstolerant to drought stress through mutation breeding approach would enable us to anticipate the crop yield-reducing effects of climate changes. The objective of this research was to evaluate the yield performance of mungbean mutant lines that showed tolerance to drought stress, and to analyze their genetic diversity and relationship among mutant lines using SSR markers. The study was conducted during the dry season of 2012 in the Muneng experimental farm, Probolinggo, East Java. The experiment was laid out in a randomized block design with four replications. Five mutant lines and two parental lines as control were tested for evaluation of yield and drought tolerance under twoenvironments of two irrigation systems as treatment. The two environmental conditions consisted of optimal irrigation (at least three times: at planting, flowering and during pod filling and suboptimal irrigation (two times at planting and flowering. To evaluate genetic variation among selected mutant lines and their discrimination from parental lines in molecular level, a cluster analysis was performed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA in the NTSYS software. The results showed that three mutant lines, including PsJ30, PsJ31, PsJ32 produced the highest grain yields of 1.17, 1.01, and 1.04 ton/ha, respectively, compared to the other mutant lines and the parents Gelatik (0.85 ton/ha and Perkutut (0.87 ton/ha as control check. Of those mutant lines, PSJ31 was the most tolerant to drought with sensitivity index value of 0.47. The PSJ31 has now been officially released as a new variety ( 2013, named as Muri which was identified to have high yield and tolerant to drought. Based on 23 SSR markers used for clustering analysis of those 3 selected mutant lines,9SSR markers (MBSS R033; satt137; MBSSR008; MBSSR203; MBSSR013; MBSSR021; MBSSR016; MBSSR136; and DMBSSR013 were successfully identified the three mungbean mutant

  2. Genetic diversity among Brazilian soybean cultivars based on SSR loci and pedigree data

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    Regina Helena Geribello Priolli

    2010-06-01

    Full Text Available In this study, simple sequence repeats (SSR loci and pedigree data were used to investigate the genetic relationship in a group of 168 Brazilian soybean cultivars. Eighteen SSR loci produced an average of 5.06 alleles and a mean gene diversity of 0.58 for the cultivars studied. Genetic distance (GD was determined using the modified Roger's Wright distance, and a final dendrogram was in agreement with the cultivar pedigree. A distance matrix based on the coefficient of parentage scores was also generated for the cultivars, which ranged from 0 to 1, with a mean of 0.18, whereas SSR-based genetic similarity (1- GD ranged from 0.01 to 0.90, with a mean of 0.25. Mantel's Z test showed that the similarity matrices generated from both the data sets were low, but significantly correlated (r = 0.31, pLocos microssatélites e dados de genealogia foram utilizados para avaliar a diversidade genética de um grupo de 168 cultivares brasileiras de soja. Os dezoito locos utilizados apresentaram em média 5,06 alelos por loco e coeficiente de diversidade genética médio de 0,58. O dendrograma final resultante da matriz de distância genética de Roger modificado por Wright, apresentou boa concordância com a ancestralidade dos grupos formados. Também foi estimado os coeficientes de parentesco entre as cultivares, sendo observada variação de 0 a 1 com média de 0,18, enquanto que as similaridades para os locos microssatélites (1- GD variou de 0,01 a 0,90 com média de 0,25. A correlação entre as duas matrizes obtidas determinada pelo teste Z de Mantel apresentou valor baixo, 0,31, mas significativo (p<0,001. Os resultados obtidos sugerem que os locos microssatélites aliados às informações de genealogia proporcionam melhor análise da diversidade genética de cultivares de soja.

  3. Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding.

    Science.gov (United States)

    Cubry, Philippe; Musoli, Pascal; Legnaté, Hyacinte; Pot, David; de Bellis, Fabien; Poncet, Valérie; Anthony, François; Dufour, Magali; Leroy, Thierry

    2008-01-01

    The present study shows transferability of microsatellite markers developed in the two cultivated coffee species (Coffea arabica L. and C. canephora Pierre ex Froehn.) to 15 species representing the previously identified main groups of the genus Coffea. Evaluation of the genetic diversity and available resources within Coffea and development of molecular markers transferable across species are important steps for breeding of the two cultivated species. We worked on 15 species with 60 microsatellite markers developed using different strategies (SSR-enriched libraries, BAC libraries, gene sequences). We focused our analysis on 4 species used for commercial or breeding purposes. Our results establish the high transferability of microsatellite markers within Coffea. We show the large amount of diversity available within wild species for breeding applications. Finally we discuss the consequences for future comparative mapping studies and breeding of the two cultivated species.

  4. [Chemotaxonomic characteristics of bacteria belonging to the genus Nocardia isolated from Ukrainian SSR soils].

    Science.gov (United States)

    Nesterenko, O A; Kasumova, S A; Kvasnikov, E I; Shkaruba, V V

    1976-01-01

    From soils of the Ukrainian SSR bearing oil and without it, 241 strains of Nocardia were isolated on mineral media containing n-alkanes C12-C22. The strains were divided into two groups: actinoid (N. asteroides, N. flavescens) and bacterium-like (N. rubropertincta, N. flava, N. ucrainica, N. salmonicolor, N. rubra, N. erythropolis, Nocardia ssp). Chemotaxonomic characteristics (the presence in the cells of galactose, arabinose, mesodiaminopimelic acid, lipid LCN-A) were used to differentiate Nocardia from other genera of actinomycetes and coryneforms and to confirm the taxonomy of museum strains. The majority of the Nocardia cultures belongs to the groups "asteroides" and "rhodochrous" according to location of spots of lipid LCN-A on chromatograms. The strains of N. asteroides and complex "M." rhodochrous may belong to both groups. A small number of strains belongs to the group which is represented by N. calcarea 41 (NCIB 8863).

  5. Epidemiology of allergic diseases of the respiratory passages in the Kazakh SSR

    Energy Technology Data Exchange (ETDEWEB)

    Moshkevich, V.S.

    1985-01-01

    Over a period of 20 years, the authors have been studying the distribution, aetiology and causes of increasing incidence of allergic respiratory diseases in various climatogeographic zones of the Kazakh SSR. Large groups of people living in towns and in the country were examined by various methods. The number of patients seeking advice in health service establishments because of allergic rhinitis and bronchial asthma was found to increase every year. A number of factors influencing the incidence of disease were pointed out, such as the character of diet, duration of the person's stay, vaccination against brucellosis, pollution of the atmosphere, local flora, climate, and other factors. Morbidity also depended on the methods of studying the epidemiology of respiratory allergoses. The obtained results will help health service authorities in taking specific measures to reduce morbidity from the mentioned pathological condition.

  6. Identification of SNP and SSR markers in eggplant using RAD tag sequencing

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    Valè Giampiero

    2011-06-01

    Full Text Available Abstract Background The eggplant (Solanum melongena L. genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant. Results RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci. Conclusion The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.

  7. Evaluation of rice germplasm under salt stress at the seedling stage through SSR markers

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    M. Al-Amin

    2013-06-01

    Full Text Available Twenty eight rice germplasms were used for identification of salt tolerant rice genotypes at the seedling stage at the experimental farm and Biotechnology laboratory of the Bangladesh Institute of Nuclear Agriculture (BINA, Mymensingh during February 2009 to October 2009. Phenotyping for salinity screening of the rice genotypes was done using salinized (EC level 12 dS m-1 nutrient solution in hydroponic system. Genotypes were evaluated for salinity tolerance on 1-9 scale based on seedling growth parameters following modified Standard Evaluation Scoring (SES of IRRI. Phenotypically, on the basis of SES and % total dry matter (TDM reduction of the genotypes viz. PBSAL-614, PBSAL-613, PBSAL-730, Horkuch, S-478/3 Pokkali and PBSAL (STL-15 were found to be salt tolerant; on the other hand Iratom-24, S-653/32, S-612/32, S-604/32, S-633/32, Charnock (DA6, BINA Dhan-6 and S-608/32 were identified as salt susceptible. For genotyping, ten SSR markers were used for polymorphism, where 3 primers (RM127, RM443 and RM140 were selected for evaluation of salt tolerance. In respect of Primer RM127, 7 lines were found salt tolerant and 11 lines were moderately tolerant and 10 lines were susceptible. Nine tolerant, 9 moderately tolerant and 10 susceptible lines were found when the primer RM140 was used and primer RM443 identified 8 lines as tolerant, 9 lines as moderately tolerant and 11 lines as susceptible. Thus, the salt tolerant lines can be used in further evaluation for salinity tolerance and the SSR markers used in this study are proving valuable for identifying salt tolerant genes in marker assisted breeding.

  8. Development and Integration of an SSR-Based Molecular Identity Database into Sugarcane Breeding Program

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    Yong-Bao Pan

    2016-04-01

    Full Text Available Sugarcane breeding is very difficult and it takes 12 to 14 years to develop a new cultivar for commercial production. This is because sugarcane varieties are highly polyploid, inter-specific hybrids with 100 to 130 chromosomes that may vary across geographical areas. Other obstacles/constraints include the small size of flowers that may not synchronize but may self-pollinate, difficulty in distinguishing hybrids from self progenies, extreme (G × E interactive effect, and potential variety mis-identification during vegetative propagation and varietal exchange. To help cane breeders circumvent these constraints, a simple sequence repeats (SSR-based molecular identity database has been developed at the United States Department of Agriculture-Agricultural Research Service, Sugarcane Research Unit in Houma, LA. Since 2005, approximately 2000 molecular identities have been constructed for clones of sugarcane and related Saccharum species that cover geographical areas including Argentina, Australia, Bangladesh, China, Colombia, India, Mexico, Pakistan, South Africa, Thailand, USA (Louisiana, Florida, Texas, and Hawaii, and Venezuela. The molecular identity database is updated annually and has been utilized to: (1 provide molecular descriptors to newly registered cultivars; (2 identify in a timely fashion any mislabeled or unidentifiable clones from cross parents and field evaluation plots; (3 develop de novo clones of energy cane with S. spontaneum cytoplasm; (4 provide clone-specific fingerprint information for assessing cross quality and paternity of polycross; (5 determine genetic relatedness of parental clones; (6 select F1 hybrids from (elite × wild or (wild × elite crosses; and (7 investigate the inheritance of SSR markers in sugarcane. The integration of the molecular identity database into the sugarcane breeding program may improve the overall efficacy of cultivar development and commercialization.

  9. De novo assembly and characterization of Gleditsia sinensis transcriptome and subsequent gene identification and SSR mining.

    Science.gov (United States)

    Han, S; Wu, Z; Wang, X; Huang, K; Jin, Y; Yang, W; Shi, H

    2016-01-29

    Gleditsia sinensis is a Chinese native deciduous tree with a high economic and medicinal value. However, there is limited knowledge on the molecular processes responsible for the medical properties of this species owing to lack of bioinformatic resources such as available whole-genome sequences. In the present study, RNA sequencing data were used to analyze the transcriptome of G. sinensis, and a series of bioinformatic tools was used to explore the main genes involved in important molecular processes. A total of 75.57 million paired-end reads, with a length of 101 bp, were acquired from G. sinensis. Using the assembly tool Trinity, 233,751 transcripts were discovered. Among these, 85,795 were identified as unique transcripts and 59,326 unique transcripts were found to contain coding regions. Gene ontology analysis identified 27,637 unique transcripts that were clustered into 56 functional groups. Genes involved in flavonoid and terpenoid backbone biosynthesis and those encoding transcription factors were further analyzed. Sequence analysis revealed four putative G. sinensis chalcone isomerase genes (GsCHI) encoding the enzymes for flavonoid biosynthesis. GsCHI1 was found to be phylogenetically related to the chalcone isomerase of the family Leguminosae, and its transcript levels in different tissues were higher than those of GsCHI2, GsCHI3, and GsCHI4. Furthermore, 15,014 simple sequence repeat (SSR) markers were discovered in the transcript library, and 5170 primers were generated for the SSR loci. The genetic and genomic information presented in this study will be helpful for future studies on gene discovery and molecular processes in G. sinensis.

  10. Rho-dependent termination of ssrS (6S RNA) transcription in Escherichia coli: implication for 3' processing of 6S RNA and expression of downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase).

    Science.gov (United States)

    Chae, Huiseok; Han, Kook; Kim, Kwang-sun; Park, Hongmarn; Lee, Jungmin; Lee, Younghoon

    2011-01-07

    It is well known that 6S RNA, a global regulatory noncoding RNA that modulates gene expression in response to the cellular stresses in Escherichia coli, is generated by processing from primary ssrS (6S RNA) transcripts derived from two different promoters. The 5' processing of 6S RNA from primary transcripts has been well studied; however, it remains unclear how the 3'-end of this RNA is generated although previous studies have suggested that exoribonucleolytic trimming is necessary for 3' processing. Here, we describe several Rho-dependent termination sites located ∼90 bases downstream of the mature 3'-end of 6S RNA. Our data suggest that the 3'-end of 6S RNA is generated via exoribonucleolytic trimming, rather than endoribonucleolytic cleavage, following the transcription termination events. The termination sites identified in this study are within the open reading frame of the downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase) gene, a part of the highly conserved bacterial operon ssrS-ygfA, which is up-regulated during the biofilm formation. Our findings reveal that ygfA expression, which also aids the formation of multidrug-tolerant persister cells, could be regulated by Rho-dependent termination activity in the cell.

  11. La implementación de la política pública de salud sexual y reproductiva (SSR en el Eje Cafetero colombiano: el caso del embarazo adolescente

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    Sara E. del Castillo Matamoros

    2008-05-01

    Full Text Available La política nacional de salud sexual y reproductiva (SSR definida en Colombia en 2002 por el Ministerio de la Protección Social para los años 2002 a 2006 señala los temas prioritarios en este campo: maternidad segura, planificación familiar, salud sexual y reproductiva de las y los adolescentes, cáncer de cuello uterino, infecciones de transmisión sexual y reproductiva, VIH/SIDA, y violencia doméstica y sexual. La investigación que se reporta se ha focalizado en el análisis cuantitativo y cualitativo del proceso de implementación de la política de salud sexual y reproductiva de los y las adolescentes en los tres departamentos y capitales que conforman el llamado “Eje Cafetero colombiano”. Los resultados del estudio mostraron que, si bien se mide una reducción en el número de nacimientos en adolescentes (10-19 años en la región vinculada al estudio entre 2003 y 2005, no se pudieron determinar estrategias y actividades explicativas de ello. La política ha permitido visibilizar y legitimar acciones específicas en este campo para la población adolescente. Sin embargo, se observó la existencia de importantes en las metodologías de recolección y sistematización de los datos relativos a la salud sexual y reproductiva de la población adolescente según las entidades estudiadas, así como la ausencia de retroalimentación cuantitativa utilizable para los actores de la política. En conclusión, se emiten unas recomendaciones para el ajuste de dicha política de SSR.

  12. EST2Prot: Mapping EST sequences to proteins

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    Lin David M

    2006-03-01

    Full Text Available Abstract Background EST libraries are used in various biological studies, from microarray experiments to proteomic and genetic screens. These libraries usually contain many uncharacterized ESTs that are typically ignored since they cannot be mapped to known genes. Consequently, new discoveries are possibly overlooked. Results We describe a system (EST2Prot that uses multiple elements to map EST sequences to their corresponding protein products. EST2Prot uses UniGene clusters, substring analysis, information about protein coding regions in existing DNA sequences and protein database searches to detect protein products related to a query EST sequence. Gene Ontology terms, Swiss-Prot keywords, and protein similarity data are used to map the ESTs to functional descriptors. Conclusion EST2Prot extends and significantly enriches the popular UniGene mapping by utilizing multiple relations between known biological entities. It produces a mapping between ESTs and proteins in real-time through a simple web-interface. The system is part of the Biozon database and is accessible at http://biozon.org/tools/est/.

  13. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis.

    Science.gov (United States)

    Zhang, Min; Wang, Cuiping; Lin, Qingfang; Liu, Aihua; Wang, Ting; Feng, Xuanjun; Liu, Jie; Han, Huiling; Ma, Yan; Bonea, Diana; Zhao, Rongmin; Hua, Xuejun

    2015-08-01

    Auxin polar transport mediated by a group of Pin-formed (PIN) transporters plays important roles in plant root development. However, the mechanism underlying the PIN expression and targeting in response to different developmental and environmental stimuli is still not fully understood. Here, we report a previously uncharacterized gene SSR1, which encodes a mitochondrial protein with tetratricopeptide repeat (TPR) domains, and show its function in root development in Arabidopsis thaliana. In ssr1-2, a SSR1 knock-out mutant, the primary root growth was dramatically inhibited due to severely impaired cell proliferation and cell elongation. Significantly lowered level of auxin was found in ssr1-2 roots by auxin measurement and was further supported by reduced expression of DR5-driven reporter gene. As a result, the maintenance of the root stem cell niche is compromised in ssr1-2. It is further revealed that the expression level of several PIN proteins, namely, PIN1, PIN2, PIN3, PIN4 and PIN7, were markedly reduced in ssr1-2 roots. In particular, we showed that the reduced protein level of PIN2 on cell membrane in ssr1-2 is due to impaired retrograde trafficking, possibly resulting from a defect in retromer sorting system, which destines PIN2 for degradation in vacuoles. In conclusion, our results indicated that SSR1 is functioning in root development in Arabidopsis, possibly by affecting PIN protein expression and subcellular targeting. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  14. A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.

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    Srinivasan Ramamurthy

    2009-11-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L., an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses. This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs and gene-based markers. Results A total of 20,162 (18,435 high quality drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons. Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965 had significant similarity (≤1E-05 to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut and three model plant species (rice, Arabidopsis and poplar provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3% significant unigenes, only 2,071 (32.3% unigenes could be functionally categorised according to Gene Ontology (GO descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs in 742 contigs (with ≥ 5 ESTs were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive

  15. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

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    Wang Junping

    2006-08-01

    Full Text Available Abstract Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR, Restriction Enzyme Fragment Polymorphism (RFLP and/or Sequence Tagged Site (STS markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci, with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM. More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in

  16. Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection.

    Science.gov (United States)

    Ipek, M; Ipek, A; Seker, M; Gul, M K

    2015-03-27

    The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined. The results also showed that there was a great amount of variation between the olive cultivars in terms of fatty acid composition. For example, oleic acid content ranged from 57.76 to 76.9% with standard deviation of 5.10%. Significant correlations between fatty acids of olive oil were observed. For instance, a very high negative correlation (-0.812) between oleic and linoleic acids was detected. A structured association analysis between the content of fatty acids in olive oil and SSR markers was performed. STRUCTURE analysis assigned olive cultivars to two gene pools (K = 2). Assignment of olive cultivars to these gene pools was not based on geographical origin. Association between fatty acid traits and SSR markers was evaluated using the general linear model of TASSEL. Significant associations were determined between five SSR markers and stearic, oleic, linoleic, and linolenic acids of olive oil. Very high associations (P olive.

  17. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery.

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    Tingxian Deng

    Full Text Available The Chinese swamp buffalo (Bubalis bubalis is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35% and 23,232 (37.27% unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5, respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO categories and EuKaryotic Ortholog Group (KOG cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Furthermore, 17,401 simple sequence repeats (SSRs were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65% yielded PCR amplicons and 69 primer pairs (60.00% presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead

  18. Repeats and EST analysis for new organisms

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    Jonassen Inge

    2008-01-01

    Full Text Available Abstract Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask against known repeats from other species (i.e., model organisms. There are few studies that investigate the effectiveness of this approach, or attempt to evaluate the different methods for identifying and masking repeats. Results Using zebrafish and medaka as example organisms, we show that accurate repeat masking is an important factor for obtaining a high quality clustering. Furthermore, we show that masking with standard repeat libraries based on curated genomic information from other species has little or no positive effect on the quality of the resulting EST clustering. Library based repeat masking which often constitutes a computational bottleneck in the EST analysis pipeline can therefore be reduced to species specific repeat libraries, or perhaps eliminated entirely. In contrast, substantially improved results can be achived by applying a repeat library derived from a partial reference clustering (e.g., from mapping sequences against a partially sequenced genome. Conclusion Of the methods explored, we find that the best EST clustering is achieved after masking with repeat libraries that are species specific. In the absence of such libraries, library-less masking gives results superior to the current practice of using cross-species, genome-based libraries.

  19. AFLP and SSR polymorphism in a Coffea interspecific backcross progeny [( C. heterocalyx x C. canephora) x C. canephora].

    Science.gov (United States)

    Coulibaly, I; Revol, B; Noirot, M; Poncet, V; Lorieux, M; Carasco-Lacombe, C; Minier, J; Dufour, M; Hamon, P

    2003-10-01

    An interspecific cross (BC 1) involving a species with one of the largest genomes in the Coffea genus [ Coffea heterocalyx (HET), qDNA = 1.74 pg] and a species with a medium-sized genome [ Coffea canephora (CAN), qDNA = 1.43 pg] was studied using two types of molecular markers, AFLP and SSR. One hundred and eighty eight AFLP bands and 34 SSR primer pairs were suitable for mapping. The total map length was 1,360 cM with 190 loci distributed in 15 linkage groups. The results were compared to those obtained previously on an interspecific BC 1 progeny involving a species with a medium-sized genome ( Coffea liberica var dewevrei, DEW) and a species with one of the smallest genomes ( Coffea pseudozanguebariae, PSE). They are discussed relative to three main points: (1) the relevance of the different marker types, (2) the genomic distribution of AFLP and SSR markers, and (3) the relation between AFLP polymorphism and genome size.

  20. Cluster Analysis on Japonica Rice (Oryza sativa L. with Good Eating Quality Based on SSR Markers and Phenotypic Traits

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    Chun-hong ZHANG

    2010-06-01

    Full Text Available Diversity of 60 conventional japonica rice accessions with good eating quality at home and abroad was analyzed using SSR molecular markers, agronomic traits and taste characteristics. A total of 290 alleles were detected in the 60 accessions at 72 SSR loci with the high similarity coefficients varying between 0.600 and 0.924. The loci on chromosome 5 showed the greatest value in average allele number. Additionally, most of the SSR loci could detect 3 to 4 alleles. An UPGMA dendrogram based on the cluster analysis of the genetic similarity coefficients showed that the grouping trend of part of the rice accessions was geographic-related and most of the rice accessions in Jiangsu Province, China were clustered together. Furthermore, many domestic accessions from south and north origins in China were close to the foreign japonica rice varieties, as proved by their pedigree origin from the foreign high-quality sources. For taste characteristics, part of the accessions with excellent taste were clearly clustered into one category though they came from different geographical regions, which indicates that taste characteristics of some varieties were mainly genetically determined. In addition, the agronomic traits of japonica rice with good taste might be closely related with their geographical origins, but the relationship between superior taste characteristics and agronomic traits should be further clarified.

  1. Genetic Diversity of Namibian Pennisetum glaucum (L. R. BR. (Pearl Millet Landraces Analyzed by SSR and Morphological Markers

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    Billy McBenedict

    2016-01-01

    Full Text Available Current Pennisetum glaucum (L. R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation’s food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

  2. Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia).

    Science.gov (United States)

    Wang, Shi; Zhang, Lingling; Matz, Mikhail

    2009-01-01

    Mining for microsatellites (also called simple sequence repeats [SSRs]) in public sequence databases of a common Indo-Pacific coral Acropora millepora identified 191 SSRs from 10 258 expressed sequence tag (EST) and 618 SSRs from 14 625 whole-genome shotgun (WGS) sequences. In contrast to other animals, trinucleotide repeats, rather than dinucleotide repeats, are dominant in the WGS-SSRs, and AAT is the most frequent trinucleotide motif in EST-SSRs. We successfully developed 40 polymorphic markers from EST-SSRs and WGS-SSRs. Both EST- and WGS-SSRs show high levels of polymorphism within corals from the same reef patch. Interestingly, markers WGS079 and WGS227 revealed SSR duplications in a few individuals, suggesting recent duplication events. Genotypic linkage disequilibrium was identified in 5 pairs of SSR markers, which will be invaluable for high-resolution studies of genetic admixture in natural populations of A. millepora. Transferability analysis showed that 25 of these markers can be successfully amplified in one of the most ubiquitous Indo-Pacific corals Acropora hyacinthus. The marker collection reported here is the largest ever developed for any reef-building coral. It holds great potential for addressing coral reef connectivity across the Indo-Pacific with an unprecedented precision, especially taking into account the cross-species transferability of a substantial number of markers.

  3. Development of EST-SSR markers related to disease resistance and their application in genetic diversity and evolution analysis in Gossypium.

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    Wang, B H; Rong, P; Cai, X X; Wang, W; Zhu, X Y; Chen, C J; Xu, Y Y; Huang, X J; Zhuang, Z M; Wang, C B

    2015-09-09

    Cotton (Gossypium spp) is one of the most economically important crops that provide the world's most widely used natural fiber. Diseases such as Fusarium wilt and particularly Verticillium wilt seriously affect cotton production, and thus breeding for disease resistance is one of the most important goals of cotton breeding programs. Currently, potential exists to improve disease resistance in cultivated cotton. Increasing the understanding of the distribution, structure, and organization of genes or quantitative trait loci for disease resistance will help the breeders improve crop yield even in the event of disease. To facilitate the mapping of disease-resistance quantitative trait loci to achieve disease-resistant molecular breeding in cotton, it is necessary to develop polymorphic molecular markers. The objective of this study was to develop simple sequence repeat markers based on cotton expressed sequence tags for disease resistance. The efficacy of these simple sequence repeat markers, their polymorphisms, and cross-species transferability were evaluated. Their value was further investigated based on genetic diversity and evolution analysis. In this study, the unique sequences used to develop markers were compared with the G. arboretum and G. raimondii genome sequences to investigate their position, homology, and collinearity between G. arboretum and G. raimondii.

  4. Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) based on de novo transcriptomeic assemblies

    Science.gov (United States)

    Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. Thi...

  5. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers

    Science.gov (United States)

    2011-01-01

    Background Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development. Results Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions. Conclusions This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research. PMID:21929789

  6. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers.

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    Wei, Wenliang; Qi, Xiaoqiong; Wang, Linhai; Zhang, Yanxin; Hua, Wei; Li, Donghua; Lv, Haixia; Zhang, Xiurong

    2011-09-19

    Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development. Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value sesame accessions. This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.

  7. Study of the functionality of the Helicobacter pylori trans-translation components SmpB and SsrA in an heterologous system

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    Ecobichon Chantal

    2010-03-01

    Full Text Available Abstract Background Trans-translation is a ubiquitous bacterial quality control-mechanism for both transcription and translation. With its two major partners, SsrA a small stable RNA and the SmpB protein, it promotes the release of ribosomes stalled on defective mRNAs and directs the corresponding truncated proteins to degradation pathways. We have recently shown that trans-translation is an essential function in the gastric pathogen Helicobacter pylori. Our results suggested that some properties of the H. pylori trans-translation machinery distinguishes it from the well known system in E. coli. Therefore, we decided to test the functionality of the SmpB and SsrA molecules of H. pylori in the E. coli heterologous system using two established phenotypic tests. Results H. pylori SmpB protein was found to successfully restore the E. coli ΔsmpB mutant growth defect and its capacity to propagate λimmP22 phage. We showed that in E. coli, H. pylori SsrA (Hp-SsrA was stably expressed and maturated and that this molecule could restore wild type growth to the E. coli ΔssrA mutant. Hp-SsrA mutants affected in the ribosome rescue function were not able to restore normal growth to E. coli ΔssrA supporting a major role of ribosome rescue in this phenotype. Surprisingly, Hp-SsrA did not restore the phage λimmP22 propagation capacity to the E. coli ΔssrA mutant. Conclusions These data suggest an additional role of the tag sequence that presents specific features in Hp-SsrA. Our interpretation is that a secondary role of protein tagging in phage propagation is revealed by heterologous complementation because ribosome rescue is less efficient. In conclusion, tmRNAs present in all eubacteria, have coevolved with the translational machinery of their host and possess specific determinants that can be revealed by heterologous complementation studies.

  8. SSR Polymorphism in Sterile, Low Fertile and Fertile of Different Citrus species

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    B. Golein

    2014-02-01

    Full Text Available Simple sequence repeats (SSR polymorphism in citrus including male sterile, sterile, low fertile and fertile was examined by analyzing 28 representative accessions sampled from north of Iran. Fifty four polymorphic alleles with an average of 4.2 alleles per primer were detected from eight pairs of used primers. The lowest number of alleles was observed in TAA27, CTT01, CCSM18 and ATC09 loci with only three alleles and the highest number of alleles was observed in TAA15 locus with eight alleles. Polymorphic information content (PIC values changed from 0.34 (AG14 to 0.90 (CCSM18. Genetic similarities among accessions were calculated according to Jaccard Similarity Index and used to construct a dendrogram based on the unweighted pair group method using arithmetic averages (UPGMA which put the 28 samples into four major groups (A, B, C and D. The cultivars of male sterile Satsuma mandarin were clustered into group A those of orange, grapefruit and Page (a complex hybrid into group B mandarin cultivars into group C and lemon Lisbon into group D.

  9. Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers

    Science.gov (United States)

    Hippolyte, I.; Jenny, C.; Gardes, L.; Bakry, F.; Rivallan, R.; Pomies, V.; Cubry, P.; Tomekpe, K.; Risterucci, A. M.; Roux, N.; Rouard, M.; Arnaud, E.; Kolesnikova-Allen, M.; Perrier, X.

    2012-01-01

    Background and Aims The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. Methods Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. Key Results and Conclusions We determine the closest diploid progenitors of the triploid ‘Cavendish’ and ‘Gros Michel’ subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. ‘Cavendish’, ‘Plantain’ and ‘Mutika-Lujugira’), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference. PMID:22323428

  10. A Set of 20 New SSR Markers Developed and Evaluated in Mandevilla Lindl.

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    Alev Oder

    2016-09-01

    Full Text Available Mandevilla is an ornamental crop with a bright future worldwide because of its high commercial acceptance and added value. However, as with most ornamental species, there are few molecular tools to support cultivar breeding and innovation. In this work, we report the development and analysis of 20 new Simple Sequence Repeat (SSR markers in Mandevilla. Microsatellites were isolated from two enriched small-insert genomic libraries of Mandevilla × amabilis. The diversity parameters estimated after their amplification in a group of 11 commercial genotypes illustrate the effect of two opposite drifts: the high relatedness of cultivars belonging to the same commercial group and the high divergence of other cultivars, especially M. × amabilis. Based on their different band patterns, six genotypes were uniquely distinguished, and two groups of sport mutations remained undistinguishable. The amplification of the SSRs in three wild species suggested the existence of unexploited diversity available to be introgressed into the commercial pool. This is the first report of available microsatellites in Mandevilla. The development process has provided some clues concerning the genome structure of the species, and the SSRs obtained will help to create new products and to protect existing and upcoming plant innovations.

  11. Genetic diversity and apple leaf spot disease resistance characterization assessed by SSR markers

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    Gustavo H.F. Klabunde

    2016-09-01

    Full Text Available Among the cultivation problems of apple production in Brazil, Apple Leaf Spot (ALS disease represents one of the main breeding challenges. This study aims at analyzing the genetic diversity among 152 apple scion accessions available at the Apple Gene Bank of EPAGRI, located in Caçador, Santa Catarina/ Brazil. Eleven genomic SSR loci were analyzed to assess genetic diversity of ALS resistant and susceptible accessions. Results revealed high genetic diversity of the studied accessions, being 120 exclusive alleles (67 unique from scion accessions resistant to ALS, and a mean PIC of 0.823. The locus Probability of Identity (I ranged from 0.017 to 0.089. The combined I was 4.11 x 10-16, and the Power of Exclusion was 99.99999259%. In addition, the DNA fingerprint patterns will contribute as additional descriptors to select parental for crosses and early identification of apple accessions for breeding purposes, and also for cultivar protection.

  12. Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR in Brassica juncea

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    Indra Singh

    2017-11-01

    Full Text Available Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs, transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR and Single Nucleotide Polymorphism (SNPs were identified on miRNAs (miR-SSRs and miR-SNPs and their target genes in B. juncea. Notably, one of the miR-SNP (C/T was found at the 5th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.

  13. Design And Development Of An Automatic Single Phase Protective Device Using Ssr

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    Michael E.

    2017-10-01

    Full Text Available Since the discovery of energy safety has been a paramount subject matter. This we can see in todays electrical systems where protective devices such as fuse and circuit breakers are used to prevent fire hazards resulting from overload overvoltage and short circuits. However with all the revolution in technology these options may be considered less smart since the fuse made with wire strands calculated for specific current capacity faults permanently when the specified current rating is exceeded. While the circuit breaker which is made up of mechanical switch fails as a result of carbon forming and the wearing away of the contacts because of arcing. As a means of improvement this paper presents the design and development of an automatic single phase protective device using solid state relay SSR. This study is to ensure automatic cut off from power supply in cases of overvoltage above 240 V AC or when overload and short circuit current above 8amps is detected without permanent damage of a fuse placed along current path. Also the design will ensure that there is an automatic close circuit whenever the trigger switch is momentary switch is closed. The system is achieved via the use of PIC micro-controller current sensor and other discrete components. The system is tested and works well inhibiting the frequent faulting of fuses. It also helps to prevent hazard as a result of overvoltage overload and short circuit and ensures a close circuit when the trigger switch is closed.

  14. New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh].

    Science.gov (United States)

    Bohra, Abhishek; Jha, Rintu; Pandey, Gaurav; Patil, Prakash G; Saxena, Rachit K; Singh, Indra P; Singh, D; Mishra, R K; Mishra, Ankita; Singh, F; Varshney, Rajeev K; Singh, N P

    2017-01-01

    Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R(2) = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable

  15. Generation and analysis of expressed sequence tags (ESTs for marker development in yam (Dioscorea alata L.

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    Robert Asiedu

    2011-02-01

    Full Text Available Abstract Background Anthracnose (Colletotrichum gloeosporioides is a major limiting factor in the production of yam (Dioscorea spp. worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310 and two resistant yam genotypes (TDa 87-01091, TDa 95-0328 challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. Results A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. Conclusion We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species.

  16. Development and Characterization of Novel EST-SSRs from Larix gmelinii and Their Cross-Species Transferability.

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    Zhang, Guojun; Sun, Zhenzhen; Zhou, Di; Xiong, Min; Wang, Xian; Yang, Junming; Wei, Zunzheng

    2015-07-09

    A set of 899 L. gmelinii expression sequence tags (ESTs), available at the National Center of Biotechnology Information (NCBI), was employed to address the feasibility on development of simple sequence repeat (SSR) markers for Larch species. Totally, 634 non-redundant unigenes including 145 contigs and 489 singletons were finally identified and mainly involved in biosynthetic, metabolic processes and response to stress according to BLASTX results, gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps. Approximately 11.7% (74) unigenes contained 90 candidate SSRs, which were mainly trinucleotides (29, 32.2%) and dinucleotides (26, 28.9%). A relatively high frequency of SSRs was respectively found in the Open Reading Frame (ORF, about 54.4%) and 5'-untranslated region (5'-UTR, 31.2%), while a low frequency was observed in the 3'-untranslated region (3'-UTR, about 14.4%). Of the 45 novel EST-SSRs markers, nine were found to be polymorphic at two L. gmelinii populations. The number of alleles per locus (Na) ranged from two to four, and the observed (Ho) and expected (He) heterozygosity values were 0.200-0.733 and 0.408-0.604, respectively. The inbreeding coefficients (FIS) for all loci were more than zero except Lg41. Most of these 9EST-SSR markers were transferable to its related species L. kaempferi, L. principis-rupprechtii and L. olgensis. These novel EST-SSRs will be useful for further research on comparative genomics, genetic resources conservation and molecular breeding in larch trees.

  17. Development and Characterization of Novel EST-SSRs from Larix gmelinii and Their Cross-Species Transferability

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    Guojun Zhang

    2015-07-01

    Full Text Available A set of 899 L. gmelinii expression sequence tags (ESTs, available at the National Center of Biotechnology Information (NCBI, was employed to address the feasibility on development of simple sequence repeat (SSR markers for Larch species. Totally, 634 non-redundant unigenes including 145 contigs and 489 singletons were finally identified and mainly involved in biosynthetic, metabolic processes and response to stress according to BLASTX results, gene ontology (GO categories and Kyoto Encyclopedia of Genes and Genomes (KEGG maps. Approximately 11.7% (74 unigenes contained 90 candidate SSRs, which were mainly trinucleotides (29, 32.2% and dinucleotides (26, 28.9%. A relatively high frequency of SSRs was respectively found in the Open Reading Frame (ORF, about 54.4% and 5′-untranslated region (5′-UTR, 31.2%, while a low frequency was observed in the 3′-untranslated region (3′-UTR, about 14.4%. Of the 45 novel EST-SSRs markers, nine were found to be polymorphic at two L. gmelinii populations. The number of alleles per locus (Na ranged from two to four, and the observed (Ho and expected (He heterozygosity values were 0.200–0.733 and 0.408–0.604, respectively. The inbreeding coefficients (FIS for all loci were more than zero except Lg41. Most of these 9EST-SSR markers were transferable to its related species L. kaempferi, L. principis-rupprechtii and L. olgensis. These novel EST-SSRs will be useful for further research on comparative genomics, genetic resources conservation and molecular breeding in larch trees.

  18. SSR markers to detect gene flow from upland to mocó cotton Marcadores SSR para detecção de fluxo gênico de algodoeiro herbáceo para algodoeiro mocó

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    Ana Carolina Assis Dantas

    2012-03-01

    Full Text Available Mocó cotton was the most important crop in Northeastern Brazil. Local varieties had been developed before governmental breeding programs, which should be identified and preserved as a genetic resource. The aim of this work was to select SSR markers which can be used to monitor gene flow from herbaceous to mocó cotton plants, using non transgenic upland cotton as a pollen source. Unique mocó cotton feral populations were identified in the state of Rio Grande do Norte, and mother plants and their seeds were collected. Allele frequencies were studied among fifteen plants from these populations using 64 SSR primer pairs. Ten SSR markers, with alleles exclusive to mocó or upland genotypes, were selected to monitor gene flow by paternity analysis (BNL3627; 2960; 2572; 3261; 3398; 3948; 3502; 3646 and CIR 094; 097. The collected seeds had none of the upland cotton alleles. The absence of exclusive alleles from upland cotton in the offspring showed that gene flow to mocó cotton was absent or lower than the analysis could detect. Among the mother plants, the number of homozygous individuals at four polymorphic loci was greater than expected, showing that reproduction occurs preferentially by self-fertilization or crossing among related individuals. Paternity analysis is an accurate measure of gene flow, and the methodology can be used for monitor these populations or others. Preservation of the plants is spoiled mainly by drought.O algodoeiro mocó foi a planta cultivada mais importante do Nordeste do Brasil. Variedades locais desenvolvidas anteriormente aos programas de melhoramento governamentais devem ser identificadas e preservadas como recurso genético. O objetivo deste trabalho foi selecionar marcadores SSR para monitorar o fluxo de genes do algodoeiro herbáceo para o mocó, usando plantas de algodoeiro herbáceo não transgênicas como fonte de pólen. Populações ferais de algodoeiro mocó raras foram identificadas no estado Rio Grande do

  19. Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae.

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    Rangeline Azevedo da Silva

    Full Text Available The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI- bands. The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.

  20. Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae).

    Science.gov (United States)

    da Silva, Rangeline Azevedo; Souza, Gustavo; Lemos, Lívia Santos Lima; Lopes, Uilson Vanderlei; Patrocínio, Nara Geórgia Ribeiro Braz; Alves, Rafael Moysés; Marcellino, Lucília Helena; Clement, Didier; Micheli, Fabienne; Gramacho, Karina Peres

    2017-01-01

    The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI- bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.

  1. Molecular diversity of Cuban cassava (Manihot esculenta Crantz cultivars assessed by simple sequences repeats (SSR

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    Beovides, Y.

    2015-01-01

    Full Text Available A total of 36 microsatellites (SSR markers were used to analyze the genetic diversity of 163 accessions of cultivated cassava (Manihot esculenta Crantz, 94 accessions of them from the Cuban Cassava Germplasm Collection and 69 genotypes from different countries and conserved at the International Center for Tropical Agriculture (Colombia. This study was carried out to determine genetic diversity within and between all accessions to promote their better use and conservation strategies. Thirty-four of those markers were used for the genetic diversity study based on their higher polymorphism. The Cuban cultivars showed the highest average allele number per loci with 5.8 and 100% of the loci were polymorphic, as well as those from Guatemala. The average proportion of individual heterozygocity observed (HO was high (0.5918 ± 0.0351, while the highest HO rates were observed in groups of genotypes from Cuba (0.6016 and Tanzania (0.6459. The total heterozygocity (HT was high (0.6538 ± 0.1770, but only 7.4% (GST = 0.0740 ± 0.0377 was due to differences between the five countries studied. Genetic differentiation coefficients (estimated by F-statistics were low to moderate (FST > 0.04 and 17 unique alleles with low frequency were found in Cuban cultivars. The results provide the first molecular characterization of Cuban cassava genotypes and showed a wide diversity among landraces from Cuba. Application of this valuable information can be used for genetic diversity conservation and genotype identification studies for the genetic breeding program of cassava.

  2. Genetic Biodiversity of Italian Olives (Olea europaea Germplasm Analyzed by SSR Markers

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    Innocenzo Muzzalupo

    2014-01-01

    Full Text Available The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l’Agricoltura, Centro di Ricerca per l’Olivicoltura e l’Industria Olearia (CRA-OLI, in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools.

  3. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas.

    Science.gov (United States)

    Hippolyte, Isabelle; Bakry, Frederic; Seguin, Marc; Gardes, Laetitia; Rivallan, Ronan; Risterucci, Ange-Marie; Jenny, Christophe; Perrier, Xavier; Carreel, Françoise; Argout, Xavier; Piffanelli, Pietro; Khan, Imtiaz A; Miller, Robert N G; Pappas, Georgios J; Mbéguié-A-Mbéguié, Didier; Matsumoto, Takashi; De Bernardinis, Veronique; Huttner, Eric; Kilian, Andrzej; Baurens, Franc-Christophe; D'Hont, Angélique; Cote, François; Courtois, Brigitte; Glaszmann, Jean-Christophe

    2010-04-13

    The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.

  4. Genetic Diversity Analysis of Traditional Rice Variety Pachchaperumal Using SSR Markers

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    Warusawithana T.M

    2017-08-01

    Full Text Available Assessing the genetic diversity for miniaturization of crop collections to form mini core collection will lead to greater utilization of germplasm to develop improved crop cultivars along with effective maintenance of it. It has become vital to perform this for traditional Rice Oryza sativa L. varieties when considering the arising demand for their qualities. This study was conducted to assess the genetic diversity of twenty Pachchaperumal traditional Rice accessions with two control varieties Bg360 and Suwandal Rice conserved at the Seed Genebank of Plant Genetic Resources Center Gannoruwa Sri Lanka. Morphological analysis was done using seven standard seed morphological descriptors of Rice and Molecular analysis was done using 16 SSR primers. Statistical analysis was done for morphological and molecular data using MINITAB 15 and POPGENE 1.31 softwares respectively. Strategy of bulking accessions was tested in this study relying on seed morphological clustering and those bulks were used in the molecular analysis. Results revealed a significant degree of genetic diversity among tested accessions both morphologically and molecularly and molecular results were more contributive. Two distinct accessions were identified as potential off types of Pachchaperumal accession numbers 3752 and 5547. Cluster analysis based on morphological traits generated seven major clusters at 1.62 relative distance. Depending on the pattern of clustering ten bulks were formed. The molecular analysis based on bulks generated five clusters in a relative genetic distance of 9.0. Eleven accessions were distinguished as representative set out of all 20 accessions and according to passport data 3 of them were Bg accessions 5550 5549 and 5546.

  5. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas

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    Matsumoto Takashi

    2010-04-01

    Full Text Available Abstract Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin. Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7% deviated (p Conclusions We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker

  6. Species-specific SSR alleles for studies of hybrid cattails (Typha latifolia x T. angustifolia; Typhaceae) in North America.

    Science.gov (United States)

    Snow, Allison A; Travis, Steven E; Wildová, Radka; Fér, Tomás; Sweeney, Patricia M; Marburger, Joy E; Windels, Steven; Kubátová, Barbora; Goldberg, Deborah E; Mutegi, Evans

    2010-12-01

    Studies of hybridizing species are facilitated by the availability of species-specific molecular markers for identifying early- and later-generation hybrids. Cattails are a dominant feature of wetland communities, and a better understanding of the prevalence of hybrids is needed to assess the ecological and evolutionary effects of hybridization. Hybridization between Typha angustifolia and T. latifolia produce long-lived clones, known as Typha ×glauca, which are considered to be invasive. Although morphological variation in cattails makes it difficult to recognize early- and later-generation hybrids, several dominant, species-specific RAPD markers are available. Our goal was to find codominant, species-specific markers with greater polymorphism than RAPDs, to identify later-generation hybrids more efficiently. • We screened nine SSR (simple sequence repeat) loci that were described from populations in Ukraine, and we surveyed 31 cattail populations from the upper Midwest and eastern USA. • Seven SSR loci distinguished the parent taxa and were consistent with known species-specific RAPD markers, allowing easier detection of backcrossing. We used linear discriminant analysis to show that F(1) hybrid phenotypes were intermediate between the parent taxa, while those of backcrossed plants overlapped with the hybrids and their parents. Log(leaf length/leaf width), spike gap length, spike length, and stem diameter explained much of the variation among groups. • We provide the first documentation of backcrossed plants in hybridizing cattail populations in Michigan. The diagnostic SSR loci we identified should be extremely useful for examining the evolutionary and ecology interactions of hybridizing cattails in North America.

  7. Population structure and genetic diversity in a rice core collection (Oryza sativa L. investigated with SSR markers.

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    Peng Zhang

    Full Text Available The assessment of genetic diversity and population structure of a core collection would benefit to make use of these germplasm as well as applying them in association mapping. The objective of this study were to (1 examine the population structure of a rice core collection; (2 investigate the genetic diversity within and among subgroups of the rice core collection; (3 identify the extent of linkage disequilibrium (LD of the rice core collection. A rice core collection consisting of 150 varieties which was established from 2260 varieties of Ting's collection of rice germplasm were genotyped with 274 SSR markers and used in this study. Two distinct subgroups (i.e. SG 1 and SG 2 were detected within the entire population by different statistical methods, which is in accordance with the differentiation of indica and japonica rice. MCLUST analysis might be an alternative method to STRUCTURE for population structure analysis. A percentage of 26% of the total markers could detect the population structure as the whole SSR marker set did with similar precision. Gene diversity and MRD between the two subspecies varied considerably across the genome, which might be used to identify candidate genes for the traits under domestication and artificial selection of indica and japonica rice. The percentage of SSR loci pairs in significant (P<0.05 LD is 46.8% in the entire population and the ratio of linked to unlinked loci pairs in LD is 1.06. Across the entire population as well as the subgroups and sub-subgroups, LD decays with genetic distance, indicating that linkage is one main cause of LD. The results of this study would provide valuable information for association mapping using the rice core collection in future.

  8. Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L. Based on Transcriptome Data.

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    Honglin Chen

    Full Text Available Rice bean (Vigna umbellata (Thunb. Ohwi & Ohashi is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2% showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3% could be classified into gene ontology categories, 25,451 (64.4% into Swiss-Prot categories and 21,982 (55.6% into KOG database categories (E-value < 1.0E-5. A total of 9,301 (23.5% were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%, AAG/CTT (8.1% and AGAA/TTCT (20.0% are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.

  9. DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling.

    Science.gov (United States)

    Liu, Siyang; Feuerstein, Ulf; Luesink, Wilbert; Schulze, Sabine; Asp, Torben; Studer, Bruno; Becker, Heiko C; Dehmer, Klaus J

    2018-01-22

    Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been limited by comparison with other major crops. More efficient utilisation of genetic resources and improved breeding schemes are required to advance L. perenne breeding. In an attempt to elucidate the extent of genetic diversity in L. perenne, 1384 DArT, 182 SNP and 48 SSR markers were applied to 297 accessions (Set I) contributed by three German breeding companies and the IPK Genebank. Due to the heterogeneous nature of Lolium accessions, bulk samples were used. Apart from germplasm set I, additional set II and set III was used to determine the reproducibility of marker system and judge the feasibility of bulk strategy in this study. By assessing different bulk sizes, 24 individuals per sample were shown to be a representative number of plants to discriminate different accessions. Among the 297 accessions, all marker types revealed a high polymorphism rate; 1.99, 2.00 and 8.19 alleles, were obtained per locus on average using DArTs, SNPs and SSRs, respectively. The Jaccard distance for DArT markers ranged from 0.00 to 0.73, the Modified Roger's distance (MRD) for SNP markers ranged from 0.03 to 0.52, and for SSR markers from 0.26 to 0.76. Gene diversity for dominant DArT and co-dominant SNP and SSR markers was found to be 0.26, 0.32 and 0.45, respectively. DArT markers showed the highest consistency and reproducibility. The resulting data were evaluated using a number of different classification methods, but none of the methods showed a clear differentiation into distinct genetic pools. With regard to hybrid breeding, this will possibly impede substantial progress towards increased biomass yields of L. perenne by utilising heterosis.

  10. Tagging and mapping of SSR marker for rust resistance gene in lentil (Lens culinaris Medikus subsp. culinaris).

    Science.gov (United States)

    Dikshit, H K; Singh, Akanksha; Singh, D; Aski, M; Jain, Neelu; Hegde, V S; Basandrai, A K; Basandrai, D; Sharma, T R

    2016-06-01

    Lentil, as an economical source of protein, minerals and vitamins, plays important role in nutritional security of the common man. Grown mainly in West Asia, North Africa (WANA) region and South Asia, it suffers from several biotic stresses such as wilt, rust, blight and broomrape. Lentil rust caused by autoecious fungus Uromyces viciae fabae (Pers.) Schroet is a serious lentil disease in Algeria, Bangladesh, Ethiopia, India, Italy, Morocco, Pakistan and Nepal. The disease symptoms are observed during flowering and early podding stages. Rust causes severe yield losses in lentil. It can only be effectively controlled by identifying the resistant source, understanding its inheritance and breeding for host resistance. The obligate parasitic nature of pathogen makes it difficult to maintain the pathogen in culture and to apply it to screen segregating progenies under controlled growth conditions. Hence, the use of molecular markers will compliment in identification of resistant types in different breeding programs. Here, we studied the inheritance of resistance to rust in lentil using F₁, F₂ and F₂:₃ from cross PL 8 (susceptible) x L 4149 (resistant) varieties. The phenotyping of lentil population was carried out at Sirmour, India. The result of genetic analysis revealed that a single dominant gene controls rust resistance in lentil genotype L 4149. The F2 population from this cross was used to tag and map the rust resistance gene using SSR and SRAP markers. Markers such as 270 SRAP and 162 SSR were studied for polymorphism and 101 SRAP and 33 SSRs were found to be polymorphic between the parents. Two SRAP and two SSR markers differentiated the resistant and susceptible bulks. SSR marker Gllc 527 was estimated to be linked to rust resistant locus at a distance of 5.9 cM. The Gllc 527 marker can be used for marker assisted selection for rust resistance; however, additional markers closer to rust resistant locus are required. The markers linked to the rust

  11. Repressive Actions of the State Security Against True Orthodox Church Structures in the Ukrainian SSR (1944–1953)

    OpenAIRE

    Vedeneev Dmitrii

    2016-01-01

    In the article on the basis of unknown scientific community documents of the Soviet state security bodies provides an analysis of the objectives and key areas of operational work and repressive actions of the security services communities against True Orthodox Church (TOC) in the Ukrainian SSR in 1944–1953. The characteristic of agent and operational developments NKGB–MGB–KGB of the USSR against the so-called «catacomb Church», as a form of religious and social protest against aggressive athei...

  12. A Genomic Association Analysis of Milk Production Traits in Chios Sheep Breed Using Microsatellite (SSR and SNP Markers

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    Dimitrios Chatziplis

    2013-05-01

    Full Text Available We have previously reported the possible segregation of major gene(s for milk yield and fat corrected milk (FCM in Chios sheep breed. In this study we demonstrate the association of an SNP marker, within the last exon of the Acetyl-CoA acyltransferase 2 (ACAA2 gene, with milk yield and FCM in the same breed. Moreover, we investigate the effect of this SNP marker along with other microsatellite markers. Fifteen microsatellite markers (SSR on 13 chromosomes were genotyped on 198 ewes of the Chios breed. The association analysis revealed significant association (P

  13. Analysis of genetic diversity of Sclerotinia sclerotiorum from eggplant by mycelial compatibility, random amplification of polymorphic DNA (RAPD and simple sequence repeat (SSR analyses

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    Fatih Mehmet Tok

    2016-09-01

    Full Text Available The genetic diversity and pathogenicity/virulence among 60 eggplant Sclerotinia sclerotiorum isolates collected from six different geographic regions of Turkey were analysed using mycelial compatibility groupings (MCGs, random amplified polymorphic DNA (RAPD and simple sequence repeat (SSR polymorphism. By MCG tests, the isolates were classified into 22 groups. Out of 22 MCGs, 36% were represented each by a single isolate. The isolates showed great variability for virulence regardless of MCG and geographic origin. Based on the results of RAPD and SSR analyses, 60 S. sclerotiorum isolates representing 22 MCGs were grouped in 2 and 3 distinct clusters, respectively. Analyses using RAPD and SSR markers illustrated that cluster groupings or genetic distance of S. sclerotiorum populations from eggplant were not distinctly relative to the MCG, geographical origin and virulence diversity. The patterns obtained revealed a high heterogeneity of genetic composition and suggested the occurrence of clonal and sexual reproduction of S. sclerotiorum on eggplant in the areas surveyed.

  14. High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR--an example in citrus.

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    Gaetano Distefano

    Full Text Available High resolution melting curve analysis (HRM has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs or insertions or deletions (INDELs. However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to

  15. QTL Analysis of Head Splitting Resistance in Cabbage (Brassica oleracea L. var. capitata Using SSR and InDel Makers Based on Whole-Genome Re-Sequencing.

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    Yanbin Su

    Full Text Available Head splitting resistance (HSR in cabbage is an important trait closely related to both quality and yield of head. However, the genetic control of this trait remains unclear. In this study, a doubled haploid (DH population derived from an intra-cross between head splitting-susceptible inbred cabbage line 79-156 and resistant line 96-100 was obtained and used to analyze inheritance and detect quantitative trait loci (QTLs for HSR using a mixed major gene/polygene inheritance analysis and QTL mapping. HSR can be attributed to additive-epistatic effects of three major gene pairs combined with those of polygenes. Negative and significant correlations were also detected between head Hsr and head vertical diameter (Hvd, head transverse diameter (Htd and head weight (Hw. Using the DH population, a genetic map was constructed with simple sequence repeat (SSR and insertion-deletion (InDel markers, with a total length of 1065.9 cM and average interval length of 4.4 cM between adjacent markers. Nine QTLs for HSR were located on chromosomes C3, C4, C7, and C9 based on 2 years of phenotypic data using both multiple-QTL mapping and inclusive composite interval mapping. The identified QTLs collectively explained 39.4 to 59.1% of phenotypic variation. Three major QTLs (Hsr 3.2, 4.2, 9.2 showing a relatively larger effect were robustly detected in different years or with different mapping methods. The HSR trait was shown to have complex genetic mechanisms. Results from QTL mapping and classical genetic analysis were consistent. The QTLs obtained in this study should be useful for molecular marker-assisted selection in cabbage breeding and provide a foundation for further research on HSR genetic regulation.

  16. Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

    Science.gov (United States)

    Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

    2013-01-01

    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

  17. SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

    Science.gov (United States)

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

  18. Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

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    Ngoot-Chin Ting

    Full Text Available Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR markers were developed for dura (ENL48 and pisifera (ML161, the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP and restriction fragment length polymorphism (RFLP markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs in 23 linkage groups (LGs, covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

  19. AMPLIFICAÇÃO CRUZADA DE PRIMERS SSR DE CAFEEIRO EM GENÓTIPOS DE ANTÚRIO

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    Edilson Marques Junior

    2017-04-01

    Full Text Available Anthurium andraeanum Lindl. é uma espécie florística, de grande importância na diversificação da agricultura tropical. É a segunda flor tropical no mercado mundial, no entanto há uma dificuldade para a delimitação taxonômica do gênero. Estudos com marcadores moleculares eliminam algumas dificuldades encontradas quando se trabalha com marcadores morfológicos, e dentre as várias classes de marcadores moleculares, os marcadores microssatélites (SSR apresentam interessantes características para a distinção e classificação de indivíduos. Porém, o desenvolvimento de primers específicos para uma espécie requer um longo e oneroso trabalho. Até o momento não existem estudos moleculares de sequenciamento do genoma de antúrios, impossibilitando o desenvolvimento de marcadores moleculares para a espécie A. andraeanum, como o SSR. Considerando que os SSRs encontrados em determinadas espécies podem ser transferidos para espécies correlatas, neste trabalho foram testados 20 primers SSRs desenvolvidos para o cafeeiro em 16 genótipos de antúrio. Dos 20 primers testados, dois apresentaram amplificação para a espécie A. andraeanum, o que corresponde a 10% de taxa de transferência.

  20. Precision assessment of some supervised and unsupervised algorithms for genotype discrimination in the genus Pisum using SSR molecular data.

    Science.gov (United States)

    Nasiri, Jaber; Naghavi, Mohammad Reza; Kayvanjoo, Amir Hossein; Nasiri, Mojtaba; Ebrahimi, Mansour

    2015-03-07

    For the first time, prediction accuracies of some supervised and unsupervised algorithms were evaluated in an SSR-based DNA fingerprinting study of a pea collection containing 20 cultivars and 57 wild samples. In general, according to the 10 attribute weighting models, the SSR alleles of PEAPHTAP-2 and PSBLOX13.2-1 were the two most important attributes to generate discrimination among eight different species and subspecies of genus Pisum. In addition, K-Medoids unsupervised clustering run on Chi squared dataset exhibited the best prediction accuracy (83.12%), while the lowest accuracy (25.97%) gained as K-Means model ran on FCdb database. Irrespective of some fluctuations, the overall accuracies of tree induction models were significantly high for many algorithms, and the attributes PSBLOX13.2-3 and PEAPHTAP could successfully detach Pisum fulvum accessions and cultivars from the others when two selected decision trees were taken into account. Meanwhile, the other used supervised algorithms exhibited overall reliable accuracies, even though in some rare cases, they gave us low amounts of accuracies. Our results, altogether, demonstrate promising applications of both supervised and unsupervised algorithms to provide suitable data mining tools regarding accurate fingerprinting of different species and subspecies of genus Pisum, as a fundamental priority task in breeding programs of the crop. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Science.gov (United States)

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  2. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Directory of Open Access Journals (Sweden)

    Huaiyong Luo

    Full Text Available The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  3. Validation of monthly surface solar radiation over Europe derived from the CM SAF dataset against homogenized GEBA series (1983-2005)

    Science.gov (United States)

    Sanchez-Lorenzo, Arturo; Trentmann, Joerg; Wild, Martin

    2013-05-01

    This work presents a validation of the solar surface radiation (SSR) derived from the Satellite Application Facility on Climate Monitoring (CM SAF) over Europe for a 23-years period of records on monthly basis. The derived SSR is based on the visible channel of the Meteosat First Generation satellites, providing a dataset with a high spatial resolution (0.03° × 0.03°) covering the 1983-2005 period. The CM SAF SSR dataset is compared against 47 of the longterm SSR monthly series recently homogenized from the Global Energy Balance Archive (GEBA) over Europe. The results show an excellent agreement between both datasets (r = 0.93, p < 0.01), with only a slight overestimation (bias of +5.20 Wm-2) of the CM SAF records as compared to the surface observations. Equally, there is a mean absolute bias (MAB) of 8.19 Wm-2 that is below the accuracy threshold defined by the CM SAF. There is a clear maximum and minimum MAB during the summer and winter, respectively, with an opposite cycle if the relative MAB values are considered.

  4. Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis

    Science.gov (United States)

    Dikshit, Harsh Kumar; Singh, Akanksha; Singh, Dharmendra; Aski, Muraleedhar Sidaram; Prakash, Prapti; Jain, Neelu; Meena, Suresh; Kumar, Shiv; Sarker, Ashutosh

    2015-01-01

    Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei’s genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard’s structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations. PMID:26381889

  5. Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis.

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    Harsh Kumar Dikshit

    Full Text Available Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei's genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard's structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations.

  6. Use of SSR markers to discern reciprocal outcrossing rates between weedy red rice types and rice cultivars having different degrees of flowering synchronization

    Science.gov (United States)

    A broad range of flowering synchronization between red rice and rice was established by planting rice cultivars that flowered earlier, similar to, or later than red rice. Five SSR markers were used to identify hybrids. Outcrossing rates differed greatly depending on the degree of synchronization a...

  7. An estimation of the boundaries on rock reservoirs in the productive Carboniferous beds in the Tatar Autonomous SSR based on core samples, to compute oil deposits

    Energy Technology Data Exchange (ETDEWEB)

    Gubaydullin, A.A.; Bezrodnykh, V.G.; Kozina, Ye.A.; Malyutina, M.Ya.

    1983-01-01

    A method is proposed for determining the boundaries on rock reservoirs, including absolute and conditioned boundaries. This method was used as the basis for developing a classification of carboniferous reservoirs in the Tatar SSR in terms of a comprehensive dynamic capacity parameter, as well as rock permeability and productivity.

  8. Association Analysis of SSR Markers with Phenology, Grain, and Stover-Yield Related Traits in Pearl Millet (Pennisetum glaucum (L. R. Br.

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    Baskaran Kannan

    2014-01-01

    Full Text Available Pearl millet is a staple food crop for millions of people living in the arid and semi-arid tropics. Molecular markers have been used to identify genomic regions linked to traits of interest by conventional QTL mapping and association analysis. Phenotypic recurrent selection is known to increase frequencies of favorable alleles and decrease those unfavorable for the traits under selection. This study was undertaken (i to quantify the response to recurrent selection for phenotypic traits during breeding of the pearl millet open-pollinated cultivar “CO (Cu 9” and its four immediate progenitor populations and (ii to assess the ability of simple sequence repeat (SSR marker alleles to identify genomic regions linked to grain and stover yield-related traits in these populations by association analysis. A total of 159 SSR alleles were detected across 34 selected single-copy SSR loci. SSR marker data revealed presence of subpopulations. Association analysis identified genomic regions associated with flowering time located on linkage group (LG 6 and plant height on LG4, LG6, and LG7. Marker alleles on LG6 were associated with stover yield, and those on LG7 were associated with grain yield. Findings of this study would give an opportunity to develop marker-assisted recurrent selection (MARS or marker-assisted population improvement (MAPI strategies to increase the rate of gain for pearl millet populations undergoing recurrent selection.

  9. Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations.

    Science.gov (United States)

    Bilska, Katarzyna; Szczecińska, Monika

    2016-01-01

    Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population's ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population's adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction). The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and Φ PT for SSR (20%) and Φ PT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish

  10. Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations

    Directory of Open Access Journals (Sweden)

    Katarzyna Bilska

    2016-11-01

    Full Text Available Background Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR, are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction. Methods The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. Results SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively. An analysis of molecular variance (AMOVA revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20% and ΦPT for ISJ (21% markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci and three groups (ISJ markers. Mantel test revealed correlations between the geographic distance

  11. Qui est Méduse?

    Directory of Open Access Journals (Sweden)

    Julia Kristeva

    2015-04-01

    Full Text Available Une belle histoire de têtes coupées traverse l'Antiquité grecque : celle des Gorgones, trois monstres ailés au corps de femme et à la chevelure de serpents, dont le regard changeait en pierre celui qui se risquait à les contempler – Méduse, Euryalé et Sthéno. Pour commencer, Méduse est une jeune fille qui se fait remarquer : séduite puis violée par Poséidon, elle se révèle fertile puisqu'elle accouche de faux jumeaux, le cheval Pégase et le géant Chrysaor. Une longue fable la transforme en terrible puissance. Pour simplifier, disons que le monstre est par deux fois tué : Persée assassine d'abord Méduse pour assurer la protection de sa mère, Danaé, importunée par le roi Polydectès. Ensuite, il délivre Andromède des liens méduséens qui la retiennent et, pour ce faire, tranche la tête de la Gorgone. La mer se teinte de sang, tandis que le vainqueur tient à l'écart l'épouvantail de Méduse, de peur que ne soient changés en statues de pierre ceux qui s'exposeraient à sa vue.

  12. A deep influence: United States-Colombia bilateral relations and security sector reform (SSR, 1994-2002

    Directory of Open Access Journals (Sweden)

    Javier Alberto Castrillón Riascos

    2017-05-01

    Full Text Available The internal conflict in Colombia has propelled the development of security sector reform (SSR programs; however, these programs have been usually linked to the influence of relations between the United States and Colombia in military and foreign policy terms. The main objective of this essay is to understand said interplay from the mid-1990’s to the early 2000’s, which marked the biggest transformations to the Colombian defense sector in human rights, doctrine, equipment, and human capital. The analysis shows that such influence allowed for the consolidation of an offensive strategy which helped the Colombian government turn the balance of the internal conflict in its favor.

  13. Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean.

    Science.gov (United States)

    Zargar, Sajad Majeed; Farhat, Sufia; Mahajan, Reetika; Bhakhri, Ayushi; Sharma, Arjun

    2016-01-01

    Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.

  14. Genetic diversity and population structure of the major peanut (Arachis hypogaea L. cultivars grown in China by SSR markers.

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    Xiaoping Ren

    Full Text Available One hundred and forty-six highly polymorphic simple sequence repeat (SSR markers were used to assess the genetic diversity and population structure of 196 peanut (Arachis Hypogaea L. cultivars which had been extensively planted in different regions in China. These SSR markers amplified 440 polymorphic bands with an average of 2.99, and the average gene diversity index was 0.11. Eighty-six rare alleles with a frequency of less than 1% were identified in these cultivars. The largest Fst or genetic distance was found between the cultivars that adapted to the south regions and those to the north regions in China. A neighbor-joining tree of cultivars adapted to different ecological regions was constructed based on pairwise Nei's genetic distances, which showed a significant difference between cultivars from the south and the north regions. A model-based population structure analysis divided these peanut cultivars into five subpopulations (P1a, P1b, P2, P3a and P3b. P1a and P1b included most the cultivars from the southern provinces including Guangdong, Guangxi and Fujian. P2 population consisted of the cultivars from Hubei province and parts from Shandong and Henan. P3a and P3b had cultivars from the northern provinces including Shandong, Anhui, Henan, Hebei, Jiangsu and the Yangtze River region including Sichuan province. The cluster analysis, PCoA and PCA based on the marker genotypes, revealed five distinct clusters for the entire population that were related to their germplasm regions. The results indicated that there were obvious genetic variations between cultivars from the south and the north, and there were distinct genetic differentiation among individual cultivars from the south and the north. Taken together, these results provided a molecular basis for understanding genetic diversity of Chinese peanut cultivars.

  15. Assessing the Genetic Diversity and Genealogical Reconstruction of Cypress (Cupressus funebris Endl. Breeding Parents Using SSR Markers

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    Hanbo Yang

    2016-07-01

    Full Text Available To identify genetic diversity, genetic structure and the relationship among accessions, and further establish a core collection for the long-term breeding of cypress (Cupressus funebris Endl., the genealogy of breeding parents was reconstructed using simple sequence repeat (SSR molecular markers. Seventeen SSR markers were used to detect molecular polymorphisms among 290 cypress accessions from five provinces and 53 accessions with unknown origin in China. A total of 92 alleles (Na were detected with 5.412 alleles per locus and an average polymorphism information content (PIC of 0.593. The haplotype diversity (H ranged from 0.021 to 0.832, with an average of 0.406. The number of alleles (Na and the effective number of alleles (Ne ranged from 4.294 to 5.176 and from 2.488 to 2.817 among five populations, respectively. The pairwise population matrix of Nei’s genetic distance ranged from 0.008 to 0.023. Based on the results of unweighted pair group method average (UPGMA cluster and population structure analyses, 343 breeding parents were divided into two major groups. Lower genetic differentiation coefficients and closer genetic relationships were observed among cypress breeding parents, suggesting that the genetic basis was narrow, and the genetic relationship was confused by frequent introduction and wide cultivation. Moreover, we reconstructed the genealogy between breeding parents and 30 accessions of breeding parents from an identified core collection. According to the present study, not only geographic origin but also the relationship of the individuals should be considered in future crossbreeding work.

  16. Repressive Actions of the State Security Against True Orthodox Church Structures in the Ukrainian SSR (1944–1953

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    Vedeneev Dmitrii

    2016-04-01

    Full Text Available In the article on the basis of unknown scientific community documents of the Soviet state security bodies provides an analysis of the objectives and key areas of operational work and repressive actions of the security services communities against True Orthodox Church (TOC in the Ukrainian SSR in 1944–1953. The characteristic of agent and operational developments NKGB–MGB–KGB of the USSR against the so-called «catacomb Church», as a form of religious and social protest against aggressive atheistic policy of the Communist authorities, infringement of the rights of believers. The basic forms and methods of intelligence and operational activities of the security organs, aimed at creating informer positions in the environment of the communities of the TOC, making the split in the ranks of the adepts of secret religious sects, the collection of «compromising material» as the basis for the application of harsh repressive measures against the movement of the TOC. The authors pay special attention to the organization and personnel of units of the NKGB–MGB–KGB, engaged, according to the terminology, «the struggle with the Church-sectarian counterrevolution» and «Church-monarchist underground», a leading representative of which was considered in the TOC, particularly active in Chernihiv, Sumy, and Kharkiv oblasts of the Ukrainian SSR and the Donbass, and also in the neighboring regions of the Russian black soil region and the North Caucasus. Given the author’s periodization of the development of the catacomb movement, highlights the historical conditions of its creation and release in the USSR. Through the prism of intelligence documents examines the liturgical aspect of the TOC, its governing structure, forms of secrecy and concealment from the prosecution authorities, the position of the catacomb members in relation to social life and social structure in the USSR.

  17. Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis.

    Science.gov (United States)

    Dachapak, Sujinna; Somta, Prakit; Poonchaivilaisak, Supalak; Yimram, Tarika; Srinives, Peerasak

    2017-04-01

    Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei's genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

  18. Identification of expressed resistance gene analogs (RGA and development of RGA-SSR markers in tobacco

    Directory of Open Access Journals (Sweden)

    Yuan Qinghua

    2015-01-01

    Full Text Available Tobacco is an important cash crop and an ideal experimental system for studies of plant-pathogen interactions. Identification of tobacco resistance (R genes and resistance gene analogs (RGAs is propitious to elucidate the underlying resistant mechanisms. In recent years, the public tobacco EST (expressed sequence tags data set, which provides a rich source for identifying expressed RGAs, has enlarged substantially. In this study, 149606 Uni-ESTs were assembled from 412325 tobacco ESTs available in GenBank, scanned with 112 published plant R-genes protein sequences, and 1113 Nicotiana (tobacco RGAs (NtRGAs were identified. The majority of them comprised the common R-genes domains, such as NBS-LRR, LRR-PK, LRR, PK and Mlo, while we were unable to identify 109 RGAs using published domains of R-genes. Upon sequence alignment, 1079 NtRGAs were allocated on 712 loci within the Nicotiana benthamiana genome. A total of 78 simple sequence repeats (SSRs were identified from 72 NtRGAs, and out of 64 newly designed primer pairs, 54 primer pairs generated clear bands upon PCR amplification using tobacco genomic DNA. Only nine primer pairs displayed polymorphism in 24 varieties of tobacco, with 2-4 alleles per locus (2.56 alleles on average, while 41 primer pairs were able to detect polymorphisms in six wild species of genus Nicotiana, with 2-4 alleles per locus (2.61 alleles on average.

  19. Gene mining a marama bean expressed sequence tags (ESTs ...

    African Journals Online (AJOL)

    The authors reported the identification of genes associated with embryonic development and microsatellite sequences. The future direction will entail characterization of these genes using gene over-expression and mutant assays. Key words: Namibia, simple sequence repeats (SSR), data mining, homology searches, ...

  20. Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus

    Directory of Open Access Journals (Sweden)

    Eshwar K

    2005-08-01

    Full Text Available Abstract Background Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits. Results An EST library was constructed after subtractive suppressive hybridization (SSH of root tissue from two very closely related chickpea genotypes (Cicer arietinum. A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen. Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum, secondary (C. pinnatifidum, C. bijugum and C. judaicum, and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum gene-pools. A large proportion of EST alleles (45% were only

  1. Piuria Estéril

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    Fabricio Andrés Lasso Andrade

    2017-09-01

    Full Text Available La Piuria estéril es una condición altamente frecuente en la población. Reporta una prevalencia del 29,9% en adultos y del 28,8% en niños, con un registro significativamente menor en hombres (12,8%. Se define como la presencia de 10 o más leucocitos por cada mL en una muestra de orina sin centrifugar, leucocitos en tinción Gram, el reporte positivo de prueba de esterasa leucocitaria y 3 o más leucocitos por campo de alto poder en orina centrifugada; en ausencia de bacterias y urocultivo negativo. Se pueden dividir sus causas entre infecciosas y no infecciosas. Dentro de las causas infecciosas, se ha asociado clásicamente con la tuberculosis urogenital causada por el del bacilo Mycobacterium tuberculosis, enfermedad que se reconoce como la segunda forma de tuberculosis extra pulmonar, aunque existen muchas otras infecciones, condiciones sistémicas y estructurales que pueden producir este hallazgo en el uroanálisis. Esto representa un desafío para el clínico, quien debe basar su aproximación diagnóstica en el levantamiento de una adecuada historia clínica y un prolijo examen físico. En ese contexto, la presente revisión narrativa persigue como objetivo dar a conocer las diferentes causas de la Piuria estéril teniente a describir una aproximación clínica para su abordaje diagnóstico. Sterile PyuriaAbstractSterile pyuria is a highly prevalent condition in the population, with a prevalence of 29.9% in adults and 28.8% in children, being significantly lower in men with 12.8%. This condition is defined as the presence of 10 or more leukocytes per mL of a urine sample without centrifugation, Gram stain leukocytes, positive leukocyte esterase test, 3 or more leukocytes per high power field in centrifuged urine; In the absence of bacteria and negative urine culture. Their causes can be divided into infectious and non-infectious. Within the infectious causes, this finding has been classically associated with urogenital tuberculosis

  2. La parole est à vous

    CERN Multimedia

    Staff Association

    2015-01-01

    Nous avons identifié, ci-dessous, 3 grands chapitres pour lesquelles bon nombre d’entre vous se posent des questions et ont fréquemment sollicités leurs délégués, qui n’ont pas toujours pu donner de réponses : La retraite et sa préparation. L’affiliation aux régimes sécurité sociale de nos états hôtes et ses conséquences au moment de la retraite. La fiscalité en général. Le service juridique, que nous avons interrogé récemment, n’est pas toujours informé de vos interrogations et de ce fait, il n’a pas encore pu investiguer sur ces questions auprès des services compétents. Il nous a suggéré de vous interroger afin de collecter vos questions, de les synthétiser, afin de les transmettre...

  3. RAPD and SSR based genetic diversity analysis of elite-2 set of ...

    African Journals Online (AJOL)

    Background: Synthetic hexaploid wheats are artificially reconstituted hexaploid wheats that possess high genetic variation which could be utilized for the development of new improved wheat varieties. One such group of synthetic wheats is called the Elite-II set of synthetic wheats that are derived from crossing durum wheat ...

  4. SNP-finding in pig mitochondrial ESTs

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Cirera Salicio, Susanna; Gilchrist, M.J.

    2008-01-01

    The Sino-Danish pig genome project produced 685 851 ESTs (Gorodkin et al. 2007), of which 41 499 originated from the mitochondrial genome. In this study, the mitochondrial ESTs were assembled, and 374 putative SNPs were found. Chromatograms for the ESTs containing SNPs were manually inspected...

  5. Localized infusions of the partial alpha 7 nicotinic receptor agonist SSR180711 evoke rapid and transient increases in prefrontal glutamate release

    DEFF Research Database (Denmark)

    Bortz, D M; Mikkelsen, J D; Bruno, J P

    2013-01-01

    that inhibited (threo-beta-benzyl-oxy-aspartate (TβOA), 100.0μM) or facilitated (ceftriaxalone, 200mg/kg, i.p.) excitatory amino acid transporters. TβOA slowed both the clearance (s) and rate of clearance (μM/s) by 10-fold, particularly at the mid-late stages of the return to baseline. Ceftriaxone reduced......The ability of local infusions of the alpha 7 nicotinic acetycholine receptor (α7 nAChR) partial agonist SSR180711 to evoke glutamate release in prefrontal cortex was determined in awake rats using a microelectrode array. Infusions of SSR180711 produced dose-dependent increases in glutamate levels...

  6. Changes in allelic frequency over time in European bread wheat (Triticum aestivum L.) varieties revealed using DArT and SSR markers

    DEFF Research Database (Denmark)

    Orabi, Jihad; Jahoor, Ahmed; Backes, Gunter Martin

    2014-01-01

    the genetic diversity and allelic frequencies among the accessions based on spring- versus winter-wheat type as well as between landraces and cultivars. We also analyzed the changes in genetic diversity and allelic frequencies in these samples over time. We observed separation based on both vernalization type......A collection of 189 bread wheat landraces and cultivars, primarily of European origin, released between 1886 and 2009, was analyzed using two DNA marker systems. A set of 76 SSR markers and ~7,000 DArT markers distributed across the wheat genome were employed in these analyses. All of the SSR...... and release date. Interestingly, we detected a decrease in genetic diversity in wheat accessions released over the period from 1960 to 1980. However, our results also showed that modern plant breeding have succeeded in maintaining genetic diversity in modern wheat cultivars. Studying allelic frequencies using...

  7. Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers.

    Science.gov (United States)

    Patil, Prakash G; Dubey, Jyotirmay; Bohra, Abhishek; Mishra, R K; Saabale, P R; Das, Alok; Rathore, Meenal; Singh, N P

    2017-08-01

    Pigeonpea production is severely constrained by wilt disease caused by Fusarium udum. In the current study, we discover the putative genomic regions that control resistance response to variant 2 of fusarium wilt using association mapping approach. The association panel comprised of 89 diverse pigeonpea genotypes including seven varieties, three landraces and 79 germplasm lines. The panel was screened rigorously for 3 consecutive years (2013-14, 2014-15 and 2015-2016) against variant 2 in a wilt-sick field. A total of 65 pigeonpea specific hypervariable SSR markers (HASSRs) were screened representing seven linkage groups and 29 scaffolds of the pigeonpea genome. A total of 181 alleles were detected, with average values of gene diversity and polymorphism information content (PIC) of 0.55 and 0.47, respectively. Further analysis using model based (STRUCTURE) and distance based (clustering) approaches separated the entire pigeonpea collection into two distinct subgroups (K = 2). The marker trait associations (MTAs) were established based on three-year wilt incidence data and SSR dataset using a unified mixed linear model. Consequently, six SSR markers were identified, which were significantly associated with wilt resistance and explained up to 6% phenotypic variance (PV) across the years. Among these SSRs, HASSR18 was found to be the most stable and significant, accounting for 5-6% PV across the years. To the best of our knowledge, this is the first report of identification of favourable alleles for resistance to variant 2 of Fusarium udum in pigeonpea using association mapping. The SSR markers identified here will greatly facilitate marker assisted resistance breeding against fusarium wilt in pigeonpea.

  8. Genetic architecture of purple pigmentation and tagging of some loci to SSR markers in pearl millet, Pennisetum glaucum (L. R. Br.

    Directory of Open Access Journals (Sweden)

    Pusapati Varalakshmi

    2012-01-01

    Full Text Available This report describes the construction of integrated genetic maps in pearl millet involving certain purple phenotype and simple sequence repeat (SSR markers. These maps provide a direct means of implementing DNA marker-assisted selection and of facilitating "map-based cloning" for engineering novel traits. The purple pigmentation of leaf sheath, midrib and leaf margin was inherited together 'en bloc' under the control of a single dominant locus (the 'midrib complex' and was inseparably associated with the locus governing the purple coloration of the internode. The purple panicle was caused by a single dominant locus. Each of the three characters (purple lamina, purple stigma and purple seed was governed by two complementary loci. One of the two loci governing purple seed was associated with the SSR locus Xpsmp2090 in linkage group 1, with a linkage value of 22 cM, while the other locus was associated with the SSR locus Xpsmp2270 in linkage group 6, with a linkage value of 23 cM. The locus for purple pigmentation of the midrib complex was either responsible for pigmentation of the panicle in a pleiotropic manner or was linked to it very closely and associated with the SSR locus Xpsmp2086 in linkage group 4, with a suggestive linkage value of 21 cM. A dominant allele at this locus seems to be a prerequisite for the development of purple pigmentation in the lamina, stigma and seed. These findings suggest that the locus for pigmentation of the midrib complex might regulate the basic steps in anthocyanin pigment development by acting as a structural gene while other loci regulate the formation of color in specific plant parts.

  9. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

    Science.gov (United States)

    Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

    2014-01-01

    Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

  10. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya marker-assisted selection and population genetic studies.

    Directory of Open Access Journals (Sweden)

    Newton Medeiros Vidal

    Full Text Available Carica papaya (papaya is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns. A total of 116,453 (72.6% of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement. Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes, achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12. The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

  11. Relationship between geographical origin, seed size and genetic diversity in faba bean (Vicia faba L.) as revealed by SSR markers.

    Science.gov (United States)

    Göl, Şurhan; Doğanlar, Sami; Frary, Anne

    2017-05-11

    Faba bean (Vicia faba L.) is an important legume species because of its high protein and starch content. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the nitrogen fixing bacteria in its roots. In this work, 255 faba bean germplasm accessions were characterized using 32 SSR primers which yielded 302 polymorphic fragments. According to the results, faba bean individuals were divided into two main groups based on the neighbor-joining algorithm (r = 0.91) with some clustering based on geographical origin as well as seed size. Population structure was also determined and agreed with the dendrogram analysis in splitting the accessions into two subpopulations. Analysis of molecular variance (AMOVA) revealed high levels of within population genetic variation. Genetic similarity and geographical proximity were related with separation of European accessions from African and Asian ones. Interestingly, there was no significant difference between landrace (38%) and cultivar (40%) diversity indicating that genetic variability has not yet been lost due to breeding. A total of 44 genetically well-characterized faba bean individuals were selected for a core collection to be further examined for yield and nutritional traits.

  12. Assessment of Plasmodium falciparum resistance to ferroquine (SSR97193 in field isolates and in W2 strain under pressure

    Directory of Open Access Journals (Sweden)

    Pradines Bruno

    2006-02-01

    Full Text Available Abstract Background Ferroquine (FQ, or SSR97193, is a novel antimalarial drug currently in phase I clinical trials. FQ is a unique organometallic compound designed to overcome the chloroquine (CQ resistance problem. FQ revealed to be equally active on CQ-sensitive and CQ-resistant Plasmodium falciparum laboratory strains and field isolates. FQ is also curative on rodent malaria parasites. As FQ will be tested in patients, the potential for resistance to this drug was evaluated. Methods The relationship between CQ-resistant transporter gene genotype and susceptibility to FQ were studied in 33 Cambodian P. falciparum field isolates previously studied for their in vitro response to CQ. In parallel, the ability of the CQ-resistant strain W2, to become resistant to FQ under drug pressure was assessed. Results The IC50 values for FQ in field isolates were found to be unrelated to mutations occurring in the P. falciparum chloroquine resistance transporter (PfCRT or to the level of expression of the corresponding mRNA. In vitro, under a drug pressure of 100 nM of FQ, transient survival was observed in only one of two experiments. Conclusion Field isolates studies and experimental drug pressure experiments showed that FQ overcomes CQ resistance, which reinforces the potential of this compound as a new antimalarial drug.

  13. Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers.

    Science.gov (United States)

    Ben Romdhane, Meriam; Riahi, Leila; Selmi, Ayet; Zoghlami, Nejia

    2016-01-01

    This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  14. Molecular characterization of three common olive (Olea europaea L.) cultivars in Palestine, using simple sequence repeat (SSR) markers

    Science.gov (United States)

    Obaid, Ramiz; Abu-Qaoud, Hassan; Arafeh, Rami

    2014-01-01

    Eight accessions of olive trees from three common varieties in Palestine, Nabali Baladi, Nabali Mohassan and Surri, were genetically evaluated using five simple sequence repeat (SSR) markers. A total of 17 alleles from 5 loci were observed in which 15 (88.2%) were polymorphic and 2 (11.8%) were monomorphic. An average of 3.4 alleles per locus was found ranging from 2.0 alleles with the primers GAPU-103 and DCA-9 to 5.0 alleles with U9932 and DCA-16. The smallest amplicon size observed was 50 bp with the primer DCA-16, whereas the largest one (450 bp) with the primer U9932. Cluster analysis with the unweighted pair group method with arithmetic average (UPGMA) showed three clusters: a cluster with four accessions from the ‘Nabali Baladi’ cultivar, another cluster with three accessions that represents the ‘Nabali Mohassen’ cultivar and finally the ‘Surri’ cultivar. The similarity coefficient for the eight olive tree samples ranged from a maximum of 100% between two accessions from Nabali Baladi and also in two other samples from Nabali Mohassan, to a minimum similarity coefficient (0.315) between the Surri and two Nabali Baladi accessions. The results in this investigation clearly highlight the genetic dissimilarity between the three main olive cultivars that have been misidentified and mixed up in the past, based on conventional morphological characters. PMID:26019564

  15. De novo characterization of Larimichthys crocea transcriptome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development

    Science.gov (United States)

    Han, Zhaofang; Xiao, Shijun; Liu, Xiande; Liu, Yang; Li, Jiakai; Xie, Yangjie; Wang, Zhiyong

    2017-03-01

    The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. crocea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats (SSRs) were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions (PCR). To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs (40.0%) exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transcriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding of L. crocea.

  16. Sexual genetic and simple sequence repeat (SSR) analysis for molecular marker development on the all hermaphrodite papaya.

    Science.gov (United States)

    Chiu, C T; Wang, C W; Chen, F C; Chin, S W; Liu, C C; Lee, M J; Chung, W C; Chien, Y W; Chang, H J; Lee, C Y

    2015-03-30

    The papaya (Carica papaya L.) is one of the most important economic tropical fruits in the world, and the hermaphrodite is the preferred type in field cultures. We analyzed the sexual ratio of offspring from the cultivar 'Taiwan Seed Station No. 7' (T7) by a self-cross and its cross with Taichung Sunrise (TS). Female progeny from the T7 self-crossing were not observed. This finding may be caused by a lethal gene that is linked to females. In this study, we selected 192 simple sequence repeats (SSRs) to analyze the polymorphism between T7 and TS. A total of 37 SSRs were identified for T7 and TS. In addition, 14 SSRs served as the molecular makers for identification of T7, TS and their hybrid offsprings. Thus, the results show that the genetic similarity between T7 and TS is rather high. This suggests that T7 may be a mutant of TS. Phylogenetic analysis from the SSR polymorphisms of the above parent strains and 15 F1 offspring revealed the genetic distance of the F1 offspring located between T7 and TS. The results of this study may provide an opportunity for elucidating the genetic characteristics of all hermaphrodites via identification of molecular makers.

  17. The characterisation of Vitis vinifera ’Refošk’ with AFLP and SSR molecular markers and ampelographic traits

    Directory of Open Access Journals (Sweden)

    Matjaž HLADNIK

    2015-12-01

    Full Text Available The genetic diversity and ampelographic variability of autochthonous red wine cultivar ‘Refošk’ (Vitis vinifera L. grown in Slovenia were evaluated with AFLP molecular markers and OIV descriptors, respectively. SSR molecular markers were employed to confirm cultivar identity of analysed samples. Eight AFLP primer combinations, one was monomorphic, produced 16 polymorphic markers in 41 out of 113 samples, what classified samples into monomorphic and polymorphic group. Dendrogram constructed with simple matching coefficient and unweighted pair-group method analysis presented genetic diversity within polymorphic group. Refošk biotypes from monomorphic and polymorphic groups were evaluated with 22 OIV descriptors related to bunch, berry and must, but on the basis of ampelographic characterization samples were not differentiated among two major groups obtained with AFLP analysis. Results of genetic analysis indicated that ‘Refošk’ originated from closely related plants that are phenotypically very similar. With regard to low observed genetic diversity more attention should be dedicated to the selection in order to conserve remaining genetic diversity.

  18. Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

    Science.gov (United States)

    Nayak, Spurthi N.; Zhu, Hongyan; Varghese, Nicy; Datta, Subhojit; Choi, Hong-Kyu; Horres, Ralf; Jüngling, Ruth; Singh, Jagbir; Kavi Kishor, P. B.; Sivaramakrishnan, S.; Hoisington, Dave A.; Kahl, Günter; Winter, Peter; Cook, Douglas R.

    2010-01-01

    This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1265-1) contains supplementary material, which is

  19. De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl.

    Science.gov (United States)

    Liu, Congcong; Dou, Ying; Guan, Xuelian; Fu, Qiang; Zhang, Ze; Hu, Zenghui; Zheng, Jian; Lu, Yizeng; Li, Wei

    2017-01-01

    Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species. Here, we applied RNA-seq for sequencing S. pohuashanensis leaves and obtained a total of 137,506 clean reads. After assembly, 96,213 unigenes with an average length of 770 bp were obtained. We found that 64.5% of the unigenes could be annotated using bioinformatics tools to analyze gene function and alignment with the NCBI database. Overall, 59,089 unigenes were annotated using the Nr database(non-redundant protein database), 35,225 unigenes were annotated using the GO (Gene Ontology categories) database, and 33,168 unigenes were annotated using COG (Cluster of Orthologous Groups). Analysis of the unigenes using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database indicated that 13,953 unigenes were involved in 322 metabolic pathways. Finally, simple sequence repeat (SSR) site detection identified 6,604 unigenes that included EST-SSRs and a total of 7,473 EST-SSRs in the unigene sequences. Fifteen polymorphic SSRs were screened and found to be of use for future genetic research. These unigene sequences will provide important genetic resources for genetic improvement and investigation of biochemical processes in S. pohuashanensis.

  20. De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance Hedl.

    Directory of Open Access Journals (Sweden)

    Congcong Liu

    Full Text Available Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq technology have provided an effective means to obtain genomic information from non-model species. Here, we applied RNA-seq for sequencing S. pohuashanensis leaves and obtained a total of 137,506 clean reads. After assembly, 96,213 unigenes with an average length of 770 bp were obtained. We found that 64.5% of the unigenes could be annotated using bioinformatics tools to analyze gene function and alignment with the NCBI database. Overall, 59,089 unigenes were annotated using the Nr database(non-redundant protein database, 35,225 unigenes were annotated using the GO (Gene Ontology categories database, and 33,168 unigenes were annotated using COG (Cluster of Orthologous Groups. Analysis of the unigenes using the KEGG (Kyoto Encyclopedia of Genes and Genomes database indicated that 13,953 unigenes were involved in 322 metabolic pathways. Finally, simple sequence repeat (SSR site detection identified 6,604 unigenes that included EST-SSRs and a total of 7,473 EST-SSRs in the unigene sequences. Fifteen polymorphic SSRs were screened and found to be of use for future genetic research. These unigene sequences will provide important genetic resources for genetic improvement and investigation of biochemical processes in S. pohuashanensis.

  1. Hemoglobin derivatives

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003371.htm Hemoglobin derivatives To use the sharing features on this page, please enable JavaScript. Hemoglobin derivatives are altered forms of hemoglobin . Hemoglobin is ...

  2. Releyendo Frankfurt: la Experiencia Estética en Adorno

    Directory of Open Access Journals (Sweden)

    Stra, Sebastián Matías

    2013-01-01

    Full Text Available [es]Intentaremos en este trabajo explorar la noción de Experiencia Estética en la obra de Theodor Adorno, entendiéndola como una compleja mediación conceptual que nos puede permitir dar cuenta de las oscuras configuraciones de la relación entre arte, cultura y conocimiento en la producción del pensador de Frankfurt. En este marco, cruzaremos las reflexiones estéticas adornianas con lecturas más cercanas a nuestro campo disciplinar, como la noción de Industria Cultural y la interpretación del mito y su derivación en la conformación de la racionalidad moderna. [en] In this work, we will try to explore the notion of Aesthetic Experience in Theodor Adorno`s work, understanding it as a complex conceptual mediation that can allow us getting in the dark settings of the relationship between art, culture and knowledge in the production of Frankfurt`s thinker. Like this, we are going to cross adornians aesthetic reflections with readings that are going to be closer to our disciplinary field, as the notion of cultural industry and the interpretation of myth and its derivation in the configuration of modern rationality.

  3. Villa d'Este i Tivoli

    DEFF Research Database (Denmark)

    Bach-Nielsen, Carsten

    2012-01-01

    Om Villa d'Este, en renæssancehave ved Rom, der tematiserer Herkules' valg mellem dydens og lastens vej......Om Villa d'Este, en renæssancehave ved Rom, der tematiserer Herkules' valg mellem dydens og lastens vej...

  4. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability.

    Science.gov (United States)

    Isobe, Sachiko N; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

    2013-02-01

    The cultivated strawberry (Fragaria × ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA'A'BBB'B' model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.

  5. Black Locust (Robinia pseudoacacia L. Root Cuttings: Diversity and Identity Revealed by SSR Genotyping: A Case Study

    Directory of Open Access Journals (Sweden)

    Maria Emilia Malvolti

    2015-10-01

    Full Text Available Background and Purpose: Black locust (Robinia pseudoacacia L. is a valuable species native to North America and today widely planted throughout the world for biomass production. In Hungary, where Robinia has great importance in the forest management, the clones have been selected for plantations on good, medium and poor quality sites. To conserve the identity, superior clones are vegetatively propagated by root cuttings. At times the collection of root cuttings can cause uncertainty for clonal identity because of the overlap of roots from neighboring plants. This can occur especially when the repository is damaged from severe environmental accidents and the planting layout has been lost. The aim of this study has been to verify by molecular markers the diversity or identity of black locust clones by root cuttings harvested in a damaged trial. Materials and Methods: Root cuttings of 91 clones belonging to five cultivars were collected in a trial severely damaged by storms and flooding periods. The obtained plantlets were analyzed with nine microsatellite (SSR markers and the genetic identity/diversity within and among the plants was tested using the software GenAlEx version 6. Results: Multilocus genotypes (MLG and the Paetkau’s assignation test (1985 revealed genetic variability among the samples: the analyzed plantlets were grouped in four classes instead of the five expected. In addition, 6 unique genotypes have been detected. Conclusions: This study remarks problems that may arise during the harvest of Robinia’s root cuttings, especially when the planting layout has been confused. Molecular analyses can be successfully used to control the germplasm before its sale as guaranty for nurseries, farmers and stakeholders.

  6. Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers.

    Science.gov (United States)

    Wee, Alison K S; Takayama, Koji; Chua, Jasher L; Asakawa, Takeshi; Meenakshisundaram, Sankararamasubramanian H; Onrizal; Adjie, Bayu; Ardli, Erwin Riyanto; Sungkaew, Sarawood; Malekal, Norhaslinda Binti; Tung, Nguyen Xuan; Salmo, Severino G; Yllano, Orlex Baylen; Saleh, M Nazre; Soe, Khin Khin; Tateishi, Yoichi; Watano, Yasuyuki; Baba, Shigeyuki; Webb, Edward L; Kajita, Tadashi

    2015-03-29

    Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers. Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting

  7. Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus.

    Science.gov (United States)

    Shokeen, Bhumika; Choudhary, Shalu; Sethy, Niroj Kumar; Bhatia, Sabhyata

    2011-08-01

    Catharanthus roseus is a plant of great medicinal importance, yet inadequate knowledge of its genome structure and the unavailability of genomic resources have been major impediments in the development of improved varieties. The aims of this study were to develop co-dominant sequence-tagged microsatellite sites (STMS) and gene-targeted markers (GTMs) and utilize them for the construction of a framework intraspecific linkage map of C. roseus. For simple sequence repeat (SSR) isolation, a genomic library enriched for (GA)(n) repeats was constructed from C. roseus 'Nirmal' (CrN1). In addition, GTMs were also designed from 12 genes of the TIA (terpenoid indole alkaloid) pathway - the medicinally most significant pathway in C. roseus. An F(2) mapping population was also generated by crossing two diverse accessions of C. roseus CrN1 (Nirmal)×CrN82 (Kew). A new set of 314 STMS markers and 64 GTMs were developed in this study. A segregating F(2) mapping population consisting of 111 F(2) individuals was generated. For generating the linkage map, a set of 423 co-dominant markers (378 newly developed and 45 published earlier) were screened for polymorphism between the parental genotypes, of which 134 were identified to be polymorphic. A total of 114 markers were mapped on eight linkage groups that spanned a 632·7 cM region of the genome with an average marker distance of 5·55 cM. Further, the mechanism of hypervariability at the gene-targeted loci was investigated at the sequence level. For the first time, a large array of STMS markers and GTMs was generated in the model medicinal plant C. roseus. Moreover, the first microsatellite marker-based linkage map was described in this study. Together, these will serve as a foundation for future genomics studies related to quantitative trait loci analysis and molecular breeding in C. roseus.

  8. SSR marker-based molecular characterization and genetic diversity analysis of aromatic landreces of rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    ABDUL M. SAJIB

    2012-01-01

    Full Text Available Molecular characterization of the genotypes gives precise information about the extent of genetic diversity which helps in the development of an appropriate breeding program. In the present study, a total of 24 SSR markers were used across 12 elite aromatic rice genotypes for their characterization and discrimination. Among these 24 markers 9 microsatellite markers were showed polymorphism. The number of alleles per locus ranged from 2 alleles (RM510, RM244, and RM277 to 6 alleles (RM 163, with an average of 3.33 alleles across 9 loci obtained in the study. The polymorphic information content values ranged from 0.14 (RM510 to 0.71 (RM163 in all 9 loci with an average of 0.48. RM163 was found the best marker for the identification of 12 genotypes as revealed by PIC values. The frequency of most common allele at each locus ranged from 41% (RM163, RM590, and RM413 to 91% (RM510. The pair-wise genetic dissimilarity co-efficient indicated that the highest genetic distance was obtained between Basmati PNR 346 and Deepa; Basmati PNR 346 and Patnai-23; Dolargura and Sugandha; Bhogganijia and Sugandha; and finally between Dolargura and Chinikani (88.89%. Opchaya, Basmati PNR 346 and Sugandha had close similarity among them but showed wide dissimilarity with other genotypes. Being grouped into distant clusters Dolargura and Opchaya could be utilized as potential parents for the improvement of fine grain aromatic rice varieties. Genotypes Deepa and Patnai-23 (having zero dissimilarity might have possessed somewhat similar genetic background and more markers are needed to discriminate them. The microsatellite marker based molecular fingerprinting could serve as a sound basis in the identification of genetically distant accessions as well as in the duplicate sorting of the morphologically close accessions.

  9. Repressive Actions of the State Security Communities Against ≪True Orthodox Church≫ Structuries in the Ukrainian SSR (1944–1953) (continued)

    OpenAIRE

    Vedeneev Dmitrii

    2016-01-01

    In the article on the basis of unknown scientific community documents of the Soviet state security bodies provides an analysis of the objectives and key areas of operational work and repressive actions of the security services communities against «True Orthodox Church» (TOC) in the Ukrainian SSR in 1944–1953. The characteristic of agent and operational developments NKGB-MGB-KGB of the USSR against the so-called «catacomb Church», as a form of religious and social protest against aggressive ath...

  10. The nicotinic alpha7 acetylcholine receptor agonist ssr180711 is unable to activate limbic neurons in mice overexpressing human amyloid-beta1-42

    DEFF Research Database (Denmark)

    Soderman, A.; Spang-Thomsen, Mogens; Hansen, H.

    2008-01-01

    systemic administration of the alpha7 nAChR agonist SSR180711 (10 mg/kg) result in a significant increase in Fos protein levels in the shell of nucleus accumbens in wild-type mice, but has no effect in the transgene mice. There were fewer cell bodies expressing Fos in the prefrontal cortex of transgene...... that clinical trials testing alpha7 nAChR agonists should be related to the content of Abeta peptides in the patient's nervous system Udgivelsesdato: 2008/8/28...

  11. Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species.

    Science.gov (United States)

    Ziya Motalebipour, Elmira; Kafkas, Salih; Khodaeiaminjan, Mortaza; Çoban, Nergiz; Gözel, Hatice

    2016-12-07

    Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species. To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.

  12. Rapid and not culture-dependent assay based on multiplex PCR-SSR analysis for monitoring inoculated yeast strains in industrial wine fermentations.

    Science.gov (United States)

    Cordero-Bueso, Gustavo; Rodríguez, María Esther; Garrido, Carlos; Cantoral, Jesús Manuel

    2017-01-01

    Wine industry needs a simple method for rapid diagnosis of the dominance of inoculated strains that could be performed routinely during the fermentation process. We present a suitable, high-throughput, and low-cost method to monitor rapidly the dominance of inoculated yeast strains in industrial fermentations of red and white wines using an activated carbon cleaning pretreatment, and a rapid DNA extraction method plus multiplex PCR-SSR analysis. We apply this technique directly to samples of fermenting wines without previously isolating yeast colonies. Results are obtained in a maximum time of 4.5 h.

  13. Estética, cine y tragedia.

    OpenAIRE

    Pérez, Berta M.

    2010-01-01

    Este trabajo propone caracterizar como «estética contramoderna» una línea de pensamiento que, desde el último Kant hasta Heidegger, se enfrenta al dominio de la teoría y reivindica la vinculación del ámbito estético a una verdad radicalmente trágica. Presenta después el fenómeno cinematográfico como un medio que la estética moderna interpreta según su propia concepción del arte para integrarlo en el orden y la ideología del capitalismo avanzado. Y, por último, ar...

  14. octene derivatives

    Indian Academy of Sciences (India)

    Ultrasonication; trimethylsilyloxy-derivatives; bicyclo[2.2.2]octene; Diels–Alder reaction; crystal structure; C–H. . . O and π...π interactions. 1. ... of silyl- derivatives were studied.8 The structural studies indicated a self-assembly ..... Technology (DST), New Delhi, India for the financial assistance. References. 1. Zhao F, Zhang ...

  15. Financial Derivatives

    DEFF Research Database (Denmark)

    Wigan, Duncan

    2013-01-01

    Contemporary derivatives mark the development of capital and constitute a novel form of ownership. By reconfiguring the temporal, spatial and legal character of ownership derivatives present a substantive challenge to the tax collecting state. While fiscal systems are nationally bounded and inheren...

  16. EST Reading Curriculum & Instruction: An Alignment Analysis

    Directory of Open Access Journals (Sweden)

    Lubna Ali Mohammed

    2015-02-01

    Full Text Available In order for a curriculum to achieve its goals, it is imperative that the curriculum is coherent at all levels. In order to determine the coherency of a curriculum, the alignment of its theoretical underpinning and the label of a curriculum is one of the aspects that can be examined. The purpose of the current study was to examine if the theoretical grounding of the Yemeni EST senior secondary curriculum is in alignment with its communicative-based curriculum label. In line with its label, the reading curriculum embedded in the EST curriculum should be developed and designed based on the Communicative Language Teaching (CLT, which should be reflected in the EST reading instructional practice. In analysing the alignment of the communicative language teaching approach in the EST senior secondary school reading curriculum, the primary focus of the analysis was on the major SLA theories and L2 reading theories and the related instructional approaches. The data for this study were collected via an ESP textbook review as well as from the observation of the EST reading classroom instruction. The findings show that the EST senior secondary reading curriculum was not developed based on the socio-cognitive and socio-cultural theories which are the grounding principles of the communicative approach. Instead, the findings show that the EST senior secondary reading curriculum was primarily developed based on the cognitive information processing theory, in which teaching instruction reflects the student as an individual information processor and the focus on teaching vocabulary and grammatical rules using reading texts in non-communicative manner. Keywords: Communicative Approach, SLA Theories, L2 Reading Theories

  17. Transcriptomic Identification of Drought-Related Genes and SSR Markers in Sudan Grass Based on RNA-Seq

    Directory of Open Access Journals (Sweden)

    Yongqun Zhu

    2017-05-01

    Full Text Available Sudan grass (Sorghum sudanense is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis. A total of 80,686 unigenes were obtained via de novo assembly of the clean reads including 45,065 unigenes (55.9% that were identified as coding sequences (CDSs. According to Gene Ontology analysis, 31,444 unigenes were annotated, 11,778 unigenes were identified to 25 categories in the clusters of orthologous groups of proteins (KOG classification, and 11,223 unigenes were assigned to 280 Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Additionally, there were 2,329 DEGs under a short-term of 25% polyethylene glycol (PEG treatment, while 5,101 DEGs were identified under the long-term of 25% PEG treatment. DEGs were enriched in pathways of carbon fixation in photosynthetic organisms and plant hormone signal transduction which played a leading role in short-term of drought stress. However, DEGs were mainly enriched in pathway of plant hormone signal transduction that played an important role under long-term of drought stress. To increase accuracy, we excluded all the DEGs of all controls, specifically, five DEGs that were associated with high PEG concentrations were found through RNA-Seq. All five genes were up-regulated under drought stress, but the functions of the genes remain unclear. In addition, we identified 17,548 SSRs obtained from 80,686 unigenes. The newly identified drought tolerance DEGs will contribute to transgenic breeding efforts, while

  18. Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers.

    Science.gov (United States)

    Xie, Chaotian; Li, Bing; Xu, Yan; Ji, Dehua; Chen, Changsheng

    2013-02-16

    novel gene discovery and gene expression profiling analyses under different physiological conditions. A number of the cSSR markers identified can be used for molecular markers and will facilitate marker assisted selection in P. haitanensis breeding. These sequences and markers will provide valuable resources for further P. haitanensis studies.

  19. EST-PAC a web package for EST annotation and protein sequence prediction

    Directory of Open Access Journals (Sweden)

    Strahm Yvan

    2006-10-01

    Full Text Available Abstract With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1 searching local or remote biological databases for sequence similarities using Blast services, 2 predicting protein coding sequence from EST data and, 3 annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

  20. [A clinical study on the comparison of the performance of stainless steel ring (SSR), uterine cavity-shaped device (UCD), MLCu250 and TCu220C].

    Science.gov (United States)

    Li, Y

    1988-01-01

    In Dafeng County, Jiangsu Province, 710 healthy peasant women, ages 22- 32, were randomly allocated to the use of several different IUDs for periods of 3-9 months postpartum. Although this single-blind study continued for 2 years, only 1 year's worth of data is presented in this paper. The total termination rate was lowest with the MLCu 250, followed by the UCD, and then the TCu220c. The UCD is an inert, stainless steel device which assumes an isosceles shape to conform to the uterine cavity. The SSR had the highest termination rate (see table 1). There was a significant difference between the total termination rates of the SSR and each of the other 3 IUDs, while no significant difference was seen between those of the 3 themselves. The removals due to bleeding and pain were much higher in the TCu220c than in the MLCu250. The results of this study seem dissimilar to those obtained in IUD trials carried out among housewives and office workers. Clearly, in women performing strenuous physical tasks, the straight and rigid transverse arms of the TCu220c may impose more stimulation on the uterine wall than the soft and curved arms of the MLCu250. (author's modified)

  1. Analysis of the Genetic Diversity and Population Structure of Latvian Ash (Fraxinus excelsior L. Stands using Nuclear and Chloroplast SSR Markers

    Directory of Open Access Journals (Sweden)

    Ruņģis Dainis

    2016-06-01

    Full Text Available Common ash (Fraxinus excelsior L. has a widespread distribution throughout Europe, and Latvia is almost at the north eastern edge of the distribution range. In Europe, ash is threatened by ash dieback, a disease caused by the introduced ascomycete Hymenoscyphus fraxineus. Chloroplast and nuclear DNA markers have been used to study the genetic diversity and population structure of ash both in a broader pan-European context as well as in more restricted regions. Some of the markers analysed in these previously published reports were also utilised in this study, enabling comparisons of the genetic parameters calculated from the nuclear SSR marker data and of the haplotypes identified with the chloroplast markers. Analysis of chloroplast markers revealed one dominant haplotype in Latvian stands, which corresponds to the haplotype previously found in Eastern Europe and Scandinavia. A second haplotype, corresponding to a previously reported central European haplotype was found in all individuals from the Ķemeri stand, indicating that this stand was naturally established from introduced germplasm, which was planted in a neighbouring park. The nuclear SSR markers revealed low levels of differentiation of Latvian F. excelsior stands, probably due efficient pollen flow between stands. The analysis of both chloroplast and nuclear DNA markers has revealed different aspects of the structure and provenance of Latvian F. excelsior populations.

  2. An SSR-based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico.

    Science.gov (United States)

    Hayano-Kanashiro, Corina; Martínez de la Vega, Octavio; Reyes-Valdés, M Humberto; Pons-Hernández, José-Luis; Hernández-Godinez, Fernando; Alfaro-Laguna, Emigdia; Herrera-Ayala, José Luis; Vega-Sánchez, Ma Cristina; Carrera-Valtierra, José Alfredo; Simpson, June

    2017-03-01

    As maize was domesticated in Mexico around 9,000 years ago, local farmers have selected and maintained seed stocks with particular traits and adapted to local conditions. In the present day, many of these landraces are still cultivated; however, increased urbanization and migration from rural areas implies a risk that this invaluable maize germplasm may be lost. In order to implement an efficient mechanism of conservation in situ, the diversity of these landrace populations must be estimated. Development of a method to select the minimum number of samples that would include the maximum number of alleles and identify germplasm harboring rare combinations of particular alleles will also safeguard the efficient ex-situ conservation of this germplasm. To reach this goal, a strategy based on SSR analysis and a novel algorithm to define a minimum collection and rare genotypes using landrace populations from Puebla State, Mexico, was developed as a "proof of concept" for methodology that could be extended to all maize landrace populations in Mexico and eventually to other native crops. The SSR-based strategy using bulked DNA samples allows rapid processing of large numbers of samples and can be set up in most laboratories equipped for basic molecular biology. Therefore, continuous monitoring of landrace populations locally could easily be carried out. This methodology can now be applied to support incentives for small farmers for the in situ conservation of these traditional cultivars.

  3. SSR markers associated to early leaf spot disease resistance through selective genotyping and single marker analysis in groundnut (Arachis hypogaea L.

    Directory of Open Access Journals (Sweden)

    Adama Zongo

    2017-09-01

    Full Text Available Groundnut (Arachis hypogaea L. is an important oilseed and food crop of the world. Breeding for disease resistance is one of major objectives in groundnut breeding. Early leaf spot (ELS is one of the major destructive diseases worldwide and in West Africa, particularly in Burkina Faso causing significant yield losses. Conventional breeding approaches have been employed to develop improved varieties resistant to ELS. Molecular dissection of resistance traits using QTL analysis can improve the efficiency of resistance breeding. In the present study, an ELS susceptible genotype QH243C and an ELS resistant genotype NAMA were crossed and the F2 population genotypic and F3 progenies phenotypic data were used for marker-trait association analysis. Parents were surveyed with 179 simple sequence repeat (SSR markers out of which 103 SSR markers were found to be polymorphic between the parents. These polymorphic markers were utilized to genotype the F2 population followed by marker-trait analysis through single marker analysis (SMA and selective genotyping of the population using 23 resistant and 23 susceptible genotypes. The SMA revealed 13 markers while the selective genotyping method identified 8 markers associated with ELS resistance. Four markers (GM1911, GM1883, GM1000 and Seq13E09 were found common between the two trait mapping methods. These four markers could be employed in genomics-assisted breeding for selection of ELS resistant genotypes in groundnut breeding.

  4. Global Derivatives

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    approaches to dealing in the global business environment." - Sharon Brown-Hruska, Commissioner, Commodity Futures Trading Commission, USA. "This comprehensive survey of modern risk management using derivative securities is a fine demonstration of the practical relevance of modern derivatives theory to risk......""In Global Derivatives: A Strategic Risk Management Perspective", Torben Juul Andersen has succeeded to gather in one book a complete and thorough summary and an easy-to-read explanation of all types of derivative instruments and their background, and their use in modern management of risk......." - Steen Parsholt, Chairman and CEO, Aon Nordic Region. "Andersen has done a wonderful job of developing a comprehensive text that deals with risk management in global markets. I would recommend this book to any student or businessman who has a need to better understand the risks and risk management...

  5. Turismo y estética formativa

    Directory of Open Access Journals (Sweden)

    Clara Inés Sánchez Arciniegas

    2002-11-01

    Full Text Available ¿Existe alguna armonía entre el conocimiento y la estética? Sin duda alguna el hombre con conocimiento y sin virtud de la estética es un autómata; este necesita de las diferentes manifestaciones en las que se encuentra plasmada y necesita recordarlas continuamente. La estética como doctrina de conocimiento no es reciente, en el siglo xviii cuando por primera vez se define teóricamente hasta nuestros días en la Universidad actual. Esta última aparentemente menos evidente debido a las nuevas formas de aprendizaje con herramientas tecnológicas muy avanzadas y contraria a la imagen del universitario que hace dos siglos como complemento a su educación se distraía a través del Gran Tour, partida que tiene el turismo para fomentar el goce estético. ¿Cuál es entonces la relación entre distracción y formación? Se debe entonces reflexionar y comprender que el conocimiento interdisciplinario y la metodología debe procurar en los hombres actitudes adecuadas frente a la cultura y el arte a través del conocimiento.

  6. Estética del rock

    OpenAIRE

    Rey, Sebastián

    2014-01-01

    El objetivo del presente artículo es el de analizar la estética del Rock en términos de la experiencia que ofrece este género musical. En primer lugar se construirá una relación entre el Nacimiento de la tragedia de Nietzsche y el surgimiento del Rock, bajo la premisa de que el origen del Rock es eminentemente dionisíaco; luego se mostrará una forma de la experiencia en la vida cotidiana de quien escucha Rock, en donde se da cuenta de la necesidad de expresar los sentimientos de placer y disp...

  7. SSR markers among cassava

    African Journals Online (AJOL)

    user

    2011-03-07

    Mar 7, 2011 ... (Rallo et al., 2003) and Poaceae (Kuleung et al., 2004). These studies have revealed that chromosome segments are conserved among related taxa. Whankaew et al. 1769. In Euphorbiaceae, a few studies on cross-genera transferability have been undertaken (Feng et al., 2009;. Kumar et al., 2010; Raji et ...

  8. Derivative chameleons

    Energy Technology Data Exchange (ETDEWEB)

    Noller, Johannes, E-mail: johannes.noller08@imperial.ac.uk [Theoretical Physics, Blackett Laboratory, Imperial College London, Prince Consort Road, London, SW7 2BZ (United Kingdom)

    2012-07-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field φ, but also of its derivatives via higher order co-ordinate invariants (such as ∂{sub μ}φ∂{sup μ}φ,□φ,...). Specifically we consider the first such non-trivial conformal factor A(φ,∂{sub μ}φ∂{sup μ}φ). The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for φ → φ+c. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning, stable derivative models are in fact typically anti-chameleons that suppress the field's mass in dense environments. Furthermore we investigate modifications to the thin-shell regime and prove a no-go theorem for chameleon effects in non-conformal geometries of the disformal type.

  9. Electricity derivatives

    CERN Document Server

    Aïd, René

    2015-01-01

    Offering a concise but complete survey of the common features of the microstructure of electricity markets, this book describes the state of the art in the different proposed electricity price models for pricing derivatives and in the numerical methods used to price and hedge the most prominent derivatives in electricity markets, namely power plants and swings. The mathematical content of the book has intentionally been made light in order to concentrate on the main subject matter, avoiding fastidious computations. Wherever possible, the models are illustrated by diagrams. The book should allow prospective researchers in the field of electricity derivatives to focus on the actual difficulties associated with the subject. It should also offer a brief but exhaustive overview of the latest techniques used by financial engineers in energy utilities and energy trading desks.

  10. An EST database from saffron stigmas

    Science.gov (United States)

    D'Agostino, Nunzio; Pizzichini, Daniele; Chiusano, Maria Luisa; Giuliano, Giovanni

    2007-01-01

    Background Saffron (Crocus sativus L., Iridaceae) flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part – the stigmas – are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron. Results We produced 6,603 high quality Expressed Sequence Tags (ESTs) from a saffron stigma cDNA library. This collection is accessible and searchable through the Saffron Genes database http://www.saffrongenes.org. The ESTs have been grouped into 1,893 Clusters, each corresponding to a different expressed gene, and annotated. The complete set of raw EST sequences, as well as of their electopherograms, are maintained in the database, allowing users to investigate sequence qualities and EST structural features (vector contamination, repeat regions). The saffron stigma transcriptome contains a series of interesting sequences (putative sex determination genes, lipid and carotenoid metabolism enzymes, transcription factors). Conclusion The Saffron Genes database represents the first reference collection for the genomics of Iridaceae, for the molecular biology of stigma biogenesis, as well as for the metabolic pathways underlying saffron secondary metabolism. PMID:17925031

  11. An EST database from saffron stigmas

    Directory of Open Access Journals (Sweden)

    Chiusano Maria Luisa

    2007-10-01

    Full Text Available Abstract Background Saffron (Crocus sativus L., Iridaceae flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part – the stigmas – are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron. Results We produced 6,603 high quality Expressed Sequence Tags (ESTs from a saffron stigma cDNA library. This collection is accessible and searchable through the Saffron Genes database http://www.saffrongenes.org. The ESTs have been grouped into 1,893 Clusters, each corresponding to a different expressed gene, and annotated. The complete set of raw EST sequences, as well as of their electopherograms, are maintained in the database, allowing users to investigate sequence qualities and EST structural features (vector contamination, repeat regions. The saffron stigma transcriptome contains a series of interesting sequences (putative sex determination genes, lipid and carotenoid metabolism enzymes, transcription factors. Conclusion The Saffron Genes database represents the first reference collection for the genomics of Iridaceae, for the molecular biology of stigma biogenesis, as well as for the metabolic pathways underlying saffron secondary metabolism.

  12. An EST database from saffron stigmas.

    Science.gov (United States)

    D'Agostino, Nunzio; Pizzichini, Daniele; Chiusano, Maria Luisa; Giuliano, Giovanni

    2007-10-09

    Saffron (Crocus sativus L., Iridaceae) flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part - the stigmas - are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron. We produced 6,603 high quality Expressed Sequence Tags (ESTs) from a saffron stigma cDNA library. This collection is accessible and searchable through the Saffron Genes database http://www.saffrongenes.org. The ESTs have been grouped into 1,893 Clusters, each corresponding to a different expressed gene, and annotated. The complete set of raw EST sequences, as well as of their electopherograms, are maintained in the database, allowing users to investigate sequence qualities and EST structural features (vector contamination, repeat regions). The saffron stigma transcriptome contains a series of interesting sequences (putative sex determination genes, lipid and carotenoid metabolism enzymes, transcription factors). The Saffron Genes database represents the first reference collection for the genomics of Iridaceae, for the molecular biology of stigma biogenesis, as well as for the metabolic pathways underlying saffron secondary metabolism.

  13. Hidden treasures in unspliced EST data.

    Science.gov (United States)

    Engelhardt, J; Stadler, P F

    2012-05-01

    Several classes of exclusively--or at least predominantly--unspliced non-coding RNAs have been described in the last years, including totally and partially intronic transcripts and long intergenic RNAs. Functionally, they appear to be involved in regulating gene expression, at least in part by associating with the chromatin. Intron-less transcripts have received little attention, even though recent findings indicate that intron-less protein-coding genes have several features that set them apart from the more abundant and much better understood spliced mRNAs. Even less is known about unspliced non-coding transcripts. Thus we systematically analyze the distribution of unspliced ESTs in the human genome. These form a large source of transcriptomic data that is almost always excluded from detailed studies. Most unspliced ESTs appear in clusters overlapping, or located in the close vicinity of, annotated RefSeq genes. Partially intronic unspliced ESTs show complex patterns of overlap with the intron/exon structure of the RefSeq gene. Distinctive patterns of CAGE tags indicate that a large class of unspliced EST clusters is forming long extensions of 3'UTRs, at least several hundreds of which probably appear also as independent 3'UTR-associated RNAs.

  14. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    Expressed Sequence Tags (ESTs) and Single Nucleotide Polymorphisms (SNPs) are providing in depth knowledge in plant biology, breeding and biotechnology. The emergence of many novel molecular marker techniques are changing and accelerating the process of producing mutations in plant molecular biology ...

  15. The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42

    DEFF Research Database (Denmark)

    Aparicio, Tomás; Ingemann Jensen, Sheila; Nielsen, Alex Toftgaard

    2016-01-01

    of reference strain KT2440) is still a time-consuming endeavor. In this work we have investigated the in vivo activity of the Ssr protein encoded by the open reading frame T1E_1405 from Pseudomonas putida DOT-T1E, a plausible functional homologue of the β protein of the Red recombination system of λ phage...

  16. Development of ESTs and data mining of pineapple EST-SSRs.

    Science.gov (United States)

    Ong, W D; Voo, C L Y; Kumar, S V

    2012-05-01

    Improving the quality of the non-climacteric fruit, pineapple, is possible with information on the expression of genes that occur during the process of fruit ripening. This can be made known though the generation of partial mRNA transcript sequences known as expressed sequence tags (ESTs). ESTs are useful not only for gene discovery but also function as a resource for the identification of molecular markers, such as simple sequence repeats (SSRs). This paper reports on firstly, the construction of a normalized library of the mature green pineapple fruit and secondly, the mining of EST-SSRs markers using the newly obtained pineapple ESTs as well as publically available pineapple ESTs deposited in GenBank. Sequencing of the clones from the EST library resulted in 282 good sequences. Assembly of sequences generated 168 unique transcripts (UTs) consisting of 34 contigs and 134 singletons with an average length of ≈500 bp. Annotation of the UTs categorized the known proteins transcripts into the three ontologies as: molecular function (34.88%), biological process (38.43%), and cellular component (26.69%). Approximately 7% (416) of the pineapple ESTs contained SSRs with an abundance of trinucleotide SSRs (48.3%) being identified. This was followed by dinucleotide and tetranucleotide SSRs with frequency of 46 and 57%, respectively. From these EST-containing SSRs, 355 (85.3%) matched to known proteins while 133 contained flanking regions for primer design. Both the ESTs were sequenced and the mined EST-SSRs will be useful in the understanding of non-climacteric ripening and the screening of biomarkers linked to fruit quality traits.

  17. Highly informative single-copy nuclear microsatellite DNA markers developed using an AFLP-SSR approach in black spruce (Picea mariana and red spruce (P. rubens.

    Directory of Open Access Journals (Sweden)

    Yong-Zhong Shi

    Full Text Available Microsatellites or simple sequence repeats (SSRs are highly informative molecular markers for various biological studies in plants. In spruce (Picea and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana and red spruce (Picea rubens using a simple but efficient method based on a combination of AFLP and microsatellite technologies.A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean = 0.67 in black spruce and from 0.161 to 0.851 (mean = 0.62 in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies.The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce and other Picea species for

  18. Complex derivatives

    Science.gov (United States)

    Battiston, Stefano; Caldarelli, Guido; Georg, Co-Pierre; May, Robert; Stiglitz, Joseph

    2013-03-01

    The intrinsic complexity of the financial derivatives market has emerged as both an incentive to engage in it, and a key source of its inherent instability. Regulators now faced with the challenge of taming this beast may find inspiration in the budding science of complex systems.

  19. The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.

    Directory of Open Access Journals (Sweden)

    Byregowda Munishamappa

    2010-03-01

    .8% in molecular function. Further, 19 genes were identified differentially expressed between FW- responsive genotypes and 20 between SMD- responsive genotypes. Generated ESTs were compiled together with 908 ESTs available in public domain, at the time of analysis, and a set of 5,085 unigenes were defined that were used for identification of molecular markers in pigeonpea. For instance, 3,583 simple sequence repeat (SSR motifs were identified in 1,365 unigenes and 383 primer pairs were designed. Assessment of a set of 84 primer pairs on 40 elite pigeonpea lines showed polymorphism with 15 (28.8% markers with an average of four alleles per marker and an average polymorphic information content (PIC value of 0.40. Similarly, in silico mining of 133 contigs with ≥ 5 sequences detected 102 single nucleotide polymorphisms (SNPs in 37 contigs. As an example, a set of 10 contigs were used for confirming in silico predicted SNPs in a set of four genotypes using wet lab experiments. Occurrence of SNPs were confirmed for all the 6 contigs for which scorable and sequenceable amplicons were generated. PCR amplicons were not obtained in case of 4 contigs. Recognition sites for restriction enzymes were identified for 102 SNPs in 37 contigs that indicates possibility of assaying SNPs in 37 genes using cleaved amplified polymorphic sequences (CAPS assay. Conclusion The pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance. Sequence analyses of this dataset have showed conservation of a considerable number of pigeonpea transcripts across legume and model plant species analysed as well as some putative pigeonpea specific genes. Validation of identified biotic stress responsive genes should provide candidate genes for allele mining as well as candidate markers for molecular breeding.

  20. La estética en Marcuse

    OpenAIRE

    Cuevas Ruíz, Rafael

    2014-01-01

    Trabajo de Fin de Máster. Máster Universitario en Filosofía Teórica y Práctica. Especialidad de Filosofía Práctica El presente trabajo tiene por objeto recapitular y sistematizar dentro de la obra de Marcuse, aquellos materiales que configuran su reflexión en el campo de la estética. Para ello y por orden cronológico, hemos ido realizando distintos recesos, deteniéndonos con más hincapié en los textos que consideramos más determinantes en cuanto a su importancia en este tema: Acerca del ca...

  1. FRIEDMAN Thomas, La terre est plate

    OpenAIRE

    Kociemba, Valérie

    2008-01-01

    « L’Église dit que la terre est plate, mais j’ai vu l’ombre sur la lune et j’ai plus foi en l’ombre qu’en l’église. » (Ferdinand Magellan) Bien des siècles plus tard, Thomas Friedman réitère l’affirmation en titre de son dernier ouvrage : La terre est plate, Une brève histoire du xxie siècle. À quelle Église appartient donc ce brillant éditorialiste du « New York Times » ? À l’Église de la toute puissance des nouvelles technologies de l’information, et il n’en fait pas mystère puisqu’il décla...

  2. An EST database from saffron stigmas

    OpenAIRE

    Chiusano Maria Luisa; Pizzichini Daniele; D'Agostino Nunzio; Giuliano Giovanni

    2007-01-01

    Abstract Background Saffron (Crocus sativus L., Iridaceae) flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part – the stigmas – are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron. Results We produced 6,603 high quality Expressed Sequence Tags (ESTs) from a saffron stigma cDNA library. This collection is access...

  3. QuEST: Robust Quantum Gadgets

    Science.gov (United States)

    2013-02-28

    of novel and robust perturbation theory gadgets , the construction of scalable stabilizer Hamiltonians, and methods for achieving the fault-tolerant... theory gadgets 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 1 19a. NAME OF RESPONSIBLE PERSON Aram Harrow a...AFRL-OSR-VA-TR-2013-0170 QuEST: Robust Quantum Gadgets Aram Harrow University of Washington Computer Science & Engineering Box 352350 Seattle, WA

  4. Estética, Subjetividad y Conocimiento

    Directory of Open Access Journals (Sweden)

    López Avendaño, Olimpia

    2002-12-01

    Full Text Available Este artículo trata de la tradicional dicotomía conocimiento objetivo-subjetivo. En él se analiza la posición de diferentes autores en búsqueda de los elementos que conducen al nacimiento de un nuevo paradigma, integrador, que supere la antinomia y permita visualizar al conocimiento pero sobre todo al individuo que lo produce, integralmente.

  5. Amar por cartas - este inferno de amara

    Directory of Open Access Journals (Sweden)

    Matildes Demetrio dos Santos

    1999-10-01

    Full Text Available Este trabalho tem por objetivo estudar o amor nas Folhas caídas e nas Cartas de amor à Viscondessa da Luz, de Almeida Garrett.Seus poemas cheios de erotismo e sensua lidade, inspirados numa mulher casada, Rosa Montúrar Infante, escandalizaram a sociedade portuguesado sécu lo XIX. Suas cartas de amor, em segredo, criavam uma ficção de características místicas.

  6. Les tueries à l’Est

    OpenAIRE

    Jurgenson, Luba

    2015-01-01

    Colloques synchrones. Deux colloques, l’un à Paris, l’autre à Bruxelles, sont venus interroger la Shoah à l’Est. Nouveaux acquis, relectures critiques. Two conferences, one held in Paris and the other one in Brussels, dedicated to the Holocaust in the East. New insights, critical analyses. Twee colloquia, het ene in Parijs en het andere in Brussel, buigen zich over de Holocaust in het Oosten. Nieuwe inzichten, kritische analyses.

  7. Development and Positioning Accuracy Assessment of Single-Frequency Precise Point Positioning Algorithms by Combining GPS Code-Pseudorange Measurements with Real-Time SSR Corrections

    Directory of Open Access Journals (Sweden)

    Miso Kim

    2017-06-01

    Full Text Available We have developed a suite of real-time precise point positioning programs to process GPS pseudorange observables, and validated their performance through static and kinematic positioning tests. To correct inaccurate broadcast orbits and clocks, and account for signal delays occurring from the ionosphere and troposphere, we applied State Space Representation (SSR error corrections provided by the Seoul Broadcasting System (SBS in South Korea. Site displacements due to solid earth tide loading are also considered for the purpose of improving the positioning accuracy, particularly in the height direction. When the developed algorithm was tested under static positioning, Kalman-filtered solutions produced a root-mean-square error (RMSE of 0.32 and 0.40 m in the horizontal and vertical directions, respectively. For the moving platform, the RMSE was found to be 0.53 and 0.69 m in the horizontal and vertical directions.

  8. The nicotinic alpha7 acetylcholine receptor agonist ssr180711 is unable to activate limbic neurons in mice overexpressing human amyloid-beta1-42

    DEFF Research Database (Denmark)

    Søderman, Andreas; Thomsen, Morten S; Hansen, Henrik H

    2008-01-01

    through the use of co-immunoprecipitation that human Abeta-immunoreactive peptides bind to mice alpha7 nAChR in vivo. Agonists of the alpha7 nAChR improve memory and attentional properties and increase immediate early gene expression in the prefrontal cortex and the nucleus accumbens. We show that acute...... systemic administration of the alpha7 nAChR agonist SSR180711 (10 mg/kg) result in a significant increase in Fos protein levels in the shell of nucleus accumbens in wild-type mice, but has no effect in the transgene mice. There were fewer cell bodies expressing Fos in the prefrontal cortex of transgene...

  9. Gnathostome phylogenomics utilizing lungfish EST sequences.

    Science.gov (United States)

    Hallström, Björn M; Janke, Axel

    2009-02-01

    The relationship between the Chondrichthyes (cartilaginous fishes), the Actinopterygii (ray-finned fishes), and the piscine Sarcopterygii (lobe-finned fishes) and how the Tetrapoda (four-limbed terrestrial vertebrates) are related to these has been a contentious issue for more than a century. A general consensus about the relationship of these vertebrate clades has gradually emerged among morphologists, but no molecular study has yet provided conclusive evidence for any specific hypothesis. In order to examine these relationships on the basis of more extensive sequence data, we have produced almost 1,000,000 bp of expressed sequence tags (ESTs) from the African marbled lungfish, Protopterus aethiopicus. This new data set yielded 771 transcribed nuclear sequences that had not been previously described. The lungfish EST sequences were combined with EST data from two cartilaginous fishes and whole genome data from an agnathan, four ray-finned fishes, and four tetrapods. Phylogenomic analysis of these data yielded, for the first time, significant maximum likelihood support for a traditional gnathostome tree with a split between the Chondrichthyes and remaining (bone) gnathostomes. Also, the sister group relationship between Dipnoi (lungfishes) and Tetrapoda received conclusive support. Previously proposed hypotheses, such as the monophyly of fishes, could be rejected significantly. The divergence time between lungfishes and tetrapods was estimated to 382-388 Ma by the current data set and six calibration points.

  10. Comparative study of methods for DNA preparation from olive oil samples to identify cultivar SSR alleles in commercial oil samples: possible forensic applications.

    Science.gov (United States)

    Breton, Catherine; Claux, Delphine; Metton, Isabelle; Skorski, Gilbert; Bervillé, André

    2004-02-11

    Virgin olive oil is made from diverse cultivars either mixed or single. Those ensure different tastes and typicity, and these may be also enhanced by the region of production of cultivars. The different olive oil labels correspond to their chemical composition and acidity. Labels also may correspond to a protected origin indication, and thus, such oils contain a given composition in cultivars. To verify the main cultivars used at the source of an olive oil sample, our method is based on DNA technology. DNA is present in all olive oil samples and even in refined oil, but the quantity may depend on the oil processing technology and oil conservation conditions. Thus, several supports were used to retain DNA checking different techniques (silica extraction, hydroxyapatite, magnetic beads, and spun column) to prepare DNA from variable amounts of oil. At this stage, it was usable for amplification through PCR technology and especially with the magnetic beads, and further purification processes were checked. Finally, the final method used magnetic beads. DNA is released from beads in a buffer. Once purified, we showed that it did not contain compounds inhibiting PCR amplification using SSR primers. Aliquot dilution fractions of this solution were successfully routinely used through PCR with different SSR primer sets. This enables confident detection of eventual alien alleles in oil samples. First applied to virgin oil samples of known composition, either single cultivars or mixtures of them, the method was verified working on commercial virgin oil samples using bottles bought in supermarkets. Last, we defined a protocol starting from 2 x 40 mL virgin olive oil, and DNA was prepared routinely in about 5 h. It was convenient to genotype together several loci per sample to check whether alleles were in accordance with those of expected cultivars. Thus, forensic applications of our method are expected. However, the method needs further improvement to work on all oil samples.

  11. Ultrastructure and ssrRNA sequencing of Myxidium amazonense n. sp. a myxosporean parasite of Corydoras melini from the Rio Negro river, Amazonas state, Brazil.

    Science.gov (United States)

    Mathews, Patrick D; Silva, Marcia R M; Maia, Antônio A M; Adriano, Edson A

    2015-12-01

    In a survey of myxozoan parasites of ornamental freshwater fish from the Rio Negro river, it was found that seven of 30 (23.3 %) Corydoras melini specimens examined had plasmodia of a new Myxidium species (Myxidium amazonense n. sp.) in the gallbladder. The fish were caught in the Rio Negro river, in the municipality of Santa Isabel do Rio Negro, in the state of Amazonas, Brazil. The plasmodia had a tubular shape, which was organized as a spiral spring with several turns in the gallbladder. The development of the myxospores was asynchronic, with disporic pansporoblasts. Mature myxospores were elongated, with 17.0 ± 0.9 (16.1-17.9) μm in length and 3.7 ± 0.7 (3.0-4.4) μm in width, and lightly arcuate from the valval view, with their bodies tapering slowly until ending in rounded extremities. The valval surface had nine to ten grooves in each valve. The polar capsules, one at either end of the spore, had a length of 5.4 ± 0.5 (4.9-5.9) μm and a width of 3.4 ± 0.6 (2.8-4.0) μm. Ultrastructural analysis showed that the wall of the plasmodia had numerous microvilli-like structures, pinocytotic canals, and cytoplasmic bridges connecting the pansporoblasts to each other and to the ectoplasm zone. Phylogenetic analysis, based on a small subunit ribosomal RNA (ssrRNA), identified the new species as a sister species of Myxidiumceccarelli, the unique South American Myxidium species whose ssrRNA sequence is available in the NCBI database. This study is the first description of Myxidium species in ornamental freshwater fish from Amazon.

  12. Repressive Actions of the State Security Communities Against ≪True Orthodox Church≫ Structuries in the Ukrainian SSR (1944–1953 (continued

    Directory of Open Access Journals (Sweden)

    Vedeneev Dmitrii

    2016-06-01

    Full Text Available In the article on the basis of unknown scientific community documents of the Soviet state security bodies provides an analysis of the objectives and key areas of operational work and repressive actions of the security services communities against «True Orthodox Church» (TOC in the Ukrainian SSR in 1944–1953. The characteristic of agent and operational developments NKGB-MGB-KGB of the USSR against the so-called «catacomb Church», as a form of religious and social protest against aggressive atheistic policy of the Communist authorities, infringement of the rights of believers. The basic forms and methods of intelligence and operational activities of the security organs, aimed at creating informer positions in the environment of the communities of the TOC, making the split in the ranks of the adepts of secret religious sects, the collection of «compromising material» as the basis for the application of harsh repressive measures against the movement of the TOC. The authors pay special attention to the organization and personnel of units of the NKGB-MGB-KGB, engaged, according to the terminology, «the struggle with the Church-sectarian counterrevolution» and «Church-monarchist underground», a leading representative of which was considered in the TOC, particularly active in Chernihiv, Sumy, and Kharkiv oblasts of the Ukrainian SSR and the Donbass, and also in the neighboring regions of the Russian black soil region and the North Caucasus. Given the author’s periodization of the development of the catacomb movement, highlights the historical conditions of its creation and release in the USSR. Through the prism of intelligence documents examines the liturgical aspect of the TOC, its governing structure, forms of secrecy and concealment from the prosecution authorities, the position of the catacomb members in relation to social life and social structure in the USSR.

  13. AcEST(EST sequences of Adiantum capillus-veneris and their annotation) - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us AcEST AcEST(EST sequences of Adiantum capillus-veneris and their annotation) Data detail Dat...a name AcEST(EST sequences of Adiantum capillus-veneris and their annotation) DOI 10.18908/lsdba.nbdc00839-0...01 Description of data contents EST sequence of Adiantum capillus-veneris and its annotation (clone ID, libr...le search URL http://togodb.biosciencedbc.jp/togodb/view/archive_acest#en Data acquisition method Capillary ...ainst UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases) Number of data entries Adiantum capillus-veneris

  14. ClEST cluster :Cl_singleton0908 [ClEST

    Lifescience Database Archive (English)

    Full Text Available Cl_singleton0908 bone marrow stromal cell-derived ubiquitin-like protein Cimex lectularius nuclear gene...TCCTCTTGT fs15049 1 PREDICTED: similar to bone marrow stromal cell-derived ubiquitin-like protein [Tribolium

  15. Mater semper incertus est: who's your mummy?

    Science.gov (United States)

    D'alton-Harrison, Rita

    2014-01-01

    In English law, the legal term for father has been given a broad definition but the definition of mother remains rooted in biology with the Roman law principle mater semper certa est (the mother is always certain) remaining the norm. However, motherhood may be acquired through giving birth to a child, by donation of gametes or by caring and nurturing a child so that the identity of the mother is no longer certain particularly in the case of surrogacy arrangements. While the law in the UK may automatically recognise the parental status of a commissioning father in a traditional surrogacy arrangement, the parental status of the commissioning mother is not automatically recognised in either a traditional or a gestational surrogacy arrangement. Thus the maxim mater est quam gestation demonstrat (meaning the mother is demonstrated by gestation) is also not approached consistently in the legal interpretation of parentage or motherhood in surrogacy as against other assisted reproduction methods. This raises questions about the extent to which motherhood should be affected by the method of reproduction and whether the sociological and philosophical concept of motherhood should, in the case of surrogacy, give rise to a new principle of 'mater semper incertus est' (the mother is uncertain). This article will argue that the time has come to move away from a legal definition of 'mother' that is based on biology to one that recognises the different forms of motherhood. © The Author [2014]. Published by Oxford University Press; all rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Beleza e cirurgia estética

    OpenAIRE

    Vilas Bôas, Luana Michele da Silva

    2012-01-01

    Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas. Programa de Pós-Graduação em Psicologia O objetivo desse estudo foi identificar as representações sociais de homens e mulheres com diferentes formações acadêmicas a respeito de beleza e da cirurgia estética. Trata-se de um estudo de natureza descritiva e comparativa, com delineamento transversal, com a participação de 120 universitários dos cursos de Educação Física, Artes e Exatas, dis...

  17. REDVET está indexada en Scirus

    OpenAIRE

    veterinaria.org

    2009-01-01

    ResumenA veces, la búsqueda en Internet de artículos científicos se convierte en una pesadilla, por lo que es conveniente recurrir a buscadores temáticos y en este aspecto Scirus es una buena opción ya que es uno de los mejores buscadores de temática científica de la Red pues busca en más de 450 millones de páginas web científicas con una búsqueda muy rápida y con resultados sorprendentes.

  18. Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

    Directory of Open Access Journals (Sweden)

    Koh Eunhee

    2007-07-01

    Full Text Available Abstract Background EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information. Results Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1. Conclusion Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.

  19. Signaling pathways in a Citrus EST database

    Directory of Open Access Journals (Sweden)

    Angela Mehta

    2007-01-01

    Full Text Available Citrus spp. are economically important crops, which in Brazil are grown mainly in the State of São Paulo. Citrus cultures are attacked by several pathogens, causing severe yield losses. In order to better understand this culture, the Millenium Project (IAC Cordeirópolis was launched in order to sequence Citrus ESTs (expressed sequence tags from different tissues, including leaf, bark, fruit, root and flower. Plants were submitted to biotic and abiotic stresses and investigated under different development stages (adult vs. juvenile. Several cDNA libraries were constructed and the sequences obtained formed the Citrus ESTs database with almost 200,000 sequences. Searches were performed in the Citrus database to investigate the presence of different signaling pathway components. Several of the genes involved in the signaling of sugar, calcium, cytokinin, plant hormones, inositol phosphate, MAPKinase and COP9 were found in the citrus genome and are discussed in this paper. The results obtained may indicate that similar mechanisms described in other plants, such as Arabidopsis, occur in citrus. Further experimental studies must be conducted in order to understand the different signaling pathways present.

  20. Sequencing and Analysis of Common Bean ESTs. Building a Foundation for Functional Genomics1[w

    Science.gov (United States)

    Ramírez, Mario; Graham, Michelle A.; Blanco-López, Lourdes; Silvente, Sonia; Medrano-Soto, Arturo; Blair, Matthew W.; Hernández, Georgina; Vance, Carroll P.; Lara, Miguel

    2005-01-01

    Although common bean (Phaseolus vulgaris) is the most important grain legume in the developing world for human consumption, few genomic resources exist for this species. The objectives of this research were to develop expressed sequence tag (EST) resources for common bean and assess nodule gene expression through high-density macroarrays. We sequenced a total of 21,026 ESTs derived from 5 different cDNA libraries, including nitrogen-fixing root nodules, phosphorus-deficient roots, developing pods, and leaves of the Mesoamerican genotype, Negro Jamapa 81. The fifth source of ESTs was a leaf cDNA library derived from the Andean genotype, G19833. Of the total high-quality sequences, 5,703 ESTs were classified as singletons, while 10,078 were assembled into 2,226 contigs producing a nonredundant set of 7,969 different transcripts. Sequences were grouped according to 4 main categories, metabolism (34%), cell cycle and plant development (11%), interaction with the environment (19%), and unknown function (36%), and further subdivided into 15 subcategories. Comparisons to other legume EST projects suggest that an entirely different repertoire of genes is expressed in common bean nodules. Phaseolus-specific contigs, gene families, and single nucleotide polymorphisms were also identified from the EST collection. Functional aspects of individual bean organs were reflected by the 20 contigs from each library composed of the most redundant ESTs. The abundance of transcripts corresponding to selected contigs was evaluated by RNA blots to determine whether gene expression determined by laboratory methods correlated with in silico expression. Evaluation of root nodule gene expression by macroarrays and RNA blots showed that genes related to nitrogen and carbon metabolism are integrated for ureide production. Resources developed in this project provide genetic and genomic tools for an international consortium devoted to bean improvement. PMID:15824284

  1. Update of the Diatom EST Database: a new tool for digital transcriptomics

    Science.gov (United States)

    Maheswari, Uma; Mock, Thomas; Armbrust, E. Virginia; Bowler, Chris

    2009-01-01

    The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3. PMID:19029140

  2. Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene Pl19in confection sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Zhang, Z W; Ma, G J; Zhao, J; Markell, S G; Qi, L L

    2017-01-01

    A new downy mildew resistance gene, Pl 19 , was identified from wild Helianthus annuus accession PI 435414, introduced to confection sunflower, and genetically mapped to linkage group 4 of the sunflower genome. Wild Helianthus annuus accession PI 435414 exhibited resistance to downy mildew, which is one of the most destructive diseases to sunflower production globally. Evaluation of the 140 BC 1 F 2:3 families derived from the cross of CMS CONFSCLB1 and PI 435414 against Plasmopara halstedii race 734 revealed that a single dominant gene controls downy mildew resistance in the population. Bulked segregant analysis conducted in the BC 1 F 2 population with 860 simple sequence repeat (SSR) markers indicated that the resistance derived from wild H. annuus was associated with SSR markers located on linkage group (LG) 4 of the sunflower genome. To map and tag this resistance locus, designated Pl 19 , 140 BC 1 F 2 individuals were used to construct a linkage map of the gene region. Two SSR markers, ORS963 and HT298, were linked to Pl 19 within a distance of 4.7 cM. After screening 27 additional single nucleotide polymorphism (SNP) markers previously mapped to this region, two flanking SNP markers, NSA_003564 and NSA_006089, were identified as surrounding the Pl 19 gene at a distance of 0.6 cM from each side. Genetic analysis indicated that Pl 19 is different from Pl 17 , which had previously been mapped to LG4, but is closely linked to Pl 17 . This new gene is highly effective against the most predominant and virulent races of P. halstedii currently identified in North America and is the first downy mildew resistance gene that has been transferred to confection sunflower. The selected resistant germplasm derived from homozygous BC 2 F 3 progeny provides a novel gene for use in confection sunflower breeding programs.

  3. Fractional Derivative as Fractional Power of Derivative

    OpenAIRE

    Tarasov, Vasily E.

    2007-01-01

    Definitions of fractional derivatives as fractional powers of derivative operators are suggested. The Taylor series and Fourier series are used to define fractional power of self-adjoint derivative operator. The Fourier integrals and Weyl quantization procedure are applied to derive the definition of fractional derivative operator. Fractional generalization of concept of stability is considered.

  4. Estesícoro y Tartessos

    OpenAIRE

    Cruz Andreotti, Gonzalo

    1991-01-01

    La escueta mención al río Tartessos (dentro del mito Heracles-Gerión) por parte de Estesícoro puede analizarse, en primer lugar, desde un punto de vista ideológico: constituiría un tipo de legitimación de un proceso colonizador a través de la figura del héroe civilizador por excelencia. Pero, y en segundo lugar, se podría lanzar la hipótesis de que sería también el eco del desarrollo de la confluencia en el sur peninsular de personajes greco-indígenas alrededor de lugares de culto compartidos...

  5. Marketing! Onde está o Paradigma?

    Directory of Open Access Journals (Sweden)

    Deosir Flávio Lobo de Castro Júnior

    2015-09-01

    Full Text Available O debate quantitativo-qualitativo, não é uma discussão recente. O objetivo desse trabalho, portanto, é verificar por meio do conceito de paradigma, novas perspectivas de compreender as pesquisas acadêmicas em marketing, a evolução do pensamento de marketing e as metodologias utilizadas nos estudos da qualidade de serviço. Sem a pretensão de esgotar este assunto e apresentar uma conclusão final, são apresentadas pesquisas que apontam para a necessidade e a importância da pesquisa qualitativa, uma vez que auxilia ao pesquisador uma melhor compreensão da natureza complexa do mundo social em que vivemos. Segundo Santana e Gomes (2007, após análise da discussão de Hegel e Kant, concluem que a razão e a própria epistemologia são construções históricas e evoluem a partir de contradições. O presente artigo está dividido em cinco momentos. Na primeira parte apresenta-se além da introdução a constituição dos objetivos desse ensaio teórico. Na segunda parte apresenta-se uma breve discussão a respeito do conceito de paradigma e o marketing. Na terceira parte apresenta-se uma retrospectiva histórica do marketing e sua evolução de suas escolas a partir dos estudos de Miranda e Arruda (2004. Na quarta parte, são apresentadas as metodologias dos estudos sobre qualidade de serviços e finalmente na quinta parte apresenta-se as considerações finais.

  6. High-density mapping of the major FHB resistance gene Fhb7 derived from Thinopyrum ponticum and its pyramiding with Fhb1 by marker-assisted selection.

    Science.gov (United States)

    Guo, Jun; Zhang, Xiuli; Hou, Yanlin; Cai, Jinjin; Shen, Xiaorong; Zhou, Tingting; Xu, Huihui; Ohm, Herbert W; Wang, Hongwei; Li, Anfei; Han, Fangpu; Wang, Honggang; Kong, Lingrang

    2015-11-01

    Wheat lines with shortened Th. ponticum chromatin carrying Fhb7 and molecular markers linked to Fhb7 will accelerate the transfer of Fhb7 to breeding lines and provide an important resource for future map-based cloning of this gene. Fusarium head blight is a major wheat disease globally. A major FHB resistance gene, designated as Fhb7, derived from Thinopyrum ponticum, was earlier transferred to common wheat, but was not used in wheat breeding due to linkage drag. The aims of this study were to (1) saturate this FHB resistance gene region; (2) develop and characterize secondary translocation lines with shortened Thinopyrum segments carrying Fhb7 using ph1b; (3) pyramid Fhb7 and Fhb1 by marker-assisted selection. Fhb7 was mapped in a 1.7 cM interval that was flanked by molecular markers XsdauK66 and Xcfa2240 with SSR, diversity arrays technology, EST-derived and conserved markers. KS24-2 carrying Fhb7 was analyzed with molecular markers and genomic in situ hybridization, confirming it was a 7DS.7el2L Robertsonian translocation. To reduce the Thinopyrum chromatin segments carrying Fhb7, a BC1F2 population (Chinese Spring ph1bph1b*2/KS24-2) was developed and genotyped with the markers linked to Fhb7. Two new translocation lines (SDAU1881 and SDAU1886) carrying Fhb7 on shortened alien segments (approximately 16.1 and 17.3% of the translocation chromosome, respectively) were developed. Furthermore, four wheat lines (SDAU1902, SDAU1903, SDAU1904, and SDAU1906) with the pyramided markers flanking Fhb1 and Fhb7 were developed and the FHB responses indicated lines with mean NDS ranging from 1.3 to 1.6 had successfully combined Fhb7 and Fhb1. Three new molecular markers associated with Fhb7 were identified and validated in 35 common wheat varieties. The translocation lines with shortened alien segments carrying Fhb7 (and Fhb1) and the markers closely linked to Fhb7 will be useful for improving wheat scab resistance.

  7. Evaluation of a novel real-time PCR test based on the ssrA gene for the identification of group B streptococci in vaginal swabs.

    LENUS (Irish Health Repository)

    Wernecke, Martina

    2009-01-01

    BACKGROUND: Despite the implementation of prevention guidelines, early-onset group B streptococci (GBS) disease remains a cause of neonatal morbidity and mortality worldwide. Strategies to identify women who are at risk of transmitting GBS to their infant and the administration of intrapartum antibiotics have greatly reduced the incidence of neonatal GBS disease. However, there is a requirement for a rapid diagnostic test for GBS that can be carried out in a labour ward setting especially for women whose GBS colonisation status is unknown at the time of delivery. We report the design and evaluation of a real-time PCR test (RiboSEQ GBS test) for the identification of GBS in vaginal swabs from pregnant women. METHODS: The qualitative real-time PCR RiboSEQ GBS test was designed based on the bacterial ssrA gene and incorporates a competitive internal standard control. The analytical sensitivity of the test was established using crude lysate extracted from serial dilutions of overnight GBS culture using the IDI Lysis kit. Specificity studies were performed using DNA prepared from a panel of GBS strains, related streptococci and other species found in the genital tract environment. The RiboSEQ GBS test was evaluated on 159 vaginal swabs from pregnant women and compared with the GeneOhm StrepB Assay and culture for the identification of GBS. RESULTS: The RiboSEQ GBS test is specific and has an analytical sensitivity of 1-10 cell equivalents. The RiboSEQ GBS test was 96.4% sensitive and 95.8% specific compared to "gold standard" culture for the identification of GBS in vaginal swabs from pregnant women. In this study, the RiboSEQ GBS test performed slightly better than the commercial BD GeneOhm StrepB Assay which gave a sensitivity of 94.6% and a specificity of 89.6% compared to culture. CONCLUSION: The RiboSEQ GBS test is a valuable method for the rapid, sensitive and specific detection of GBS in pregnant women. This study also validates the ssrA gene as a suitable and

  8. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using insertion-deletion (InDel) and simple sequence repeat (SSR) markers.

    Science.gov (United States)

    Wu, Kun; Yang, Minmin; Liu, Hongyan; Tao, Ye; Mei, Ju; Zhao, Yingzhong

    2014-03-19

    Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design. Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines. This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic

  9. Estudios de estética medioeval. La estética de la luz

    Directory of Open Access Journals (Sweden)

    Anónimo Anónimo

    1959-10-01

    Full Text Available Reproducción parcial del capítulo I, Libro 1 V -El Siglo XIII - de la obra "Estudios de Estética Medioeval" de Edgar De Bruyne. Biblioteca Hispánica de Filosofía. Editorial Credo. Madrid, 1959, para la versión castellana.

  10. On $n$-derivations

    Directory of Open Access Journals (Sweden)

    Mohammad Hossein Sattari

    2016-06-01

    Full Text Available In this article, the notion of $n-$derivation is introduced for all integers $ngeq 2$. Although all derivations are $n-$derivations,  in general these notions are not equivalent. Some properties of ordinary derivations are  investigated for $n-$derivations. Also, we show that under certain mild condition  $n-$derivations are derivations.

  11. Le discours fantastique est-il rationnel ?

    Directory of Open Access Journals (Sweden)

    Anouck Linck

    2011-01-01

    Full Text Available L’importance de la contradiction dans la composition du discours fantastique a été signalée par la critique et le carré sémiotique de Greimas assigne au fantastique une place de choix – non reconnue encore à ce jour. Le rôle structurant de la contradiction est confirmé par notre méthode d’investigation, qui envisage l’acte de lecture sur le mode de l’élaboration d’un acte démonstratif. Cette méthode, appliquée à trois textes emblématiques du discours fantastique, aboutit en effet à l’élaboration de théories inconsistantes (contenant une contradiction du type p  p mais non triviales, au sein desquelles le principe aristotélicien de non-contradiction n’est pas valable. Nous touchons là aux limites de la raison classique, d’où notre questionnement : le discours fantastique est-il rationnel ? Plutôt que de répondre par la négative, nous montrons que la non-absurdité du discours fantastique invite au dépassement des limites de la raison classique et à une extension de cette dernière, car il se place sous l’égide d’une logique formelle moins contraignante et plus générale que la logique classique : la logique paraconsistante de Newton da Costa.La crítica ha señalado la importancia de la contradicción en lo que se refiere a la composición de la narrativa fantástica y ésta tiene su lugar asignado dentro del cuadrado semiótico de Greimas – un lugar hasta ahora no identificado como tal. Al considerar el acto de lectura como elaboración un acto demostrativo, nuestro método de investigación resalta ese papel fundamental de la contradicción. Dicho método, aplicado a tres textos emblemáticos de la narrativa fantástica, desemboca en efecto en la elaboración de teorías inconsistentes (que contienen una contradicción de tipo p  p pero no triviales, dentro de las cuales el principio aristotélico de no-contradicción no es válido. Con esto llegamos al límite de la racionalidad

  12. APOSENTADORIA: como professores vivenciam este momento?

    Directory of Open Access Journals (Sweden)

    Cristiane Nervis Conrado Machado

    2017-05-01

    Full Text Available O presente artigo buscou compreender as implicações que a aposentadoria causa na vida de professores, levando em conta o significado que a aposentadoria representa à estes, considerando os pontos de maior mudança após a aposentadoria, bem como os aspectos positivos e negativos causados pela aposentadoria na percepção dos sujeitos da pesquisa. Para tanto, foi realizada uma pesquisa qualitativa caracterizada como exploratória e descritiva com professores aposentados por mais de dois anos, com idade entre 58 e 66 anos, através de entrevistas individuais, com roteiros semiestruturados. A análise dos dados foi por meio da análise de conteúdo de Bardin (2011. Entre os principais resultados, destaca-se o significado de “liberdade” que a aposentadoria representa, a rotina como maior mudança e flexibilidade de horários dentre os pontos positivos e a falta dos alunos como aspecto negativo, contudo, pode-se perceber que a aposentadoria possibilitou e contribuiu para que os professores pudessem desfrutar de momentos de lazer, dedicando cuidado à família e realizando seus anseios e vontades.

  13. Combined use of a new SNP-based assay and multilocus SSR markers to assess genetic diversity of Xylella fastidiosa subsp. pauca infecting citrus and coffee plants.

    Science.gov (United States)

    Montes-Borrego, Miguel; Lopes, Joao R S; Jiménez-Díaz, Rafael M; Landa, Blanca B

    2015-03-01

    Two haplotypes of Xylella fastidiosa subsp. pauca (Xfp) that correlated with their host of origin were identified in a collection of 90 isolates infecting citrus and coffee plants in Brazil, based on a single-nucleotide polymorphism in the gyrB sequence. A new single-nucleotide primer extension (SNuPE) protocol was designed for rapid identification of Xfp according to the host source. The protocol proved to be robust for the prediction of the Xfp host source in blind tests using DNA from cultures of the bacterium, infected plants, and insect vectors allowed to feed on Xfp-infected citrus plants. AMOVA and STRUCTURE analyses of microsatellite data separated most Xfp populations on the basis of their host source, indicating that they were genetically distinct. The combined use of the SNaPshot protocol and three previously developed multilocus SSR markers showed that two haplotypes and distinct isolates of Xfp infect citrus and coffee in Brazil and that multiple, genetically different isolates can be present in a single orchard or infect a single tree. This combined approach will be very useful in studies of the epidemiology of Xfp-induced diseases, host specificity of bacterial genotypes, the occurrence of Xfp host jumping, vector feeding habits, etc., in economically important cultivated plants or weed host reservoirs of Xfp in Brazil and elsewhere. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

  14. Genetic variation and relationships among Ulex (Fabaceae) species in southern Spain and northern Morocco assessed by chloroplast microsatellite (cpSSR) markers.

    Science.gov (United States)

    Cubas, Paloma; Pardo, Cristina; Tahiri, Hikmat

    2005-12-01

    Genetic variation in 27 populations of Ulex species from southern Spain and northern Morocco (Betic-Rif arc) was assessed using 11 chloroplast microsatellite (cpSSR) markers, which revealed 47 different haplotypes. These nonrecombinant, haploid markers allow measurement of genetic variation in closely related species of Ulex where molecular phylogenetic analyses have not provided a clear view of interspecific relationships. Discriminant analysis indicates that the haplotypes are useful to differentiate among species, and analysis of molecular variance (AMOVA) shows high levels of differentiation among populations. The minimum spanning tree (MST), that represents the connections between the haplotypes, suggests that the eastern Rifean U. africanus haplotypes are more genetically related than those from southern Spain. The latter may have lost genetic diversity while colonizing new habitats, eventually differentiating into U. baeticus and U. scaber. Hybridization between these populations, followed by polyploidization, may have originated the tetraploids (U. congestus and U. borgiae) that colonized new habitats associated with acidic rocks. Separate groupings of U. scaber populations may indicate multiple origins from different stocks. Diversification in this group of Ulex species could be related to the opening of the Alboran Sea by Middle Miocene, when the populations from Morocco and Spain became isolated from each other.

  15. SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

    Science.gov (United States)

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

  16. Kohvik-restoran C'est La Vie = Cafe-restaurant C'est La Vie

    Index Scriptorium Estoniae

    2008-01-01

    Kohvik-restorani C'est La Vie (Suur-Karja 5, Tallinn) sisekujundusest. Sisearhitekt: Maile Grünberg, kes kavandas ka valdavalt mööbli. Laevalgusti disainis Tõnis Vellama. Skulptuuride (koopiad) autor on keraamik Ülle Rajasalu. Maile Grünbergist, tema viimased tööd. Keldrikorruse ja I korruse plaan, 8 värv. vaadet, foto M. Grünbergist

  17. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

    Science.gov (United States)

    Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

    2008-04-10

    Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  18. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

    Directory of Open Access Journals (Sweden)

    Pardinas Jose R

    2008-04-01

    Full Text Available Abstract Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  19. A milestone in the doubled haploid pathway of cassava: a milestone in the doubled haploid pathway of cassava (Manihot esculenta Crantz): cellular and molecular assessment of anther-derived structures.

    Science.gov (United States)

    Perera, P I P; Ordoñez, C A; Lopez-Lavalle, L A Becerra; Dedicova, B

    2014-01-01

    This study was aimed at inducing androgenesis in cultured anthers of cassava (Manihot esculenta Crantz) to develop a protocol for the production of doubled haploids. Microspore reprogramming was induced in cassava by cold or heat stress of anthers. Since the anthers contain both haploid microspores and diploid somatic cells, it was essential to verify the origin of anther-derived calli. The origin of anther-derived calli was assessed by morphological screening followed by histological analysis and flow cytometry (FCM). Additionally, simple sequence repeat (SSR) and amplified fragmented length polymorphism (AFLP) assays were used for the molecular identification of the microspore-derived calli. The study clearly demonstrated the feasibility of producing microspore-derived calli using heat- or cold-pretreated anthers. Histological studies revealed reprogramming of the developmental pathway of microspores by symmetrical division of the nucleus. Flow cytometry analysis revealed different ploidy level cell types including haploids, which confirmed their origin from the microspores. The SSR and AFLP marker assays independently confirmed the histological and FCM results of a haploid origin of the calli at the DNA level. The presence of multicellular microspores in the in vitro system indicated a switch of developmental program, which constitutes a crucial step in the design of protocols for the regeneration of microspore-derived embryos and plants. This is the first detailed report of calli, embryos, and abnormal shoots originated from the haploid cells in cassava, leading to the development of a protocol for the production of doubled haploid plants in cassava.

  20. Algunas observaciones sobre el "control del estímulo"

    OpenAIRE

    Ribes Iñesta,Emilio

    2011-01-01

    Se reflexiona sobre el concepto de control del estímulo en la teoría del condicionamiento operante y, en especial, sobre el concepto de estímulo discriminativo. Para ello se señalan los problemas lógicos y definicionales que reviste el uso del concepto de estímulo en general y el de estímulo discriminativo en particular. Se reseñan diversos experimentos del autor para mostrar la incapacidad del concepto de estímulo discriminativo para dar cuenta de una serie de datos que muestran las insufici...

  1. The Alveolate Perkinsus marinus: Biological Insights from EST Gene Discovery

    Directory of Open Access Journals (Sweden)

    El-Sayed Najib M

    2010-04-01

    Full Text Available Abstract Background Perkinsus marinus, a protozoan parasite of the eastern oyster Crassostrea virginica, has devastated natural and farmed oyster populations along the Atlantic and Gulf coasts of the United States. It is classified as a member of the Perkinsozoa, a recently established phylum considered close to the ancestor of ciliates, dinoflagellates, and apicomplexans, and a key taxon for understanding unique adaptations (e.g. parasitism within the Alveolata. Despite intense parasite pressure, no disease-resistant oysters have been identified and no effective therapies have been developed to date. Results To gain insight into the biological basis of the parasite's virulence and pathogenesis mechanisms, and to identify genes encoding potential targets for intervention, we generated >31,000 5' expressed sequence tags (ESTs derived from four trophozoite libraries generated from two P. marinus strains. Trimming and clustering of the sequence tags yielded 7,863 unique sequences, some of which carry a spliced leader. Similarity searches revealed that 55% of these had hits in protein sequence databases, of which 1,729 had their best hit with proteins from the chromalveolates (E-value ≤ 1e-5. Some sequences are similar to those proven to be targets for effective intervention in other protozoan parasites, and include not only proteases, antioxidant enzymes, and heat shock proteins, but also those associated with relict plastids, such as acetyl-CoA carboxylase and methyl erythrithol phosphate pathway components, and those involved in glycan assembly, protein folding/secretion, and parasite-host interactions. Conclusions Our transcriptome analysis of P. marinus, the first for any member of the Perkinsozoa, contributes new insight into its biology and taxonomic position. It provides a very informative, albeit preliminary, glimpse into the expression of genes encoding functionally relevant proteins as potential targets for chemotherapy, and evidence

  2. Efficient clustering of large EST data sets on parallel computers.

    Science.gov (United States)

    Kalyanaraman, Anantharaman; Aluru, Srinivas; Kothari, Suresh; Brendel, Volker

    2003-06-01

    Clustering expressed sequence tags (ESTs) is a powerful strategy for gene identification, gene expression studies and identifying important genetic variations such as single nucleotide polymorphisms. To enable fast clustering of large-scale EST data, we developed PaCE (for Parallel Clustering of ESTs), a software program for EST clustering on parallel computers. In this paper, we report on the design and development of PaCE and its evaluation using Arabidopsis ESTs. The novel features of our approach include: (i) design of memory efficient algorithms to reduce the memory required to linear in the size of the input, (ii) a combination of algorithmic techniques to reduce the computational work without sacrificing the quality of clustering, and (iii) use of parallel processing to reduce run-time and facilitate clustering of larger data sets. Using a combination of these techniques, we report the clustering of 168 200 Arabidopsis ESTs in 15 min on an IBM xSeries cluster with 30 dual-processor nodes. We also clustered 327 632 rat ESTs in 47 min and 420 694 Triticum aestivum ESTs in 3 h and 15 min. We demonstrate the quality of our software using benchmark Arabidopsis EST data, and by comparing it with CAP3, a software widely used for EST assembly. Our software allows clustering of much larger EST data sets than is possible with current software. Because of its speed, it also facilitates multiple runs with different parameters, providing biologists a tool to better analyze EST sequence data. Using PaCE, we clustered EST data from 23 plant species and the results are available at the PlantGDB website.

  3. SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomes.

    Science.gov (United States)

    Khanal, Sameer; Kim, Changsoo; Auckland, Susan A; Rainville, Lisa K; Adhikari, Jeevan; Schwartz, Brian M; Paterson, Andrew H

    2017-04-01

    We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F1 progeny of a cross between the two parents. The T89 map is based on 291 loci on 34 cosegregating groups (CGs), with an average marker spacing of 12.5 cM. The T574 map is based on 125 loci on 14 CGs, with an average marker spacing of 10.7 cM. Six T89 and one T574 CG(s) deviated from disomic inheritance. Furthermore, marker segregation data and linkage phase analysis revealed partial residual polysomic inheritance in T89, suggesting that common bermudagrass is undergoing diploidization following whole genome duplication (WGD). Twenty-six T89 CGs were coalesced into 9 homo(eo)logous linkage groups (LGs), while 12 T574 CGs were assembled into 9 LGs, both putatively representing the basic chromosome complement (x = 9) of the species. Eight T89 and two T574 CGs remain unassigned. The marker composition of bermudagrass ancestral chromosomes was inferred by aligning T89 and T574 homologs, and used in comparisons to sorghum and rice genome sequences based on 108 and 91 significant blast hits, respectively. Two nested chromosome fusions (NCFs) shared by two other chloridoids (i.e., zoysiagrass and finger millet) and at least three independent translocation events were evident during chromosome number reduction from 14 in the polyploid common ancestor of Poaceae to 9 in Cynodon.

  4. Sequencing and de novo assembly of visceral mass transcriptome of the critically endangered land snail Satsuma myomphala: Annotation and SSR discovery.

    Science.gov (United States)

    Kang, Se Won; Patnaik, Bharat Bhusan; Hwang, Hee-Ju; Park, So Young; Chung, Jong Min; Song, Dae Kwon; Patnaik, Hongray Howrelia; Lee, Jae Bong; Kim, Changmu; Kim, Soonok; Park, Hong Seog; Park, Seung-Hwan; Park, Young-Su; Han, Yeon Soo; Lee, Jun Sang; Lee, Yong Seok

    2017-03-01

    Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis. We identified 103,774 unigenes of which 37,959, 12,890, and 17,699 were annotated in the PANM (Protostome DB), Unigene, and COG (Clusters of Orthologous Groups) databases, respectively. In addition, 14,451 unigenes were predicted under Gene Ontology functional categories, with 4581 assigned to a single category. Furthermore, 3369 sequences with 646 having Enzyme Commission (EC) numbers were mapped to 122 pathways in the Kyoto Encyclopedia of Genes and Genomes Pathway database. The prominent protein domains included the Zinc finger (C2H2-like), Reverse Transcriptase, Thioredoxin-like fold, and RNA recognition motif domain. Many unigenes with homology to immunity, defense, and reproduction-related genes were screened in the transcriptome. We also detected 3120 putative simple sequence repeats (SSRs) encompassing dinucleotide to hexanucleotide repeat motifs from >1kb unigene sequences. A list of PCR primers of SSR loci have been identified to study the genetic polymorphisms. The transcriptome data represents a valuable resource for further investigations on the species genome structure and biology. The unigenes information and microsatellites would provide an indispensable tool for conservation of the species in natural and adaptive environments. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L. Germplasm for Early Seedling Vigor (ESV Using Trait Linked SSR Markers.

    Directory of Open Access Journals (Sweden)

    Annamalai Anandan

    Full Text Available Early seedling vigor (ESV is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS. It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM and mixed linear model (MLM approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.

  6. SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers.

    Directory of Open Access Journals (Sweden)

    Hilal Betul Kaya

    Full Text Available BACKGROUND: The olive tree (Olea europaea L. is a diploid (2n = 2x = 46 outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP discovery in olive. The objectives of this study were (1 to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2 to characterize 96 olive genotypes originating from different regions of Turkey. METHODOLOGY/PRINCIPAL FINDINGS: Next-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP and simple sequence repeats (SSR markers. CONCLUSIONS/SIGNIFICANCE: This study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL analysis, association mapping and map-based gene cloning in the olive. High levels

  7. Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σE-regulated SPI-2 gene expression

    Directory of Open Access Journals (Sweden)

    Jie eLi

    2015-02-01

    Full Text Available The extracytoplasmic functioning sigma factor σE is known to play an essential role for Salmonella enterica serovar Typhimurium to survive and proliferate in macrophages and mice. However, its regulatory network is not well characterized, especially during infection. Here we used microarray to identify genes regulated by σE in Salmonella grown in three conditions: a nutrient-rich condition and two others that mimic early and late intracellular infection. We found that in each condition σE regulated different sets of genes, and notably, several global regulators. When comparing nutrient-rich and infection-like conditions, large changes were observed in the expression of genes involved in Salmonella pathogenesis island (SPI-1 type-three secretion system (TTSS, SPI-2 TTSS, protein synthesis, and stress responses. In total, the expression of 58% of Salmonella genes was affected by σE in at least one of the three conditions. An important finding is that σE up-regulates SPI-2 genes, which are essential for Salmonella intracellular survival, by up-regulating SPI-2 activator ssrB expression at the early stage of infection and down-regulating SPI-2 repressor hns expression at a later stage. Moreover, σE is capable of countering the silencing of H-NS, releasing the expression of SPI-2 genes. This connection between E and SPI-2 genes, combined with the global regulatory effect of σE, may account for the lethality of rpoE-deficient Salmonella in murine infection.

  8. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

    Directory of Open Access Journals (Sweden)

    Huihui Yu

    Full Text Available Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs and simple sequence repeats (SSRs, thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs from low-coverage sequences of a recombinant inbred line (RIL population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.

  9. Le développement durable : est-il possible? est-il mesurable?

    Directory of Open Access Journals (Sweden)

    Belmokaddem MOSTEFA

    2011-04-01

    Full Text Available A la première question, nous répondrons bien sûr, par l’affirmative puisque tous les pays sont engagés dans une nouvelle approche du développement qui ne consiste pas seulement à produire le plus de biens et au moindre coût, afin de vendre beaucoup et réaliser de grands profits. C’était la vision en vigueur dans toutes les techniques de gestion mais on s’est rendu compte que cette production, supposée au moindre coût, était en fait, souvent d’un coût exorbitant, relativement aux dégâts occasionnés dans l’environnement et dans les nuisances occasionnées à la santé de l’homme et à sa tranquillité. Il est temps d’inclure d’autres variables dans le calcul du prix de revient tout en revoyant certaines techniques de production trop salissantes, dangereuses ou grosses consommatrices d’énergie. Nous répondrons aussi par la négative quand on pense qu’au niveau micro économique, les comportements sont édictés par les satisfactions immédiates et les maximisations des profits. Ces comportements qui ne s’intéressent qu’aux résultats à court terme, ne s’intègrent pas facilement dans les plans de développement visant les équilibres macro économiques à long terme.A la deuxième question, nous dirons qu’il y a effectivement des indicateurs pour tester les niveaux de qualité dans l’éducation, la santé, les ressources naturelles... et les gains tirés au niveau social mais les calculs économiques qui déterminent la rentabilité des projets, les profits espérés, les risques financiers encourus ne sont pas toujours en rapport avec les efforts pour réaliser le développement durable qui, eux dépassent la simple notion d’efficacité et de satisfaction. Quand on pense aux générations futures, ce n’est pas seulement en termes de durée dans le temps mais aussi dans la manière d’apprécier les gains espérés.Notre recherche repose sur ces questions qui minent bien des efforts alors qu

  10. Analysis of Expressed Sequence Tags (EST) in Date Palm.

    Science.gov (United States)

    Al-Faifi, Sulieman A; Migdadi, Hussein M; Algamdi, Salem S; Khan, Mohammad Altaf; Al-Obeed, Rashid S; Ammar, Megahed H; Jakse, Jerenj

    2017-01-01

    Expressed sequence tags (EST) were generated from a normalized cDNA library of the date palm Sukkari cv. to understand the high-quality and better field performance of this well-known commercial cultivar. A total of 6943 high-quality ESTs were generated, out of them 6671 are submitted to the GenBank dbEST (LIBEST_028537). The generated ESTs were assembled into 6362 unigenes, consisting of 494 (14.4%) contigs and 5868 (84.53%) singletons. The functional annotation shows that the majority of the ESTs are associated with binding (44%), catalytic (40%), transporter (5%), and structural molecular (5%) activities. The blastx results show that 73% of unigenes are significantly similar to known plant genes and 27% are novel. The latter could be of particular interest in date palm genetic studies. Further analysis shows that some ESTs are categorized as stress/defense- and fruit development-related genes. These newly generated ESTs could significantly enhance date palm EST databases in the public domain and are available to scientists and researchers across the globe. This knowledge will facilitate the discovery of candidate genes that govern important developmental and agronomical traits in date palm. It will provide important resources for developing genetic tools, comparative genomics, and genome evolution among date palm cultivars.

  11. EST data - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...st.zip File URL: ftp://ftp.biosciencedbc.jp/archive/red/LATEST/red_est.zip File size: 629 KB Simple search U...ase Database Description Download License Update History of This Database Site Policy | Contact Us EST data - RED | LSDB Archive ...

  12. Annotation and BAC/PAC localization of nonredundant ESTs from ...

    Indian Academy of Sciences (India)

    Unknown

    2002-04-25

    Apr 25, 2002 ... Keywords. ESTs; annotation; Oryza sativa; indica rice; cDNA libraries; rice genome; drought tolerance. *For correspondence. ... Here we describe the annotation of this nonredundant set of ESTs generated from ...... Plant Physiol. 1283, 896–910. Goff S. A., Ricke D., Lan T., Presting G., Wang R., Dunn M.

  13. Interest rate derivatives

    DEFF Research Database (Denmark)

    Svenstrup, Mikkel

    This Ph.D. thesis consists of four self-contained essays on valuation of interest rate derivatives. In particular derivatives related to management of interest rate risk care are considered.......This Ph.D. thesis consists of four self-contained essays on valuation of interest rate derivatives. In particular derivatives related to management of interest rate risk care are considered....

  14. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas

    Directory of Open Access Journals (Sweden)

    Huang Lifei

    2010-12-01

    Full Text Available Abstract Background The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweetpotato root for gene discovery and molecular marker development. Results In this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02% genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG indicated that 17,598 (31.14% unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests. Conclusion This study generated a substantial fraction of sweetpotato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers

  15. Generalized Riemann derivative

    Directory of Open Access Journals (Sweden)

    Sorin Radulescu

    2013-03-01

    Full Text Available Initiated by Marshall Ash in 1966, the study of generalized Riemann derivative draw significant attention of the mathematical community and numerous studies where carried out since then. One of the major areas that benefits from these developments is the numerical analysis, as the use of generalized Riemann derivatives leads to solving a wider class of problems that are not solvable with the classical tools. This article studies the generalized Riemann derivative and its properties and establishes relationships between Riemann generalized derivative and the classical one. The existence of classical derivative implies the existence of the Riemann generalized derivative, and we study conditions necessary for the generalized Riemann derivative to imply the existence of the classical derivative. Furthermore, we provide conditions on the generalized Riemann derivative that are sufficient for the existence of the classical derivative.

  16. Comparative mapping in the Fagaceae and beyond with EST-SSRs

    Directory of Open Access Journals (Sweden)

    Bodénès Catherine

    2012-08-01

    Full Text Available Abstract Background Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. Results We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs and located 397 markers (EST-SSRs and genomic SSRs on the 12 oak chromosomes (2n = 2x = 24 on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak and Quercus petraea (sessile oak. Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. Conclusions This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping

  17. Comparative mapping in the Fagaceae and beyond with EST-SSRs

    Science.gov (United States)

    2012-01-01

    Background Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. Results We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. Conclusions This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the

  18. Synthetic Bioluminescent Coelenterazine Derivatives.

    Science.gov (United States)

    Nishihara, Ryo; Citterio, Daniel; Suzuki, Koji

    2016-01-01

    The development of coelenterazine (CTZ) derivatives resulting in superior optical characteristics is an efficient method to extend the range of its possible applications. Here, we describe the synthesis of three C-6 substituted CTZ derivatives retaining the recognition by Renilla luciferase (RLuc) and its derivatives. The novel derivatives are useful as bright blue-shifted CTZ derivatives, which can be used as an alternative to hitherto reported compound DeepBlueC™.

  19. Esferas estáticas en relatividad general

    Directory of Open Access Journals (Sweden)

    J. Ospino

    2007-01-01

    Full Text Available Recientemente K. Lake ha presentado un algoritmo que permit e obtener todas las soluciones estáticas de las ecuaciones de Einstein, para el caso de un fluido perfecto con simetría esférica, a partir de u na sola función dada. Este algoritmo se extiende al caso de un fluido localmen te anisótropo. Como era de esperar, este nuevo formalismo requiere del cono cimiento de dos funciones en lugar de una. Para ilustrar el método se dedu cen de nuevo algunas soluciones conocidas.

  20. Estágio curricular na empresa Consulfrio

    OpenAIRE

    Mateus, Filipe Pêgo

    2015-01-01

    Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica Este relatório apresenta-se como Trabalho Final de Mestrado, realizado no âmbito do Mestrado em Engenharia Mecânica no Instituto Superior de Engenharia de Lisboa e tem como objetivo a exposição das atividades desenvolvidas durante o estágio curricular. O estágio teve a duração de nove meses, tendo-se iniciado em outubro de 2014, e foi realizado na empresa Consulfrio, na qual o estagiário integro...

  1. Relatório de estágio: Labamaro

    OpenAIRE

    Faria, Sónia Raquel Mota

    2010-01-01

    Relatório de estágio de mestrado, Análises Clínicas, Universidade de Lisboa, Faculdade de Farmácia, 2010 Este relatório de estágio do Mestrado de Análises Clínicas pretende descrever todas as actividades na qual estive envolvida durante o período de estágio em Labamaro. Na primeira parte, são descritos os métodos usados na execução de análises nas várias secções do laboratório (hematologia, bioquímica, imunologia e microbiologia) e a respectiva interpretação de resultados. Na segunda...

  2. ¿Están subvencionados los aceites vegetales argentinos?

    OpenAIRE

    Fernández-Baca, Jorge

    2001-01-01

    Los fabricantes nacionales de aceites vegetales están tratando de obstruir el ingreso de sus similares argentinos, alegando que estos tienen una subvención de 10% otorgada por el Gobierno argentino, que les permite competir deslealmente con la producción nacional y han solicitado al Indecopi una sobretasa arancelaria que los proteja contra este subsidio. El presente trabajo pretende analizar la validez de estas afirmaciones y la conveniencia de atender el pedido de los denunciantes. The pe...

  3. ¿Están subvencionados los aceites vegetales argentinos?

    OpenAIRE

    Fernández-Baca, Jorge Mariano

    2014-01-01

    Los fabricantes nacionales de aceites vegetales están tratando de obstruir el ingreso de sus similares argentinos, alegando que estos tienen una subvención de 10% otorgada por el Gobierno argentino, que les permite competir deslealmente con la producción nacional y han solicitado al Indecopi una sobretasa arancelaria que los proteja contra este subsidio. El presente trabajo pretende analizar la validez de estas afirmaciones y la conveniencia de atender el pedido de los denunciantes.

  4. The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections

    Directory of Open Access Journals (Sweden)

    Milanesi Luciano

    2009-10-01

    Full Text Available Abstract Background The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs. This wide collection represents an important source of information for gene expression studies, provided it can be inspected according to biologically relevant criteria. EST data can be browsed using different dedicated web resources, which allow to investigate library specific gene expression levels and to make comparisons among libraries, highlighting significant differences in gene expression. Nonetheless, no tool is available to examine distributions of quantitative EST collections in Gene Ontology (GO categories, nor to retrieve information concerning library-dependent EST involvement in metabolic pathways. In this work we present the Human EST Ontology Explorer (HEOE http://www.itb.cnr.it/ptp/human_est_explorer, a web facility for comparison of expression levels among libraries from several healthy and diseased tissues. Results The HEOE provides library-dependent statistics on the distribution of sequences in the GO Direct Acyclic Graph (DAG that can be browsed at each GO hierarchical level. The tool is based on large-scale BLAST annotation of EST sequences. Due to the huge number of input sequences, this BLAST analysis was performed with the aid of grid computing technology, which is particularly suitable to address data parallel task. Relying on the achieved annotation, library-specific distributions of ESTs in the GO Graph were inferred. A pathway-based search interface was also implemented, for a quick evaluation of the representation of libraries in metabolic pathways. EST processing steps were integrated in a semi-automatic procedure that relies on Perl scripts and stores results in a MySQL database. A PHP-based web interface offers the possibility to simultaneously visualize, retrieve and compare data from the different libraries. Statistically significant differences in GO categories among user selected libraries can

  5. Intrarectal artemisinin derivatives

    NARCIS (Netherlands)

    Nosten, F.; van Vugt, M.; White, N. J.

    1998-01-01

    The artemisinin derivatives are the most potent antimalarials. They are rapidly absorbed orally, parenterally and intra-rectally. The latter mode of administration is particularly interesting in rural tropics. Preliminary studies have shown that artemisinin and its derivatives artesunate and

  6. Aproximaciones a una estética de lo americano

    Directory of Open Access Journals (Sweden)

    María del Milagro Casalla

    2010-01-01

    Full Text Available El legado filosófico que nos ha dejado Rodolfo Kusch tiene cada vez más presencia y valor en este largo itinerario de descubrirnos como americanos. La pasión de este pensador por la América profunda es una fuente de ins- piración para quienes creemos que vivir en América no es simplemente un episodio geográfico sino un horizonte desde y a partir del cual construimos nuestra identidad. En este trabajo se pretende recrear sus consideracio - nes estéticas recogidas en su ensayo “Anotaciones para una estética de lo americano”, escrito en el año 1955. Aunque se trata de uno de los primeros escritos de Rodolfo Kusch, en el mismo se encuentran presentes numerosos conceptos que luego serán tematizados extensamente a lo largo de toda su obra. Considero que el abordaje a sus consideraciones estéticas no ha sido tan frecuentado como sí otros aspectos de su pensamiento (ser-estar, geocultura, símbolo y religión, etc.. Por ello, creo que este trabajo puede constituir una orientación preeliminar para futuras interpretaciones y, a la vez, ser un humilde homenaje a su filosofía, que, a lo largo de los años, sigue estimulando a antiguas y nuevas generaciones de pensadores dedicados a la filosofía latinoamericana.

  7. Wheat EST resources for functional genomics of abiotic stress

    Directory of Open Access Journals (Sweden)

    Links Matthew G

    2006-06-01

    Full Text Available Abstract Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets. Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in

  8. activismo y estéticas en experimento

    Directory of Open Access Journals (Sweden)

    Omar Rincón

    2005-01-01

    Full Text Available Podemos comunicarlo todo: tenemos las tecnologías de la comunicación cada vez más cerca; pero no podemos contar nada, porque no tenemos nada qué decir, ni sabemos cómo decirlo. Hay que inventarlo todo, intervenir de nuevo la sociedad desde la comunicación. Es necesario convertir los medios en experiencia estética, social y política. ¿Cómo? Usando a las tecnologías para el activismo y el experimento; recurriendo a los llamado retro, porque no es lo más actual, lo más mercado, como experiencia de inspiración y emoción. Hay que volver a las estéticas, a los modos de narrar y a las historias que están inscritas en nuestras identidades locales; en nuestras sensibilidades femeninas, juveniles o sexuales; en nuestras tradiciones étnicas, o en nuestros modos urbanos. Sólo basta una minicámara para inventar el universo. En este ensayo se realiza un alegato contra los universos estético-narrativopolíticos construidos por la máquina televisiva y la homogeneidad del mercado. En este texto se argumenta a favor del activismo comunicativo, de la exploración tecnológica y de la inspiración étnica como estrategias para generar una mayor conciencia sobre el valor social de la comunicación, la intervención estético-narrativa de la sociedad y la importancia política de los medios de la gente.

  9. The Ungraded Derived Category

    OpenAIRE

    Stai, Torkil Utvik

    2012-01-01

    By means of the ungraded derived category we prove that the orbit category of the bounded derived category of an iterated tilted algebra with respect to translation is triangulated in such a way that the canonical functor from the bounded derived category to the orbit category becomes a triangle functor.

  10. Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis

    Directory of Open Access Journals (Sweden)

    Wegnez Maurice

    2007-05-01

    Full Text Available Abstract Background The western African clawed frog Xenopus tropicalis is an anuran amphibian species now used as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more amenable to systematic transcriptome surveys. We initiated a large-scale partial cDNA sequencing project to provide a functional genomics resource on genes expressed in the nervous system during early embryogenesis and metamorphosis in X. tropicalis. Results A gene index was defined and analysed after the collection of over 48,785 high quality sequences. These partial cDNA sequences were obtained from an embryonic head and retina library (30,272 sequences and from a metamorphic brain and spinal cord library (27,602 sequences. These ESTs are estimated to represent 9,693 transcripts derived from an estimated 6,000 genes. Comparison of these cDNA sequences with protein databases indicates that 46% contain their start codon. Further annotation included Gene Ontology functional classification, InterPro domain analysis, alternative splicing and non-coding RNA identification. Gene expression profiles were derived from EST counts and used to define transcripts specific to metamorphic stages of development. Moreover, these ESTs allowed identification of a set of 225 polymorphic microsatellites that can be used as genetic markers. Conclusion These cDNA sequences permit in silico cloning of numerous genes and will facilitate studies aimed at deciphering the roles of cognate genes expressed in the nervous system during neural development and metamorphosis. The genomic resources developed to study X. tropicalis biology will accelerate exploration of amphibian physiology and genetics. In particular, the model will facilitate analysis of key questions related to anuran embryogenesis and metamorphosis and its associated regulatory processes.

  11. El leviatán estético

    Directory of Open Access Journals (Sweden)

    Jorge Peñuela

    2011-05-01

    Full Text Available En este ensayo exploro algunos argumentos de Hannah Arendt, con el fin de mostrar las razones que explican el odio que se manifestaba en las discusiones artísticas de comienzos del siglo XX, odio que persiste aún en muchos escenarios artísticos actuales. Con Arendt sostengo que este fenómeno no está superado, porque el odio es la herramienta que despliega el Capital, para amalgamar a todos los desheredados que ha creado. Contextualizo en la práctica artística colombiana el siguiente argumento de Arendt: el capitalismo creó una amalgama de frustrados sociales, políticos y estéticos que destruye la esfera pública como lugar para el acontecer de la política, amalgama que denominó populacho. Introduzco la categoría de populacho estético, para hablar del odio que ha animado las prácticas artísticas en Colombia desde 1940.

  12. Estética en prótesis removibles

    Directory of Open Access Journals (Sweden)

    LVM Lucas

    2010-06-01

    Full Text Available La estética actualmente recibe una importante consideración en el contexto social. Una sonrisa atractiva es aspiración de la mayoría de los pacientes que precisan tratamiento protésico. Los implantes propiciaron una mejoría significativa, con relación a las prótesis removibles, debido a su funcionalidad. El objetivo de este estudio fue explorar en la literatura científica moderna, a fin de hallar aspectos relacionados con la estética en la rehabilitación mediante prótesis removibles. Fueron encontrados factores importantes como: la selección de los dientes artificiales, la disposición de los mismos, la caracterización de la base de resina acrílica, además de los tipos de retenedores para las prótesis parciales removibles. La planificación y aplicación apropiada de este procedimiento, con criterios estéticos correctos, debe ser responsabilidad del profesional.

  13. Taxation of Derivatives

    DEFF Research Database (Denmark)

    Dyppel, Katja Joo

    2013-01-01

    The main objective for this thesis is to analyse and systematise the Danish legislation on taxation of derivatives. According to financial terminology, a derivative is a financial instrument. Its value is derived from changes in the value of one or more underlying assets.The most common derivatives...... with the scope of sections 29-33 of the Danish Act on Taxation of Gains and Losses on Claims and Debt and the tax consequences for the covered financial contracts. In the analysis of taxation of derivatives, the fundamental issues of qualification and tax treatment of the instruments are dealt with....... are known as futures, forwards, options and swaps. Derivatives are traded for the purpose of hedging financial or business risk, speculating in future spot prices and taking advantage of arbitrage opportunities. This market has increased tremendously in recent years. The term derivative is not used...

  14. #RevueltasEstéticas: Del #yosoy132 a #Ayotzinapa

    OpenAIRE

    Córdova Rojas, Alba Citlali

    2016-01-01

    El objetivo de este artículo es situar en las estéticas de protesta los dispositivos que se despliegan en manifestaciones sociales como prácticas artísticas contemporáneas. En dos casos en México, el movimiento “yo soy 132” y las manifestaciones por los 43 estudiantes desaparecidos de Ayotzinapa. Se aborda la relación entre política y estética desde el planteamiento de que el arte contribuye a la formación de subjetividades políticas, y la forma en que estas prácticas críticas se han desplega...

  15. Construction, database integration, and application of an Oenothera EST library.

    Science.gov (United States)

    Mrácek, Jaroslav; Greiner, Stephan; Cho, Won Kyong; Rauwolf, Uwe; Braun, Martha; Umate, Pavan; Altstätter, Johannes; Stoppel, Rhea; Mlcochová, Lada; Silber, Martina V; Volz, Stefanie M; White, Sarah; Selmeier, Renate; Rudd, Stephen; Herrmann, Reinhold G; Meurer, Jörg

    2006-09-01

    Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.

  16. Relatório de estágio

    OpenAIRE

    Loureiro, Lurdes Filipa Crisóstomo Santos

    2012-01-01

    O presente relatório encontra-se inserido no Curso de Mestrado em Enfermagem na área de Especialização em Enfermagem de Saúde Infantil e Pediátrica. Este visa refletir sobre o percurso realizado nos diferentes módulos de estágio, ao nível de aquisição e desenvolvimento de competências profissionais como futura Enfermeira Especialista em Enfermagem de Saúde da Criança e do Jovem. O tema transversal a este percurso é a “Promoção de Hábitos de Sono Saudáveis na Criança”. O sono adequado é ...

  17. SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera

    Directory of Open Access Journals (Sweden)

    Sabourault Cécile

    2006-06-01

    Full Text Available Abstract Background The Lepidoptera Spodoptera frugiperda is a pest which causes widespread economic damage on a variety of crop plants. It is also well known through its famous Sf9 cell line which is used for numerous heterologous protein productions. Species of the Spodoptera genus are used as model for pesticide resistance and to study virus host interactions. A genomic approach is now a critical step for further new developments in biology and pathology of these insects, and the results of ESTs sequencing efforts need to be structured into databases providing an integrated set of tools and informations. Description The ESTs from five independent cDNA libraries, prepared from three different S. frugiperda tissues (hemocytes, midgut and fat body and from the Sf9 cell line, are deposited in the database. These tissues were chosen because of their importance in biological processes such as immune response, development and plant/insect interaction. So far, the SPODOBASE contains 29,325 ESTs, which are cleaned and clustered into non-redundant sets (2294 clusters and 6103 singletons. The SPODOBASE is constructed in such a way that other ESTs from S. frugiperda or other species may be added. User can retrieve information using text searches, pre-formatted queries, query assistant or blast searches. Annotation is provided against NCBI, UNIPROT or Bombyx mori ESTs databases, and with GO-Slim vocabulary. Conclusion The SPODOBASE database provides integrated access to expressed sequence tags (EST from the lepidopteran insect Spodoptera frugiperda. It is a publicly available structured database with insect pest sequences which will allow identification of a number of genes and comprehensive cloning of gene families of interest for scientific community. SPODOBASE is available from URL: http://bioweb.ensam.inra.fr/spodobase

  18. Dia mundial da espirometria na ESTeSL

    OpenAIRE

    Dias, Hermínia Brites; Carolino, Elisabete

    2011-01-01

    Objectivos do estudo: associar a ESTeSL e a AC de CPL às comemorações do Dia Mundial da Espirometria promovidas pela Fundação Europeia do Pulmão; realizar o maior número possível de espirometrias; consciencializar a comunidade para o papel da espirometria no diagnóstico precoce da patologia respiratória; colocar a ESTeSL, enquanto entidade formadora de Técnicos de Cardiopneumologia, na primeira linha das iniciativas relacionadas com o estudo espirométrico; identificar possíveis alter...

  19. La grande vitesse est-elle toujours sur les rails ?

    OpenAIRE

    Libourel, Eloïse; Ruggeri, Charlotte; Schorung, Matthieu

    2016-01-01

    National audience; Depuis le milieu du XXème, la grande vitesse ferroviaire est considérée comme une innovation révolutionnaire pour le transport de voyageurs. Elle renvoie une image de modernité à tous les acteurs institutionnels et à la société civile, et elle permet également aux États d’afficher une image de puissance technique et industrielle. L’objectif est de capitaliser sur l’objet « grande vitesse » pour valoriser l’avancée technologique d’un pays, d’une région, et pour promouvoir de...

  20. Niemeyer e as ideias estéticas

    Directory of Open Access Journals (Sweden)

    Vladimir Vieira

    2012-09-01

    Full Text Available O objetivo desse texto é discutir o artigo “Estética da arquitetura, Kant e Niemeyer: aproximações em investigação”, de Miguel Gally. Meu comentário ressalta o papel que a noção kantiana de ideia de estética desempenha para leitura proposta por Gally, e considera possivéis incongruências da obra do filósofo, bem como problemas mais gerais que podem ser suscitados pela abordagem escolhida para tratar da obra de Oscar Niemeyer.