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.

[SSR loci information analysis in transcriptome of Andrographis paniculata].

Science.gov (United States)

Li, Jun-Ren; Chen, Xiu-Zhen; Tang, Xiao-Ting; He, Rui; Zhan, Ruo-Ting

2018-06-01

To study the SSR loci information and develop molecular markers, a total of 43 683 Unigenes in transcriptome of Andrographis paniculata were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software, SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 14 135 SSR loci were found in the transcriptome of A. paniculata, which distributed in 9 973 Unigenes with a distribution frequency of 32.36%. Di-nucleotide and Tri-nucleotide repeat were the main types, accounted for 75.54% of all SSRs. The repeat motifs of AT/AT and CCG/CGG were the predominant repeat types of Di-nucleotide and Tri-nucleotide, respectively. A total of 4 740 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. Ten pairs of primers in 20 pairs of randomly picked primers produced fragments with expected molecular size. The gene function of Unigenes containing SSR were mostly related to the basic metabolism function of A. paniculata. The SSR markers in transcriptome of A. paniculata show rich type, strong specificity and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. Copyright© by the Chinese Pharmaceutical Association.

Development and characterization of genomic SSR markers in Cynodon transvaalensis Burtt-Davy.

Science.gov (United States)

Tan, Chengcheng; Wu, Yanqi; Taliaferro, Charles M; Bell, Greg E; Martin, Dennis L; Smith, Mike W

2014-08-01

Simple sequence repeat (SSR) markers are a major molecular tool for genetic and genomic research that have been extensively developed and used in major crops. However, few are available in African bermudagrass (Cynodon transvaalensis Burtt-Davy), an economically important warm-season turfgrass species. African bermudagrass is mainly used for hybridizations with common bermudagrass [C. dactylon var. dactylon (L.) Pers.] in the development of superior interspecific hybrid turfgrass cultivars. Accordingly, the major objective of this study was to develop and characterize a large set of SSR markers. Genomic DNA of C. transvaalensis '4200TN 24-2' from an Oklahoma State University (OSU) turf nursery was extracted for construction of four SSR genomic libraries enriched with [CA](n), [GA](n), [AAG](n), and [AAT](n) as core repeat motifs. A total of 3,064 clones were sequenced at the OSU core facility. The sequences were categorized into singletons and contiguous sequences to exclude redundancy. From the two sequence categories, 1,795 SSR loci were identified. After excluding duplicate SSRs by comparison with previously developed SSR markers using a nucleotide basic local alignment tool, 1,426 unique primer pairs (PPs) were designed. Out of the 1,426 designed PPs, 981 (68.8 %) amplified alleles of the expected size in the donor DNA. Polymorphisms of the SSR PPs tested in eight C. transvaalensis plants were 93 % polymorphic with 544 markers effective in all genotypes. Inheritance of the SSRs was examined in six F(1) progeny of African parents 'T577' × 'Uganda', indicating 917 markers amplified heritable alleles. The SSR markers developed in the study are the first large set of co-dominant markers in African bermudagrass and should be highly valuable for molecular and traditional breeding research.

(SSR) markers

African Journals Online (AJOL)

acer

2013-06-26

Jun 26, 2013 ... analysis was in general agreement with PCoA in discrimi- nating the cultivars. Conclusions. Estimation of morphological diversity may provide addi- tional information on the present finding. Nonetheless, the 29 SSR markers provided considerable genetic reso- lution and this genetic diversity analysis ...

(SSR) markers

African Journals Online (AJOL)

SAM

2014-07-30

Jul 30, 2014 ... India and the country is currently the leading producer, consumer and exporter of ... registration with the competent authority for plant variety protection. Conventionally ... detection of duplicates, parental verification in crosses, gene tagging in .... allelic patterns as revealed by the current set of SSR markers.

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

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Lu, X; Zhou, H; Pan, Y-B; Chen, C Y; Zhu, J R; Chen, P H; Li, Y-R; Cai, Q; Chen, R K

2015-12-28

No information is available on segregation analysis of DNA markers involving both pollen and self-progeny. Therefore, we used capillary electrophoresis- and fluorescence-based DNA fingerprinting together with single pollen collection and polymerase chain reaction (PCR) to investigate simple sequence repeat (SSR) marker segregation among 964 single pollens and 288 self-progenies (S1) of sugarcane cultivar LCP 85-384. Twenty SSR DNA fragments (alleles) were amplified by five polymorphic SSR markers. Only one non-parental SSR allele was observed in 2392 PCRs. SSR allele inheritance was in accordance with Mendelian laws of segregation and independent assortment. Highly significant correlation coefficients were found between frequencies of observed and expected genotypes in pollen and S1 populations. Within the S1 population, the most frequent genotype of each SSR marker was the parental genotype of the same marker. The number of genotypes was higher in pollen than S1 population. PIC values of the five SSR markers were greater in pollen than S1 populations. Eleven of 20 SSR alleles (55%) were segregated in accordance with Mendelian segregation ratios expected from pollen and S1 populations of a 2n = 10x polyploid. Six of 20 SSR alleles were segregated in a 3:1 (presence:absence) ratio and were simplex markers. Four and one alleles were segregated in 77:4 and 143:1 ratios and considered duplex and triplex markers, respectively. Segregation ratios of remaining alleles were unexplainable. The results provide information about selection of crossing parents, estimation of seedling population optimal size, and promotion of efficient selection, which may be valuable for sugarcane breeders.

Generation and application of SSR markers in avocado

International Nuclear Information System (INIS)

Sharon, D.; Lavi, U.; Cregan, P.B.; Hillel, J.

1998-01-01

Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author)

Generation and application of SSR markers in avocado

Energy Technology Data Exchange (ETDEWEB)

Sharon, D; Lavi, U [Institute of Horticulture, ARO Volcani Center, Bet-Dagan (Israel); Cregan, P B [United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland (United States); Hillel, J [Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot (Israel)

1998-10-01

Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author) 20 refs, 3 figs, 8 tabs

SSR markers: a tool for species identification in Psidium (Myrtaceae).

Science.gov (United States)

Tuler, A C; Carrijo, T T; Nóia, L R; Ferreira, A; Peixoto, A L; da Silva Ferreira, M F

2015-11-01

Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies.

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

Indian Academy of Sciences (India)

We recently initiated a programme 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). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be ...

New device based on the super spatial resolution (SSR) method

International Nuclear Information System (INIS)

Soluri, A.; Atzeni, G.; Ucci, A.; Bellone, T.; Cusanno, F.; Rodilossi, G.; Massari, R.

2013-01-01

Recently it have been described that innovative methods, namely Super Spatial Resolution (SSR), can be used to improve the scintigraphic imaging. The aim of SSR techniques is the enhancement of the resolution of an imaging system, using information from several images. In this paper we describe a new experimental apparatus that could be used for molecular imaging and small animal imaging. In fact we present a new device, completely automated, that uses the SSR method and provides images with better spatial resolution in comparison to the original resolution. Preliminary small animal imaging studies confirm the feasibility of a very high resolution system in scintigraphic imaging and the possibility to have gamma cameras using the SSR method, to perform the applications on functional imaging. -- Highlights: • Super spatial resolution brings a high resolution image from scintigraphic images. • Resolution improvement depends on the signal to noise ratio of the original images. • The SSR shows significant improvement on spatial resolution in scintigraphic images. • The SSR method is potentially utilizable for all scintigraphic devices

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

Directory of Open Access Journals (Sweden)

Meryem Ipek

2015-02-01

Full Text Available Only a limited number of simple sequence repeat (SSR markers is available for the genome of garlic (Allium sativum L. despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.

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

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

Indian Academy of Sciences (India)

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 AFLP primer combinations and 177 SSR primer pairs tested, 32 AFLP and four SSR primers were chosen for genotyping F2 ...

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

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.

Large-scale development of PIP and SSR markers and their complementary applied in Nicotiana.

Science.gov (United States)

Huang, L; Cao, H; Yang, L; Yu, Yu; Wang, Yu

2013-08-01

PIP (Potential Intron Polymorphism) and SSR (Simple Sequence Repeats) were used in many species, but large-scale development and combined use of these two markers have not been reported in tobacco. In this study, a total of 12,388 PIP and 76,848 SSR markers were designed and uploaded to a web-accessible database (http://yancao.sdau.edu.cn/tgb/). E-PCR analysis showed that PIP and SSR rarely overlapped and were strongly complementary in the tobacco genome. The density was 3.07 PIP and 1.72 SSR markers per 10 kb of the known sequences. A total of 153 and 166 alleles were detectedby 22 PIP and 22 SSR markers in 64 Nicotiana accessions. SSR produced higher PIC (polymorphism information content) values and identified more alleles than PIP, whereas PIP could identify larger numbers of rare alleles. Mantel testing demonstrated a high correlation coefficient (r = 0.949, P SSR. The UPGMA dendrogram created from the combined PIP and SSR markers was clearer and more reliable than the individual PIP or SSR dendrograms. It suggested that PIP and SSR can make up the deficiency of molecular markers not only in tobacco but other plant.

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 ...

Development of genic SSR markers from transcriptome sequencing of pear buds.

Science.gov (United States)

Yue, Xiao-yan; Liu, Guo-qin; Zong, Yu; Teng, Yuan-wen; Cai, Dan-ying

2014-04-01

A total of 8375 genic simple sequence repeat (SSR) loci were discovered from a unigene set assembled from 116282 transcriptomic unigenes in this study. Dinucleotide repeat motifs were the most common with a frequency of 65.11%, followed by trinucleotide (32.81%). A total of 4100 primer pairs were designed from the SSR loci. Of these, 343 primer pairs (repeat length ≥15 bp) were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions. After the preliminary test, 104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11% (101) of these. Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions. These markers displayed a high level of polymorphism. The number of alleles at these SSR loci ranged from 2 to 17, with a mean of 9.43 alleles per locus, and the polymorphism information content (PIC) values ranged from 0.26 to 0.91. The UPGMA (unweighted pair-group method with arithmetic average) cluster analysis grouped the 28 Pyrus accessions into two groups: Oriental pears and Occidental pears, which are congruent to the traditional taxonomy, demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships, enriching rare Pyrus EST-SSR resources, and confirming the potential value of a pear transcriptome database for the development of new SSR markers.

SSR: Its Effects on Students' Reading Habits after They Complete the Program.

Science.gov (United States)

Wiesendanger, Katherine D.; Bader, Lois

1989-01-01

Studies the effect of sustained silent reading (SSR) on recreational reading habits after termination of instruction. Finds that SSR students read more than those not in the program, and that SSR has no impact on above average readers, great impact on average readers, and little impact on below average readers. (RS)

Development and characterization of genomic SSR markers for Anneslea fragrans (Pentaphylacaceae).

Science.gov (United States)

Sun, Lijing; Meng, Kaikai; Liao, Boyong; Li, Chunmei; Zhang, Yue; Liao, Wenbo; Chen, Sufang

2017-10-01

The genus Anneslea (Pentaphylacaceae) contains four species and six varieties, most of which are locally endemic. Here, simple sequence repeat (SSR) markers were developed for the conservation of these species. The genome of A. fragrans was sequenced and de novo assembled into 445,162 contigs, of which 30,409 SSR loci were detected. Primers for 100 SSR loci were validated with PCR amplification in three populations of A. fragrans . Seventy-nine loci successfully amplified, and 30 were polymorphic. The mean number of alleles, observed heterozygosity, and expected heterozygosity were 7.01 ± 1.60, 0.817 ± 0.241, and 0.796 ± 0.145, respectively. Most primers could be amplified in Ternstroemia gymnanthera , T. kwangtungensis , and Cleyera pachyphylla . Our study demonstrated that shotgun genome sequencing is an efficient way to develop genomic SSR markers for nonmodel species. These genomic SSR loci will be valuable in population genetic studies in Anneslea and its relatives.

On the status of Ukrainian SSR before the beginning of perestroika

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А. А. Омарова

2014-12-01

Full Text Available The article studies legal status of Ukrainian SSR before the beginning of Perestroika. Constitutional acts, laws and other regulatory acts are analyzed which fixed the status of Ukrainian SSR within USSR. On the basis of study of regulatory sources and monographs we came to conclusion that a contradiction existed between legally fixed and actual status of Ukrainian SSR within USSR before the beginning of Perestroika.

A set of tetra-nucleotide core motif SSR markers for efficient identification of potato (Solanum tuberosum) cultivars.

Science.gov (United States)

Kishine, Masahiro; Tsutsumi, Katsuji; Kitta, Kazumi

2017-12-01

Simple sequence repeat (SSR) is a popular tool for individual fingerprinting. The long-core motif (e.g. tetra-, penta-, and hexa-nucleotide) simple sequence repeats (SSRs) are preferred because they make it easier to separate and distinguish neighbor alleles. In the present study, a new set of 8 tetra-nucleotide SSRs in potato ( Solanum tuberosum ) is reported. By using these 8 markers, 72 out of 76 cultivars obtained from Japan and the United States were clearly discriminated, while two pairs, both of which arose from natural variation, showed identical profiles. The combined probability of identity between two random cultivars for the set of 8 SSR markers was estimated to be 1.10 × 10 -8 , confirming the usefulness of the proposed SSR markers for fingerprinting analyses of potato.

DNA profiling of pineapple cultivars in Japan discriminated by SSR markers

Science.gov (United States)

Shoda, Moriyuki; Urasaki, Naoya; Sakiyama, Sumisu; Terakami, Shingo; Hosaka, Fumiko; Shigeta, Narumi; Nishitani, Chikako; Yamamoto, Toshiya

2012-01-01

We developed 18 polymorphic simple sequence repeat (SSR) markers in pineapple (Ananas comosus) by using genomic libraries enriched for GA and CA motifs. The markers were used to genotype 31 pineapple accessions, including seven cultivars and 11 breeding lines from Okinawa Prefecture, 12 foreign accessions and one from a related species. These SSR loci were highly polymorphic: the 31 accessions contained three to seven alleles per locus, with an average of 4.1. The values of expected heterozygosity ranged from 0.09 to 0.76, with an average of 0.52. All 31 accessions could be successfully differentiated by the 18 SSR markers, with the exception of ‘N67-10’ and ‘Hawaiian Smooth Cayenne’. A single combination of three markers TsuAC004, TsuAC010 and TsuAC041, was enough to distinguish all accessions with one exception. A phenogram based on the SSR genotypes did not show any distinct groups, but it suggested that pineapples bred in Japan are genetically diversed. We reconfirmed the parentage of 14 pineapple accessions by comparing the SSR alleles at 17 SSR loci in each accession and its reported parents. The obtained information will contribute substantially to protecting plant breeders’ rights. PMID:23341750

simple sequence repeat (SSR)

African Journals Online (AJOL)

In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

Factors Affecting SSR in Holstein Dairy Cows

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Alireza Heravi Mosavi

2016-08-01

reports have shown that high environmental temperature and higher rates of evaporation from a week to a month before conception secondary sex ratio was increased. Materials and method The demographic, production and reproduction data of six large dairy farms between years 1375 and 1389 were used. The rolling average of 305 d fat corrected milk yield was 8145 kg with a range of 7578 to 8670 Kg. Breeding Center of Iran and the herds covered by the registration and recording them on a regular basis carried out by experts dairy cooperatives. The flocks were in the area northeast of the country. Production data (date corrected milk production and the cumulative production by 60 and 305 days of lactation, reproductive data (such as calving year, calving season, type of birth, sex of calf, the latest information on AI, days open , and details the possible removal of the flock or death were recorded. Data were collected from flocks before the analysis was re-verification. Used by sperm, sperm into four groups: Iranian, Canadian, American and other countries (including sperm taken from European countries groups. The data were analyzed using multivariate logistic regression model. Statistics 0/05 was used to ensure meaningful results. Results and discussion Results showed that the ratio of males to females was 53 to 47. Origin of the sires (including Iranian, American, or Canadian had no impact on secondary sex ratio. Type of calving (eutocia vs. non-eutocia calving including dystocia and still birth had significant impact on SSR (P

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.

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.

Genetic Assessment of Moroccan Tomato (Solanum lycopersicum L. Genotypes by RAPD and SSR Markers

Directory of Open Access Journals (Sweden)

Rajae Amraoui

2017-06-01

Full Text Available For the first time eight local tomato cultivars collected from four different regions of Morocco were assessed with RAPD and SSR methods. Most of RAPD markers give monomorphic banding profiles. Only OPU03 marker showed a total of 4 polymorphic amplicons out of 8 recorded in FIGUIG2 cultivar. The analysis with SSR markers gives more polymorphism. The number of alleles amplified assessed from 2 to 5 alleles among cultivars. The similarity matrix subjected by the unweighted pairgroup arithmetic method (UPGMA clustering grouped the cultivars in four groups where FIGUIG2 cultivar formed a separate and more distant cluster. In addition this cultivar holds the very high percentage of uniformity (99% indicating that is an homogeneous traditional cultivar with high purity. This genotype can be conserved and used in breeding programs. More traditional Moroccan cultivars must be collected in order to determine their genetic structure.

SSR-Based DNA Fingerprinting and Diversity Assessment Among Indian Germplasm of Euryale ferox: an Aquatic Underutilized and Neglected Food Crop.

Science.gov (United States)

Kumar, Nitish; Shikha, Divya; Kumari, Swati; Choudhary, Binod Kumar; Kumar, Lokendra; Singh, Indu Shekhar

2017-10-30

Euryale ferox is native to Southeast Asia and China, and it is one of the important aquatic food crops propagated mostly in eastern part of India. The aim of the present study was to characterize and evaluate the genetic diversity of ex situ collections of E. ferox germplasm from different geographical states of India using microsatellite (simple sequence repeats (SSRs)) markers. Ten SSR markers were analyzed to assess DNA fingerprinting and genetic diversity of 16 cultivated germplasm of E. ferox. Total 37 polymorphic alleles were recorded with an average of 3.7 allele frequency per primer. The polymorphic information content value varied from 0.204 to 0.735 with mean of 0.448. A high range of heterozygosity (Ho 0.228; He 0.512) was detected in the present study. The neighbor-joining (N-J) tree and the principle coordinate analysis showed that the germplasm divided in to three main clusters. The results of the present investigation comply that SSR markers are effective for computing genetic assessment of genetic diversity and similarity with classifying cultivated varieties of E. ferox. Evaluation of genetic diversity among Indian E. ferox germplasm could provide useful information for genetic improvement.

(SSR) markers for analysis of genetic diversity in African rice ...

African Journals Online (AJOL)

Bonny Oloka

2015-05-06

May 6, 2015 ... and conservation. To address this knowledge gap, 10 highly polymorphic rice simple sequence repeat. (SSR) markers were used to characterize 99 rice genotypes to determine their diversity and place them in their different population groups. The SSR markers were multiplexed in 3 panels to increase their.

An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

Science.gov (United States)

Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

2016-01-01

Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

SSR-based association mapping of salt tolerance in cotton (Gossypium hirsutum L.).

Science.gov (United States)

Zhao, Y L; Wang, H M; Shao, B X; Chen, W; Guo, Z J; Gong, H Y; Sang, X H; Wang, J J; Ye, W W

2016-05-25

The identification of simple sequence repeat (SSR) markers associated with salt tolerance in cotton contributes to molecular assisted selection (MAS), which can improve the efficiency of traditional breeding. In this study, 134 samples of upland cotton cultivars were selected. The seedling emergence rates were tested under 0.3% NaCl stress. A total of 74 SSR markers were used to scan the genomes of these samples. To identify SSR markers associated with salt tolerance, an association analysis was performed between salt tolerance and SSR markers using TASSEL 2.1, based on the analysis of genetic structure using Structure 2.3.4. The results showed that the seedling emergence rates of 134 cultivars were significantly different, and 27 salt-sensitive and 10 salt-tolerant cultivars were identified. A total of 148 loci were found in 74 SSR markers involving 246 allelic variations, which ranged from 2 to 7 with an average of 3.32 per SSR marker. The gene diversity ranged from 0.0295 to 0.4959, with the average being 0.2897. The polymorphic information content ranged from0.0290 to 0.3729, with the average being 0.2381. This natural population was classified into two subgroups by Structure 2.3.4, containing 89 and 45 samples, respectively. Finally, eight SSR sites associated with salt tolerance ware found through an association analysis, with the rate of explanation ranging from 2.91 to 7.82% and an average of 4.32%. These results provide reference data for the use MAS for salt tolerance in cotton.

Genetic diversity of wild and cultivated genotypes of pigeonpea through RAPD and SSR markers.

Science.gov (United States)

Walunjkar, Babasaheb C; Parihar, Akarsh; Singh, Nirbhay Kumar; Parmar, L D

2015-03-01

Eight wild and four cultivated pigeonpea genotypes were subjected to RAPD and microsatellite analysis, with 40 primers each. Out of these, eight RAPD and five SSR primers were found polymorphic. RAPD primers showed 100% polymorphism and produced a total of 517 DNA fragments, whereas SSR primers produced 67 fragments and they too showed 100% polymorphism. The RAPD markers revealed highest similarity co-efficient of 0.93 (GT-100 and ICPL-87), whereas the highest similarity co-efficient obtained with SSR markers was 1.00 (GTH-1 and GT-100). Average PIC value obtained with RAPD and SSR were 0.90 and 0.18, respectively. The arithmetic mean heterozygosity and marker index were 0.90 and 22.47 respectively with RAPD marker, whereas the corresponding values for SSR markers were 0.18 and 33.66. Moreover; the four wild genotypes (Cajanus scarabaeoides, Rhyncosia rufescence, Cajanus cajanifolius and Rhyncosia canna) and the four cultivars (GTH-1, GT-100, ICPL-87 and GT-1) grouped distinctly in the same subgroups of the dendrograms obtained with both RAPD and SSR analysis. Therefore, the findings of SSR supplement and validate the results obtained with RAPD analysis.

Development and characterization of EST-SSR markers in Bombax ceiba (Malvaceae).

Science.gov (United States)

Ju, Miao-Miao; Ma, Huan-Cheng; Xin, Pei-Yao; Zhou, Zhi-Li; Tian, Bin

2015-04-01

Bombax ceiba (Malvaceae), commonly known as silk cotton tree, is a multipurpose tree species of tropical forests. Novel expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for the species using transcriptome analysis. A total of 33 new EST-SSR markers were developed for B. ceiba, of which 13 showed polymorphisms across the 24 individuals from four distant populations tested in the study. The results showed that the number of alleles per polymorphic locus ranged from two to four, and the expected heterozygosity and observed heterozygosity per locus varied from 0.043 to 0.654 and from 0 to 0.609, respectively. These newly developed EST-SSR markers can be used in phylogeographic and population genetic studies to investigate the origin of B. ceiba populations. Furthermore, these EST-SSR markers could also greatly promote the development of molecular breeding studies pertaining to silk cotton tree.

The CRF₁ receptor antagonist SSR125543 prevents stress-induced long-lasting sleep disturbances in a mouse model of PTSD: comparison with paroxetine and d-cycloserine.

Science.gov (United States)

Philbert, Julie; Beeské, Sandra; Belzung, Catherine; Griebel, Guy

2015-02-15

The selective CRF₁ (corticotropin releasing factor type 1) receptor antagonist SSR125543 has been previously shown to attenuate the long-term behavioral and electrophysiological effects produced by traumatic stress exposure in mice. Sleep disturbances are one of the most commonly reported symptoms by people with post-traumatic stress disorder (PTSD). The present study aims at investigating whether SSR125543 (10 mg/kg/day/i.p. for 2 weeks) is able to attenuate sleep/wakefulness impairment induced by traumatic stress exposure in a model of PTSD in mice using electroencephalographic (EEG) analysis. Effects of SSR125543 were compared to those of the 5-HT reuptake inhibitor, paroxetine (10 mg/kg/day/i.p.), and the partial N-methyl-d-aspartate (NMDA) receptor agonist, d-cycloserine (10 mg/kg/day/i.p.), two compounds which have demonstrated clinical efficacy against PTSD. Baseline EEG recording was performed in the home cage for 6h prior to the application of two electric foot-shocks of 1.5 mA. Drugs were administered from day 1 post-stress to the day preceding the second EEG recording session, performed 14 days later. Results showed that at day 14 post-stress, shocked mice displayed sleep fragmentation as shown by an increase in the occurrence of both non-rapid eye movement (NREM) sleep and wakefulness bouts. The duration of wakefulness, NREM and REM sleep were not significantly affected. The stress-induced effects were prevented by repeated administration of SSR125543, paroxetine and D-cycloserine. These findings confirm further that the CRF₁ receptor antagonist SSR125543 is able to attenuate the deleterious effects of traumatic stress exposure. Copyright © 2014 Elsevier B.V. All rights reserved.

Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family.

Science.gov (United States)

Sen, Surojit; Dehury, Budheswar; Sahu, Jagajjit; Rathi, Sunayana; Yadav, Raj Narain Singh

2018-04-06

Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO. A total 12,878 number of SSRs were detected from 101,701 number of EST sequences. SSR density ranged from 1 SSR/3.22 kb to 1 SSR/15.65 kb. A total of 1873 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR-ESTs could be assigned a significant match to the protein database. 3037 unique SSR-FDM were assigned and IPR003657 (WRKY Domain) was found to be the most dominant FDM among the members. 1810 unique GO terms obtained were further subjected to enrichment analysis to obtain 513 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were, GO:0003824 for molecular function, GO:0006350 for biological process and GO:0005886 for cellular component, justifying the richness of defensive secondary metabolites and phytomedicine within the family. The results from this study provides tangible insight to genetic make-up and distribution of SSRs. Functional annotation corresponded many genes of unknown functions which may be considered as novel genes or genes responsible for stress specific secondary metabolites. Further studies are required to understand stress specific genes accountable for leveraging the synthesis of secondary metabolites.

Cultivar identification and genetic relationship of pineapple (Ananas comosus) cultivars using SSR markers.

Science.gov (United States)

Lin, Y S; Kuan, C S; Weng, I S; Tsai, C C

2015-11-25

The genetic relationships among 27 pineapple [Ananas comosus (L.) Merr.] cultivars and lines were examined using 16 simple sequence repeat (SSR) markers. The number of alleles per locus of the SSR markers ranged from 2 to 6 (average 3.19), for a total of 51 alleles. Similarity coefficients were calculated on the basis of 51 amplified bands. A dendrogram was created according to the 16 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed most of the cultivars and lines to be distinguished, with the exception of vegetative clones. According to the dendrogram, the 27 pineapple cultivars and lines were clustered into three main clusters and four individual clusters. As expected, the dendrogram showed that derived cultivars and lines are closely related to their parental cultivars; the genetic relationships between pineapple cultivars agree with the genealogy of their breeding history. In addition, the analysis showed that there is no obvious correlation between SSR markers and morphological characters. In conclusion, SSR analysis is an efficient method for pineapple cultivar identification and can offer valuable informative characters to identify pineapple cultivars in Taiwan.

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

An accurate and efficient method for large-scale SSR genotyping and applications.

Science.gov (United States)

Li, Lun; Fang, Zhiwei; Zhou, Junfei; Chen, Hong; Hu, Zhangfeng; Gao, Lifen; Chen, Lihong; Ren, Sheng; Ma, Hongyu; Lu, Long; Zhang, Weixiong; Peng, Hai

2017-06-02

Accurate and efficient genotyping of simple sequence repeats (SSRs) constitutes the basis of SSRs as an effective genetic marker with various applications. However, the existing methods for SSR genotyping suffer from low sensitivity, low accuracy, low efficiency and high cost. In order to fully exploit the potential of SSRs as genetic marker, we developed a novel method for SSR genotyping, named as AmpSeq-SSR, which combines multiplexing polymerase chain reaction (PCR), targeted deep sequencing and comprehensive analysis. AmpSeq-SSR is able to genotype potentially more than a million SSRs at once using the current sequencing techniques. In the current study, we simultaneously genotyped 3105 SSRs in eight rice varieties, which were further validated experimentally. The results showed that the accuracies of AmpSeq-SSR were nearly 100 and 94% with a single base resolution for homozygous and heterozygous samples, respectively. To demonstrate the power of AmpSeq-SSR, we adopted it in two applications. The first was to construct discriminative fingerprints of the rice varieties using 3105 SSRs, which offer much greater discriminative power than the 48 SSRs commonly used for rice. The second was to map Xa21, a gene that confers persistent resistance to rice bacterial blight. We demonstrated that genome-scale fingerprints of an organism can be efficiently constructed and candidate genes, such as Xa21 in rice, can be accurately and efficiently mapped using an innovative strategy consisting of multiplexing PCR, targeted sequencing and computational analysis. While the work we present focused on rice, AmpSeq-SSR can be readily extended to animals and micro-organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The research of SSR which can be restrained by photovoltaic grid connected

Science.gov (United States)

Li, Kuan; Liu, Meng; Zheng, Wei; Li, Yudun; Wang, Xin

2018-02-01

Utilization of photovoltaic power generation has attracted considerable attention, and it is growing rapidly due to its environmental benefits. The series capacitive compensation is needed to be introduced into the lines which could improve the transmission capacity. However, the series capacitive compensation may lead to sub-synchronous resonance(SSR). This paper proposes a method to restrain the SSR based on photovoltaic grid connected which is caused by series capacitive compensation. Sub-synchronous oscillation damping controller (SSDC) is designed based on complex torque coefficient approach, and the SSDC is added to the PV power station’s main controller to damp SSR. IEEE Second benchmark model is used as simulation model based on PSCAD/EMTDC. The results show that the designed SSDC could restrain SSR and improve stability in PV grid connected effectively.

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

Directory of Open Access Journals (Sweden)

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.

Mapping of QTLs for frost tolerance and heading time using SSR ...

African Journals Online (AJOL)

STORAGESEVER

2008-10-19

Oct 19, 2008 ... using SSR markers in bread wheat. Omid Sofalian1*, Seyyed A. ... Key words: Bread wheat, frost tolerance, heading time, QTL mapping, single marker analysis, SSR. INTRODUCTION. Abiotic stresses are crucial ... cultivars are divided into two types (winter and spring growth habit) depending on their need ...

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.

simple sequence repeats (EST-SSR)

African Journals Online (AJOL)

Yomi

2012-01-19

Jan 19, 2012 ... 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat ... Cluster analysis revealed a high genetic similarity among the sugarcane (Saccharum spp.) breeding lines which could reduce the genetic gain in ..... The multiple allele characteristic of SSR com-.

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...... SSR markers was evaluated for polymorphism across nine of the 23 grass species. Four to seven of the markers were polymorphic within each species, with an average detection of 2.4 alleles per species....

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...... the SSR, damping the power system oscillation and enhancing the transient stability margin in response to different SCRs....... in the STATCOM control structure. The performances of the controllers are tested in steady state operation and in response to system contingencies, taking into account the impact of short circuit ratios (SCRs). Simulation results are presented to demonstrate the capability of the controllers for mitigating...

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

Development of advanced BWR fuel bundle with spectral shift rod (3) -transient analysis of ABWR core with SSR

International Nuclear Information System (INIS)

Ikegawa, T.; Chaki, M.; Ohga, Y.; Abe, M.

2010-01-01

The spectral shift rod (SSR) is a new type of water rod, utilized instead of the conventional water rod, in which a water level develops during core operation. The water level can be changed according to the fuel channel flow rate. In this study, ABWR plant performance with SSR fuel bundles under transient conditions has been evaluated using the TRACG code. The TRACG code, which can treat three-dimensional hydrodynamic calculations in a reactor pressure vessel, is well suited for evaluating the reactor transient performance with the SSR fuel bundles because it can calculate the water levels in the SSR at each channel grouping and therefore evaluate the core reactivity according to the water level changes in the SSR. 'Generator load rejection with total turbine bypass failure' and 'Recirculation flow control failure with increasing flow' were selected as cases which may increase the reactivity with the increasing water level in the SSR. It was found that the absolute value of the void reactivity coefficient in the SSR core was larger than that in the conventional water rod core because the core averaged void fraction in the SSR core, which has the vapor region above the water level in the SSR, was larger than that in the conventional water rod core. Therefore, AMCPR for the SSR core was a little larger than that for the conventional water rod core; however, the difference was smaller than 0.02 because the inlet of the SSR ascending path was designed to be small enough to prevent the rapid water level increase in the SSR. (authors)

[Study on quality evaluation of sequence and SSR information in transcriptome of Astragalus membranacus].

Science.gov (United States)

Chang, Yue; Yang, Song; Liu, Zhen-Peng; Ren, Wei-Chao; Liu, Jie; Ma, Wei

2016-04-01

In this study, 454/Roche GS FLX sequencing technology was used to obtain the data of the Astragalus membranaceus. Four hundred and fifty-four Sequencing System Software was applied to carry out the transcription of the group from scratch. Using MISA tools, 9 893 unigenes were selected for the sequence of the genome of A. membranaceus, and the information of SSR locus was analyzed. According to the result, the average length of reads was 413 bp, about 86% of the reads was involved in the splicing, the length of the N50 was 1 205 bp, the number of unigenes was measured by the whole transcript. 1 729 SSR loci in the A. membranaceus transcriptome were searched, the occurrence frequency of SSR was 9.24%, the frequency of SSR in the whole transcriptome was 13.42%, the average length of SSR was 7.97 kb. One hundred and twenty-seven kinds of core repeat sequences were found, the dominant type was TG/AC type of dinucleotide, it appeared to account for 4.25% of the total SSR locus. The results of the sequence of the transcription of the A. membranaceus transcriptome revealed the overall expression, and a large number of unigenessequence was obtained, and the SSR locus in the genome of the A. membranaceus is high, and the type is diverse, and the polymorphism of the gene is high. Copyright© by the Chinese Pharmaceutical Association.

A new set of validated SSR primers for application in mulberry ...

Indian Academy of Sciences (India)

user

2018-01-11

Jan 11, 2018 ... We chose 37 genomic sequences that had high number of di, tri and tetra SSR motifs from ... primers failed to produce any amplification products and ... Sericulture is a cottage industry that employs 8.03 million people across ... The resolving power of the SSR markers ranged from 0.11 (MulSatG100717) to.

Identification of molecular performance from oil palm clones based on SSR markers

Science.gov (United States)

Putri, Lollie Agustina P.; Basyuni, M.; Bayu, Eva S.; Arvita, D.; Arifiyanto, D.; Syahputra, I.

2018-03-01

In Indonesia, the oil palms are an important economic crop, producing food and raw materials for the food, confectionary, cosmetics and oleo-chemical industrial demands of oil palm products. Clonal oil palm offers the potential for greater productivity because it is possible to establish uniform tree stands comprising identical copies (clones) of a limited number of highly productive oil palms. Unfortunately, tissue culture sometimes accentuates the expression of detects in oil palm, particularly when embryogenesis is induced in particullar callus for prolonged periods. This research is conducted by taking individual tree sample of clone germplasm two years old. The purpose of this research is to molecular performance analysis of some oil palm clones based on SSR markers. A total of 30 trees oil palm clones were used for analysis. In this experiment, the DNA profile diversity was assessed using five loci of oil palm’s specific SSR markers. The results of the experiment indicated out of 3 SSR markers (FR-0779, FR-3663 and FR-0782) showed monomorphic of PCR product and 2 SSR markers (FR-0783 and FR- 3745) showed polymorphic of PCR product. There are 10 total number of PCR product. These preliminary results demonstrated SSR marker can be used to evaluate genetic relatedness among trees of oil palm clones.

Exploration of genetic diversity among medicinally important genus Epimedium species based on genomic and EST-SSR marker.

Science.gov (United States)

Yousaf, Zubaida; Hu, Weiming; Zhang, Yanjun; Zeng, Shaohua; Wang, Ying

2015-01-01

Epimedium species has gained prime importance due to their medicinal and economic values. Therefore, in this study, 26 genomic SSR and 10 EST-SSR markers were developed for 13 medicinal species of the Epimedium genus and one out-group species Vancouveria hexandra W. J. Hooker to explore the existing genetic diversity. A total of 100 alleles by genomic SSR and 65 by EST-SSR were detected. The genomic SSR markers were presented between 2-7 alleles per locus. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 4.5 and 0.0254 to 2.8108, respectively. Similarly, for EST-SSR, these values were ranged from 3.00 to 4.00 and 1.9650 to 2.7142. The number of alleles for EST-SSR markers ranged from 3 to 10 with an average of 3.51 per loci. It has been concluded that medicinally important species of the genus Epimedium possesses lower intraspecific genetic variation.

Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species.

Science.gov (United States)

Gupta, S K; Gopalakrishna, T

2010-07-01

Unigene sequences available in public databases provide a cost-effective and valuable source for the development of molecular markers. In this study, the identification and development of unigene-based SSR markers in cowpea (Vigna unguiculata (L.) Walp.) is presented. A total of 1071 SSRs were identified in 15 740 cowpea unigene sequences downloaded from the National Center for Biotechnology Information. The most frequent SSR motifs present in the unigenes were trinucleotides (59.7%), followed by dinucleotides (34.8%), pentanucleotides (4%), and tetranucleotides (1.5%). The copy number varied from 6 to 33 for dinucleotide, 5 to 29 for trinucleotide, 5 to 7 for tetranucleotide, and 4 to 6 for pentanucleotide repeats. Primer pairs were successfully designed for 803 SSR motifs and 102 SSR markers were finally characterized and validated. Putative function was assigned to 64.7% of the unigene SSR markers based on significant homology to reported proteins. About 31.7% of the SSRs were present in coding sequences and 68.3% in untranslated regions of the genes. About 87% of the SSRs located in the coding sequences were trinucleotide repeats. Allelic variation at 32 SSR loci produced 98 alleles in 20 cowpea genotypes. The polymorphic information content for the SSR markers varied from 0.10 to 0.83 with an average of 0.53. These unigene SSR markers showed a high rate of transferability (88%) across other Vigna species, thereby expanding their utility. Alignment of unigene sequences with soybean genomic sequences revealed the presence of introns in amplified products of some of the SSR markers. This study presents the distribution of SSRs in the expressed portion of the cowpea genome and is the first report of the development of functional unigene-based SSR markers in cowpea. These SSR markers would play an important role in molecular mapping, comparative genomics, and marker-assisted selection strategies in cowpea and other Vigna species.

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.

Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunfl ower (Helianthus annuus L.) under natural and water-limited states.

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Ali, Soleimani Gezeljeh; Darvishzadeh, Reza; Ebrahimi, Asa; Bihamta, Mohammad Reza

2018-03-01

Sunflower is an important source of edible oil. Drought is known as an important factor limiting the growth and productivity of field crops in most parts of the world. Agricultural biotechnology mainly aims at developing crops with higher tolerance to the challenging environmental conditions, such as drought. This study examined a number of morphological characters, along with relative water content (RWC) in 100 inbred sunflower lines. A 10 × 10 simple lattice design with two replications was employed to measure the mentioned parameters under natural and water-limited states during two successive years. In molecular trial, 30 simple sequence repeat (SSR) primer pairs, as well as 14 inter-retrotransposon amplified polymorphism (IRAP) and 14 retrotransposon-microsatellite amplified polymorphism (REMAP) primer combinations were used for DNA fingerprinting of the lines. Most of the examined characters had lower average values under water-limited than natural states. Maximum and minimum reductions were observed in the cases of yield and oil percentage, respectively. The broad-sense heritabilities for all the examined characters were 0.20-0.73 and 0.10-0.34 under natural and water-limited states, respectively. In the studied samples, 8.97% of the 435 possible locus pairs of the SSRs represented significant linkage disequilibrium (LD) levels. In the association analysis using SSR markers, 22 and 21 markers were identified (P ≤ 0.05) for the studied characters under natural and water-limited states, respectively. The corresponding values were 50 and 37 using retrotransposon-based molecular markers. Some detected markers were communal between the characters under water-limited and natural states. This was in line with the phenotypic correlations detected between the characters. Communal markers facilitate the simultaneous selection of several characters and can thus improve the efficacy of selection based on markers in the plant-breeding activities.

Genetic variation of maize (Zea mays L.) mutants based on ssr analysis

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Hongni, Qin; Yilin, Cai; Chunrong, Yang; Guoqiang, Wang [Maize Research Institute of Southwest University, Chongqing (China)

2008-12-15

52 SSR primers that gave stable profiles amplified in sample of the Maize inbred line '082' and its 48 mutants were selected from 97 primers, and produced 170 polymorphic amplified fragments. The average number of allele per SSR locus was 3.27 with a range from 2 to 6. The polymorphism information content for the SSR loci varied from 0.039 to 0.715 with an average of 0.327. Genetic similarities among the 49 materials ranged from 0.377 to 1.000 with an average of 0.823. The 49 materials were divided into 6 groups by UPGMA. The results indicated that distinct variation existed among mutants. (authors)

Genetic variation of maize (Zea mays L.) mutants based on ssr analysis

International Nuclear Information System (INIS)

Qin Hongni; Cai Yilin; Yang Chunrong; Wang Guoqiang

2008-01-01

52 SSR primers that gave stable profiles amplified in sample of the Maize inbred line '082' and its 48 mutants were selected from 97 primers, and produced 170 polymorphic amplified fragments. The average number of allele per SSR locus was 3.27 with a range from 2 to 6. The polymorphism information content for the SSR loci varied from 0.039 to 0.715 with an average of 0.327. Genetic similarities among the 49 materials ranged from 0.377 to 1.000 with an average of 0.823. The 49 materials were divided into 6 groups by UPGMA. The results indicated that distinct variation existed among mutants. (authors)

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

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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.

Genetic Diversity in Various Accessions of Pineapple [Ananas comosus (L.) Merr.] Using ISSR and SSR Markers.

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Wang, Jian-Sheng; He, Jun-Hu; Chen, Hua-Rui; Chen, Ye-Yuan; Qiao, Fei

2017-12-01

Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers were used to assess the genetic diversity of 36 pineapple accessions that were introduced from 10 countries/regions. Thirteen ISSR primers amplified 96 bands, of which 91 (93.65%) were polymorphic, whereas 20 SSR primers amplified 73 bands, of which 70 (96.50%) were polymorphic. Nei's gene diversity (h = 0.28), Shannon's information index (I = 0.43), and polymorphism information content (PIC = 0.29) generated using the SSR primers were higher than that with ISSR primers (h =  0.23, I = 0.37, PIC = 0.24), thereby suggesting that the SSR system is more efficient than the ISSR system in assessing genetic diversity in various pineapple accessions. Mean genetic similarities were 0.74, 0.61, and 0.69, as determined using ISSR, SSR, and combined ISSR/SSR, respectively. These results suggest that the genetic diversity among pineapple accessions is very high. We clustered the 36 pineapple accessions into three or five groups on the basis of the phylogenetic trees constructed based on the results of ISSR, SSR, and combined ISSR/SSR analyses using the unweighted pair-group with arithmetic averaging (UPGMA) method. The results of principal components analysis (PCA) also supported the UPGMA clustering. These results will be useful not only for the scientific conservation and management of pineapple germplasm but also for the improvement of the current pineapple breeding strategies.

WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes.

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

2018-03-16

Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (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, noncoding RNA (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 Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 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.

Study the Stability of SSR Repeats of pEA29 Plasmid of the Casual Agent of Fire Blight

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S. Baghaee Ravari

2016-02-01

Full Text Available Introduction Fire blight disease causes by Erwinia amylovora infects a wide variety of rosaceous plants. It was first recorded from pear trees in Karaj in year 1990. After that it was observed in many pear and apple orchards of the country. E. amylovora isolates differed slightly in virulence, symptoms and host range which ca be related to different plasmid content. The presence of an universal plasmid, pEA29, has been observed in majority of E. amylovora strains. Short-sequence DNA repeat with eight nt were repeated 3 to 15 times in the PstI fragment of the pEA29 plasmid. Here, the stability of SSR units and efficiency of this method to categorize strains was checked. For this reseaon two methods including amplification and cloning of whole and part of PstI fragment was done and the sequences were compared to eachother. In addition stability was evaluated based on three treatments including long time propagation, keeping strains in cold situation and re-isolation of infected tissues. Materials and Methods In this study 20 strains were purchased from the Iranian Plant Protection Research Institute. Their typical phenotypic tests were examined for all strains. All of then were checked with lateral flow immune chromatography in different serial dilutions. The pathogenicity were aassayed using complete fruit. Direct PCR with A/B primers and nested PCR with AJ75/AJ76 were applied for studied strains. Ten representative strains were selected snf part of PstI fragment amplified using RS1/RS2 primers. The PCR products were purified by QIAquick PCR purification kit (Qiagen, USA, cloned in pGEM-T and were sequenced (Macrogen Inc., Korea. Five of 10 were chosen for stability tests including long time propagation and sub culturing each two week for three months, keeping strains in refrigerator for three months and re-isolation of infected tissues. Results and Discussion In phenotypic tests all studies strains were facultative anaerobic growth, oxidase

Simple sequence repeat marker loci discovery using SSR primer.

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Robinson, Andrew J; Love, Christopher G; Batley, Jacqueline; Barker, Gary; Edwards, David

2004-06-12

Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. With the increase in the availability of DNA sequence information, an automated process to identify and design PCR primers for amplification of SSR loci would be a useful tool in plant breeding programs. We report an application that integrates SPUTNIK, an SSR repeat finder, with Primer3, a PCR primer design program, into one pipeline tool, SSR Primer. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. The results are parsed to Primer3 for locus-specific primer design. The script makes use of a Web-based interface, enabling remote use. This program has been written in PERL and is freely available for non-commercial users by request from the authors. The Web-based version may be accessed at http://hornbill.cspp.latrobe.edu.au/

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.

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

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Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

2015-01-01

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.

Development and characterization of polymorphic genomic-SSR markers in Asian long-horned beetle (Anoplophora glabripennis).

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Liu, Zhaoyang; Tao, Jing; Luo, Youqing

2017-12-01

The Asian long-horned beetle (ALB), Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae: Lamiinae), is a wood-borer and polyphagous xylophage that is native to Asia. It infests and seriously harms healthy trees, and therefore is a cause for considerable environmental concern. The analysis of population genetic structure of ALB and sibling species Anoplophora nobilis (Ganglbauer) will not only help to clarify the relationship between environmental variables and mechanisms of speciation, but also will enhance our understanding of evolutionary processes. However, the known genetic markers, particularly microsatellites, are limited for this species. SSRLocator software was used to analyze the distribution and frequencies of genomic simple sequence repeat (SSR), to infer the basic characteristics of repeat motifs, and to design primers. We developed SSR loci of 2-6 repeated units, including 10,650 perfect SSRs, and found 140 types of repeat motifs. A total of 2621 SSR markers were discovered in ALB whole-genome shotgun sequences. 48 pairs of SSR primers were randomly chosen from 2621 SSR markers, and half of these 48 pairs were polymorphic containing 4 di-, 7 tri-, 2 tetra-, and 11-hexamer SSRs. Four populations test the effectiveness of the primers. These results suggest that our method for whole-genome SSR screening is feasible and efficient, and the SSR markers developed in this study are suitable for further population genetics studies of ALB. Moreover, they may also be useful for the development of SSRs for other Coleoptera.

High-throughput development of genome-wide locus-specific informative SSR markers in wheat

Science.gov (United States)

Although simple sequence repeat (SSR) markers are not new, they are still useful and often used markers in molecular mapping and marker-assisted breeding, particularly in developing countries. However, locus-specific SSR markers could be more useful and informative in wheat breeding and genetic stud...

Characterization and multiplexing of EST-SSR primers in Cynodon (Poaceae) species1.

Science.gov (United States)

Jewell, Margaret C; Frere, Celine H; Prentis, Peter J; Lambrides, Christopher J; Godwin, Ian D

2010-10-01

Cynodon species are multiple-use grasses that display varying levels of adaptation to biotic and abiotic stress. Previously identified EST-SSR primers were characterized and multiplexed to assess the level of genetic diversity present within a collection of almost 1200 Cynodon accessions from across Australia. • Two multiplex reactions were developed comprising a total of 16 EST-SSR markers. All SSR markers amplified across different Cynodon species and different levels of ploidy. The number of alleles ranged from one to eight per locus and the total number of alleles for the germplasm collection was 79. • The 16 markers show sufficient variation for the characterization of Cynodon core collections and analysis of population genetic diversity in Cynodon grasses.

Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.].

Science.gov (United States)

Jia, Xiaoping; Zhang, Zhongbao; Liu, Yinghui; Zhang, Chengwei; Shi, Yunsu; Song, Yanchun; Wang, Tianyu; Li, Yu

2009-02-01

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F(2) population, i.e. "B100" of cultivated S. italica and "A10" of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces' grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together.

Generation of Unbiased Ionospheric Corrections in Brazilian Region for GNSS positioning based on SSR concept

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Monico, J. F. G.; De Oliveira, P. S., Jr.; Morel, L.; Fund, F.; Durand, S.; Durand, F.

2017-12-01

Mitigation of ionospheric effects on GNSS (Global Navigation Satellite System) signals is very challenging, especially for GNSS positioning applications based on SSR (State Space Representation) concept, which requires the knowledge of spatial correlated errors with considerable accuracy level (centimeter). The presence of satellite and receiver hardware biases on GNSS measurements difficult the proper estimation of ionospheric corrections, reducing their physical meaning. This problematic can lead to ionospheric corrections biased of several meters and often presenting negative values, which is physically not possible. In this contribution, we discuss a strategy to obtain SSR ionospheric corrections based on GNSS measurements from CORS (Continuous Operation Reference Stations) Networks with minimal presence of hardware biases and consequently physical meaning. Preliminary results are presented on generation and application of such corrections for simulated users located in Brazilian region under high level of ionospheric activity.

Genetic diversity of Phytophthora sojae isolates in Heilongjiang Province in China assessed by RAPD and EST-SSR

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Wu, J. J.; Xu, P. F.; Liu, L. J.; Wang, J. S.; Lin, W. G.; Zhang, S. Z.; Wei, L.

Random-amplified polymorphic DNA (RAPD) and EST-SSR markers were used to estimate the genetic relationship among thirty-nine P.sojae isolates from three locations in Heilongjiang Province, and nine isolates from Ohio in America were made as reference strains. 10 of 50 RAPD primers and 5 of 33 EST-SSR were polymorphic across 48 P.sojae isolates. Similarity values among P.sojae isolates were from 49% to 82% based on the RAPD data. The similarities based on EST-SSR markers ranged from 47% to 85%. The genetic diversity revealed by EST-SSR marker analysis was higher than that obtained from RAPD. The similarity matrices for the SSR data and the RAPD data were moderately correlated (r = 0.47). Genetic similarity coefficients were also relatively lower, which demonstrated complicated genetic background within each location. The high similarity values range revealed the ability of RAPD/EST-SSR markers to distinguish even among morphological similar phytophthora.

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

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Zhang, Haiyang; Wei, Libin; Miao, Hongmei; Zhang, Tide; Wang, Cuiying

2012-07-16

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. 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 polymorphisms between the parents, and 14

A simple ssr analysis for genetic diversity estimation of maize landraces

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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

Title XVI / Supplemental Security Record Point In Time (SSRPT)

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Social Security Administration — This is the point-in-time database to house temporary Supplemental Security Record (SSR) images produced during the course of the operating day before they can be...

Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars

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In recent years SSR markers have been used widely for genetic analysis. The objective of this study was to use an SSR-based marker system to develop the molecular fingerprints and analyze the genetic relationship of sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers wer...

Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Panicum miliaceum; Poaceae).

Science.gov (United States)

Hou, Siyu; Sun, Zhaoxia; Li, Yaoshen; Wang, Yijie; Ling, Hubin; Xing, Guofang; Han, Yuanhuai; Li, Hongying

2017-07-01

Proso millet ( Panicum miliaceum ; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers. Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple sequence repeat (SSR) markers were identified and used to detect polymorphism among 56 accessions. Population structure and genetic similarity coefficient were estimated. In total, 25,341 unique gene sequences and 4724 SSR loci were obtained from the transcriptome, of which 229 pairs of SSR primers were validated, which resulted in 14 polymorphic genic SSR primers exhibiting 43 total alleles. According to the ratio of polymorphic markers (6.1%, 14/229), there are potentially 288 polymorphic genic SSR markers available for genetic assay development in the future. Bayesian population analyses showed that the 56 accessions comprised two distinct groups. A genetic structure and cluster assay indicated that the accessions from the Loess Plateau of China shared a high genetic similarity coefficient with those from other regions and that there was no correlation between genetic diversity and geographic origin. The transcriptome sequencing data and millet-specific SSR markers developed in this study establish an excellent resource for gene discovery and may improve the development of breeding programs in proso millet in the future.

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.

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

Institute of Scientific and Technical Information of China (English)

Liwu; Zhang; Rongrong; Cai; Minhang; Yuan; Aifen; Tao; Jiantang; Xu; Lihui; Lin; Pingping; Fang; Jianmin; Qi

2015-01-01

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 Co SSR305-120 and Co SSR174-195 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.

Novel and highly informative Capsicum SSR markers and their cross-species transferability.

Science.gov (United States)

Buso, G S C; Reis, A M M; Amaral, Z P S; Ferreira, M E

2016-09-23

This study was undertaken primarily to develop new simple sequence repeat (SSR) markers for Capsicum. As part of this project aimed at broadening the use of molecular tools in Capsicum breeding, two genomic libraries enriched for AG/TC repeat sequences were constructed for Capsicum annuum. A total of 475 DNA clones were sequenced from both libraries and 144 SSR markers were tested on cultivated and wild species of Capsicum. Forty-five SSR markers were randomly selected to genotype a panel of 48 accessions of the Capsicum germplasm bank. The number of alleles per locus ranged from 2 to 11, with an average of 6 alleles. The polymorphism information content was on average 0.60, ranging from 0.20 to 0.83. The cross-species transferability to seven cultivated and wild Capsicum species was tested with a set of 91 SSR markers. We found that a high proportion of the loci produced amplicons in all species tested. C. frutescens had the highest number of transferable markers, whereas the wild species had the lowest. Our results indicate that the new markers can be readily used in genetic analyses of Capsicum.

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

Science.gov (United States)

Chen, Honglin; Liu, Liping; Wang, Lixia; Wang, Suhua; Somta, Prakit; Cheng, Xuzhen

2015-01-01

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.

Assessment of inter- and intra-cultivar variations in olive using SSR markers

Directory of Open Access Journals (Sweden)

Ahmet Ipek

2012-10-01

Full Text Available Olive (Olea europaea L. production in the world has been made by using many cultivars, and the genetic uniformity of commercial cultivars is important for standard olive oil and table olive production. The genetic variation among and within commonly cultivated olive cultivars in Turkey was analyzed using SSR markers. A total of 135 leaf samples were collected from 11 commonly cultivated olive cultivars from 11 provinces in four geographical regions of Turkey. Seven SSR primer pairs generated 46 SSR markers, and the number of SSR markers per primer pair ranged from 4 (UDO-14 to 9 (GAPU-89 with an average of 6.57. This high level of SSR polymorphism suggests that olive production in Turkey has been made using genetically diverse olive cultivars and this high level of genetic variation is probably due to the location of Turkey in the center of the origin of olive. The UPGMA dendrogram, developed to visualize the estimated genetic relationships among the 135 samples, demonstrated that the clustering of olive cultivars was not based on geographical regions of cultivation. Presence of genetic variation was detected within a nationwide grown Turkish olive cultivar, called 'Gemlik'. Olive growers successfully discriminated olive cultivars with distinct morphological and pomological characters. However, there was some confusion about the identification of cultivars with similar phenotypic traits. To prevent misidentification of olive cultivars and to minimize intra-cultivar variation, certified propagation materials which were characterized using DNA based molecular markers should be used during the establishment of new olive orchards.

GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.

Science.gov (United States)

Wang, Xuewen; Wang, Le

2016-01-01

Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

Genetic Diversity and Identification of Chinese-Grown Pecan Using ISSR and SSR Markers

Directory of Open Access Journals (Sweden)

Zhong-Ren Guo

2011-12-01

Full Text Available Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic in the range of 140–1,950 bp for the ISSR and 70 amplified bands (100% polymorphic in the range of 50–350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.

Science.gov (United States)

Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

2011-12-06

Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

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 ...

78 FR 43258 - Privacy Act; System of Records: Human Resources Records, State-31

Science.gov (United States)

2013-07-19

... DEPARTMENT OF STATE [Public Notice 8384] Privacy Act; System of Records: Human Resources Records... system of records, Human Resources Records, State- 31, pursuant to the provisions of the Privacy Act of... State proposes that the current system will retain the name ``Human Resources Records'' (previously...

Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

Science.gov (United States)

Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

2016-01-22

In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea.

Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes.

Science.gov (United States)

Moon, Suyun; Lee, Hwa-Yong; Shim, Donghwan; Kim, Myungkil; Ka, Kang-Hyeon; Ryoo, Rhim; Ko, Han-Gyu; Koo, Chang-Duck; Chung, Jong-Wook; Ryu, Hojin

2017-06-01

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

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.

SSR markers reveal genetic variation between improved cassava ...

African Journals Online (AJOL)

SERVER

2007-12-03

Dec 3, 2007 ... Numerical Taxonomy and Multivariate Analysis System software .... DNA extraction and polymerase chain reaction with SSR .... Primers that have PIC value falling between 0.50 to 0.70 ..... Woodman, Lee M, Porter K (2000).

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.

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.

Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers.

Science.gov (United States)

Dar, Aejaz Ahmad; Mudigunda, Sushma; Mittal, Pramod Kumar; Arumugam, Neelakantan

2017-05-01

Sesame (Sesamum indicum L.) is an ancient oilseed crop known for its nutty seeds and high-quality edible oil. It is an unexplored crop with a great economic potential. The present study deals with assessment of genetic diversity in the crop. Twenty two RAPD and 18 SSR primers were used for analysis of the 47 different sesame accessions grown in different agroclimatic zones of India. A total of 256 bands were obtained with RAPD primers, of which 191 were polymorphic. SSR primers gave 64 DNA bands, of which all of were polymorphic. The Jaccard's similarity coefficient of RAPD, SSR, and pooled RAPD and SSR data ranged from 0.510 to 0.885, 0.167 to 0.867, and 0.505 to 0.853, respectively. Maximum polymorphic information content was reported with SSRs (0.194) compared to RAPDs (0.186). Higher marker index was observed with RAPDs (1.426) than with SSRs (0.621). Similarly, maximum resolving power was found with RAPD (4.012) primers than with SSRs (0.884). The RAPD primer RPI-B11 and SSR primer S16 were the most informative in terms of describing genetic variability among the varieties under study. At a molecular level, the seed coat colour was distinguishable by the presence and absence of a group of marker amplicon/s. White and brown seeded varieties clustered close to each other, while black seeded varieties remained distanced from the cluster. In the present study, we found higher variability in Sesamum indicum L. using RAPD and SSR markers and these could assist in DNA finger printing, conservation of germplasm, and crop improvement.

Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties.

Science.gov (United States)

Singh, Nivedita; Choudhury, Debjani Roy; Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R K; Singh, N K; Singh, Rakesh

2013-01-01

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.

JPRS Report, Soviet Union, Political Affairs.

Science.gov (United States)

1989-11-30

with recordings of popular and modern music . In secondary school No. 6, not far from Lenin Square, we are preparing for the festive opening of a...Kirghiz SSR State Committee for Physical Culture and Sport into a Kirghiz SSR State Committee for Physical Culture, Sport, and Tourism . Ratification...Comrade Eshim Kutmanalnev as chairman of the Kir- ghiz SSR State Committee for Physical Culture and Tourism , Comrade Dzhumakadyr Ubyshev, as

Generation of human auditory steady-state responses (SSRs). II: Addition of responses to individual stimuli.

Science.gov (United States)

Santarelli, R; Maurizi, M; Conti, G; Ottaviani, F; Paludetti, G; Pettorossi, V E

1995-03-01

In order to investigate the generation of the 40 Hz steady-state response (SSR), auditory potentials evoked by clicks were recorded in 16 healthy subjects in two stimulating conditions. Firstly, repetition rates of 7.9 and 40 Hz were used to obtain individual middle latency responses (MLRs) and 40 Hz-SSRs, respectively. In the second condition, eight click trains were presented at a 40 Hz repetition rate and an inter-train interval of 126 ms. We extracted from the whole train response: (1) the response-segment taking place after the last click of the train (last click response, LCR), (2) a modified LCR (mLCR) obtained by clearing the LCR from the amplitude enhancement due to the overlapping of the responses to the clicks preceding the last within the stimulus train. In comparison to MLRs, the most relevant feature of the evoked activity following the last click of the train (LCRs, mLCRs) was the appearance in the 50-110 ms latency range of one (in 11 subjects) or two (in 2 subjects) additional positive-negative deflections having the same periodicity as that of MLR waves. The grand average (GA) of the 40 Hz-SSRs was compared with three predictions synthesized by superimposing: (1) the GA of MLRs, (2) the GA of LCRs, (3) the GA of mLCRs. Both the MLR and mLCR predictions reproduced the recorded signal in amplitude while the LCR prediction amplitude resulted almost twice that of the 40 Hz-SSR. With regard to the phase, the MLR, LCR and mLCR closely predicted the recorded signal. Our findings confirm the effectiveness of the linear addition mechanism in the generation of the 40 Hz-SSR. However the responses to individual stimuli within the 40 Hz-SSR differ from MLRs because of additional periodic activity. These results suggest that phenomena related to the resonant frequency of the activated system may play a role in the mechanisms which interact to generate the 40 Hz-SSR.

Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Panicum miliaceum; Poaceae)1

Science.gov (United States)

Hou, Siyu; Sun, Zhaoxia; Li, Yaoshen; Wang, Yijie; Ling, Hubin; Xing, Guofang; Han, Yuanhuai; Li, Hongying

2017-01-01

Premise of the study: Proso millet (Panicum miliaceum; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers. Methods: Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple sequence repeat (SSR) markers were identified and used to detect polymorphism among 56 accessions. Population structure and genetic similarity coefficient were estimated. Results: In total, 25,341 unique gene sequences and 4724 SSR loci were obtained from the transcriptome, of which 229 pairs of SSR primers were validated, which resulted in 14 polymorphic genic SSR primers exhibiting 43 total alleles. According to the ratio of polymorphic markers (6.1%, 14/229), there are potentially 288 polymorphic genic SSR markers available for genetic assay development in the future. Bayesian population analyses showed that the 56 accessions comprised two distinct groups. Discussion: A genetic structure and cluster assay indicated that the accessions from the Loess Plateau of China shared a high genetic similarity coefficient with those from other regions and that there was no correlation between genetic diversity and geographic origin. The transcriptome sequencing data and millet-specific SSR markers developed in this study establish an excellent resource for gene discovery and may improve the development of breeding programs in proso millet in the future. PMID:28791202

78 FR 8217 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

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2013-02-05

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0071] Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations of Unfairness, Prejudice, Partiality, Bias... the third column, the fourth line under the ``Summary'' heading, change ``SSR-13-Xp'' to ``SSR-13-1p...

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.

Development and mapping of a public reference set of SSR markers in Lolium perenne L.

NARCIS (Netherlands)

Bach, J.L.; Muylle, H.; Arens, P.F.P.; Andersen, C.H.; Bach Holm, P.; Ghesquiere, M.; Julier, B.; Lubberstedt, T.; Nielsen, K.K.; Riek, de J.; Roldán-Ruiz, I.; Roulund, N.; Taylor, C.; Vosman, B.J.; Barre, P.

2005-01-01

We report on the characterization and mapping of 76 simple sequence repeat (SSR) markers for Lolium perenne. These markers are publicly available or obtained either from genomic libraries enriched for SSR motifs or L. perenne expressed sequence tag (EST) clones. Four L. perenne mapping populations

Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers.

Science.gov (United States)

Pandey, Sudhakar; Ansari, Waquar Akhter; Pandey, Maneesh; Singh, Bijendra

2018-02-01

In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37-46.9, number of fruits/plant (1.33-5.80), average fruit weight (41-333), vine length (36-364), relative water content (58.5-92.7), electrolyte leakage (15.9-37.1), photosynthetic efficiency (0.40-0.75) and chlorophyll concentration index (11.1-28.6). The pair wise Jaccard similarity coefficient ranged from 0.00 to 0.27 for quantitative traits and 0.24 to 0.96 for EST-SSR markers indicating that the accessions represent genetically diverse populations. With twenty-one EST-SSR markers, polymorphism revealed among 40 cucumber genotypes, number of alleles varied 2-6 with an average 3.05. Polymorphism information content varied from 0.002 to 0.989 (mean = 0.308). The number of effective allele (Ne), expected heterozygosity (He) and unbiased expected heterozygosity (uHe) of these EST-SSRs were 1.079-1.753, 0.074-0.428 and 0.074-0.434, respectively. Same 21 EST-SSR markers transferability checked in four other Cucumis species: snapmelon ( Cucumis melo var. momordica ), muskmelon ( Cucumis melo L.), pickling melon ( Cucumis melo var. conomon ) and wild muskmelon ( Cucumis melo var. agrestis ) with frequency of 61.9, 95.2, 76.2, and 76.2%, respectively. Present study provides useful information on variability, which can assist geneticists with desirable traits for cucumber germplasm utilization. Observed physiological parameters may assists in selection of genotype for abiotic stress tolerance also, EST-SSR markers may be useful for genetic studies in related species.

Chromosomal location of genomic SSR markers associated

Indian Academy of Sciences (India)

Among the same earlier tested 230 primers, one SSR marker (Xgwm311) also amplified a fragment which is present in the resistant parent and in the resistant bulks, but absent in the susceptible parent and in the susceptible bulks. To understand the chromosome group location of these diagnostic markers, Xgwm382 and ...

Development and characterization of EST-SSR markers for Ottelia acuminata var. jingxiensis (Hydrocharitaceae).

Science.gov (United States)

Li, Zhi-Zhong; Lu, Meng-Xue; Saina, Josphat K; Gichira, Andrew W; Wang, Qing-Feng; Chen, Jin-Ming

2017-11-01

Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis . One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata , and 12 amplified in each of the other three varieties of O. acuminata . These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata .

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

Indian Academy of Sciences (India)

2014-08-18

Aug 18, 2014 ... RESEARCH NOTE. Physical location of SSR regions and cytogenetic instabilities in Pinus ... first cytogenetic study in Scots pine using SSRs in FISH experiments. ... Science, Mannheim, Germany) according to manufacturer's.

Characterization of variable EST SSR markers for Norway spruce (Picea abies L.

Directory of Open Access Journals (Sweden)

Spiess Nadine

2011-10-01

Full Text Available Abstract Background Norway spruce is widely distributed across Europe and the predominant tree of the Alpine region. Fast growth and the fact that timber can be harvested cost-effectively in relatively young populations define its status as one of the economically most important tree species of Northern Europe. In this study, EST derived simple sequence repeat (SSR markers were developed for the assessment of putative functional diversity in Austrian Norway spruce stands. Results SSR sequences were identified by analyzing 14,022 publicly available EST sequences. Tri-nucleotide repeat motifs were most abundant in the data set followed by penta- and hexa-nucleotide repeats. Specific primer pairs were designed for sixty loci. Among these, 27 displayed polymorphism in a testing population of 16 P. abies individuals sampled across Austria and in an additional screening population of 96 P. abies individuals from two geographically distinct Austrian populations. Allele numbers per locus ranged from two to 17 with observed heterozygosity ranging from 0.075 to 0.99. Conclusions We have characterized variable EST SSR markers for Norway spruce detected in expressed genes. Due to their moderate to high degree of variability in the two tested screening populations, these newly developed SSR markers are well suited for the analysis of stress related functional variation present in Norway spruce populations.

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

Indian Academy of Sciences (India)

Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. CHUANXIANG LIU, DAOJUN YUAN and ZHONGXU LIN. ∗. National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan),. Huazhong Agricultural University, Wuhan ...

Tibiofemoral subchondral surface ratio (SSR) is a predictor of osteoarthritis symptoms and radiographic progression: data from the Osteoarthritis Initiative (OAI).

Science.gov (United States)

Everhart, J S; Siston, R A; Flanigan, D C

2014-06-01

Symptomatic knee osteoarthritis (OA) is poorly correlated with radiographic severity, but subchondral bone measures may be useful for risk assessment as bone shape is grossly unaffected at early radiographic stages. We sought to determine whether compartment-specific size mismatch in the naturally asymmetric tibiofemoral joint, measured as tibiofemoral subchondral surface ratio (SSR): (1) predicts incident symptoms, (2) predicts incident or progressive OA, (3) is reproducible and time invariant. OA Initiative participants with baseline MRIs and up to 48-month follow-up (n = 1,338) were analyzed. Logistic regression was used to determine the association between SSR and incident symptoms, incident OA, and progression of OA after adjusting for demographic, radiologic, injury-related, and lifestyle-related factors. Reproducibility was assessed as % coefficient of variation (CV) on repeat MRI studies at baseline and 24 months. Increased medial SSR is protective against incident symptoms at 48 months (per 0.1 increase: OR 0.48 CI 0.30, 0.75; P = 0.001). Increased lateral SSR values are protective against lateral OA incidence (OR 0.23 CI 0.06, 0.77; P = 0.016) or progression (OR 0.66 CI 0.43, 0.99; P = 0.049) at 24 months. Both medial and lateral SSR are stable over time (medial: mean change 0.001 SD 0.016; lateral: mean change 0.000 SD 0.017) and are highly reproducible (3.0% CV medial SSR; 2.7% CV lateral SSR). A larger medial SSR is protective against developing OA-related symptoms. A larger lateral SSR is protective against lateral OA incidence or progression. Finally, lateral and medial SSR are stable over time and are highly reproducible across MRI studies. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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

2016-01-01

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 genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5-8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs.

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.

Development and characterization of genic SSR markers from low ...

Indian Academy of Sciences (India)

Development and characterization of genic SSR markers from low depth genome ... A variety of molecular markers are currently ... chloroform method (Sambrook et al. 1989). ..... Available online, http://www.iucnredlist.org/details/168255/0.

Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties.

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Nivedita Singh

Full Text Available Simple sequence repeat (SSR and Single Nucleotide Polymorphic (SNP, the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.

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.

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

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Dai, Yueting; Su, Wenying; Song, Bing; Li, Yu; Fu, Yongping

2017-01-01

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. PMID:29149037

Engaging Non-State Security Providers: Whither the Rule of Law?

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Timothy Donais

2017-07-01

Full Text Available The primacy of the rule of law has long been seen as one of the essential principles of security sector reform (SSR programming, and part of the larger gospel of SSR is that the accountability of security providers is best guaranteed by embedding security governance within a rule of law framework. Acknowledging the reality of non-state security provision, however, presents a challenge to thinking about SSR as merely the extension of the rule of law into the security realm, in large part because whatever legitimacy non-state security providers possess tends to be grounded in 'extralegal' foundations. This paper – more conceptual than empirical in its approach – considers the implications of hybrid forms of security governance for thinking about the relationship between SSR and rule of law promotion, and argues that the rule of law still provides a useful source of strategic direction for SSR programming.

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

Indian Academy of Sciences (India)

1Department of Molecular Biology and Genetic Engineering, 2Ranichauri Hill Campus, G. B. Pant University of Agriculture ... Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the ...... project programme.

Supplementary data: Development of SSR markers and construction ...

Indian Academy of Sciences (India)

Supplementary data: Development of SSR markers and construction of a linkage map in jute. Moumita Das, Sumana Banerjee, Raman Dhariwal, Shailendra Vyas, Reyazul R. Mir, Niladri Topdar, Avijit Kundu, Jitendra P. Khurana, Akhilesh K. Tyagi,. Debabrata Sarkar, Mohit K. Sinha, Harindra S. Balyan and Pushpendra K.

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

Science.gov (United States)

Gil, Jinsu; Um, Yurry; Kim, Serim; Kim, Ok Tae; Koo, Sung Cheol; Reddy, Chinreddy Subramanyam; Kim, Seong-Cheol; Hong, Chang Pyo; Park, Sin-Gi; Kim, Ho Bang; Lee, Dong Hoon; Jeong, Byung-Hoon; Chung, Jong-Wook; Lee, Yi

2017-09-21

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 ( H O ) values, and the expected heterozygosity ( H E ) 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.

1 Tbit/inch2 Recording in Angular-Multiplexing Holographic Memory with Constant Signal-to-Scatter Ratio Schedule

Science.gov (United States)

Hosaka, Makoto; Ishii, Toshiki; Tanaka, Asato; Koga, Shogo; Hoshizawa, Taku

2013-09-01

We developed an iterative method for optimizing the exposure schedule to obtain a constant signal-to-scatter ratio (SSR) to accommodate various recording conditions and achieve high-density recording. 192 binary images were recorded in the same location of a medium in approximately 300×300 µm2 using an experimental system embedded with a blue laser diode with a 405 nm wavelength and an objective lens with a 0.85 numerical aperture. The recording density of this multiplexing corresponds to 1 Tbit/in.2. The recording exposure time was optimized through the iteration of a three-step sequence consisting of total reproduced intensity measurement, target signal calculation, and recording energy density calculation. The SSR of pages recorded with this method was almost constant throughout the entire range of the reference beam angle. The signal-to-noise ratio of the sampled pages was over 2.9 dB, which is higher than the reproducible limit of 1.5 dB in our experimental system.

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

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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.

GENETIC DIVERSITY OF S3 MAIZE GENOTYPES RESISTANT TO DOWNY MILDEW BASED ON SSR MARKERS

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Amran Muis

2016-02-01

Full Text Available The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and  genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.

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

Indian Academy of Sciences (India)

All results were adjusted for multiple simul- taneous ... ated from HWE after Bonferroni correction (adjusted P = 0.0017) ... ity test of the designed SSR markers. In the 30 examined. S. undulata samples, the PIC value of the 29 newly devel-.

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.

77 FR 65049 - Privacy Act; System of Records: Translator and Interpreter Records, State-37

Science.gov (United States)

2012-10-24

... DEPARTMENT OF STATE [Public Notice 8066] Privacy Act; System of Records: Translator and... an existing system of records, Translator and Interpreter Records, State-37, pursuant to the... INFORMATION: The Department of State proposes that the current system will retain the name ``Translator and...

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

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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

Differential transferability of EST-SSR primers developed from diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Th. elongatum

Science.gov (United States)

Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid T...

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".

Simple sequence repeat (SSR)-based genetic variability among ...

African Journals Online (AJOL)

The objective of this study was to compare if simple sequence repeat (SSR) markers could correctly identify peanut genotypes with difference in specific leaf weight (SLW) and relative water content (RWC). Four peanut genotypes and two water regimes (FC and 1/3 available water; 1/3 AW) were arranged in factorial ...

Insight into the genetic variability analysis and cultivar identification of tall fescue by using SSR markers.

Science.gov (United States)

Fu, Kaixin; Guo, Zhihui; Zhang, Xinquan; Fan, Yan; Wu, Wendan; Li, Daxu; Peng, Yan; Huang, Linkai; Sun, Ming; Bai, Shiqie; Ma, Xiao

2016-01-01

Genetic diversity of 19 forage-type and 2 turf-type cultivars of tall fescue ( Festuca arundinacea Schreb.) was revealed using SSR markers in an attempt to explore the genetic relationships among them, and examine potential use of SSR markers to identify cultivars by bulked samples. A total of 227 clear band was scored with 14 SSR primers and out of which 201 (88.6 %) were found polymorphic. The percentage of polymorphic bands (PPB) per primer pair varied from 62.5 to 100 % with an average of 86.9 %. The polymorphism information content (PIC) value ranged from 0.116 to 0.347 with an average of 0.257 and the highest PIC value (0.347) was noticed for primer NFA040 followed by NFA113 (0.346) whereas the highest discriminating power (D) of 1 was shown in NFA037 and LMgSSR02-01C. A Neighbor-joining dendrogram and the principal component analysis identified six major clusters and grouped the cultivars in agreement with their breeding histories. STRUCTURE analysis divided these cultivars into 3 sub-clades which correspond to distance based groupings. These findings indicates that SSR markers by bulking strategy are a useful tool to measure genetic diversity among tall fescue cultivars and could be used to supplement morphological data for plant variety protection.

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.

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

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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.

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

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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.

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

Science.gov (United States)

Chen, Honglin; Wang, Lixia; Wang, Suhua; Liu, Chunji; Blair, Matthew Wohlgemuth; Cheng, Xuzhen

2015-01-01

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 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 or comparative mapping and genetic analyses of various Vigna species.

Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers.

Science.gov (United States)

Siew, Ging Yang; Ng, Wei Lun; Tan, Sheau Wei; Alitheen, Noorjahan Banu; Tan, Soon Guan; Yeap, Swee Keong

2018-01-01

Durian ( Durio zibethinus ) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, H E  = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10 -3 . Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called "clones", "varieties", or "cultivars". Such matters have a direct impact on the regulation and management of durian genetic resources in the region.

Characterization and compilation of polymorphic simple sequence repeat (SSR markers of peanut from public database

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Zhao Yongli

2012-07-01

Full Text Available Abstract Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L. genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5% within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5% was the most abundant followed by AAG (12.1%, AAT (10.9%, and AT (10.3%.The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

Repressive Actions of the State Security Communities Against ≪True Orthodox Church≫ Structuries in the Ukrainian SSR (1944–1953 (continued

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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.

Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

Science.gov (United States)

Bosamia, Tejas C.; Mishra, Gyan P.; Thankappan, Radhakrishnan; Dobaria, Jentilal R.

2015-01-01

With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81%) sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86%) were the most abundant followed by di-nucleotide repeats (27.51%) while AG/CT (20.7%) and AAG/CTT (13.25%) were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62%) primer pairs yielded clear and scorable PCR products and 39 (10.66%) primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut. PMID:26046991

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.

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.

Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers.

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Filippi, Carla V; Aguirre, Natalia; Rivas, Juan G; Zubrzycki, Jeremias; Puebla, Andrea; Cordes, Diego; Moreno, Maria V; Fusari, Corina M; Alvarez, Daniel; Heinz, Ruth A; Hopp, Horacio E; Paniego, Norma B; Lia, Veronica V

2015-02-13

Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent

76 FR 52378 - Privacy Act; System of Records: State-76, Personal Services Contractor Records

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2011-08-22

... Services Contractor Records SUMMARY: Notice is hereby given that the Department of State proposes to create a new system of records, Personal Services Contractor Records, State-76, pursuant to the provisions... July 20, 2011. It is proposed that the new system be named ``Personal Services Contractor Records.'' It...

Your Lung Operation: After Your Operation

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Full Text Available ... Features of the SSR CMS MIPS ABS Continuous Certification Requirements SSR Login MIPS Resources and Education Quality ... State Legislation Tracked by the College Maintenance of Certification Quality Quality Quality Electronic Health Records (EHR) Incentive ...

Ostomy Home Skills Program

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Full Text Available ... Features of the SSR CMS MIPS ABS Continuous Certification Requirements SSR Login MIPS Resources and Education Quality ... State Legislation Tracked by the College Maintenance of Certification Quality Quality Quality Electronic Health Records (EHR) Incentive ...

Three vibrio-resistance related EST-SSR markers revealed by selective genotyping in the clam Meretrix meretrix.

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Nie, Qing; Yue, Xin; Chai, Xueliang; Wang, Hongxia; Liu, Baozhong

2013-08-01

The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker-trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P SSR markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits.

Science.gov (United States)

Hazra, Anjan; Dasgupta, Nirjhar; Sengupta, Chandan; Das, Sauren

2017-07-06

Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program.

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.

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

[EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

Science.gov (United States)

Yuan, Can; Peng, Fang; Yang, Ze-Mao; Zhong, Wen-Juan; Mou, Fang-Sheng; Gong, Yi-Yun; Ji, Pei-Cheng; Pu, De-Qiang; Huang, Hai-Yan; Yang, Xiao; Zhang, Chao

2017-09-01

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding. Copyright© by the Chinese Pharmaceutical Association.

Development of novel EST-SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus.

Science.gov (United States)

Feng, Bing; Yi, Soojin V; Zhang, Manman; Zhou, Xiaoyun

2018-01-01

The co-existence of several ploidy types in natural populations makes the cyprinid loach Misgurnus anguillicaudatus an exciting model system to study the genetic and phenotypic consequences of ploidy variations. A first step in such effort is to identify the specific ploidy of an individual. Currently popular methods of karyotyping via cytological preparation or flow cytometry require a large amount of tissue (such as blood) samples, which can be damaging or fatal to the fishes. Here, we developed novel microsatellite markers (SSR markers) from M. anguillicaudatus and show that they can effectively discriminate ploidy using samples collected in a minimally invasive way. Specifically, we generated whole genome transcriptomes from multiple M. anguillicaudatus using the Illumina paired-end sequencing. Approximately 150 million raw reads were assembled into 76,544 non-redundant unigenes. A total of 8,194 potential SSR markers were identified. We selected 98 pairs with more than five tandem repeats for further assays. Out of 45 putative EST-SSR markers that successfully amplified and harbored polymorphism in diploids, 11 markers displayed high variability in tetraploids. We further demonstrate that a set of five EST-SSR markers selected from these are sufficient to distinguish ploidy levels, by first validating them on 69 reference specimens with known ploidy levels and then subsequently using fresh-collected 96 ploidy-unknown specimens. The results from EST-SSR markers are highly concordant with those from independent flow cytometry analysis. The novel EST-SSR markers developed here should facilitate genetic studies of polyploidy in the emerging model system M. anguillicaudatus.

Analysis of esterase isozyme and SSR for mutagenic progenies induced by space mutation in mustard

International Nuclear Information System (INIS)

Shen Jinjuan; Liu Yihua; Zhang Zhaorong; Ran Guangkui; Zhao Shouzhong; Xiao Li

2012-01-01

Seeds of five mustard (Brassica juncea Coss) varieties were carried into outer space by 'Shijian No.8' satellite. After five years' consecutive planting and selection, ten relatively stable mutant lines were obtained, which had significant variation in agronomic and economic characters. The mutant lines and their original varieties without space mutation treatment as control were studied by esterase isozyme and SSR analyses. Electrophoresis analysis of esterase isozymes indicated that there were differences between mutant lines and their controls in enzyme types and enzyme activity. Different mustard varieties had different enzymographs, and so did the mutants induced by space mutation, which shows different sensitivity among different mustard varieties. The SSR analysis showed that large differences were found in the SSR loci between mutant lines and their original variety, the variation frequency was between 9.52% and 57.14% with an average frequency of 26.19% for all the mutant lines. Among the mutant SSR loci, about 56.36% showed changes in band number and 43.64% in molecular weight. These results indicated that the ten mutant lines had large genetic difference in phenotype, genomic sequence and gene expression, and the outer space mutation would be an effective method to develop new mustard germplasm and variety. (authors)

Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco.

Science.gov (United States)

Tong, Zhijun; Xiao, Bingguang; Jiao, Fangchan; Fang, Dunhuang; Zeng, Jianmin; Wu, Xingfu; Chen, Xuejun; Yang, Jiankang; Li, Yongping

2016-06-01

Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date.

Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication.

Science.gov (United States)

Xia, Xinyao; Luan, Lin Lin; Qin, Guanghua; Yu, Li Fang; Wang, Zhi Wei; Dong, Wan Chen; Song, Yumin; Qiao, Yuling; Zhang, Xian Sheng; Sang, Ya Lin; Yang, Long

2017-12-20

Molecular markers are efficient tools for breeding and genetic studies. However, despite their ecological and economic importance, their development and application have long been hampered. In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences. Larger motifs, including hexamers and heptamers, accounted for most of the seven different types of SSR loci. Within these loci, A/T bases comprised a significantly larger proportion of sequence than G/C. SSR and ILP markers exhibited an alternative distribution pattern. Most SSRs were monomorphic markers, and the proportions of polymorphic markers were positively correlated with genome size. By verifying with all 16 tree species, 54 SSR, 418 ILP, and four PIP universal markers were obtained, and their efficiency was examined by PCR. A combination of five SSR and six ILP markers were used for the phylogenetic analysis of 30 willow samples, revealing a positive correlation between genetic diversity and geographic distance. We also found that SSRs can be used as tools for duplication analysis. Our findings provide important foundations for the development of breeding and genetic studies in tree species.

76 FR 76215 - Privacy Act; System of Records: State-78, Risk Analysis and Management Records

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2011-12-06

... a system of records, Risk Analysis and Management Records, State-78, pursuant to the provisions of... INFORMATION: The Department of State proposes that the new system will be ``Risk Analysis and Management.... These standard routine uses apply to State-78, Risk Analysis and Management Records. POLICIES AND...

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers.

Science.gov (United States)

Korir, N K; Diao, W; Tao, R; Li, X; Kayesh, E; Li, A; Zhen, W; Wang, S

2014-01-08

The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

Development of a simple sequence repeat (SSR) marker set to ...

African Journals Online (AJOL)

GREGORY

2010-08-23

Aug 23, 2010 ... varieties. Tuber seeds of most of these varieties are not produced and distributed in an organized way ... races from Canary Islands using 19 SSR markers. The ... The aim of the current study was to determine a set of.

Linkage Map of a Gene Controlling Zero Tannins (zt-1 in Faba Bean (Vicia faba L. with SSR and ISSR Markers

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Wanwei Hou

2018-05-01

Full Text Available Faba bean (Vicia faba L., a partially allogamous species, is rich in protein. Condensed tannins limit the use of faba beans as food and feed. Two recessive genes, zt-1 and zt-2, control the zero tannin content in faba bean and promote a white flower phenotype. To determine the inheritance and develop a linkage map for the zt-1 gene in the faba bean germplasm M3290, F2 and F3 progenies were derived from the purple flower and high tannin content genotypes Qinghai12 and zt-1 line M3290, respectively. Genetic analysis verified a single recessive gene for zero tannin content and flower colour. In total, 596 SSR markers and 100 ISSR markers were used to test the polymorphisms between the parents and bulks for the contrasting flower colour via Bulked Segregant Analysis (BSA. Subsequently, six SSR markers and seven ISSR markers were used to genotype the entire 413 F2 population. Linkage analysis showed that the zt-1 gene was closely linked to the SSR markers SSR84 and M78, with genetic distances of 2.9 and 5.8 cM, respectively. The two flanked SSR markers were used to test 34 faba bean genotypes with different flower colours. The closely linked SSR marker SSR84 predicted the zt-1 genotypes with absolute accuracy. The results from the marker-assisted selection (MAS from this study could provide a solid foundation for further faba bean breeding programmes.

Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

Science.gov (United States)

Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

2012-01-01

Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function. PMID:22368382

The Non-Peptide Vasopressin V1b Receptor Antagonist, SSR149415, Ameliorates Spermatogenesis Function in a Mouse Model of Chronic Social Defeat Stress.

Science.gov (United States)

Wang, Bin; Zhou, Jian; Zhuang, Yan-Yan; Wang, Liang-Liang; Pu, Jin-Xian; Huang, Yu-Hua; Xia, Fei; Lv, Jin-Xing

2017-11-01

To determine the effects of SSR149415 on testis and spermatogenesis in male mice subjected to chronic social defeat stress, C57BL/6 male mice were divided into two groups: Control and Stress. Then Stress group was subdivided into four subgroups administered water, SSR149415 (1 mg/kg/day), SSR149415 (10 mg/kg/day), SSR149415 (30 mg/kg/day), respectively. The behavioral alterations revealed by social interaction test and open field test were measured. The physical indices, including body weight and gonad weight (testis and epididymis) as well as testis/body weight and cauda epididymis/body weight were detected. Serum hormones, including testosterone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH) were determined. Sperm count and abnormality as well as testicular histology structure were assessed. The germ cells apoptosis were also evaluated. Chronic social defeat stress-induced behavioral abnormality, as well as gonad atrophy (testis and epididymis) was significantly alleviated in stressed male mice exposed to SSR149415. Regressed serum testosterone levels and elevated serum FSH and LH levels exhibited by stressed male mice were observably reversed following SSR149415 administration. Chronic social defeat stress-induced damage in testicular histology structure and semen quality were also improved after SSR149415 administration. In addition, SSR149415 significantly reversed chronic social defeat stress-induced germ cells apoptosis. Overall, we provide clear evidence indicating the amelioration of chronic social defeat stress-induced behavioral abnormality and testicular dysfunction via SSR149415, promoting the development of drug-directed therapy against this disease. J. Cell. Biochem. 118: 3891-3898, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers

Science.gov (United States)

Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

2016-01-01

Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies. PMID:26960153

Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers.

Science.gov (United States)

Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

2016-01-01

Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies.

Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species.

Science.gov (United States)

Satya, Pratik; Paswan, Pramod Kumar; Ghosh, Swagata; Majumdar, Snehalata; Ali, Nasim

2016-06-01

Cross-species transferability is a quick and economic method to enrich SSR database, particularly for minor crops where little genomic information is available. However, transferability of SSR markers varies greatly between species, genera and families of plant species. We assessed confamiliar transferability of SSR markers from cotton (Gossypium hirsutum) and jute (Corchorus olitorius) to 22 species distributed in different taxonomic groups of Malvaceae. All the species selected were potential industrial crop species having little or no genomic resources or SSR database. Of the 14 cotton SSR loci tested, 13 (92.86 %) amplified in G. arboreum and 71.43 % exhibited cross-genera transferability. Nine out of 11 jute SSRs (81.81 %) showed cross-transferability across genera. SSRs from both the species exhibited high polymorphism and resolving power in other species. The correlation between transferability of cotton and jute SSRs were highly significant (r = 0.813). The difference in transferability among species was also significant for both the marker groups. High transferability was observed at genus, tribe and subfamily level. At tribe level, transferability of jute SSRs (41.04 %) was higher than that of cotton SSRs (33.74 %). The tribe Byttnerieae exhibited highest SSR transferability (48.7 %). The high level of cross-genera transferability (>50 %) in ten species of Malvaceae, where no SSR resource is available, calls for large scale transferability testing from the enriched SSR databases of cotton and jute.

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

International Nuclear Information System (INIS)

Wang Tiegu; Huang Qunce; Feng Weisen

2007-01-01

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

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.

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

Energy Technology Data Exchange (ETDEWEB)

Tiegu, Wang [Henan Provincial Key Laboratory of Ion Beam Bio-Engineering, Zhengzhou University, Zhengzhou 450052 (China); Qunce, Huang [Henan Provincial Key Laboratory of Ion Beam Bio-Engineering, Zhengzhou University, Zhengzhou 450052 (China); Weisen, Feng [Luoyang Institute of Agricultural Science, Luoyang 471022 (China)

2007-10-15

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.

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh

Science.gov (United States)

2011-01-01

Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR

SSR: What's in "School Science Review" for "PSR" Readers?

Science.gov (United States)

Lakin, Liz

2004-01-01

This article summarises ideas and developments in teaching and learning in science of relevance to "Primary Science Review" ("PSR") readers from three recent issues (309, 310, and 311) of "School Science Review" ("SSR"), the ASE journal for science education 11-19. The themes running through these are: ICT, the implications for science education…

Optimization of the Geometric Beta for the SSR2 Cavities of the Project X

International Nuclear Information System (INIS)

Solyak, N.; Vostrikov, A.; Yakovlev, V.P.; Awida, M.H.; Berrutti, P.; Gonin, I.V.

2012-01-01

Project X based on the 3 GeV CW superconducting Linac and is currently in the R and D phase. The CW SC Linac starts from a low-energy SCRF section (2.1 - 165 MeV) containing three different types of resonators. HWR f = 162.5 MHz (2.1 - 11 MeV) having beta= 0.11, SSR1 f = 325 MHz (11 - 35 MeV) having beta = 0.21. In this paper we present the analysis that lead to the final design of SSR2 f = 325 MHz cavity (35 - 165 MeV). We present the results of optimization of the geometric beta and the comparison between single, double and triple spoke resonators used in Project X frontend. A β optimization has been carried out for the last spoke cavity section of Project X front end. The optimization process of β opt for a single spoke resonator family SSR2 shown that β opt = 0.47 looks better than the previous choice, which is β opt = 0.4. This change can save some cavities and provide the same final energy for this section, 160 MeV. Single double and triple spoke resonator performances have been compared. The best option is the single spoke resonator SSR2 because the NTTF of a multi-spoke resonator is much narrower than a single one. In the energy range considered (40-160 MeV) the most efficient resonator is the single spoke one.

Genetic diversity and population structure of Brassica oleracea germplasm in Ireland using SSR markers.

Science.gov (United States)

El-Esawi, Mohamed A; Germaine, Kieran; Bourke, Paula; Malone, Renee

2016-01-01

The most economically important Brassica oleracea species is endangered in Ireland, with no prior reported genetic characterization studies. This study assesses the genetic diversity, population structure and relationships of B. oleracea germplasm in Ireland using microsatellite (SSRs) markers. A total of 118 individuals from 25 accessions of Irish B. oleracea were genotyped. The SSR loci used revealed a total of 47 alleles. The observed heterozygosity (0.699) was higher than the expected one (0.417). Moreover, the average values of fixation indices (F) were negative, indicating excess of heterozygotes in all accessions. Polymorphic information content (PIC) values of SSR loci ranged from 0.27 to 0.66, with an average of 0.571, and classified 10 loci as informative markers (PIC>0.5) to differentiate among the accessions studied. The genetic differentiation among accessions showed that 27.1% of the total genetic variation was found among accessions, and 72.9% of the variation resided within accessions. The averages of total heterozygosity (H(T)) and intra-accession genetic diversity (H(S)) were 0.577 and 0.442, respectively. Cluster analysis of SSR data distinguished among kale and Brussels sprouts cultivars. This study provided a new insight into the exploitation of the genetically diverse spring cabbages accessions, revealing a high genetic variation, as potential resources for future breeding programs. SSR loci were effective for differentiation among the accessions studied. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Characterization of genetic diversity in chickpea using SSR markers, Start Codon Targeted Polymorphism (SCoT) and Conserved DNA-Derived Polymorphism (CDDP).

Science.gov (United States)

Hajibarat, Zahra; Saidi, Abbas; Hajibarat, Zohreh; Talebi, Reza

2015-07-01

To evaluate the genetic diversity among 48 genotypes of chickpea comprising cultivars, landraces and internationally developed improved lines genetic distances were evaluated using three different molecular marker techniques: Simple Sequence Repeat (SSR); Start Codon Targeted (SCoT) and Conserved DNA-derived Polymorphism (CDDP). Average polymorphism information content (PIC) for SSR, SCoT and CDDP markers was 0.47, 0.45 and 0.45, respectively, and this revealed that three different marker types were equal for the assessment of diversity amongst genotypes. Cluster analysis for SSR and SCoT divided the genotypes in to three distinct clusters and using CDDP markers data, genotypes grouped in to five clusters. There were positive significant correlation (r = 0.43, P SSR markers. These results suggest that efficiency of SSR, SCOT and CDDP markers was relatively the same in fingerprinting of chickpea genotypes. To our knowledge, this is the first detailed report of using targeted DNA region molecular marker (CDDP) for genetic diversity analysis in chickpea in comparison with SCoT and SSR markers. Overall, our results are able to prove the suitability of SCoT and CDDP markers for genetic diversity analysis in chickpea for their high rates of polymorphism and their potential for genome diversity and germplasm conservation.

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 < 0.001) between ssrOeUA-DCA14 and stearic acid and between GAPU71B and oleic acid indicated that these markers could be used for marker-assisted selection in olive.

Comparative analysis of genetic diversity among Chinese watermelon germplasmsusing SSR and SRAP markers, and implications for future genetic improvement

OpenAIRE

WANG, PANGQIAO; LI, QIONG; Hu, Jianbin; SU, YAN

2015-01-01

The genetic diversity of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] in China, the world's largest producer of watermelon fruits, has not been examined. Two molecular markers, sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR), were used to investigate the genetic variation and genetic relationship among 54 Chinese watermelon accessions, as well as 7 accessions from Africa, the United States, and Japan. SRAP assay generated 312 bands, ...

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'.

Development of SSR markers for a Tibetan medicinal plant, Lancea tibetica (Phrymaceae), based on RAD sequencing.

Science.gov (United States)

Tian, Zunzhe; Zhang, Faqi; Liu, Hairui; Gao, Qingbo; Chen, Shilong

2016-11-01

Lancea tibetica (Phrymaceae), a Tibetan medicinal plant, is endemic to the Qinghai-Tibet Plateau. The over-exploitation of wild L. tibetica has led to the destruction of many populations. To enhance protection and management, biological research, especially population genetic studies, should be carried out on L. tibetica . Simple sequence repeat (SSR) markers of L. tibetica were developed to analyze population diversity. Four thousand four hundred and forty-one SSR loci were identified for L. tibetica based on restriction-site associated DNA (RAD) sequencing on the Illumina HiSeq platform. One hundred SSR loci were arbitrarily selected for primer design, and 38 of them were successfully amplified. These markers were tested on 56 individuals from three populations of L. tibetica , and 10 markers displayed polymorphisms. The total number of alleles per locus ranged from three to eight, and observed and expected heterozygosities ranged from 0.200 to 1.000 and 0.683 to 0.879, respectively. We tested for cross-amplification of these 10 markers in the related species L. hirsuta and found that nine could be successfully amplified. The SSR markers characterized here are the first to be developed and tested in L. tibetica . They will be useful for future population genetic studies on L. tibetica and closely related species.

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 ...

Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae).

Science.gov (United States)

Zhou, Tao; Li, Zhong-Hu; Bai, Guo-Qing; Feng, Li; Chen, Chen; Wei, Yue; Chang, Yong-Xia; Zhao, Gui-Fang

2016-02-23

Dipteronia Oliver (Aceraceae) is an endangered Chinese endemic genus consisting of two living species, Dipteronia sinensis and Dipteronia dyeriana. However, studies on the population genetics and evolutionary analyses of Dipteronia have been hindered by limited genomic resources and genetic markers. Here, the generation, de novo assembly and annotation of transcriptome datasets, and a large set of microsatellite or simple sequence repeat (SSR) markers derived from Dipteronia have been described. After Illumina pair-end sequencing, approximately 93.2 million reads were generated and assembled to yield a total of 99,358 unigenes. A majority of these unigenes (53%, 52,789) had at least one blast hit against the public protein databases. Further, 12,377 SSR loci were detected and 4179 primer pairs were designed for experimental validation. Of these 4179 primer pairs, 435 primer pairs were randomly selected to test polymorphism. Our results show that products from 132 primer pairs were polymorphic, in which 97 polymorphic SSR markers were further selected to analyze the genetic diversity of 10 natural populations of Dipteronia. The identification of SSR markers during our research will provide the much valuable data for population genetic analyses and evolutionary studies in Dipteronia.

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel.

Science.gov (United States)

Huang, Ling; Deng, Xiaohui; Li, Ronghua; Xia, Yanshi; Bai, Guihua; Siddique, Kadambot H M; Guo, Peiguo

2018-04-20

Simple Sequence Repeat (SSR) is one of the most effective markers used in plant and animal genetic research and molecular breeding programs. Silver staining is a widely used method for the detection of SSR markers in a polyacrylamide gel. However, conventional protocols for silver staining are technically demanding and time-consuming. Like many other biological laboratory techniques, silver staining protocols have been steadily optimized to improve detection efficiency. Here, we report a simplified silver staining method that significantly reduces reagent costs and enhances the detection resolution and picture clarity. The new method requires two major steps (impregnation and development) and three reagents (silver nitrate, sodium hydroxide, and formaldehyde), and only 7 min of processing for a non-denaturing polyacrylamide gel. Compared to previously reported protocols, this new method is easier, quicker and uses fewer chemical reagents for SSR detection. Therefore, this simple, low-cost, and effective silver staining protocol will benefit genetic mapping and marker-assisted breeding by a quick generation of SSR marker data.

Cranberry SSR multiplexing panels for DNA horticultural fingerprinting and genetic studies

Science.gov (United States)

Cranberry (Vaccinium macrocarpon) is in need of inexpensive high-throughput DNA fingerprinting methods for genetic research and germplasm purity testing for agricultural purposes. Therefore, we designed and validated 16-multiplexing panels containing 61 evenly distributed simple sequence (SSR) marke...

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.

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).

Science.gov (United States)

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

Fingerprinting and genetic purity assessment of F1 barley hybrids and their salt-tolerant parental lines using nSSR molecular markers.

Science.gov (United States)

Ben Romdhane, Mériam; Riahi, Leila; Jardak, Rahma; Ghorbel, Abdelwahed; Zoghlami, Nejia

2018-01-01

Hybridity and the genuineness of hybrids are prominent characteristics for quality control of seeds and thereby for varietal improvement. In the current study, the cross between two local barley genotypes (Ardhaoui: female; Testour: male) previously identified as susceptible/tolerant to salt stress in Tunisia was achieved. The hybrid genetic purity of the generated F 1 putative hybrids and the fingerprinting of the parents along with their offspring were assessed using a set of 17 nuclear SSR markers. Among the analyzed loci, 11 nSSR were shown polymorphic among the parents and their offspring. Based on the applied 11 polymorphic SSR loci, a total of 28 alleles were detected with an average of 2.54 alleles per locus. The locus HVM33 presented the highest number of alleles. The highest polymorphism information content value was detected for the locus HVM33 (0.6713) whereas the lowest PIC value (0.368) was revealed by the loci BMAC0156 , EBMAC0970 and BMAG0013 with a mean value of 0.4619. The probabilities of identical genotypes PI for the 11 microsatellite markers were 8.63 × 10 -7 . Banding patterns among parents and hybrids showed polymorphic fragments. The 11 SSR loci had produced unique fingerprints for each analyzed genotype and segregate between the two parental lines and their four hybrids. Parentage analysis confirms the hybrid purity of the four analyzed genotypes. Six Tunisian barley accessions were used as an outgroup in the multivariate analysis to confirm the efficiency of the employed 11 nSSR markers in genetic differentiation among various barley germplasms. Thus, neighbor joining and factorial analysis revealed clearly the discrimination among the parental lines, the four hybrids and the outgroup accessions. Out of the detected polymorphic 11 nuclear SSR markers, a set of five markers ( HVM33 , WMC1E8 , BMAC0154 , BMAC0040 and BMAG0007 ) were shown to be sufficient and informative enough to discriminate among the six genotypes representing the two

Identification of SSR and RAPD markers associated with QTLs of ...

African Journals Online (AJOL)

SERVER

2008-04-03

Apr 3, 2008 ... Parents and. F3 families had significant differences in studied traits (p ≤. 0.01). In this study, SSR and RAPD markers were used together for constructing linkage groups and rescanning the genome of rapeseed to identify QTLs controlling winter survival and related traits. For this, the parental polymorphism ...

Genome-Wide Development of MicroRNA-Based SSR Markers in Medicago truncatula with Their Transferability Analysis and Utilization in Related Legume Species.

Science.gov (United States)

Min, Xueyang; Zhang, Zhengshe; Liu, Yisong; Wei, Xingyi; Liu, Zhipeng; Wang, Yanrong; Liu, Wenxian

2017-11-18

Microsatellite (simple sequence repeats, SSRs) marker is one of the most widely used markers in marker-assisted breeding. As one type of functional markers, MicroRNA-based SSR (miRNA-SSR) markers have been exploited mainly in animals, but the development and characterization of miRNA-SSR markers in plants are still limited. In the present study, miRNA-SSR markers for Medicago truncatula ( M. truncatula ) were developed and their cross-species transferability in six leguminous species was evaluated. A total of 169 primer pairs were successfully designed from 130 M. truncatula miRNA genes, the majority of which were mononucleotide repeats (70.41%), followed by dinucleotide repeats (14.20%), compound repeats (11.24%) and trinucleotide repeats (4.14%). Functional classification of SSR-containing miRNA genes showed that all targets could be grouped into three Gene Ontology (GO) categories: 17 in biological process, 11 in molecular function, and 14 in cellular component. The miRNA-SSR markers showed high transferability in other six leguminous species, ranged from 74.56% to 90.53%. Furthermore, 25 Mt - miRNA-SSR markers were used to evaluate polymorphisms in 20 alfalfa accessions, and the polymorphism information content (PIC) values ranged from 0.39 to 0.89 with an average of 0.71, the allele number per marker varied from 3 to 18 with an average of 7.88, indicating a high level of informativeness. The present study is the first time developed and characterized of M. truncatula miRNA-SSRs and demonstrated their utility in transferability, these novel markers will be valuable for genetic diversity analysis, marker-assisted selection and genotyping in leguminous species.

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.

Molecular characterization of a peanut variety and its derivatives based on SSR and COP analysis

Institute of Scientific and Technical Information of China (English)

Xiaoping REN; Boshou LIAO; Huifang JIANG; Zhongyuan YUAN; Yuning CHEN; Xiaojing ZHOU; Li HUANG; Jiaquan HUANG; Yong LEI; Liying YAN

2016-01-01

Despite the economic importance of the peanut,no studies have been carried out to determine the correlation between genetic distances based on molecular markers and on coefficient of parentage (COP) data.In this study,simple sequence repeat (SSR) and pedigree data were used to assess the genetic distance between the Fuhuasheng variety and its derivative cultivars.A total of 39 SSR polymorphism primers were used,and 151 bands were obtained,with an average of 2.04 bands in each primer.The genetic SSR-based distance (GD) values ranged from 0.02 to 0.81,while the COP-based GD ranged from 0.25 to 0.98.Certain Fuhuasheng loci displayed higher transmission rates.These loci or nearby chromosomal regions might be associated with desirable traits in Fuhuasheng variety,thus being frequently selected in breeding programs.Therefore,it can be suggested that COP analysis should be the preferred method for estimating genetic diversity invarieties with available complete pedigree information and parents.In this case,marker analysis would provide the best estimations.

Identification and differentiation of Ricinus communis L. using SSR markers

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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.

Molecular genetic alterations in egfr CA-SSR-1 microsatellite and egfr copy number changes are associated with aggressiveness in thymoma.

Science.gov (United States)

Conti, Salvatore; Gallo, Enzo; Sioletic, Stefano; Facciolo, Francesco; Palmieri, Giovannella; Lauriola, Libero; Evoli, Amelia; Martucci, Robert; Di Benedetto, Anna; Novelli, Flavia; Giannarelli, Diana; Deriu, Gloria; Granone, Pierluigi; Ottaviano, Margaret; Muti, Paola; Pescarmona, Edoardo; Marino, Mirella

2016-03-01

The key role of egfr in thymoma pathogenesis has been questioned following the failure in identifying recurrent genetic alterations of egfr coding sequences and relevant egfr amplification rate. We investigated the role of the non-coding egfr CA simple sequence repeat 1 (CA-SSR-1) in a thymoma case series. We used sequencing and egfr-fluorescence in situ hybridization (FISH) to genotype 43 thymomas; (I) for polymorphisms and somatic loss of heterozygosity of the non-coding egfr CA-SSR-1 microsatellite and (II) for egfr gene copy number changes. We found two prevalent CA-SSR-1 genotypes: a homozygous 16 CA repeat and a heterozygous genotype, bearing alleles with 16 and 20 CA repeats. The average combined allele length was correlated with tumor subtype: shorter sequences were significantly associated with the more aggressive WHO thymoma subtype group including B2/B3, B3 and B3/C histotypes. Four out of 29 informative cases analysed for somatic CA-SSR-1 loss of heterozygosity showed allelic imbalance (AI), 3/4 with loss of the longer allele. By egfr-FISH analysis, 9 out of 33 cases were FISH positive. Moreover, the two integrated techniques demonstrated that 3 out of 4 CA-SSR-1-AI positive cases with short allele relative prevalence showed significantly low or high chromosome 7 "polysomy"/increased gene copy number by egfr-FISH. Our molecular and genetic and follow up data indicated that CA-SSR-1-allelic imbalance with short allele relative prevalence significantly correlated with EGFR 3+ immunohistochemical score, increased egfr Gene Copy Number, advanced stage and with relapsing/metastatic behaviour in thymomas.

Identification of SSR and RAPD markers associated with QTLs of ...

African Journals Online (AJOL)

Because of importance of winter survival in winter type of Brassica napus, this study was performed to identify the QTLs controlling winter survival and related traits using SSR and RAPD markers. For this, an F2:3 population of 200 families derived from crossing between cv. 'SLMO46' (winter type and cold resistant) and cv.

Development and mapping of SSR markers linked to resistance-gene homologue clusters in common bean

Institute of Scientific and Technical Information of China (English)

Luz; Nayibe; Garzon; Matthew; Wohlgemuth; Blair

2014-01-01

Common bean is an important but often a disease-susceptible legume crop of temperate,subtropical and tropical regions worldwide. The crop is affected by bacterial, fungal and viral pathogens. The strategy of resistance-gene homologue(RGH) cloning has proven to be an efficient tool for identifying markers and R(resistance) genes associated with resistances to diseases. Microsatellite or SSR markers can be identified by physical association with RGH clones on large-insert DNA clones such as bacterial artificial chromosomes(BACs). Our objectives in this work were to identify RGH-SSR in a BAC library from the Andean genotype G19833 and to test and map any polymorphic markers to identify associations with known positions of disease resistance genes. We developed a set of specific probes designed for clades of common bean RGH genes and then identified positive BAC clones and developed microsatellites from BACs having SSR loci in their end sequences. A total of 629 new RGH-SSRs were identified and named BMr(bean microsatellite RGH-associated markers). A subset of these markers was screened for detecting polymorphism in the genetic mapping population DOR364 × G19833. A genetic map was constructed with a total of 264 markers,among which were 80 RGH loci anchored to single-copy RFLP and SSR markers. Clusters of RGH-SSRs were observed on most of the linkage groups of common bean and in positions associated with R-genes and QTL. The use of these new markers to select for disease resistance is discussed.

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

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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.

Identification of new SSR markers linked to leaf chlorophyll content, flag leaf senescence and cell membrane stability traits in wheat under water stressed condition.

Science.gov (United States)

Barakat, Mohamed N; Saleh, Mohamed; Al-Doss, Abdullah A; Moustafa, Khaled A; Elshafei, Adel A; Al-Qurainy, Fahed H

2015-03-01

Segregating F4 families from the cross between drought sensitive (Yecora Rojo) and drought tolerant (Pavon 76) genotypes were made to identify SSR markers linked to leaf chlorophyll content, flag leaf senescence and cell membrane stability traits in wheat (Triticum aestivum L.) under water-stressed condition and to map quantitative trait locus (QTL) for the three physiological traits. The parents and 150 F4 families were evaluated phenotypically for drought tolerance using two irrigation treatments (2500 and 7500 m3/ha). Using 400 SSR primers tested for polymorphism in testing parental and F4 families genotypes, the results revealed that QTL for leaf chlorophyll content, flag leaf senescence and cell membrane stability traits were associated with 12, 5 and 12 SSR markers, respectively and explained phenotypic variation ranged from 6 to 42%. The SSR markers for physiological traits had genetic distances ranged from 12.5 to 25.5 cM. These SSR markers can be further used in breeding programs for drought tolerance in wheat.

Two discrete components of the 20 Hz steady-state response are distinguished through the modulation of activation level

DEFF Research Database (Denmark)

Griskova, Inga; Mørup, Morten; Parnas, Josef

2009-01-01

Objective: To investigate the modulation of amplitude and phase precision of the auditory steady-state response (SSR) to 20 Hz stimulation in two conditions varying in the level of activation. Methods: Click stimuli (20 Hz) were applied while subjects were sitting upright silently reading a book......-negative multi-way factorization (NMWF). Results: The NMWF decomposition of amplitude and phase precision measures resulted in the observation of two distinct components: a component at the frequency of stimulation – 20 Hz SSR and a component emerging at 40 Hz – 20 Hz SSR-related 40 Hz activity. Modulation...... by the activation level was observed only for 20 Hz SSR-related 40 Hz activity as increased amplitude and phase precision during low activation level. No such effects were observed for 20 Hz SSR. Conclusion: The discrete components of the 20 Hz SSR are distinguished through modulation of activation level, 20 Hz SSR...

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.

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.

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.

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

Science.gov (United States)

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango. PMID:27736892

Identification of SSR markers closely linked to the yellow seed coat color gene in heading Chinese cabbage (Brassica rapa L. ssp. pekinensis).

Science.gov (United States)

Ren, Yanjing; Wu, Junqing; Zhao, Jing; Hao, Lingyu; Zhang, Lugang

2017-02-15

Research on the yellow-seeded variety of heading Chinese cabbage will aid in broadening its germplasm resources and lay a foundation for AA genome research in Brassica crops. Here, an F 2 segregating population of 1575 individuals was constructed from two inbred lines (brown-seeded '92S105' and yellow-seeded '91-125'). This population was used to identify the linkage molecular markers of the yellow seed coat trait using simple sequence repeat (SSR) techniques combined with a bulk segregant analysis (BSA). Of the 144 SSR primer pairs on the A01-A10 chromosomes from the Brassica database (http://brassicadb.org/brad/), two pairs located on the A06 chromosome showed polymorphic bands between the bulk DNA pools of eight brown-seeded and eight yellow-seeded F 2 progeny. Based on the genome sequence, 454 SSR markers were designed to A06 to detect these polymorphic bands and were synthesized. Six SSR markers linked to the seed coat color gene were successfully selected for fine linkage genetic map construction, in which the two closest flanking markers, SSR449a and SSR317, mapped the Brsc-ye gene to a 40.2 kb region with distances of 0.07 and 0.06 cM, respectively. The molecular markers obtained in this report will assist in the marker-assisted selection and breeding of yellow-seeded lines in Brassica rapa L. and other close species. © 2017. Published by The Company of Biologists Ltd.

A high density barley microsatellite consensus map with 775 SSR loci

NARCIS (Netherlands)

Varshney, R.K.; Marcel, T.C.; Ramsay, L.; Russell, J.; Roder, M.S.; Stein, N.; Waugh, R.; Langridge, P.; Niks, R.E.; Graner, A.

2007-01-01

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWBDom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for

High levels of heterozygosity found for 15 SSR loci in Solanum chacoense

Science.gov (United States)

Genetic variation is a necessary prerequisite for improving domesticated plants through breeding; without it, breeding progress would be impossible. Genetic variation can be readily ascertained with co-dominant DNA markers, such as simple sequence repeats (SSRs). Twenty-four SSR markers specifically...

Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice.

Science.gov (United States)

Tabkhkar, Narjes; Rabiei, Babak; Samizadeh Lahiji, Habibollah; Hosseini Chaleshtori, Maryam

2018-02-24

Drought is one of the major abiotic stresses, which hampers the production of rice worldwide. Informative molecular markers are valuable tools for improving the drought tolerance in various varieties of rice. The present study was conducted to evaluate the informative simple sequence repeat (SSR) markers in a diverse set of rice genotypes. The genetic diversity analyses of the 83 studied rice genotypes were performed using 34 SSR markers closely linked to the major quantitative trait loci (QTLs) of grain yield under drought stress (qDTYs). In general, our results indicated high levels of polymorphism. In addition, we screened these rice genotypes at the reproductive stage under both drought stress and nonstressful conditions. The results of the regression analysis demonstrated a significant relationship between 11 SSR marker alleles and the plant paddy weight under stressful conditions. Under the nonstressful conditions, 16 SSR marker alleles showed a significant correlation with the plant paddy weight. Finally, four markers (RM279, RM231, RM166, and RM231) demonstrated a significant association with the plant paddy weight under both stressful and nonstressful conditions. These informative-associated alleles may be useful for improving the crop yield under both drought stress and nonstressful conditions in breeding programs.

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

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...

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 ...

Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers.

Science.gov (United States)

Mujaju, C; Sehic, J; Werlemark, G; Garkava-Gustavsson, L; Fatih, M; Nybom, H

2010-08-01

Low polymorphism in cultivated watermelon has been reported in previous studies, based mainly on US Plant Introductions and watermelon cultivars, most of which were linked to breeding programmes associated with disease resistance. Since germplasm sampled in a putative centre of origin in southern Africa may harbour considerably higher variability, DNA marker-based diversity was estimated among 81 seedlings from eight accessions of watermelon collected in Zimbabwe; five accessions of cow-melons (Citrullus lanatus var. citroides) and three of sweet watermelons (C. lanatus var. lanatus). Two molecular marker methods were used, random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) also known as microsatellite DNA. Ten RAPD primers produced 138 markers of which 122 were polymorphic. Nine SSR primer pairs detected a total of 43 alleles with an average of 4.8 alleles per locus. The polymorphic information content (PIC) ranged from 0.47 to 0.77 for the RAPD primers and from 0.39 to 0.97 for the SSR loci. Similarity matrices obtained with SSR and RAPD, respectively, were highly correlated but only RAPD was able to provide each sample with an individual-specific DNA profile. Dendrograms and multidimensional scaling (MDS) produced two major clusters; one with the five cow-melon accessions and the other with the three sweet watermelon accessions. One of the most variable cow-melon accessions took an intermediate position in the MDS analysis, indicating the occurrence of gene flow between the two subspecies. Analysis of molecular variation (AMOVA) attributed most of the variability to within-accessions, and contrary to previous reports, sweet watermelon accessions apparently contain diversity of the same magnitude as the cow-melons.

Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.

Science.gov (United States)

Gong, L.; Stift, G.; Kofler, R.; Pachner, M.

2008-01-01

Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Ölkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety “Lady Godiva” (O5) and the Italian crookneck variety “Bianco Friulano” (CN), which are the parents of our previous F2 mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0750-2) contains supplementary material, which is available to authorized users. PMID:18379753

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

Directory of Open Access Journals (Sweden)

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

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

Science.gov (United States)

2012-01-01

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 and number of SSR

Development and characterization of polymorphic EST based SSR markers in barley (Hordeum vulgare).

Science.gov (United States)

Jo, Won-Sam; Kim, Hye-Yeong; Kim, Kyung-Min

2017-08-01

In barley, breeding using good genetic characteristics can improve the quality or quantity of crop characters from one generation to the next generation. The development of effective molecular markers in barley is crucial for understanding and analyzing the diversity of useful alleles. In this study, we conducted genetic relationship analysis using expressed sequence tag-simple sequence repeat (EST-SSR) markers for barley identification and assessment of barley cultivar similarity. Seeds from 82 cultivars, including 31 each of naked and hulled barley from the Korea Seed and Variety Service and 20 of malting barley from the RDA-Genebank Information Center, were analyzed in this study. A cDNA library of the cultivar Gwanbori was constructed for use in analysis of genetic relationships, and 58 EST-SSR markers were developed and characterized. In total, 47 SSR markers were employed to analyze polymorphisms. A relationship dendrogram based on the polymorphism data was constructed to compare genetic diversity. We found that the polymorphism information content among the examined cultivars was 0.519, which indicates that there is low genetic diversity among Korean barley cultivars. The results obtained in this study may be useful in preventing redundant investment in new cultivars and in resolving disputes over seed patents. Our approach can be used by companies and government groups to develop different cultivars with distinguishable markers. In addition, the developed markers can be used for quantitative trait locus analysis to improve both the quantity and the quality of cultivated barley.

Development of an SSR-based identification key for Tunisian local almonds

Directory of Open Access Journals (Sweden)

Hassouna Gouta

2012-04-01

Full Text Available Ten simple sequence repeat (SSR loci were used to study polymorphism in 54 almond genotypes. All genotypes used in this study originated from almond-growing areas in Tunisia with different climatic conditions ranging from the sub-humid to the arid and are preserved in the national collection at Sidi Bouzid. Using ten SSR, 130 alleles and 250 genotypes were revealed. In order to develop an identification key for each accession, the data were analysed separately for each microsatellite marker. The most polymorphic microsatellite (CPDCT042 was used as a first marker. Two microsatellite loci (CPDCT042 and CPDCT025 were sufficient to discriminate among all accessions studied. Neighbour-joining clustering and principal coordinate analysis were performed to arrange the genotypes according to their genetic relationships and origin. The results are discussed in the context of almond collection management, conformity checks, identification of homonyms, and screening of the local almond germplasm. Furthermore, this microsatellite-based key is a first step toward a marker-assisted identification almond database.

Analysis of cold resistance and identification of SSR markers linked to cold resistance genes in Brassica rapa L.

Science.gov (United States)

Huang, Zhen; Zhang, Xuexian; Jiang, Shouhua; Qin, Mengfan; Zhao, Na; Lang, Lina; Liu, Yaping; Tian, Zhengshu; Liu, Xia; Wang, Yang; Zhang, Binbin; Xu, Aixia

2017-06-01

Currently, cold temperatures are one of the main factors threatening rapeseed production worldwide; thus, it is imperative to identify cold-resistant germplasm and to cultivate cold-resistant rapeseed varieties. In this study, the cold resistance of four Brassica rapa varieties was analyzed. The cold resistance of Longyou6 and Longyou7 was better than that of Tianyou2 and Tianyou4. Thus, an F 2 population derived from Longyou6 and Tianyou4 was used to study the correlation of cold resistance and physiological indexes. Our results showed that the degree of frost damage was related to the relative conductivity and MDA content (r1 = 0.558 and r2 = 0.447, respectively). In order to identify the markers related to cold resistance, 504 pairs of SSR (simple sequence repeats) primers were used to screen the two parents and F 2 population. Four and five SSR markers had highly significant positive correlation to relative conductivity and MDA, respectively. In addition, three of these SSR markers had a highly significant positive correlation to both of these two indexes. These three SSR markers were subsequently confirmed to be used to distinguish between cold-resistant and non-cold-resistant varieties. The results of this study will lay a solid foundation for the mapping of cold-resistant genes and molecular markers assisted selection for the cold-resistance.

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

Phylogenetic and Diversity Analysis of Dactylis glomerata Subspecies Using SSR and IT-ISJ Markers.

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Yan, Defei; Zhao, Xinxin; Cheng, Yajuan; Ma, Xiao; Huang, Linkai; Zhang, Xinquan

2016-10-31

The genus Dactylis , an important forage crop, has a wide geographical distribution in temperate regions. While this genus is thought to include a single species, Dactylis glomerata , this species encompasses many subspecies whose relationships have not been fully characterized. In this study, the genetic diversity and phylogenetic relationships of nine representative Dactylis subspecies were examined using SSR and IT-ISJ markers. In total, 21 pairs of SSR primers and 15 pairs of IT-ISJ primers were used to amplify 295 polymorphic bands with polymorphic rates of 100%. The average polymorphic information contents (PICs) of SSR and IT-ISJ markers were 0.909 and 0.780, respectively. The combined data of the two markers indicated a high level of genetic diversity among the nine D. glomerata subspecies, with a Nei's gene diversity index value of 0.283 and Shannon's diversity of 0.448. Preliminarily phylogenetic analysis results revealed that the 20 accessions could be divided into three groups (A, B, C). Furthermore, they could be divided into five clusters, which is similar to the structure analysis with K = 5. Phylogenetic placement in these three groups may be related to the distribution ranges and the climate types of the subspecies in each group. Group A contained eight accessions of four subspecies, originating from the west Mediterranean, while Group B contained seven accessions of three subspecies, originating from the east Mediterranean.

AFLP/SSR mapping of resistance genes to Alectra vogelii in cowpea ...

African Journals Online (AJOL)

To find and map the resistance gene to A. vogelii in cowpea, a F2 population from a cross involving a resistant parent IT81D-994 and a susceptible TVX3236 was screened. Amplified fragment length polymorphism (AFLP) in combination with Single Sequence Repeat (SSR) analysis was used to identify markers that may be ...

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes.

Science.gov (United States)

An, Jianyu; Yin, Mengqi; Zhang, Qin; Gong, Dongting; Jia, Xiaowen; Guan, Yajing; Hu, Jin

2017-09-11

Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica , about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N 50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both "Zheda 23" and "Zheda 83". Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species.

Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.).

Science.gov (United States)

Mornkham, T; Wangsomnuk, P P; Mo, X C; Francisco, F O; Gao, L Z; Kurzweil, H

2016-10-24

Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. Our results show that 43 primers are polymorphic for the six studied populations, while the remaining 36 were either monomorphic or failed to amplify. These 43 SSR loci exhibited a high level of genetic diversity among populations, with allele numbers varying from 2 to 7, with an average of 3.95 alleles per loci. Heterozygosity ranged from 0.096 to 0.774, with an average of 0.536; polymorphic index content ranged from 0.096 to 0.854, with an average of 0.568. Principal component analysis and neighbor-joining analysis revealed that the six populations could be divided into six clusters. Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus.

Development of SSR markers for the short arm of rye chromosome 1

Czech Academy of Sciences Publication Activity Database

Kofler, R.; Stift, G.; Gong, L.; Suchánková, Pavla; Šimková, Hana; Doležel, Jaroslav; Lelley, T.

2007-01-01

Roč. 71, - (2007), s. 279-281 ISSN 0723-7812 R&D Projects: GA ČR GA521/04/0607 Institutional research plan: CEZ:AV0Z50380511 Source of funding: V - iné verejné zdroje Keywords : SSR markers * rye chromosome 1 Subject RIV: GE - Plant Breeding

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

Directory of Open Access Journals (Sweden)

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

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.

Simple sequence repeat (SSR) markers are effective for identifying ...

African Journals Online (AJOL)

DNA was extracted from newly formed leaves and amplified using 21 simple sequence repeat (SSR) markers (NH001c, NH002b, NH005b, NH007b, NH008b, NH009b, NH011b, NH013b, NH012a, NH014a, NH015a, NH017a, KA4b, KA5, KA14, KA16, KB16, KU10, BGA35, BGT23b and HGA8b). The data was analyzed by ...

In vivo imaging of neuroinflammation in the rodent brain with [{sup 11}C]SSR180575, a novel indoleacetamide radioligand of the translocator protein (18 kDa)

Energy Technology Data Exchange (ETDEWEB)

Chauveau, Fabien [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Universite Paris Sud, INSERM U1023, Orsay (France); Universite Lyon 1, Creatis, CNRS UMR 5220, INSERM U630, INSA Lyon, Lyon (France); Boutin, Herve [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Universite Paris Sud, INSERM U1023, Orsay (France); University of Manchester, Faculty of Life Sciences, Manchester (United Kingdom); Camp, Nadja van; Tavitian, Bertrand [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Universite Paris Sud, INSERM U1023, Orsay (France); Thominiaux, Cyrille; Dolle, Frederic [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Hantraye, Philippe [CEA, DSV, IBM, MIRCEN, Fontenay-aux-Roses (France); Rivron, Luc [Sanofi-Aventis, GMPK-Global Isotope Chemistry and Metabolite Synthesis Department (ICMS), Paris (France); Marguet, Frank; Castel, Marie-Noelle; Rooney, Thomas; Benavides, Jesus [Sanofi-Aventis, CNS Department, Paris (France)

2011-03-15

Neuroinflammation is involved in neurological disorders through the activation of microglial cells. Imaging of neuroinflammation with radioligands for the translocator protein (18 kDa) (TSPO) could prove to be an attractive biomarker for disease diagnosis and therapeutic evaluation. The indoleacetamide-derived 7-chloro-N,N,5-trimethyl-4-oxo-3-phenyl-3,5-dihydro-4H-pyridazino[4,5-b]indole-1-acetamide, SSR180575, is a selective high-affinity TSPO ligand in human and rodents with neuroprotective effects. Here we report the radiolabelling of SSR180575 with {sup 11}C and in vitro and in vivo imaging in an acute model of neuroinflammation in rats. The image contrast and the binding of [{sup 11}C]SSR180575 are higher than that obtained with the isoquinoline-based TSPO radioligand, [{sup 11}C]PK11195. Competition studies demonstrate that [{sup 11}C]SSR180575 has high specific binding for the TSPO. [{sup 11}C]SSR180575 is the first PET radioligand for the TSPO based on an indoleacetamide scaffold designed for imaging neuroinflammation in animal models and in the clinic. (orig.)

Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

Science.gov (United States)

The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers ...

Effective damping for SSR analysis of parallel turbine-generators

International Nuclear Information System (INIS)

Agrawal, B.L.; Farmer, R.G.

1988-01-01

Damping is a dominant parameter in studies to determine SSR problem severity and countermeasure requirements. To reach valid conclusions for multi-unit plants, it is essential that the net effective damping of unequally loaded units be known. For the Palo Verde Nuclear Generating Station, extensive testing and analysis have been performed to verify and develop an accurate means of determining the effective damping of unequally loaded units in parallel. This has led to a unique and simple algorithm which correlates well with two other analytic techniques

Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa).

Science.gov (United States)

Mondal, Tapan Kumar; Ganie, Showkat Ahmad

2014-02-10

Salinity is an important abiotic stress that affects agricultural production and productivity. It is a complex trait that is regulated by different molecular mechanisms. miRNAs are non-coding RNAs which are highly conserved and regulate gene expression. Simple sequence repeats (SSRs) are robust molecular markers for studying genetic diversity. Although several SSR markers are available now, challenge remains to identify the trait-specific SSRs which can be used for marker assisted breeding. In order to understand the genetic diversity of salt responsive-miRNA genes in rice, SSR markers were mined from 130 members of salt-responsive miRNA genes of rice and validated among the contrasting panels of tolerant as well as susceptible rice genotypes, each with 12 genotypes. Although 12 miR-SSRs were found to be polymorphic, only miR172b-SSR was able to differentiate the tolerant and susceptible genotypes in 2 different groups. It had also been found that miRNA genes were more diverse in susceptible genotypes than the tolerant one (as indicated by polymorphic index content) which might interfere to form the stem-loop structure of premature miRNA and their subsequent synthesis in susceptible genotypes. Thus, we concluded that length variations of the repeats in salt responsive miRNA genes may be responsible for a possible sensitivity to salinity adaptation. This is the first report of characterization of trait specific miRNA derived SSRs in plants. Copyright © 2013 Elsevier B.V. All rights reserved.

SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions.

Science.gov (United States)

Choudhary, Shashi Bhushan; Sharma, Hariom Kumar; Kumar, Arroju Anil; Maruthi, Rangappa Thimmaiah; Mitra, Jiban; Chowdhury, Isholeena; Singh, Binay Kumar; Karmakar, Pran Gobinda

2017-02-01

A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI=0.46; He=0.31; P=85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P=0.01. The maximum Nei's unbiased genetic distance (D=0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm. Copyright © 2016 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

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 ( H e = 0.609, H e = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters F ST 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

Characterization of functional SSR markers in Prosopis alba and their transferability across Prosopis species

Directory of Open Access Journals (Sweden)

María F. Pomponio

2015-08-01

Full Text Available Aim of study: The aim of the study was to characterize functional microsatellite markers in Prosopis alba and examine the transferability to species from the Prosopis genus. Area of the study: samples were obtained from natural populations of Argentina. Material and Methods: Eleven SSR functional markers related to stress and metabolism were amplified in a sample of 152 genotypes from P.alba, P. denudans, P. hassleriP. chilensis, P. flexuosa, and interspecific hybrids. Main results: In P. alba, the PIC average value was 0.36; and 6 out of the 11 primers showed high values of polymorphism ranging from 0.40 to 0.71. The cross-species transferability was high with high percentages of polymorphic loci. Research highlights: The SSR markers developed in P.alba were easily transferred to other Prosopis species which did not have functional markers.

Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

Science.gov (United States)

In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

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.

Rapid identification of red-flesh loquat cultivars using EST-SSR markers based on manual cultivar identification diagram strategy.

Science.gov (United States)

Li, X Y; Xu, H X; Chen, J W

2014-04-29

Manual cultivar identification diagram is a new strategy for plant cultivar identification based on DNA markers, providing information to efficiently separate cultivars. We tested 25 pairs of apple EST-SSR primers for amplification of PCR products from loquat cultivars. These EST-SSR primers provided clear amplification products from the loquat cultivars, with a relatively high transferability rate of 84% to loquat; 11 pairs of primers amplified polymorphic products. After analysis of 24 red-fleshed loquat accessions, we found that only 7 pairs of primers could clearly separate all of them. A cultivar identification diagram of the 24 cultivars was constructed using polymorphic bands from the DNA fingerprints and EST-SSR primers. Any two of the 24 cultivars could be rapidly separated from each other, according to the polymorphic bands from the cultivars; the corresponding primers were marked in the correct position on the cultivar identification diagram. This red-flesh loquat cultivar identification diagram can separate the 24 red-flesh loquat cultivars, which is of benefit for loquat cultivar identification for germplasm management and breeding programs.

Analysis of genetic diversity among rapeseed cultivars and breeding lines by srap and ssr molecular markers

International Nuclear Information System (INIS)

Channa, S.A.; Tian, H.

2016-01-01

The knowledge of genetic diversity is very important for developing new rapeseed (Brassica napus L.) cultivars. The genetic diversity among 77 rapeseed accessions, including 22 varieties and 55 advanced breeding lines were analyzed by 47 sequence-related amplified polymorphism (SRAP) and 56 simple sequence repeat (SSR) primers. A total of 270 SRAP and 194 SSR polymorphic fragments were detected with an average of 5.74 and 3.46 for SRAP and SSR primer, respectively. The cluster analysis grouped the 77 accessions into five major clusters. Cluster I contained spring and winter type varieties from Czech Republic and semi-winter varieties and their respective breeding lines from China. The 16 elite breeding lines discovered in Cluster II, III, IV and V indicated higher genetic distance than accessions in Cluster I. The principal component analysis and structure analysis exhibited similar results to the cluster analysis. Analysis of molecular variance revealed that genetic diversity of the selected breeding lines was comparable to the rapeseed varieties, and variation among varieties and lines was significant. The diverse and unique group of 16 elite breeding lines detected in this study can be utilized in the future breeding program as a source for development of commercial varieties with more desirable characters. (author)

[SSR analysis on stress effect of transgenic hybrid poplar 741 on Clostera anachoreta (Fabricius) (Lepidoptera: Notodontidae)].

Science.gov (United States)

Liu, Jun Xia; Song, Xiao Ying; Jiang, Wen Hu; Zhou, Guo Na; Gao, Bao Jia

2016-12-01

The genetic differentiation of the experimental population of Clostera anachoreta fed on different resistant transgenic 741 poplar leaves was analyzed by SSR molecular marker technique to investigate stress effect of transgenic poplar Bt gene as food on target insect. The experimental population of C. anachoreta fed on transgenic 741 poplar high resistant strains 'Pb29', medium resis-tant strains 'Pb17' and non-transgenic poplar (CK), and the screened ten pairs of SSR primers were used. The results showed that 76 alleles were observed in ten pairs of primers. The average allele was 7.6, the average effective number of alleles was 2.2, the average observed heterozygosity was 0.5167, the average expected heterozygosity was 0.5167, and the average percentage of polymorphic loci was 96.7%. The genetic diversity level of C. anachoreta experimental population fed on transgenic poplar 741 was significantly higher than that fed on non-transgenic populations, and C. anachoreta fed on high resistance had the lowest genetic similarity with CK samples, which showed an increasing trend of the genetic diversity of the experimental population fed on transgenic Bt poplar. It was thus clear that transgenic hybrid poplar 741 had stress effects on genetic differentiation of C. anachoreta experimental population by SSR.

In vivo imaging of neuro-inflammation in the rodent brain with [11C]SSR180575, a novel indoleacetamide radioligand of the translocator protein (18 kDa)

International Nuclear Information System (INIS)

Chauveau, F.; Boutin, H.; Van Camp, N.; Thominiaux, C.; Dolle, F.; Tavitian, B.; Chauveau, F.; Boutin, H.; Van Camp, N.; Tavitian, B.; Hantraye, P.; Rivron, L.; Marguet, F.; Castel, M.N.; Rooney, T.; Benavides, J.; Chauveau, F.; Boutin, H.

2011-01-01

Purpose Neuro-inflammation is involved in neurological disorders through the activation of micro-glial cells. Imaging of neuro-inflammation with radioligands for the translocator protein (18 kDa) (TSPO) could prove to be an attractive bio-marker for disease diagnosis and therapeutic evaluation. The indoleacetamide-derived 7-chloro-N, N, 5- trimethyl-4-oxo-3-phenyl-3, 5-dihydro-4H-pyridazino[4, 5-b] indole-1-acetamide, SSR180575, is a selective high-affinity TSPO ligand in human and rodents with neuro-protective effects. Methods Here we report the radiolabelling of SSR180575 with 11 C and in vitro and in vivo imaging in an acute model of neuro-inflammation in rats. Results The image contrast and the binding of [ 11 C] SSR180575 are higher than that obtained with the isoquinoline- based TSPO radioligand, [ 11 C]PK11195. Competition studies demonstrate that [ 11 C]SSR180575 has high specific binding for the TSPO. Conclusion [ 11 C]SSR180575 is the first PET radioligand for the TSPO based on an indoleacetamide scaffold designed for imaging neuro-inflammation in animal models and in the clinic. (authors)

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

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

Genetic diversity analysis of Amomum tsao-ko in Jinping County of Yunnan Province using SSR markers

Science.gov (United States)

Ma, Mengli; Wang, Tiantao; Lei, En; Meng, Hengling; Xie, Linyan; Zhu, Kunlong; Duan, Shaoze; Li, Wenqiang; Lu, Bingyue

2017-08-01

Genetic diversity analysis is very important for germplasm resources conservation and utilization. The objective of this study was to assess the genetic diversity among 44 individuals of Amomum tsao-ko from Jinping County of Yunnan Province using 5 selected SSR (simple sequence repeat) markers. A total of 23 polymorphic loci were detected among these germplasms, with an average of 4.6 polymorphic loci per SSR primer combination. The percentage of polymorphic loci was 100%, whereas the mean effective number of alleles (Ne), observed heterozygosity(Ho), expected heterozygosity (He), Shannon's information index (I), and the mean polymorphism information content (PIC) were 3. 410, 0. 491, 0. 679, 1.266 and 0. 672, respectively, indicating that the Amomum tsao-ko germplasms from Jinping County had high genetic diversity.

Development of a core set of SSR markers for the characterization of Gossypium germplasm

Science.gov (United States)

Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm collections. Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are us...

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species.

Science.gov (United States)

Kumari, Kajal; Muthamilarasan, Mehanathan; Misra, Gopal; Gupta, Sarika; Subramanian, Alagesan; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

2013-01-01

Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

Simple sequence repeat (SSR) vs. sequence-related amplified polymorphism (SRAP) markers for Cynara cardunculus characterization

Energy Technology Data Exchange (ETDEWEB)

Casadevall, R.; Martin, E.; Cravero, V.

2011-07-01

A little is known about the genetic variability present in globe artichoke, cultivated and wild cardoons. This knowledge is very important for efficient genetic resources utilization, and to gain a better understanding of genetic structure of this botanical varieties. With the aims to determine genetic distances between Cynara cardunculus accessions and to compare two molecular markers systems for their efficiency to differ between botanical varieties, a molecular characterization of sixteen accessions from different geographical origins was performed. Seven SSR and seven SRAP markers were used for varieties characterization and to calculate genetic distances between them. Both distance matrices were subjected to cluster analysis. Exclusive SSR alleles were found for globe artichoke and for wild cardoon, but non exclusive alleles were found for cultivated cardoon. For both markers systems two major groups were identified, one of them included mostly globe artichoke accessions and the other one grouped mainly cardoons. The differences observed in the sub-cluster conformation with each marker systems may be due to intrinsic characteristics of the markers. Concluding, both kind of molecular markers are valuable tools for studying genetic distances between C. cardunculus accessions although they give different information. Nevertheless, SSR electrophoretic profiles are simpler to score than SRAP markers because they consist of just a few bands. As well, bands are highly informative because of the great number of alleles existing in population and they are codominant markers. In addition, SSRs use would reduce time and costs. (Author) 31 refs.

SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis.

Science.gov (United States)

Han, Zhengzhou; Ma, Xinye; Wei, Min; Zhao, Tong; Zhan, Ruoting; Chen, Weiwen

2018-04-25

Chrysanthemum indicum L., an important ancestral species of the flowering plant chrysanthemum, can be used as medicine and for functional food development. Due to the lack of hereditary information for this species and the difficulty of germplasm identification, we herein provide new genetic insight from the perspective of intraspecific transcriptome comparison and present single sequence repeat (SSR) molecular marker recognition technology. Through the study of a diploid germplasm (DIWNT) and a tetraploid germplasm (DIWT), the following outcome were obtained. (1) A significant difference in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations for specific homologous genes was observed using the OrthoMCL method for the identification of homologous gene families between the two cytotypes. Ka/Ks analysis of common, single-copy homologous family members also revealed a greater difference among genes that experienced positive selection than among those experiencing positive selection. (2) Of more practical value, 2575 SSR markers were predicted and partly verified. We used TaxonGap as a visual tool to inspect genotype uniqueness and screen for high-performance molecular loci; we recommend four primers of 65 randomly selected primers with a combined identification success rate of 88.6% as priorities for further development of DNA fingerprinting of C. indicum germplasm. The SSR technology based on next-generation sequencing was proved to be successful in the identification of C. indicum germplasms. And the information on the intraspecfic genetic divergence generated by transcriptome comparison deepened the understanding of this complex species' nature.

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

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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.

Assessment of genetic diversity in ragi [Eleusine coracana (L.) Gaertn] using morphological, RAPD and SSR markers.

Science.gov (United States)

Prabhu, Kalapad Santosh; Das, Anath Bandhu; Dikshit, Nilamani

2018-04-25

Finger millet (Eleusine coracana L. Gaertn., 2n=36) is one of the most important minor crops, commonly known as 'ragi' and used as a staple food grain in more than 25 countries including Africa and south Asia. Twenty-seven accessions of ragi were collected from different parts of India and were evaluated for morpho-genetic diversity studies. Simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) markers were used for assessment of genetic diversity among 27 genotypes of E. coracana. High degree of similarity (90%) was obtained between 'IC49979A' and 'IC49974B' genotypes, whereas low level of similarity (9.09%) was found between 'IC204141' and 'IC49985' as evident in morphological and DNA markers. A total of 64 SSR and 301 RAPD amplicons were produced, out of which 87.50% and 77.20% DNA fragments showed polymorphism, respectively. The clustering pattern obtained among the genotypes corresponded well with their morphological and cytological data with a monophyletic origin of this species which was further supported by high bootstrap values and principal component analysis. Cluster analysis showed that ragi accessions were categorised into three distinct groups. Genotypes IC344761, IC340116, IC340127, IC49965 and IC49985 found accession specific in RAPD and SSR markers. The variation among ragi accessions might be used as potential source of germplasm for crop improvement.

Genetic Characterization of Turkish Snake Melon (Cucumis melo L. subsp. melo flexuosus Group) Accessions Revealed by SSR Markers.

Science.gov (United States)

Solmaz, Ilknur; Kacar, Yildiz Aka; Simsek, Ozhan; Sari, Nebahat

2016-08-01

Snake melon is an important cucurbit crop especially in the Southeastern and the Mediterranean region of Turkey. It is consumed as fresh or pickled. The production is mainly done with the local landraces in the country. Turkey is one of the secondary diversification centers of melon and possesses valuable genetic resources which have different morphological characteristics in case of snake melon. Genetic diversity of snake melon genotypes collected from different regions of Turkey and reference genotypes obtained from World Melon Gene Bank in Avignon-France was examined using 13 simple sequence repeat (SSR) markers. A total of 69 alleles were detected, with an average of 5.31 alleles per locus. The polymorphism information content of SSR markers ranged from 0.19 to 0.57 (average 0.38). Based on cluster analysis, two major groups were defined. The first major group included only one accession (61), while the rest of all accessions grouped in the second major group and separated into different sub-clusters. Based on SSR markers, cluster analysis indicated that considerably high genetic variability exists among the examined accessions; however, Turkish snake melon accessions were grouped together with the reference snake melon accessions.

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

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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

40 CFR 142.14 - Records kept by States.

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2010-07-01

... determination, the State's findings based on the supporting data and any additional bases for the determination... may be kept or data may be transferred to tabular summaries, provided that the information retained... decision allows a system to avoid monitoring without receiving State approval in each instance, records of...

Table 1. Details of SSR loci genotyped in E. tereticornis (Et86)

Indian Academy of Sciences (India)

Welcome

Details of SSR loci genotyped in E. tereticornis (Et86) × E. grandis (Eg9) mapping population showing allelic pattern, annealing temperature (oC) and linkage group (LG). Marker name. Et86. Eg9. Annealing temperature. (oC). LG. 1. EMBRA2 ab cd. 56. 11. 2. EMBRA9 nn np. 57. 5. 3. EMBRA17 lm ll. 56. 9. 4. EMBRA19 lm.

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species.

Directory of Open Access Journals (Sweden)

Kajal Kumari

Full Text Available Foxtail millet (Setariaitalica L. is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2% eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65 obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%, maize (~61% and rice (~42% chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

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

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...... markers were found to be polymorphic, whereas only 2,532 of the ~7,000 DArT markers were polymorphic. A Mantel test between the genetic distances calculated based on the SSR and DArT data showed a strong positive correlation between the two marker types, with a Pearson's value (r) of 0.66. We assessed...... 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...

Analysis of average standardized SSR allele size supports domestication of soybean along the Yellow River

NARCIS (Netherlands)

Li, Y.H.; Zhang, C.; Smulders, M.J.M.; Li, W.; Ma, Y.S.; Xu, Qu; Chang, R.Z.; Qiu, Li-Juan

2013-01-01

Soybean (Glycine max) was domesticated in China from its wild progenitor G. soja. The geographic region of domestication is, however, not exactly known. Here we employed the directional evolution of SSR (microsatellite) repeats (which mutate preferentially into longer alleles) to analyze the

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2010-08-27

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Genetic Diversity and Association of EST-SSR and SCoT Markers with Rust Traits in Orchardgrass (Dactylis glomerata L.).

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Yan, Haidong; Zhang, Yu; Zeng, Bing; Yin, Guohua; Zhang, Xinquan; Ji, Yang; Huang, Linkai; Jiang, Xiaomei; Liu, Xinchun; Peng, Yan; Ma, Xiao; Yan, Yanhong

2016-01-08

Orchardgrass (Dactylis glomerata L.), is a well-known perennial forage species; however, rust diseases have caused a noticeable reduction in the quality and production of orchardgrass. In this study, genetic diversity was assessed and the marker-trait associations for rust were examined using 18 EST-SSR and 21 SCoT markers in 75 orchardgrass accessions. A high level of genetic diversity was detected in orchardgrass with an average genetic diversity index of 0.369. For the EST-SSR and SCoT markers, 164 and 289 total bands were obtained, of which 148 (90.24%) and 272 (94.12%) were polymorphic, respectively. Results from an AMOVA analysis showed that more genetic variance existed within populations (87.57%) than among populations (12.43%). Using a parameter marker index, the efficiencies of the EST-SSR and SCoT markers were compared to show that SCoTs have higher marker efficiency (8.07) than EST-SSRs (4.82). The results of a UPGMA cluster analysis and a STRUCTURE analysis were both correlated with the geographic distribution of the orchardgrass accessions. Linkage disequilibrium analysis revealed an average r² of 0.1627 across all band pairs, indicating a high extent of linkage disequilibrium in the material. An association analysis between the rust trait and 410 bands from the EST-SSR and SCoT markers using TASSEL software revealed 20 band panels were associated with the rust trait in both 2011 and 2012. The 20 bands obtained from association analysis could be used in breeding programs for lineage selection to prevent great losses of orchardgrass caused by rust, and provide valuable information for further association mapping using this collection of orchardgrass.

Transferability of Newly Developed Pear SSR Markers to Other Rosaceae Species.

Science.gov (United States)

Fan, L; Zhang, M-Y; Liu, Q-Z; Li, L-T; Song, Y; Wang, L-F; Zhang, S-L; Wu, J

2013-01-01

A set of 120 simple sequence repeats (SSRs) was developed from the newly assembled pear sequence and evaluated for polymorphisms in seven genotypes of pear from different genetic backgrounds. Of these, 67 (55.8 %) primer pairs produced polymorphic amplifications. Together, the 67 SSRs detected 277 alleles with an average of 4.13 per locus. Sequencing of the amplification products from randomly picked loci NAUPy31a and NAUpy53a verified the presence of the SSR loci. When the 67 primer pairs were tested on 96 individual members of eight species in the Rosaceae family, 61.2 % (41/67) of the tested SSRs successfully amplified a PCR product in at least one of the Rosaceae genera. The transferability from pear to different species varied from 58.2 % (apple) to 11.9 % (cherry). The ratio of transferability also reflected the closer relationships within Maloideae over Prunoideae. Two pear SSR markers, NAUpy43c and NAUpy55k, could distinguish the 20 different apple genotypes thoroughly, and UPGMA cluster analysis grouped them into three groups at the similarity level of 0.56. The high level of polymorphism and good transferability of pear SSRs to Rosaceae species indicate their promise for application to future molecular screening, map construction, and comparative genomic studies among pears and other Rosaceae species.

High-density Integrated Linkage Map Based on SSR Markers in Soybean

Science.gov (United States)

Hwang, Tae-Young; Sayama, Takashi; Takahashi, Masakazu; Takada, Yoshitake; Nakamoto, Yumi; Funatsuki, Hideyuki; Hisano, Hiroshi; Sasamoto, Shigemi; Sato, Shusei; Tabata, Satoshi; Kono, Izumi; Hoshi, Masako; Hanawa, Masayoshi; Yano, Chizuru; Xia, Zhengjun; Harada, Kyuya; Kitamura, Keisuke; Ishimoto, Masao

2009-01-01

A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding. PMID:19531560

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.

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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Guo, Qi; Wang, Jin-Xing; Su, Li-Zhuo; Lv, Wei; Sun, Yu-Han; Li, Yun

2017-07-07

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.

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

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McBenedict, Billy; Chimwamurombe, Percy; Kwembeya, Ezekeil; Maggs-Kölling, Gillian

2016-01-01

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.

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.

Irradiation facilities on the TRIGA-SSR thermal column

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Roth, C; Aioanei, L; Preda, M; Gugiu, D [Institute for Nuclear Research, Pitesti (Romania); Garlea, I; Kelerman, C; Garlea, C [SENDRA ' Nuclear Technologies' ltd. Bucharest (Romania)

2004-07-01

The development of thermal and intermediate energy neutron irradiation facilities at the steady state core of the Romanian TRIGA Reactor is described. The reference thermal neutron irradiation facility consists of a dry spherical cavity placed into the graphite thermal column of the SSR core and the intermediate energy neutron irradiation facility is a {sigma}{sigma} system located into the thermal flux cavity. The implementation of the irradiation facilities into the under-water thermal column represented an important challenge from the standpoint of instrumentation solutions. The neutron flux and spectrum measurements were performed using foil activation techniques and fission rate measurements by sealed fission chambers, followed by spectrum unfolding procedure. The absolute fission reaction measurements, using calibrated fission chambers, allow the neutron flux density unit transfer from international reference neutron fields. The MCNP-4C code package was used for neutron spectrum computations in the thermal flux cavity and in the {sigma}{sigma} system. The neutron characterization program demonstrates the accuracy of the spectrum characteristics and neutron flux densities reported to the local monitoring system count rates. Some discrepancies, as compared to other similar facilities, were identified and discussed. These are caused by thermal column particularities: the presence of a water layer between the graphite cells (thermal neutron absorption) and smaller geometrical dimensions (neutron escape phenomena). Based on these results the metrological certification process, according to Romanian metrological laws requirements, is now in progress. (nevyjel)

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

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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

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

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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...

De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L. Hepper].

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J Souframanien

Full Text Available Black gram [V. mungo (L. Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes pathways were identified, of which majority of TCS are grouped into purine metabolism (678 followed by pyrimidine metabolism (263. A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35% followed by di-nucleotide repeats (32%. PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS and untranslated regions (UTRs respectively. Tri-nucleotide repeats (57.3% were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.

De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L.) Hepper

Science.gov (United States)

Souframanien, J.; Reddy, Kandali Sreenivasulu

2015-01-01

Black gram [V. mungo (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram. PMID

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice.

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Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K; Agarwal, Pinky; Parida, Swarup K; Tyagi, Akhilesh K

2016-01-01

Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus , and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region ( OsqGW5.1 ) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis -regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse

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.

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.

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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.

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.

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Chen, Jingfang; Li, Ronghua; Xia, Yanshi; Bai, Guihua; Guo, Peiguo; Wang, Zhiliang; Zhang, Hua; Siddique, Kadambot H M

2017-01-01

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.

Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

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Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

2016-01-01

Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

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

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Hao, Xiaopeng; Yang, Tao; Liu, Rong; Hu, Jinguo; Yao, Yang; Burlyaeva, Marina; Wang, Yan; Ren, Guixing; Zhang, Hongyan; Wang, Dong; Chang, Jianwu; Zong, Xuxiao

2017-01-01

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 NextSeq TM 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.

Development of polymorphic genic-SSR markers by cDNA library sequencing in boxwood, Buxus spp. (Buxaceae)

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Genic microsatellites or simple sequence repeat (genic-SSR) markers were developed in boxwood (Buxus taxa) for genetic diversity analysis, identification of taxa, and to facilitate breeding. cDNA libraries were developed from mRNA extracted from leaves of Buxus sempervirens ‘Vardar Valley’ and seque...

Genotype-specific microsatellite (SSR) markers for the sugarcane germplasm in the Karst region of Guizhou, China

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It is the first report on SSR-based molecular evaluation of genetic variability among sugarcane genotypes from the Karst region of China that provides useful information for local sugarcane improvement. Eighteen sugarcane genotypes including 13 active cultivars and five elite QT-series clones bred l...

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.

Development of Simple Sequence Repeats (SSR) markers in Setaria italica (Poaceae) and cross-amplification in related species.

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Lin, Heng-Sheng; Chiang, Chih-Yun; Chang, Song-Bin; Kuoh, Chang-Sheng

2011-01-01

Foxtail millet is one of the world's oldest cultivated crops. It has been adopted as a model organism for providing a deeper understanding of plant biology. In this study, 45 simple sequence repeats (SSR) markers of Setaria italica were developed. These markers showing polymorphism were screened in 223 samples from 12 foxtail millet populations around Taiwan. The most common dinucleotide and trinucleotide repeat motifs are AC/TG (84.21%) and CAT (46.15%). The average number of alleles (N(a)), the average heterozygosities observed (H(o)) and expected (H(e)) are 3.73, 0.714, 0.587, respectively. In addition, 24 SSR markers had shown transferability to six related Poaceae species. These new markers provide tools for examining genetic relatedness among foxtail millet populations and other related species. It is suitable for germplasm management and protection in Poaceae.

Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweet potato (Ipomoea batatas (L.) Lam).

Science.gov (United States)

Kim, Jin-Hee; Chung, Il Kyung; Kim, Kyung-Min

2017-01-01

The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis. According to those, the Four QTLs were identified, and The LOD score was 3.0. Further studies need to develop molecular markers in terms of EST-SSR markers for doing to be capable of efficient breeding. The genetic map created here using EST-SSR markers will facilitate planned breeding of sweet potato cultivars with various desirable traits.

Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas L.

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Kai eZhang

2016-03-01

Full Text Available 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 1,824 SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato, and designed 1,476 primer pairs based on SSR-containing sequences. We mapped 214 pairs of primers in a natural population comprised of 239 germplasms, and identified 1,278 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.

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

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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.

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

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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.

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.

Molecular characterization of barley (Hordeum vulgare L. accessions of the Serbian GeneBank by SSR fingerprinting

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Šurlan-Momirović Gordana

2013-01-01

Full Text Available Molecular diversity of 145 barley (Hordeum vulgare subsp. vulgare L. accessions from the Serbian GenBank was assessed by single sequence repeats (SSR markers. A set of 15 SSRs, covering all chromosomes of the diploid barley genome with 2-3 SSR markers per chromosome, with a range of 4-18 alleles per locus were used. In total, 15 loci and 119 alleles were detected, with an average of 7.93 alleles per locus. The Polymorphic information content value ranged from 0.220 to 0.782 with a mean value of 0.534. Regarding the growth habit and row type groups, gene diversity was comparatively higher for the spring (0.616 and six-rowed accessions (0.616 than for the winter and two- rowed accessions (0.322 and 0.478, respectively. Analysis of molecular variance showed that all sources of variation were significant (P < 0.01, but the between-group component was predominant (76.85% for growth habit and 89.45% for row type. Unweighted Pair Group Method with Arithmetic Mean (UPGMA cluster analysis based on the shared allele distance (DSA matrix estimated on the SSR data assigned the genotypes into two clusters - the first smaller consisting of the six 6-rowed spring cultivars and the second comprising six subclusters. Genotype MBR1012 was separated from all other genotypes that constitute UPGMA tree. The associations of genotypes belonging to different growth habit and row type groups were assessed using Principal Coordinate Analysis revealing separation of winter growth habit group from facultative one. The use of the STRUCTURE clustering algorithm allowed the identification of 2 subpopulations of genotypes. [Projekat Ministarstva nauke Republike Srbije, br. TR31092

76 FR 76103 - Privacy Act; Notice of Proposed Rulemaking: State-78, Risk Analysis and Management Records

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2011-12-06

... Rulemaking: State-78, Risk Analysis and Management Records SUMMARY: Notice is hereby given that the... portions of the Risk Analysis and Management (RAM) Records, State-78, system of records contain criminal...) * * * (2) * * * Risk Analysis and Management Records, STATE-78. * * * * * (b) * * * (1) * * * Risk Analysis...

[An evaluation of the economic loss from intestinal helminthiases in the Uzbek SSR].

Science.gov (United States)

Abdiev, T A; Zubitskaia, M A; Kovalenko, A F; Fuzaĭlov, Iu M; Baratov, R D; Ziganshina, N Kh; Isaeva, Kh B; Borukhov, S M; Priezzhaeva, N G; Musaeva, G A

1990-01-01

Calculations of economic loss costs due to procedures for helminth detection and the out-patient treatment of recognized cases of enterobiasis, hymenolepiasis, taeniasis, ascariasis, trichocephaliasis in the Uzbek SSR in 1985 were made as were the costs of inpatient treatment in the specialized clinics in 1986 with account for the loss due to the related decrease in the national output and payments for disability. Their total turned to be about 1.8 million rubles.

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.

Phylogeny and sequence variability of the Sarcocystis singaporensis Zaman and Colley, (1975) 1976 ssrDNA

Czech Academy of Sciences Publication Activity Database

Šlapeta, Jan Roger; Kyselová, Iveta; Richardson, A. O.; Modrý, David; Lukeš, Julius

2002-01-01

Roč. 88, č. 9 (2002), s. 810-815 ISSN 0932-0113 R&D Projects: GA ČR GA524/00/P015; GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6022909 Keywords : Sarcocystis * phylogeny * ssrDNA Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.046, year: 2002

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. PMID:26808306

Development of Simple Sequence Repeats (SSR Markers in Setaria italica (Poaceae and Cross-Amplification in Related Species

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Chih-Yun Chiang

2011-11-01

Full Text Available Foxtail millet is one of the world’s oldest cultivated crops. It has been adopted as a model organism for providing a deeper understanding of plant biology. In this study, 45 simple sequence repeats (SSR markers of Setaria italica were developed. These markers showing polymorphism were screened in 223 samples from 12 foxtail millet populations around Taiwan. The most common dinucleotide and trinucleotide repeat motifs are AC/TG (84.21% and CAT (46.15%. The average number of alleles (Na, the average heterozygosities observed (Ho and expected (He are 3.73, 0.714, 0.587, respectively. In addition, 24 SSR markers had shown transferability to six related Poaceae species. These new markers provide tools for examining genetic relatedness among foxtail millet populations and other related species. It is suitable for germplasm management and protection in Poaceae.

Language Policy, Tacit Knowledge, and Institutional Learning: The Case of the Swiss Public Service Broadcaster SRG SSR

Science.gov (United States)

Perrin, Daniel

2011-01-01

"Promoting public understanding" is what the programming mandate asks the Swiss public broadcasting company SRG SSR to do. From a sociolinguistic perspective, this means linking speech communities with other speech communities, both between and within the German-, French-, Italian-, and Romansh-speaking parts of Switzerland. In the…

Functional molecular markers (EST-SSR) in the full-sib reciprocal recurrent selection program of maize (Zea mays L.).

Science.gov (United States)

Galvão, K S C; Ramos, H C C; Santos, P H A D; Entringer, G C; Vettorazzi, J C F; Pereira, M G

2015-07-03

This study aimed to improve grain yield in the full-sib reciprocal recurrent selection program of maize from the North Fluminense State University. In the current phase of the program, the goal is to maintain, or even increase, the genetic variability within and among populations, in order to increase heterosis of the 13th cycle of reciprocal recurrent selection. Microsatellite expressed sequence tags (EST-SSRs) were used as a tool to assist the maximization step of genetic variability, targeting the functional genome. Eighty S1 progenies of the 13th recur-rent selection cycle, 40 from each population (CIMMYT and Piranão), were analyzed using 20 EST-SSR loci. Genetic diversity, observed heterozygosity, information content of polymorphism, and inbreeding co-efficient were estimated. Subsequently, analysis of genetic dissimilarity, molecular variance, and a graphical dispersion of genotypes were conducted. The number of alleles in the CIMMYT population ranged from 1 to 6, while in the Piranão population the range was from 2 to 8, with a mean of 3.65 and 4.35, respectively. As evidenced by the number of alleles, the Shannon index showed greater diversity for the Piranão population (1.04) in relation to the CIMMYT population (0.89). The genic SSR markers were effective in clustering genotypes into their respective populations before selection and an increase in the variation between populations after selection was observed. The results indicate that the study populations have expressive genetic diversity, which cor-responds to the functional genome, indicating that this strategy may contribute to genetic gain, especially in association with the grain yield of future hybrids.

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

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Saba Jasim Aljumaili

2018-01-01

Full Text Available Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak with 3 released varieties as a control using the 32 simple sequence repeat (SSR markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816 from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers.

Science.gov (United States)

Jasim Aljumaili, Saba; Rafii, M Y; Latif, M A; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

2018-01-01

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index ( I ) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity ( H e ) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

Science.gov (United States)

Jasim Aljumaili, Saba; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

2018-01-01

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development. PMID:29736396

Screening of the White Button Mushroom (Agaricusbisporus Homokaryons and Producing New Hybrid Strain by SSR Markers

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marzieh nourashrafeddin

2018-02-01

Full Text Available Introduction: Edible white button mushroom (Agaricusbisporus is the most common edible mushroom in Iran and the world. The yield of this mushroom is less than the average of yield in the world because of strain degeneration and using strains with low yield. Most of the current hybrids are either identical or very similar to the first hybrids. Ongoing breeding programs are exploiting the variability in Agaricus germplasm to produce new varieties with better traits including higher yield and resistance to biotic and abiotic stresses. One of the breeding programs is F1 production from parental homokaryons crossing. These homokaryonsis were isolated among germinated basidiospores on the culture media. During the last decades, various molecular markers based on nucleic acid polymorphisms (such as Restriction Fragment Length Polymorphism, Random Amplification of Polymorphic DNA, Amplified fragment of Length Polymorphism, Inter Simple Sequence Repeat, Simple Sequence Repeat markers have been used to differentiate homokaryons and heterokaryons. Microsatellites consist of short tandem repeat motifs distributed throughout the genome. Microsatellites are usually highly polymorphic due to a high degree of variation in the number of repeats among individuals. Microsatellite markers are multiallelic and co-dominant and thus tend to be more informative than other marker systems. Microsatellite markers have been widely developed in animals and plants and more recently in fungal species. The presence of microsatellites in the genome of A. bisporus was previously reported. Materials and Methods: In this research, 160 germinated basidiospores were collected from commercially cultivated strain A15 and they were grown on compost extract agar (CEA. The mycelial growth rate of these160 isolates was evaluated at 25°C on CEA medium. 18 isolates with slow growing rate were selected from 160 isolates. In the next step, co-dominant SSR markers were used to homokaryons

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.

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.

SSR allelic variation of rice variety Hangxiangnuo bred by space mutation

International Nuclear Information System (INIS)

Yang Tifeng; Liu Chuanguang; Pan Dajian; Fan Zhilan; Li Chen; Chen Jianyou; Liu Bin; Jiang Yijun; Gao Yun; Zhou Hanqin

2011-01-01

Hangxiangnuo, an indica fragrant glutinous rice mutant, was induced by space environment. Comparing with its wild type Nanfengnuo, the yield and blast resistance of Hangxiangnuo are improved significantly and the grain shape became slender and with fragrance. To understand the mechanisms of space mutation and identify the changes at molecular level associated with phenotypic variations, SSR allelic variation analysis were performed on Hangxiangnuo and Nanfengnuo in this study. The results showed that 45 loci were polymorphic among the 156 SSR loci tested throughout the genome, the frequency of variation was 28.85%. Among the polymorphic loci, 42 loci only showed variations in the molecular weight of the amplified bands, only on locus increased the number of amplification bands in Hangxiangnuo and two loci were differed by heterozygous loci (with two amplification bands at one locus) detected in Nanfengnuo and homozygous loci in Hangxiangnuo. It suggests that the change of some loci in mutants was due to the normal segregation and recombination of heterozygous loci of the wild type. The variation frequencies among different chromosomes were quite different, with the highest one at 50.00% detected on chromosomes 7, 8 and 12, and the lowest at 6.25% on chromosome 6. The polymorphic loci were clustered on chromosomes throughout the genome indicating that large DNA segments mutation is one of the major variation patterns induced by space environment. Some of reported QTLs involved in grain shape, yield, fragrance and blast resistance were found to be located exactly in the mutated regions. Therefore, further study is needed to confirm that these QTLs are responsible for the trait variations. (authors)

Characterization of functional SSR markers in Prosopis alba and their transferability across Prosopis species

OpenAIRE

María F. Pomponio; Cintia Acuña; Vivien Pentreath; Diego L. Lauenstein; Susana M. Poltri; Susana Torales

2015-01-01

Aim of study: The aim of the study was to characterize functional microsatellite markers in Prosopis alba and examine the transferability to species from the Prosopis genus. Area of the study: samples were obtained from natural populations of Argentina. Material and Methods: Eleven SSR functional markers related to stress and metabolism were amplified in a sample of 152 genotypes from P.alba, P. denudans, P. hassleriP. chilensis, P. flexuosa, and interspecific hybrids. Main res...

Assessment of genetic diversity in Brassica juncea Brassicaceae genotypes using phenotypic differences and SSR markers

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Vinu V.

2013-12-01

Full Text Available Las especies de mostaza del género Brassica representan uno de los cultivos de semillas oleaginosas más importantes en India, sin embargo, su diversidad genética es poco conocida. Para la utilización de genotipos en programas de cultivos resulta esencial un mayor conocimiento sobre este tema. Debido a ello, se evaluó la diversidad genética entre 44 genotipos de mostaza de la India Brassica juncea incluyendo variedades y líneas puras de diferentes zonas agro-climáticas de la India y algunos genotipos exóticos Australia, Polonia y China. Para ello, se utilizaron marcadores SSR específicos del genoma A y B y datos fenotípicos del rendimiento de 12 cosechas y sus características. De los 143 primers evaluados, 134 reportaron polimorfismo y un total de 355 alelos fueron amplificados. Se generaron dendrogramas a partir de los coeficientes de similitud de Jaccard y de disimilitud Manhattan, basados en un algoritmo de vinculación promedio UPGMA. Se utilizaron datos de marcadores genéticos y datos fenotípicos. Los genotipos se agruparon en cuatro grupos basados en las distancias genéticas. Ambos patrones de agrupamiento, tanto los basados en los coeficientes de similitud de Jaccard como los basados en los de disimilitud Manhattan, separaron independientemente los genotipos por su genealogía y origen, de una manera efectiva. El PCoA reveló que la agrupación de genotipos basada en datos de marcadores SSR, es más convincente que los datos fenotípicos, sin embargo, se observó que la correlación entre las matrices de distancia fenotípica y genética resultó muy baja r=0.11. Por lo tanto, para estudios de diversidad basados en marcadores moleculares es necesario realizar más pruebas. Los marcadores SSR constituyen herramientas más eficientes para discriminar entre genotipos de B. juncea, que las características cuantitativas.

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

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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

78 FR 9987 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

Science.gov (United States)

2013-02-12

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0071] Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations of Unfairness, Prejudice, Partiality, Bias, Misconduct, or Discrimination by Administrative Law Judges (ALJs); Correction AGENCY: Social Security...

78 FR 22361 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

Science.gov (United States)

2013-04-15

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0071] Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations of Unfairness, Prejudice, Partiality, Bias, Misconduct, or Discrimination by Administrative Law Judges (ALJs); Correction AGENCY: Social Security...

Reptilia, Squamata, Gymnophthalmidae, Arthrosaura reticulata (O'Shaughnessy, 1881: Distribution extension and new state record.

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Mott, T.

2011-01-01

Full Text Available Arthrosaura reticulata (O´Shaugnessy, 1881 is reported from two localities in Mato Grosso, Brazil. It representsthe first state record for the species, extending its known distribution in 830 km southeastern of the southernmost recordin the state of Amazonas and 470 km eastern of the state of Rondônia, the southernmost record of the species.

Genetic variability assessment in the genus Passiflora by SSR markers

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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.

Synthesis and carbon-11-labeling of p-MeO-SSR180575, a novel indoleacetamide-based candidate for PET imaging of the peripheral benzodiazepine receptor (TSPO 18 kDa)

International Nuclear Information System (INIS)

Damont, A.; Le Helleix, St.; Kuhnast, B.; Boisgard, R.; Tavitian, B.; Dolle, F.; Marguet, F.; Puech, F.

2011-01-01

Complete text of publication follows: Objectives: The 3-iso-quinolinecarboxamide [ 11 C]PK11195, despite its low brain uptake and high level of nonspecific binding, is still the most widely used PET-radioligand for the in vivo imaging of the peripheral benzodiazepine receptor (PBR or TSPO 18 kDa). Several new PBR radioligands are currently developed to replace [ 11 C]PK11195, e.g the pyrazolo[1, 5-a]pyrimidine-acetamides [ 11 C]DPA-713 and [ 18 F]DPA-714, the imidazo[1, 2-a]pyridine-acetamides [ 11 C]CLINME and [ 18 F]PBR111 and the N-benzyl-N-(2-phenoxy-aryl)- acetamides [ 11 C]PBR28 and [ 18 F]FEDAA1106. Another attractive newly identified chemical class of structures are the indole-acetamides and notably compounds derived from the lead compound SSR180575. Herein are reported the synthesis and the labelling with the positron-emitter carbon-11 (half-life: 20.38 min) of a novel derivative of SSR180575, bearing a para methoxy function on its phenyl ring. Methods: p-MeO-SSR180575 (1) was synthesized from commercially available 4-chloro-2-nitrotoluene in 10 steps. O-demethylation, performed with a boron tribromide solution in dichloromethane at low temperature, afforded the free phenol derivative 2. Carbon-11 labeling of p-MeO-SSR180575 (1) was performed using a TRACERLab FX-C Pro synthesizer (GEMS) and comprised (1) trapping of [ 11 C]MeOTf at -10 C in acetone (0.3 mL) containing the nor-derivative 2 (O-demethylated, 0.6-0.9 mg) and aq. 3N NaOH (8 μL); (2) heating at 110 C for 2 min; (3) concentration to dryness and taking up the residue in 1.0 mL of the HPLC mobile phase; (4) purification using semi-preparative reversed-phase HPLC (Waters Symmetry C-18 - eluent: CH 3 CN / H 2 O / TFA: 50 / 50 / 0.1 (v:v:v) - flow rate: 5 mL/min - detection at 254 nm) and (5) SepPak R Plus C-18-based formulation for i.v. injection. Results: p-MeO-SSR180575 (1) was obtained in 10% overall yield. The tricky and low-yielding step in our approach was the pyridazine ring formation

Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry

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A database of Louisiana sugarcane molecular identity has been constructed and is being updated annually using FAM or HEX or NED fluorescence- and capillary electrophoresis (CE)-based microsatellite (SSR) fingerprinting information. The fingerprints are PCR-amplified from leaf DNA samples of current ...

Development and Characterization of Simple Sequence Repeat (SSR) Markers Based on RNA-Sequencing of Medicago sativa and In silico Mapping onto the M. truncatula Genome

Science.gov (United States)

Wang, Zan; Yu, Guohui; Shi, Binbin; Wang, Xuemin; Qiang, Haiping; Gao, Hongwen

2014-01-01

Sufficient codominant genetic markers are needed for various genetic investigations in alfalfa since the species is an outcrossing autotetraploid. With the newly developed next generation sequencing technology, a large amount of transcribed sequences of alfalfa have been generated and are available for identifying SSR markers by data mining. A total of 54,278 alfalfa non-redundant unigenes were assembled through the Illumina HiSeqTM 2000 sequencing technology. Based on 3,903 unigene sequences, 4,493 SSRs were identified. Tri-nucleotide repeats (56.71%) were the most abundant motif class while AG/CT (21.7%), AGG/CCT (19.8%), AAC/GTT (10.3%), ATC/ATG (8.8%), and ACC/GGT (6.3%) were the subsequent top five nucleotide repeat motifs. Eight hundred and thirty- seven EST-SSR primer pairs were successfully designed. Of these, 527 (63%) primer pairs yielded clear and scored PCR products and 372 (70.6%) exhibited polymorphisms. High transferability was observed for ssp falcata at 99.2% (523) and 71.7% (378) in M. truncatula. In addition, 313 of 527 SSR marker sequences were in silico mapped onto the eight M. truncatula chromosomes. Thirty-six polymorphic SSR primer pairs were used in the genetic relatedness analysis of 30 Chinese alfalfa cultivated accessions generating a total of 199 scored alleles. The mean observed heterozygosity and polymorphic information content were 0.767 and 0.635, respectively. The codominant markers not only enriched the current resources of molecular markers in alfalfa, but also would facilitate targeted investigations in marker-trait association, QTL mapping, and genetic diversity analysis in alfalfa. PMID:24642969

Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers.

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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.

Development and Characterization of 1,906 EST-SSR Markers from Unigenes in Jute (Corchorus spp..

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Liwu Zhang

Full Text Available Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively. The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute.

Investigating the Effect of Sympathetic Skin Response Parameters on the Psychological Test Scores in Patients with Fibromyalgia Syndrome by Using ANNS

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Murat Yıldız

2013-01-01

Full Text Available In this study, psychological tests such as Visual Analogue Pain Scale, Verbal Pain Scale, Beck Depression Inventory, Beck Anxiety Inventory, Hamilton Depression Rating Scale and Hamilton Anxiety Scale were applied to the selected healthy subjects and patients with Fibromyalgia Syndrome (FMS in Suleyman Demirel University, Faculty of Medicine, Department of Physical Medicine and Rehabilitation and the scores were recorded. A measurement system was established in the same department of the university to measure the sympathetic skin response (SSR from the subjects. The SSR was measured and recorded. The parameters such as latency time, maximum amplitude and the elapsed time were calculated by using Matlab software from the recorded SSR data. SSR parameters were added to the scores and diagnosis accuracy percentages of the FMS calculated by using artificial neural networks (ANNs. Obtained results from the simulations showed that the specified parameters of the SSR and FMS were concerned and these parameters can be used as a diagnostic method in FMS.

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

NARCIS (Netherlands)

Ting, N.C.; Jansen, J.; Nagappan, J.; Ishak, Z.; Chin, C.W.; Tan, S.G.; Cheah, S.C.; Singh, R.

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)

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

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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...

Synthesis and carbon-11-labeling of p-MeO-SSR180575, a novel indoleacetamide-based candidate for PET imaging of the peripheral benzodiazepine receptor (TSPO 18 kDa)

International Nuclear Information System (INIS)

Damont, A.L.; Le Helleix, St.; Kuhnast, B.; Boisgard, R.; Tavitian, B.; Dolle, F.; Marguet, F.; Puech, F.

2011-01-01

Complete text of publication follows: Objectives: The 3-iso-quinolinecarboxamide [ 11 C]PK11195, despite its low brain uptake and high level of nonspecific binding, is still the most widely used PET-radioligand for the in vivo imaging of the peripheral benzodiazepine receptor (PBR or TSPO 18 kDa). Several new PBR radioligands are currently developed to replace [ 11 C]PK11195 [1], e.g the pyrazolo[1, 5-a]pyrimidine-acetamides [ 11 C]DPA-713 and [ 18 F]DPA-714, the imidazo[1, 2-a]pyridine-acetamides [ 11 C]CLINME and [ 18 F]PBR111 and the N-benzyl-N-(2-phenoxy-aryl)- acetamides [ 11 C]PBR28 and [ 18 F]FEDAA1106. Another attractive newly identified chemical class of structures are the indole-acetamides and notably compounds derived from the lead compound SSR180575 [2]. Herein are reported the synthesis and the labelling with the positron-emitter carbon-11 (half-life: 20.38 min) of a novel derivative of SSR180575, bearing a para methoxy function on its phenyl ring. Methods: p-MeO-SSR180575 (1) was synthesized from commercially available 4-chloro-2-nitrotoluene in 10 steps. O-demethylation, performed with a boron tribromide solution in dichloromethane at low temperature, afforded the free phenol derivative 2. Carbon-11 labeling of p-MeO-SSR180575 (1) was performed using a TRACERLab FX-C Pro synthesizer (GEMS) and comprised (1) trapping of [ 11 C]MeOTf at -10 C in acetone (0.3 mL) containing the nor-derivative 2 (O-demethylated, 0.6-0.9 mg) and aq. 3N NaOH (8 μL); (2) heating at 110 C for 2 min; (3) concentration to dryness and taking up the residue in 1.0 mL of the HPLC mobile phase; (4) purification using semi-preparative reversed-phase HPLC (Waters Symmetry R C-18 - eluent: CH 3 CN / H 2 O / TFA: 50 / 50 / 0.1 (v:v:v) - flow rate: 5 mL/min - detection at 254 nm) and (5) SepPak Plus R C-18-based formulation for i.v. injection approach was the pyridazine ring formation reaction that proceeded partially: the maximum conversion of the intermediate diester-indole reacting

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species.

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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.

The assessment of genetic diversity between and within brassica species and their wild relative (eruca sativa) using ssr markers

International Nuclear Information System (INIS)

Kanwal, M.; Farhatullah, A.; Iqbal, S.; Fayyaz, L.; Rabbani, M.A.

2014-01-01

Microsatellites markers were tested for their ability to distinguish genomic distribution of the Brassica species of the U Triangle and E. sativa. The objectives of the present study were to investigate the genetic diversity of six Brassica species from U-Triangle (representing three genomes, A, B, C) and one from genus Eruca and to identify promising sources of genetic variation for breeding purposes. A total of 54 SSR markers were analyzed in order to detect variation between and within the selected genomes. Three primer pairs depicted the greatest genetic diversity showing 97% polymorphism between Brassica and Eruca genomes (2.55 alleles per locus). Polymorphic Information Content (PIC) values ranged from 0.40 (SSR primer Na14-DO7) to 0.79 (NA10-G09). For comparison within Brassica genomes and Eruca, all the genomes were grouped in three modules i.e., ABE, ACE and BCE (Fig. 1). The tetraploid originating from their parental diploids along-with Eruca was considered in the same module. For the estimation of relatedness within and among genomes, dice coefficients were computed as a measure of genetic similarity matrix. On the basis of genetic distances, dendrogram was constructed through cluster analysis. Two major clusters at coefficient of similarity level (0.47) were observed. One cluster comprised of all Brassica genomes and their accessions, while another consisting of all accessions of Eruca genome. The cluster containing Brassica genomes was further subdivided into four sub-groups that contained diploid and tetraploid species in a way that tetraploid species were grouped in between their diploid parental species with varying genetic distances. Present findings confirmed the validity of SSR markers in genomic studies. (author)

Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki.

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Luo, C; Zhang, F; Zhang, Q L; Guo, D Y; Luo, Z R

2013-01-09

We developed and characterized expressed sequence tags (ESTs)-simple sequence repeats (SSRs) and targeted region amplified polymorphism (TRAP) markers to examine genetic relationships in the persimmon genus Diospyros gene pool. In total, we characterized 14 EST-SSR primer pairs and 36 TRAP primer combinations, which were amplified across 20 germplasms of 4 species in the genus Diospyros. We used various genetic parameters, including effective multiplex ratio (EMR), diversity index (DI), and marker index (MI), to test the utility of these markers. TRAP markers gave higher EMR (24.85) but lower DI (0.33), compared to EST-SSRs (EMR = 3.65, DI = 0.34). TRAP gave a very high MI (8.08), which was about 8 times than the MI of EST-SSR (1.25). These markers were utilized for phylogenetic inference of 20 genotypes of Diospyros kaki Thunb. and allied species, with a result that all kaki genotypes clustered closely and 3 allied species formed an independent group. These markers could be further exploited for large-scale genetic relationship inference.

Assessment of Genetic Diversity in Opuntia spp. Portuguese Populations Using SSR Molecular Markers

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Carlos M. G. Reis

2018-04-01

Full Text Available The Opuntia spp., most likely few individuals, were introduced in the Iberian Peninsula in the beginning of the 16th century, after the discovery of America, spreading afterwards throughout the Mediterranean basin. We analysed, for the first time, the genetic diversity in a set of 19 Portuguese Opuntia spp. populations from the species O. ficus-indica, O. elata, O. dillenii and O. robusta using nuclear microsatellite (nuSSR markers. The Italian cultivars ‘Bianca’, ‘Gialla’ and ‘Rossa’ were included in the study for comparison purposes. The nuSSR amplifications produced from five to 16 alleles, with an average of 9.2 alleles per primer pair, and average polymorphism information content of 0.71. The estimated Dice coefficient among populations varied from 0.26 to 1.0, indicating high interspecific genetic diversity but low genetic diversity at the intraspecific level. The hierarchical clustering analysis revealed four major groups that clearly separated the four Opuntia species. Among the O. ficus-indica populations, two sub-clusters were found, one including the white pulp fruits (with cv. Bianca and the other with the orange pulp ones and including the cv. Gialla, the cv. Rossa, and one pale yellow pulp population. No genetic differences were found between the inermis form, O. ficus-indica f. ficus-indica, and the rewilded spiny one, O. ficus-indica f. amyclaea. The dendrogram indicated that the clustering pattern was unrelated to geographical origin. The results revealed a low level of genetic diversity among the Portuguese populations of O. ficus-indica.

The Development Strategies of Electronic Records: United States, Canada, United Kingdom and Australia as Examples

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Chiao-Min Lin

2004-09-01

Full Text Available The development of electronic records have been an indicator of modern government all over the world. The format of public records of government agencies have been gradually transformed to digitalform. How to manage the life cycle of electronic records have became an important issue. In this paper, the development strategies in electronic records of the United States, Canada, United Kingdom and Australia are taken as examples to explain their state-of-the-art. Several suggestions are proposed as the reference for Taiwan’s government. [Article content in Chinese

Using SSR-HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice.

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Li, Jingjian; Xiong, Chao; He, Xia; Lu, Zhaocen; Zhang, Xin; Chen, Xiaoyang; Sun, Wei

2018-01-01

Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci. We tested this method on licorice, a traditional herbal medicine with a long history. Results showed that nine simple sequence repeat (SSR) markers produced distinct melting curve profiles for the five licorice species investigated using HRM analysis. These results were validated by capillary electrophoresis. We applied this protocol to commercially available licorice products, thus enabling the consistent identification of 11 labels with non-declared Glycyrrhiza species. This novel strategy may thus facilitate DNA barcoding as a method of identification of closely related species in herbal medicine products. Based on this study, a brief operating procedure for using the SSR-HRM protocol for herbal authentication is provided.

Identification of SSR and RAPD markers linked to a resistance allele for angular leaf spot in the common bean (Phaseolus vulgaris line ESAL 550

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Gilvan Ferreira da Silva

2003-12-01

Full Text Available The objective of this study was to identify RAPD and SSR markers associated with a resistant allele for angular leaf spot (Phaeoisariopsis griseola from the line 'ESAL 550', derived from the Andean 'Jalo EEP 558' cultivar, to assist selection of resistant genotypes. The resistant line 'ESAL 550' and the susceptible cultivar 'Carioca MG' were crossed to generate F1 and F2 populations. One hundred and twenty F2:3 families were evaluated. The DNA of the 12 most resistant families was bulked and the same was done with the DNA of the 10 most susceptible, generating two contrasting bulks. One RAPD and one SSR marker was found to be linked in coupling phase to the resistant allele. The SSR marker was amplified by the primer PV-atct001(282C, and its distance from the resistant allele was 7.6 cM. This is the most useful marker for indirect selection of resistant plants in segregating populations. The RAPD marker was amplified by the primer OPP07(857C linked in coupling phase to the resistant allele, and distant 24.4 cM. Therefore, this RAPD marker is not so useful in assisting selection because it is too far from the resistant allele.

Analysis of genetic stability at SSR loci during somatic embryogenesis in maritime pine (Pinus pinaster).

Science.gov (United States)

Marum, Liliana; Rocheta, Margarida; Maroco, João; Oliveira, M Margarida; Miguel, Célia

2009-04-01

Somatic embryogenesis (SE) is a propagation tool of particular interest for accelerating the deployment of new high-performance planting stock in multivarietal forestry. However, genetic conformity in in vitro propagated plants should be assessed as early as possible, especially in long-living trees such as conifers. The main objective of this work was to study such conformity based on genetic stability at simple sequence repeat (SSR) loci during somatic embryogenesis in maritime pine (Pinus pinaster Ait.). Embryogenic cell lines (ECLs) subjected to tissue proliferation during 6, 14 or 22 months, as well as emblings regenerated from several ECLs, were analyzed. Genetic variation at seven SSR loci was detected in ECLs under proliferation conditions for all time points, and in 5 out of 52 emblings recovered from somatic embryos. Three of these five emblings showed an abnormal phenotype consisting mainly of plagiotropism and loss of apical dominance. Despite the variation found in somatic embryogenesis-derived plant material, no correlation was established between genetic stability at the analyzed loci and abnormal embling phenotype, present in 64% of the emblings. The use of microsatellites in this work was efficient for monitoring mutation events during the somatic embryogenesis in P. pinaster. These molecular markers should be useful in the implementation of new breeding and deployment strategies for improved trees using SE.

De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development.

Science.gov (United States)

Chen, Honglin; Wang, Lixia; Liu, Xiaoyan; Hu, Liangliang; Wang, Suhua; Cheng, Xuzhen

2017-07-11

Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus. Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions. This transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species.

4-(2-Chloro-4-methoxy-5-methylphenyl)-N-[(1S)-2-cyclopropyl-1-(3-fluoro-4-methylphenyl)ethyl]5-methyl-N-(2-propynyl)-1,3-thiazol-2-amine hydrochloride (SSR125543A): a potent and selective corticotrophin-releasing factor(1) receptor antagonist. I. Biochemical and pharmacological characterization.

Science.gov (United States)

Gully, Danielle; Geslin, Michel; Serva, Laurence; Fontaine, Evelyne; Roger, Pierre; Lair, Christine; Darre, Valerie; Marcy, Claudine; Rouby, Pierre-Eric; Simiand, Jacques; Guitard, Josette; Gout, Georgette; Steinberg, Regis; Rodier, Daniel; Griebel, Guy; Soubrie, Philippe; Pascal, Marc; Pruss, Rebecca; Scatton, Bernard; Maffrand, Jean-Pierre; Le Fur, Gerard

2002-04-01

4-(2-Chloro-4-methoxy-5-methylphenyl)-N-[(1S)-2-cyclopropyl-1- (3-fluoro-4-methylphenyl)ethyl]5-methyl-N-(2-propynyl)-1,3-thiazol-2-amine hydrochloride (SSR125543A), a new 2-aminothiazole derivative, shows nanomolar affinity for human cloned or native corticotrophin-releasing factor (CRF)(1) receptors (pK(i) values of 8.73 and 9.08, respectively), and a 1000-fold selectivity for CRF(1) versus CRF(2 alpha) receptor and CRF binding protein. SSR125543A antagonizes CRF-induced stimulation of cAMP synthesis in human retinoblastoma Y 79 cells (IC(50) = 3.0 +/- 0.4 nM) and adrenocorticotropin hormone (ACTH) secretion in mouse pituitary tumor AtT-20 cells. SSR125543A is devoid of agonist activity in these models. Its brain penetration was demonstrated in rats by using an ex vivo [(125)I-Tyr(0)] ovine CRF binding assay. SSR125543A displaced radioligand binding to the CRF(1) receptor in the brain with an ID(50) of 6.5 mg/kg p.o. (duration of action >24 h). SSR125543A also inhibited the increase in plasma ACTH levels elicited in rats by i.v. CRF (4 microg/kg) injection (ID(50) = 1, 5, or 5 mg/kg i.v., i.p., and p.o., respectively); this effect lasted for more than 6 h when the drug was given orally at a dose of 30 mg/kg. SSR125543A (10 mg/kg p.o.) reduced by 73% the increase in plasma ACTH levels elicited by a 15-min restraint stress in rats. Moreover, SSR125543A (20 mg/kg i.p.) also antagonized the increase of hippocampal acetylcholine release induced by i.c.v. injection of 1 microg of CRF in rats. Finally, SSR125543A reduced forepaw treading induced by i.c.v. injection of 1 microg of CRF in gerbils (ID(50) = approximately 10 mg/kg p.o.). Altogether, these data indicate that SSR125543A is a potent, selective, and orally active CRF(1) receptor antagonist.

SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India.

Science.gov (United States)

Ashraf, Humaira; Husaini, Amjad M; Ashraf Bhat, M; Parray, G A; Khan, Salim; Ganai, Nazir A

2016-10-01

A set of 24 of SSR markers were used to estimate the genetic diversity in 16 rice genotypes found in Western Himalayas of Kashmir and Himachal Pradesh, India. The level of polymorphism among the genotypes of rice was evaluated from the number of alleles and PIC value for each of the 24 SSR loci. A total of 68 alleles were detected across the 16 genotypes through the use of these 24 SSR markers The number of alleles per locus generated varied from 2 (RM 338, RM 452, RM 171) to 6 (RM 585, RM 249, RM 481, RM 162). The PIC values varied from 0.36 (RM 1) to 0.86 (RM 249) with an average of 0.62 per locus. Based on information generated, the genotypes got separated in six different clusters. Cluster 1 comprised of 4 genotypes viz; Zag 1, Zag 13, Pusa sugandh 3, and Zag 14, separated from each other at a similarity value of 0.40. Cluster second comprised of 3 landraces viz; Zag 2. Zag 4 and Zag10 separated from each other at a similarity value of 0.45. Cluster third comprised of 3 genotypes viz; Grey rice, Mushk budji and Kamad separated from each other at a similarity value of 0.46. Cluster fourth had 2 landraces viz; Kawa kreed and Loual anzul, and was not sub clustered. Fifth cluster had 3 genotypes viz; Zag 12, Purple rice and Jhelum separated from each other at a similarity value of 0.28. Cluster 6 comprised of a single popular variety i.e. Shalimar rice 1 with independent lineage.

Disomic Inheritance and Segregation Distortion of SSR Markers in Two Populations of Cynodon dactylon (L.) Pers. var. dactylon.

Science.gov (United States)

Guo, Yuanwen; Wu, Yanqi; Anderson, Jeff A; Moss, Justin Q; Zhu, Lan

2015-01-01

Common bermudagrass [C. dactylon (L.) Pers. var. dactylon] is economically and environmentally the most important member among Cynodon species because of its extensive use for turf, forage and soil erosion control in the world. However, information regarding the inheritance within the taxon is limited. Accordingly, the objective of this study was to determine qualitative inheritance mode in common bermudagrass. Two tetraploid (2n = 4x = 36), first-generation selfed (S1) populations, 228 progenies of 'Zebra' and 273 from A12359, were analyzed for segregation with 21 and 12 simple sequence repeat (SSR) markers, respectively. It is concluded that the inheritance mode of tetraploid bermudagrass was complete or near complete disomic. It is evident that the two bermudagrass parents had an allotetraploid genome with two distinct subgenomes since 33 SSR primer pairs amplified 34 loci, each having two alleles. Severe transmission ratio distortions occurred in the Zebra population while less so in the A12359 population. The findings of disomic inheritance and segregation ratio distortion in common bermudagrass is significant in subsequent linkage map construction, quantitative trait locus mapping and marker-assisted selection in the species.

Report on the development of putative functional SSR and SNP markers in passion fruits.

Science.gov (United States)

da Costa, Zirlane Portugal; Munhoz, Carla de Freitas; Vieira, Maria Lucia Carneiro

2017-09-06

Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.

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

Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers.

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Shanmugapriya Arumugasundaram

Full Text Available Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r(2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r(2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.

Decadal variations in estimated surface solar radiation over Switzerland since the late 19th century

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A. Sanchez-Lorenzo

2012-09-01

Full Text Available Our knowledge on trends in surface solar radiation (SSR involves uncertainties due to the scarcity of long-term time series of SSR, especially with records before the second half of the 20th century. Here we study the trends of all-sky SSR from 1885 to 2010 in Switzerland, which have been estimated using a homogenous dataset of sunshine duration series. This variable is shown to be a useful proxy data of all-sky SSR, which can help to solve some of the current open issues in the dimming/brightening phenomenon. All-sky SSR has been fairly stable with little variations in the first half of the 20th century, unlike the second half of the 20th century that is characterized also in Switzerland by a dimming from the 1950s to the 1980s and a subsequent brightening. Cloud cover changes seem to explain the major part of the decadal variability observed in all-sky SSR, at least from 1885 to the 1970s; at this point, a discrepancy in the sign of the trend is visible in the all-sky SSR and cloud cover series from the 1970s to the present. Finally, an attempt to estimate SSR series for clear-sky conditions, based also on sunshine duration records since the 1930s, has been made for the first time. The mean clear-sky SSR series shows no relevant changes between the 1930s to the 1950s, then a decrease, smaller than the observed in the all-sky SSR, from the 1960s to 1970s, and ends with a strong increase from the 1980s up to the present. During the three decades from 1981 to 2010 the estimated clear-sky SSR trends reported in this study are in line with previous findings over Switzerland based on direct radiative flux measurements. Moreover, the signal of the El Chichón and Pinatubo volcanic eruption visible in the estimated clear-sky SSR records further demonstrates the potential to infer aerosol-induced radiation changes from sunshine duration observations.

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

NARCIS (Netherlands)

Dijk, van T.; Pagliarani, G.; Pikunova, A.; Noordijk, Y.; Yilmaz-Temel, H.; Meulenbroek, B.; Visser, R.G.F.; Weg, van de W.E.

2014-01-01

Background Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map

Nineteenth Century Long-Term Instrumental Records, Examples From the Southeastern United States

Science.gov (United States)

Mock, C. J.

2001-12-01

Early instrumental records in the United States, defined as those operating before 1892 which is regarded the period prior to the modern climate record, provide a longer perspective of climatic variability at decadal and interannual timescales. Such reconstructions also provide a means of verification for other proxy data. This paper provides a American perspective of historical climatic research, emphasizing the urgent need to properly evaluate data quality and provide necessary corrections to make them compatible with the modern record. Different fixed observation times, different practices of weather instrument exposures, and statistical methods for calibration are the main issues in applying corrections and conducting proper climatic interpretations. I illustrate several examples on methodologies of this historical climatic research, focusing on the following in the Southeastern United States: daily reconstructed temperature time-series centered on Charleston SC and Natchez MS back to the late eighteenth century, and precipitation frequency reconstructions during the antebellum period for the Gulf Coast and coastal Southeast Atlantic states. Results indicate several prominent extremes unprecedented as compared to the modern record, such as the widespread warm winter of 1827-28, and the severe cold winters of 1856 and 1857. The reconstructions also yield important information concerning responses to past ENSO events, the PNA, NAO, and the PDO, particularly when compared with instrumental data from other regions. A high potential also exists for applying the climate reconstructions to assess historical climatic impacts on society in the Southeast, such as to understand climatic linkages to famous case studies of Yellow Fever epidemics and severe drought.

Progress along developmental tracks for electronic health records implementation in the United States

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Hollar David W

2009-03-01

Full Text Available Abstract The development and implementation of electronic health records (EHR have occurred slowly in the United States. To date, these approaches have, for the most part, followed four developmental tracks: (a Enhancement of immunization registries and linkage with other health records to produce Child Health Profiles (CHP, (b Regional Health Information Organization (RHIO demonstration projects to link together patient medical records, (c Insurance company projects linked to ICD-9 codes and patient records for cost-benefit assessments, and (d Consortia of EHR developers collaborating to model systems requirements and standards for data linkage. Until recently, these separate efforts have been conducted in the very silos that they had intended to eliminate, and there is still considerable debate concerning health professionals access to as well as commitment to using EHR if these systems are provided. This paper will describe these four developmental tracks, patient rights and the legal environment for EHR, international comparisons, and future projections for EHR expansion across health networks in the United States.

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.

Records of threatened bird and mammal species in Mato Grosso do Sul State, Brazil

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Sylvia Torrecilha

2018-04-01

Full Text Available We conducted a detailed review of threatened bird and mammal occurrence records obtained from surveys across Mato Grosso do Sul, midwestern region of Brazil which has an extent of 357,145 km2, aiming to support environmental and biodiversity conservation initiatives, as strategic plans to protect threatened species in this region. We included all records of species categorized as threatened by the Brazilian and global red list of threatened species. We collected 760 records of threatened birds and mammals in Mato Grosso do Sul State, with 319 records of 40 bird’s species and 441 records of 24 mammal’s species. The status of the 40 bird species under de Brazilian threat category were as follow: 1 Critically Threatened (CR, 6 Endangered (EN, 11 Vulnerable (VU, 11 Near Threatened (NT, and 11 species only in the IUCN red list. Under the IUCN category for the bird´s species, were as follow: 3 EN, 13 VU, 18 NT, 5 Least Concern (LC and 1 taxon has not yet been assessed for the IUCN Red List. Regarding mammal’s species under the Brazilian threat category were as follow: 2 EN, 18 VU, 2 NT and 1 only in the IUCN red list. Under the IUCN status the species ranged from 2 EN, 6 VU, 10 NT, and 6 LC. Each record identified corresponds to the existence of at least one occurrence of threatened birds or mammals in a particular region. The records of threatened species belongs to the three biomes in the state: 269 mammal’s records and 147 bird’s records from Cerrado (Neotropical Savanna biome, 117 mammal’s records and 162 bird’s records from Pantanal (Wetland biome, and 55 mammal’s records and 10 bird’s records from Atlantic Forest biome. In addition, we also included in the dataset environmental information where each record was obtained. Supplementary Files 1- Records of Threatened Mammals_MS_Brazil and Supplementary File 2. Records of Threatened Birds of_MS_Brazil Keywords: Threatened species, Protected areas, Database, Brazil

Field Performance of Five Soybean Mutants Under Drought Stress Conditions and Molecular Analysis Using SSR Markers

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Y Yuliasti

2017-08-01

Full Text Available The objectives of this research wereto evaluate (1 the performance of soybean mutant lines under drought stress conditions, and(2 the genetic diversity and relationship among the mutant lines using SSR markers.The field evaluation was conducted during the dry season of 2011 and 2012 at the experimental Farm of Mataram University, West Nusa Tenggara, Indonesia. The field experiment was set up in a randomized block design. Ten mutant lines and two control varieties were evaluated in four replications. Genetic distance among evaluated lines were determined based on allelic diversity analysis using 40 simple sequence repeat (SSR loci. Under drought stress conditions, two mutant lines, Kdl3 and Kdl8,showed a better performance compared to the other ones. The high yielding mutant lines were Kdl3and Kdl8, which yielded 1.75 t ha-1and 1.69 t ha-1, respectively, compared to the parent and national control, Panderman 1.43 t ha-1 and Muria 1.32 t ha-1. These mutant linesrequired 30.75 to 32days to flower and 79.75 to 83.75 day to harvest with relatively short plant height 28.25 and 23.35 cmrespectively. Those mutant characters were better than those of the other three mutants, the original parents, and the control soybean species. Since the evaluated soybean mutant lines yielded more under drought stress conditions than the standard varieties, they can be used and registered as drought-tolerant soybean mutants. Moreover, the evaluated soybean accessions showed a wide genetic distance. The accessions were clustered into two groups according to their genetic background, namelygroup I (the Panderman with three mutant lines and group II (the Muria with two mutant lines. Twenty-three out of 40 evaluated SSR loci, including AW31, BE806, CMAC7L, S080, S126, S57, S171, S224, S285, S294, S393, S294, S383, S511, S511, S520, S540, S547, S551, S571, S577, and S578, provided polymorphic alleles between the parents and their mutants and could be used to differentiate

First record of Mesoclemmys tuberculata (Reptilia, Testudines, Chelidae in the Cerrado area of Minas Gerais state, southeastern Brazil

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Adriano Lima Silveira

2010-12-01

Full Text Available Mesoclemmys tuberculata is a turtle species that is distributed in northeastern Brazil, recorded mainly in the Caatinga and at some localities in the Atlantic Forest and Cerrado. In this paper we report the first species record in an area of Cerrado of Minas Gerais state, and it is the only known state record in a specific location. During field sampling, a specimen of M. tuberculata was collected in the municipality of João Pinheiro, northwest state, in a Cerrado nuclear area in the São Francisco river basin. The locality of this record is the southern and western limits of M. tuberculata’s known distribution, as well as the most inland locality of species record in the Cerrado biome.

38 CFR 1.506 - Disclosure of records to Federal Government departments, State unemployment compensation agencies...

Science.gov (United States)

2010-07-01

... Federal Government departments, State unemployment compensation agencies, and the Office of Servicemembers....506 Disclosure of records to Federal Government departments, State unemployment compensation agencies... official purposes by any department or other agency of the U.S. Government or any state unemployment...

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.

Insecta, Coleoptera, Cerambycidae, Cerambycinae, Trachyderini: New state and country records from South America

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Quintino, H. Y. S.

2010-01-01

Full Text Available Based on the revision of the collections of the Museu Nacional, Universidade Federal do Rio de Janeiro andthe National Museum of Natural History, Smithsonian Institution, the current work provides new localities for 32 speciesand two subspecies of Trachyderini from South America. Thirteen new country records from Argentina, Brazil, Colombia,Ecuador, Peru, Surinam and Venezuela and 35 new state records from Brazil are registered.

Open reading frame ssr2016 is required for antimycin A-sensitive photosystem I-driven cyclic electron flow in the cyanobacterium Synechocystis sp. PCC 6803

NARCIS (Netherlands)

Yeremenko, Nataliya; Jeanjean, Robert; Prommeenate, Peerada; Krasikov, Vladimir; Nixon, Peter J.; Vermaas, Wim F. J.; Havaux, Michel; Matthijs, Hans C. P.

2005-01-01

Open reading frame ssr2016 encodes a protein with substantial sequence similarities to PGR5 identified as a component of the antimycin A-sensitive ferredoxin:plastoquinone reductase (FQR) in PSI cyclic photophosphorylation in Arabidopsis thaliana. We studied cyclic electron flow in Synechocystis sp.

Fauna of Simuliidae (Diptera from the state of Espírito Santo, Brazil: distribution, new records and list of species

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Karina Bertazo

2013-03-01

Full Text Available Fauna of Simuliidae (Diptera from the state of Espírito Santo, Brazil: Distribution, new records and list of species. The fauna of Simuliidae in Brazil is composed of 87 species, 17 of which are recorded from the state of Espírito Santo. Entomological collections were carried out in 2010-2011 with the objective of increasing the knowledge of the species richness of this family in the state. Ninety three rivers and streams were sampled, each collection being carried out in a 50m transect. During the study period 30 species were collected, 13 of which represent new records for the state, 12 of the genus Simulium and one of the genus Lutzsimulium. Among these new state records one, Simulium lobatoi, also represents a new record from southeastern Brazil. The other newly recorded species are: Lutzsimulium hirticosta, Simulium distinctum, Simulium exiguum, Simulium oyapockense, Simulium botulibranchium, Simulium petropoliense, Simulium clavibranchium, Simulium rappae, Simulium minusculum, Simulium dinellii, Simulium ochraceum and Simulium scutistriatum.

Association mapping of agro-morphological characters among the global collection of finger millet genotypes using genomic SSR markers.

Science.gov (United States)

Kalyana Babu, B; Agrawal, P K; Pandey, Dinesh; Jaiswal, J P; Kumar, Anil

2014-08-01

Identification of alleles responsible for various agro-morphological characters is a major concern to further improve the finger millet germplasm. Forty-six genomic SSRs were used for genetic analysis and population structure analysis of a global collection of 190 finger millet genotypes and fifteen agro-morphological characters were evaluated. The overall results showed that Asian genotypes were smaller in height, smaller flag leaf length, less basal tiller number, early flowering and early maturity nature, small ear head length, and smaller in length of longest finger. The 46 SSRs yielded 90 scorable alleles and the polymorphism information content values varied from 0.292 to 0.703 at an average of 0.442. The gene diversity was in the range of 0.355 to 0.750 with an average value of 0.528. The 46 genomic SSR loci grouped the 190 finger millet genotypes into two major clusters based on their geographical origin by the both phylogenetic clustering and population structure analysis by STRUCTURE software. Association mapping of QTLs for 15 agro-morphological characters with 46 genomic SSRs resulted in identification of five markers were linked to QTLs of four traits at a significant threshold (P) level of ≤ 0.01 and ≤ 0.001. The QTL for basal tiller number was strongly associated with the locus UGEP81 at a P value of 0.001 by explaining the phenotypic variance (R (2)) of 10.8%. The QTL for days to 50% flowering was linked by two SSR loci UGEP77 and UGEP90, explained 10 and 8.7% of R (2) respectively at a P value of 0.01. The SSR marker, FM9 found to have strong association to two agro-morphological traits, flag leaf width (P-0.001, R(2)-14.1 %) and plant height (P-0.001, R(2)-11.2%). The markers linked to the QTLs for above agro-morphological characters found in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of alleles into locally well

Annealing effects in solid-state track recorders

International Nuclear Information System (INIS)

Gold, R.; Roberts, J.H.; Ruddy, F.H.

1981-01-01

Current analyses of the annealing process in Solid State Track Recorders (SSTR) reveal fundamental misconceptions. The use of the Arrhenius equation to describe the decrease in track density resulting from annealing is shown to be incorrect. To overcome these deficiencies, generalized reaction rate theory is used to describe the annealing process in SSTR. Results of annealing experiments are used to guide this theoretical formulation. Within this framework, the concept of energy per etchable defect for SSTR is introduced. A general correlation between sensitivity and annealing susceptibility in SSTR is deduced. In terms of this general theory, the apparent correlation between fission track size and fission track density observed under annealing is readily explained. Based on this theoretical treatment of annealing phenomena, qualitative explanations are advanced for current enigmas in SSTR cosmic ray work

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.

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.

Solid-state reaction in Ti/Ni multilayered films studied by using magneto-optical spectroscopy

CERN Document Server

Lee, Y P; Kim, K W; Kim, C G; Kudryavtsev, Y V; Nemoshkalenko, V V; Szymanski, B

2000-01-01

A comparative study of the solid-state reaction (SSR) in a series of Ti/Ni multilayered films (MLDs) with bilayer periods of 0.65-22.2 nm and a constant Ti to Ni sublayer thickness ratio was performed by using experimental and computer-simulated magneto-optical (MO) spectroscopy based on different models of MLFs, as well as x-ray diffraction (XRD). The spectral and sublayer thickness dependences of the MO properties of the Ti/Ni MLFs were explained on the basis of the electromagnetic theory. The existence of a threshold nominal Ni-sublayer thickness of about 3 nm for the as-deposited Ti/Ni MLF to observe of the equatorial Kerr effect was explained by a solid-state reaction which formed nonmagnetic alloyed regions between pure components during the MLF deposition. The SSR in the Ti/Ni MLFs, which was caused by the low temperature annealing, led to the formation of an amorphous Ti-Ni alloy and took place mainly in the Ti/Ni MLFs with ''thick'' sublayers. For the caes of Ti/Ni MLFs, the MO approach turned out to...

Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery

Science.gov (United States)

Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Peng, Hui; Li, Pirui; Song, Aiping; Guan, Zhiyong; Fang, Weimin; Liao, Yuan; Chen, Fadi

2013-01-01

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. PMID:23626799

Sympathetic skin response and R-R interval variation in cases with rheumatoid arthritis.

Science.gov (United States)

Gozke, E; Erdogan, N; Akyuz, G; Turan, B; Akyuz, E; Us, O

2003-03-01

To investigate the autonomic nervus system involvement in cases with rheumatoid arthritis (RA) by assesing sympathetic skin response (SSR) and R-R interval variation (RRIV), 14 healthy women and 10 women with RA, all of them without clinic dysautonomies were examined. SSR's were recorded palmar surface of both hands and soles of both feet, after stimulating median and tibial nerves individually. RRIV's were assessed at rest and during six deep breathing in one minute with electrodes placed on dorsal surfaces of both hands. SSR could not be obtained from lower extremities of one case with RA. We could not find any significant difference between two groups in terms of SSR latencies. RRIV values obtained during deep breathing to those recorded at rest (D%/R%) was found to be significantly lower in RA cases than healthy controls. RRIV values increased with deep breathing in healthy subjects, while they decreased in 50% of the RA cases. We conclude that assessment of SSR and RRIV are valuble methods for revelation of subclinical autonomic involvement in cases with RA.

Mode of recording and modulation frequency effects of auditory steady state response thresholds

OpenAIRE

Jalaei, Bahram; Shaabani, Moslem; Zakaria, Mohd Normani

2017-01-01

Abstract Introduction The performance of auditory steady state response (ASSR) in threshold testing when recorded ipsilaterally and contralaterally, as well as at low and high modulation frequencies (MFs), has not been systematically studied. Objective To verify the influences of mode of recording (ipsilateral vs. contralateral) and modulation frequency (40 Hz vs. 90 Hz) on ASSR thresholds. Methods Fifteen female and 14 male subjects (aged 18–30 years) with normal hearing bilaterally were ...

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).

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 25 bp 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).

SSR240612 [(2R)-2-[((3R)-3-(1,3-benzodioxol-5-yl)-3-[[(6-methoxy-2-naphthyl)sulfonyl]amino]propanoyl)amino]-3-(4-[[2R,6S)-2,6-dimethylpiperidinyl]methyl]phenyl)-N-isopropyl-N-methylpropanamide hydrochloride], a new nonpeptide antagonist of the bradykinin B1 receptor: biochemical and pharmacological characterization.

Science.gov (United States)

Gougat, Jean; Ferrari, Bernard; Sarran, Lionel; Planchenault, Claudine; Poncelet, Martine; Maruani, Jeanne; Alonso, Richard; Cudennec, Annie; Croci, Tiziano; Guagnini, Fabio; Urban-Szabo, Katalin; Martinolle, Jean-Pierre; Soubrié, Philippe; Finance, Olivier; Le Fur, Gérard

2004-05-01

The biochemical and pharmacological properties of a novel non-peptide antagonist of the bradykinin (BK) B(1) receptor, SSR240612 [(2R)-2-[((3R)-3-(1,3-benzodioxol-5-yl)-3-[[(6-methoxy-2-naphthyl)sulfonyl]amino]propanoyl)amino]-3-(4-[[2R,6S)-2,6-dimethylpiperidinyl]methyl]phenyl)-N-isopropyl-N-methylpropanamide hydrochloride] were evaluated. SSR240612 inhibited the binding of [(3)H]Lys(0)-des-Arg(9)-BK to the B(1) receptor in human fibroblast MRC5 and to recombinant human B(1) receptor expressed in human embryonic kidney cells with inhibition constants (K(i)) of 0.48 and 0.73 nM, respectively. The compound selectivity for B(1) versus B(2) receptors was in the range of 500- to 1000-fold. SSR240612 inhibited Lys(0)-desAr(9)-BK (10 nM)-induced inositol monophosphate formation in human fibroblast MRC5, with an IC(50) of 1.9 nM. It also antagonized des-Arg(9)-BK-induced contractions of isolated rabbit aorta and mesenteric plexus of rat ileum with a pA(2) of 8.9 and 9.4, respectively. Antagonistic properties of SSR240612 were also demonstrated in vivo. SSR240612 inhibited des-Arg(9)-BK-induced paw edema in mice (3 and 10 mg/kg p.o. and 0.3 and 1 mg/kg i.p.). Moreover, SSR240612 reduced capsaicin-induced ear edema in mice (0.3, 3 and 30 mg/kg p.o.) and tissue destruction and neutrophil accumulation in the rat intestine following splanchnic artery occlusion/reperfusion (0.3 mg/kg i.v.). The compound also inhibited thermal hyperalgesia induced by UV irradiation (1 and 3 mg/kg p.o.) and the late phase of nociceptive response to formalin in rats (10 and 30 mg/kg p.o.). Finally, SSR240612 (20 and 30 mg/kg p.o.) prevented neuropathic thermal pain induced by sciatic nerve constriction in the rat. In conclusion, SSR240612 is a new, potent, and orally active specific non-peptide bradykinin B(1) receptor antagonist.

A genetic linkage map of hexaploid naked oat constructed with SSR markers

Directory of Open Access Journals (Sweden)

Gaoyuan Song

2015-08-01

Full Text Available Naked oat is a unique health food crop in China. Using 202 F2 individuals derived from a hybrid between the variety 578 and the landrace Sanfensan, we constructed a genetic linkage map consisting of 22 linkage groups covering 2070.50 cM and including 208 simple sequence repeat (SSR markers. The minimum distance between adjacent markers was 0.01 cM and the average was 9.95 cM. Each linkage group contained 2–22 markers. The largest linkage group covered 174.40 cM and the shortest one covered 36.80 cM, with an average of 94.11 cM. Thirty-six markers (17.3% showing distorted segregation were distributed across linkage groups LG5 to LG22. This map complements published oat genetic maps and is applicable for quantitative trait locus analysis, gene cloning and molecular marker-assisted selection.

The Sensetivity of Flood Frequency Analysis on Record Length in Continuous United States

Science.gov (United States)

Hu, L.; Nikolopoulos, E. I.; Anagnostou, E. N.

2017-12-01

In flood frequency analysis (FFA), sufficiently long data series are important to get more reliable results. Compared to return periods of interest, at-site FFA usually needs large data sets. Generally, the precision of at site estimators and time-sampling errors are associated with the length of a gauged record. In this work, we quantify the difference with various record lengths. we use generalized extreme value (GEV) and Log Pearson type III (LP3), two traditional methods on annual maximum stream flows to undertake FFA, and propose quantitative ways, relative difference in median and interquartile range (IQR) to compare the flood frequency performances on different record length from selected 350 USGS gauges, which have more than 70 years record length in Continuous United States. Also, we group those gauges into different regions separately based on hydrological unit map and discuss the geometry impacts. The results indicate that long record length can avoid imposing an upper limit on the degree of sophistication. Working with relatively longer record length may lead accurate results than working with shorter record length. Furthermore, the influence of hydrologic unites for the watershed boundary dataset on those gauges also be presented. The California region is the most sensitive to record length, while gauges in the east perform steady.

Genetic variability of a Brazilian Capsicum frutescens germplasm collection using morphological characteristics and SSR markers.

Science.gov (United States)

Carvalho, S I C; Bianchetti, L B; Ragassi, C F; Ribeiro, C S C; Reifschneider, F J B; Buso, G S C; Faleiro, F G

2017-07-06

Characterization studies provide essential information for the conservation and use of germplasm in plant breeding programs. In this study, 103 Capsicum frutescens L. accessions from the Active Germplasm Bank of Embrapa Hortaliças, representative of all five Brazilian geographic regions, were characterized based on morphological characteristics and microsatellite (or simple sequence repeat - SSR) molecular markers. Morphological characterization was carried out using 57 descriptors, and molecular characterization was based on 239 alleles from 24 microsatellite loci. From the estimates of genetic distances among accessions, based on molecular characterization, a cluster analysis was carried out, and a dendrogram was established. Correlations between morphological and molecular variables were also estimated. Twelve morphological descriptors were monomorphic for the set of C. frutescens accessions, and those with the highest degree of polymorphism were stem length (14.0 to 62.0 cm), stem diameter (1.0 to 4.2 cm), days to flowering (90 to 129), days to fruiting (100 to 140), fruit weight (0.1 to 1.4 g), fruit length (0.6 to 4.6 cm), and fruit wall thickness (0.25 to 1.5 mm). The polymorphism information content for the SSR loci varied from 0.36 (EPMS 417) to 0.75 (CA49), with an overall mean of 0.57. The correlation value between morphological and molecular characterization data was 0.6604, which was statistically significant. Fourteen accessions were described as belonging to the morphological type tabasco, 85 were described as malagueta, and four were malaguetinha, a morphological type confirmed in this study. The typical morphological pattern of malagueta was described. Six similarity groups were established for C. frutescens based on the dendrogram and are discussed individually. The genetic variability analyzed in the study highlights the importance of characterizing genetic resources available for the development of new C. frutescens cultivars with the potential

GEOS seismograms recorded for aftershocks of the earthquakes of December 7, 1988, near Spitak, Armenia SSR, during the time period 3 January 1989 through 2 February 1988 (UTC)

Science.gov (United States)

Borcherdt, R.D.; Glassmoyer, Gary; Cranswick, Edward

1989-01-01

The earthquakes of December 7, 1988, near Spitak, Armenia SSR, serve as another grim reminder of the serious hazard that earthquakes pose throughout the world. We extend our heartfelt sympathies to the families of the earthquake victims and intend that our cooperative scientific endeavours will help reduce losses in future earthquakes. Only through a better understanding of earthquake hazards can earthquake losses be reduced for all peoples in seismically active regions of the world.The tragic consequences of these earthquakes remind scientists and public officials alike of their urgent responsibilities to understand and mitigate the effects of earthquakes. On behalf of the U.S. Geological Survey, I would like to express appreciation to our Soviet colleagues for their kind invitation to participate in joint scientific and engineering studies. Without their cooperation and generous assistance, the conduct of these studies would not have been possible.This report provides seismologic and geologic data collected during the time period December 21, 1988, through February 2, 1989. These data are presented in their entirety to expedite analysis of the data set for inferences regarding hazard mitigation actions, applicable not only in Armenia but other regions of the world exposed to high seismic risk

Densification of Ce0.9Gd0.1O1.95 barrier layer by in-situ solid state reaction

DEFF Research Database (Denmark)

Ni, De Wei; Esposito, Vincenzo

2014-01-01

A novel methodology, called in-situ solid state reaction (SSR), is developed and achieved for the densification of gadolinia doped ceria (CGO) barrier layer (BL) within the solid oxide fuel cell (SOFC) technology. The method is based on the combined use of impregnation technique and a designed two...

Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars

NARCIS (Netherlands)

Matthies, I.E.; Hintum, van T.J.L.; Weise, S.; Röder, M.S.

2012-01-01

Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be

Top-down modulation of the auditory steady-state response in a task-switch paradigm

Directory of Open Access Journals (Sweden)

Nadia Müller

2009-02-01

Full Text Available Auditory selective attention is an important mechanism for top-down selection of the vast amount of auditory information our perceptual system is exposed to. In the present study, the impact of attention on auditory steady-state responses - previously shown to be generated in primary auditory regions - was investigated. This issue is still a matter of debate and recent findings point to a complex pattern of attentional effects on the aSSR. The present study aimed at shedding light on the involvement of ipsilateral and contralateral activations to the attended sound taking into account hemispheric differences and a possible dependency on modulation frequency. In aid of this, a dichotic listening experiment was designed using amplitude-modulated tones that were presented to the left and right ear simultaneously. Participants had to detect target tones in a cued ear while their brain activity was assessed using MEG. Thereby, a modulation of the aSSR by attention could be revealed, interestingly restricted to the left hemisphere and 20 Hz responses: Contralateral activations were enhanced while ipsilateral activations turned out to be reduced. Thus, our findings support and extend recent findings, showing that auditory attention can influence the aSSR, but only under specific circumstances and in a complex pattern regarding the different effects for ipsilateral and contralateral activations.

Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

Science.gov (United States)

Gimode, Davis; Odeny, Damaris A; de Villiers, Etienne P; Wanyonyi, Solomon; Dida, Mathews M; Mneney, Emmarold E; Muchugi, Alice; Machuka, Jesse; de Villiers, Santie M

2016-01-01

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional

Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

Directory of Open Access Journals (Sweden)

Davis Gimode

Full Text Available Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS technologies to develop both Simple Sequence Repeat (SSR and Single Nucleotide Polymorphism (SNP markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included

A New species and records of Gripopterygidae (Plecoptera) from Rio Grande do Sul State, Southern Brazil.

Science.gov (United States)

Novaes, Marcos Carneiro; Da Conceição Bispo, Pitágoras

2016-10-17

Specimens of Gripopterygidae (Plecoptera) from Rio Grande do Sul State, southern Brazil were studied. A new species, Tupiperla sepeensis n. sp. is described. Tupiperla misionera Froehlich 2002 is a new record for Brazil and Gripopteryx reticulata Brauer 1866 and Tupiperla tessellata Brauer 1866 are new records for southern Brazil.

New species and records of Perlidae (Plecoptera) from Espírito Santo State, Brazil.

Science.gov (United States)

Gonçalves, Maísa DE Carvalho; Novaes, Marcos Carneiro; Salles, Frederico Falcão

2017-06-01

Two new species of the perlid genus Anacroneuria, A. rotunda n. sp and A. pitii n. sp are described from Espírito Santo State, Brazil. Additionally, six species of Anacroneuria and four species of Kempnyia are reported for the first time from Espírito Santo State. Records are also provided for A. debilis, A. subcostalis, K. flava, K. gracilenta, and K. neotropica. An undetermined species of Macrogynoplax based on nymphs is also reported from Espírito Santo State.

Dynamic crossmodal links revealed by steady-state responses in auditory-visual divided attention.

Science.gov (United States)

de Jong, Ritske; Toffanin, Paolo; Harbers, Marten

2010-01-01

Frequency tagging has been often used to study intramodal attention but not intermodal attention. We used EEG and simultaneous frequency tagging of auditory and visual sources to study intermodal focused and divided attention in detection and discrimination performance. Divided-attention costs were smaller, but still significant, in detection than in discrimination. The auditory steady-state response (SSR) showed no effects of attention at frontocentral locations, but did so at occipital locations where it was evident only when attention was divided between audition and vision. Similarly, the visual SSR at occipital locations was substantially enhanced when attention was divided across modalities. Both effects were equally present in detection and discrimination. We suggest that both effects reflect a common cause: An attention-dependent influence of auditory information processing on early cortical stages of visual information processing, mediated by enhanced effective connectivity between the two modalities under conditions of divided attention. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Optical efficiency for fission fragment track counting in Muscovite solid state track recorders

International Nuclear Information System (INIS)

Roberts, J.H.; Ruddy, F.H.; Gold, R.

1984-01-01

In order to determine absolute fission rates from thin actinide deposits placed in direct contact with Muscovite Solid State Track Recorders, it is necessary to know the efficiency with which fission fragment tracks are recorded. In this paper, a redetermination of the 'optical efficiency', i.e. the fraction of fission events recorded and observed in the Muscovite is reported. The value obtained from a well-calibrated thin deposit of 252 Cf and Muscovite etched about 90 min. in 49% HF at room temperature, is 0.9875 +- 0.0085. Manual counting was used. Preliminary results from a deposit of 242 Pu are also reported, along with preliminary comparisons of track counting with an automated system. Reasons for the discrepancy of the optical efficiency reported here with an earlier measurement are also reported. (author)

Evaluation of Advanced Chickpea (Cicer Arietinum L.) Accessions Based on Drought Tolerance Indices and SSR Markers Against Different Water Treatments

International Nuclear Information System (INIS)

Maqbool, M. A.; Aslam, M.

2016-01-01

Chickpea is mainly grown on marginal lands and encounter the problem of erratic rainfall that causes lack of water availability especially at terminal growth stages. Forty advanced chickpea genotypes were grown under irrigated, rainfed and tunnel conditions for two years (2012-13 and 2013-14). Data were collected for seed yield and analyzed by analysis of variance. Highly significant differences among genotypes and water treatments were observed for seed yield. However, across the year differences were insignificant for seed yield of chickpea. Seed yield under rainfed was higher than under irrigated conditions. Forty genotypes were assembled in four distinct groups on the basis of PCA biplot for different drought tolerance indices. These four distinct groups were representative of genotypic performance under normal and stressed conditions. Twenty eight SSR primers were used for sortation of genotypes either as drought tolerant or susceptible and to find association with results of drought tolerance indices. Only nine SSR markers were found to be polymorphic while others were either monomorphic or not amplified. H3DO5 and TA8 with Group-I, TR19 and ICCM0035 with Group-II, ICCM0035 with Group-III and TA25 was strongly correlated with results of Group-IV. Genotypes of group-I were drought tolerant whereas, CH16/06, CH81/06 and D097-11 within this groups were more tolerant. (author)

A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. sesquipedialis and comparison with the broader species.

Directory of Open Access Journals (Sweden)

Pei Xu

Full Text Available Asparagus bean (Vigna. unguiculata ssp. sesquipedialis is a distinctive subspecies of cowpea [Vigna. unguiculata (L. Walp.] that apparently originated in East Asia and is characterized by extremely long and thin pods and an aggressive climbing growth habit. The crop is widely cultivated throughout Asia for the production of immature pods known as 'long beans' or 'asparagus beans'. While the genome of cowpea ssp. unguiculata has been characterized recently by high-density genetic mapping and partial sequencing, little is known about the genome of asparagus bean. We report here the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups (LGs, with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cM, with an average marker distance of 1.98 cM. There are four high marker-density blocks distributed on three LGs and three regions of segregation distortion (SDRs identified on two other LGs, two of which co-locate in chromosomal regions syntenic to SDRs in soybean. Synteny between asparagus bean and the model legume Lotus. japonica was also established. This work provides the basis for mapping and functional analysis of genes/QTLs of particular interest in asparagus bean, as well as for comparative genomics study of cowpea at the subspecies level.

A SNP and SSR Based Genetic Map of Asparagus Bean (Vigna. unguiculata ssp. sesquipedialis) and Comparison with the Broader Species

Science.gov (United States)

Xu, Pei; Wu, Xiaohua; Wang, Baogen; Liu, Yonghua; Ehlers, Jeffery D.; Close, Timothy J.; Roberts, Philip A.; Diop, Ndeye-Ndack; Qin, Dehui; Hu, Tingting; Lu, Zhongfu; Li, Guojing

2011-01-01

Asparagus bean (Vigna. unguiculata ssp. sesquipedialis) is a distinctive subspecies of cowpea [Vigna. unguiculata (L.) Walp.] that apparently originated in East Asia and is characterized by extremely long and thin pods and an aggressive climbing growth habit. The crop is widely cultivated throughout Asia for the production of immature pods known as ‘long beans’ or ‘asparagus beans’. While the genome of cowpea ssp. unguiculata has been characterized recently by high-density genetic mapping and partial sequencing, little is known about the genome of asparagus bean. We report here the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups (LGs), with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cM, with an average marker distance of 1.98 cM. There are four high marker-density blocks distributed on three LGs and three regions of segregation distortion (SDRs) identified on two other LGs, two of which co-locate in chromosomal regions syntenic to SDRs in soybean. Synteny between asparagus bean and the model legume Lotus. japonica was also established. This work provides the basis for mapping and functional analysis of genes/QTLs of particular interest in asparagus bean, as well as for comparative genomics study of cowpea at the subspecies level. PMID:21253606

State at War, State in War: The Nagorno-Karabakh Conflict and State-Making in Armenia, 1991-1995

Directory of Open Access Journals (Sweden)

Taline Papazian

2008-07-01

Full Text Available The Republic of Armenia’s accession to independence came along with open war with Azerbaijan over Nagorno-Karabakh, an Armenian populated enclave dispatched within the Azerbaijani SSR in 1923. These specific conditions determined state-building in Armenia, launching two complementary processes: building of a national army from a meagre Soviet heritage and accumulating scarce resources into a restricted number of state institutions, the Defence Ministry in particular. Open conflict ended in 1994, freezing Armenian advances in Nagorno-Karabakh and Azerbaijan, thus marking victory in the eyes of the Armenian military. This sense of victory coupled with the return of soldiers to civilian life transcribed into a “Karabakh syndrome”, a tentative notion for the mindset of victorious militiamen eager to be rewarded for their sacrifices in war by economic or political benefits. Starting from 1995, this syndrome weighed on the Republic’s political life, eventually resulting in the resignation of then President Levon Ter Petrossian.

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

22 CFR 92.2 - Description of overseas notarial functions of the Department of State, record of acts.

Science.gov (United States)

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Description of overseas notarial functions of the Department of State, record of acts. 92.2 Section 92.2 Foreign Relations DEPARTMENT OF STATE LEGAL... officers of the Department of State is similar to the function of a notary public in the United States. See...

Genetic variation and comparison of orchardgrass (Dactylis glomerata L.) cultivars and wild accessions as revealed by SSR markers.

Science.gov (United States)

Xie, W G; Lu, X F; Zhang, X Q; Huang, L K; Cheng, L

2012-02-24

Orchardgrass is a highly variable, perennial forage grass that is cultivated throughout temperate and subtropical regions of the world. Despite its economic importance, the genetic relationship and distance among and within cultivars are largely unknown but would be of great interest for breeding programs. We investigated the molecular variation and structure of cultivar populations, compared the level of genetic diversity among cultivars (Baoxing, Anba, Bote, and Kaimo), subspecies (Dactylis glomerata ssp Woronowii) and advanced breeding line (YA02-116) to determine whether there is still sufficient genetic diversity within presently used cultivars for future breeding progress in China. Twenty individuals were analyzed from each of six accessions using SSR markers; 114 easily scored bands were generated from 15 SSR primer pairs, with an average of 7.6 alleles per locus. The polymorphic rate was 100% among the 120 individuals, reflecting a high degree of genetic diversity. Among the six accessions, the highest genetic diversity was observed in Kaimo (H = 0.2518; I = 0.3916; P = 87.3%) and 02-116 had a lower level of genetic diversity (H = 0.1806; I = 0.2788; P = 58.73%) compared with other cultivars tested. An of molecular variance revealed a much larger genetic variation within accessions (65%) than between them (35%). This observation suggests that these cultivars have potential for providing rich genetic resource for further breeding program. Furthermore, the study also indicated that Chinese orchardgrass breeding has involved strong selection for adaptation to forage production, which may result in restricted genetic base of orchardgrass cultivar.

Development of novel SSR markers for evaluation of genetic diversity and population structure in Tribulus terrestris L. (Zygophyllaceae).

Science.gov (United States)

Kaur, Kuljit; Sharma, Vikas; Singh, Vijay; Wani, Mohammad Saleem; Gupta, Raghbir Chand

2016-12-01

Tribulus terrestris L., commonly called puncture vine and gokhru, is an important member of Zygophyllaceae. The species is highly important in context to therapeutic uses and provides important active principles responsible for treatment of various diseases and also used as tonic. It is widely distributed in tropical regions of India and the world. However, status of its genetic diversity remained concealed due to lack of research work in this species. In present study, genetic diversity and structure of different populations of T. terrestris from north India was examined at molecular level using newly developed Simple Sequence Repeat (SSR) markers. In total, 20 primers produced 48 alleles in a size range of 100-500 bp with maximum (4) fragments amplified by TTMS-1, TTMS-25 and TTMS-33. Mean Polymorphism Information Content (PIC) and Marker Index (MI) were 0.368 and 1.01, respectively. Dendrogram showed three groups, one of which was purely containing accessions from Rajasthan while other two groups corresponded to Punjab and Haryana regions with intermixing of few other accessions. Analysis of molecular variance partitioned 76 % genetic variance within populations and 24 % among populations. Bayesian model based STRUCTURE analysis detected two genetic stocks for analyzed germplasm and also detected some admixed individuals. Different geographical populations of this species showed high level of genetic diversity. Results of present study can be useful in identifying diverse accessions and management of this plant resource. Moreover, the novel SSR markers developed can be utilized for various genetic analyses in this species in future.

Peculiarities of the contamination with radionuclides of the cultured pasture grass of the Lithuanian SSR after the Chernobyl accident

International Nuclear Information System (INIS)

Nedvetskajte, T.N.; Filistovich, V.I.; Petrulis, R.A.; Dauskurdis, S.I.; Tamulenajte, O.P.; Chias, K.V.

1989-01-01

Data on the contamination of pastures in the Lithuanian SSR with 131 I after the Chernobyl accident are given on the basis of measuring the grass samples from the cultured pastures. The predominant radionculides on the grass in the north-eastern and central parts of Lithuanie were 1 31 I and 103 Ru, while in its western and southern parts the 141 Ce, 144 Ce, 134 Cs, 137 Cs and other radioisotopes as well as hot particles predominated. The value of the grass-milk transfer coefficient was specified. 2 refs.; 5 figs

Optical efficiency for fission-fragment track counting in Muscovite Solid-State Track Recorders

International Nuclear Information System (INIS)

Roberts, J.H.; Ruddy, F.H.; Gold, R.

1983-07-01

In order to determine absolute fission rates from thin actinide deposits placed in direct contact with Muscovite Solid-State Track Recorders, it is necessary to know the efficiency with which fission-fragment tracks are recorded. In this paper, a redetermination of the optical efficiency, i.e., the fraction of fission events recorded and observed in the Muscovite, is reported. The value obtained from a well-calibrated thin deposit of 252 Cf and Muscovite etched about 90 min. in 49% HF at room temperature, is 0.9875 +- 0.0085. Manual counting was used. Preliminary results from a deposit of 242 Pu are also reported, along with preliminary comparisons of track counting with an automated system. Reasons for the discrepancy of the optical efficiency reported here with an earlier measurement are also reported. 5 references, 1 figure, 3 tables

First record of Phaethornis pretrei (Birds, Trochilidae in the State of Rio Grande do Sul, Brazil.

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Rodrigo Vargas Damiani

2009-06-01

Full Text Available There are 18 species of the genus Phaethornis, Swainson 1827 (Trochilidae in Brazil. In the state of Rio Grande do Sul, to date, only Phaethornis eurynome (Lesson, 1832 has been found. This work presents the first record of Phaethornis pretrei (Lesson & Delattre, 1839 in Rio Grande do Sul. The record was made in the urban perimeter of the town of Campinas do Sul. The species was documented in three ways by use of photography, video, and the recording of a spontaneous call.

Association Analysis of Simple Sequence Repeat (SSR Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb..

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Yanhong Lou

Full Text Available Tall fescue is widely used in temperate regions throughout the world as a dominant forage grass as well as a turfgrass, in pastoral and turf industry. However, the utilization of tall fescue was limited because of its leaf roughness, poor regeneration ability and poor stress resistance. New cultivars were desirable in modern pastoral industries exceed the potential of existing cultivars. Therefore, well understanding the agronomic traits and describing germplasms would help to overcome these constraints, and morphological evaluation of tall fescue germplasm is the key component in selecting rational parents for hybridization breeding. However, describing the morphological traits of tall fescue germplasm is costly and time-consuming. Fortunately, biotechnology approaches can supplement conventional breeding efforts for tall fescue improvement. Association mapping, as a powerful approach to identify association between agronomic traits and molecular markers has been widely used for enhancing the utilization, conservation and management of the tall fescue germplasms. Therefore, in the present research, 115 tall fescue accessions from different origins (25 accessions are cultivars; 31 accessions from America; 32 accessions from European; 7 accessions from Africa; 20 accessions from Asia, were evaluated for agronomic traits and genetic diversity with 90 simple sequence repeat (SSR markers. The panel displayed significant variation in spike count per plant (SCP and spike weight (SW. However, BCS performed the lowest CV among all the observed agronomic traits. Three subpopulations were identified within the collections but no obvious relative kinship (K was found. The GLM model was used to describe the association between SSR and agronomic traits. Fifty-one SSR markers associated with agronomic traits were observed. Twelve single-associated markers were associated with PH; six single-associated markers were associated with BCS; eight single

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.

GEOS seismograms recorded for aftershocks of the earthquakes of December 7, 1988, near Spitak, Armenia SSR, during the time period 26 December 1988 14:00 through 29 December 1988 (UTC)

Science.gov (United States)

Borcherdt, R.D.; Glassmoyer, Gary; Cranswick, Edward

1989-01-01

The earthquakes of December 7, 1988, near Spitak, Armenia SSR, serve as another grim reminder of the serious hazard that earthquakes pose throughout the world. We extend our heartfelt sympathies to the families of the earthquake victims and intend that our cooperative scientific endeavours will help reduce losses in future earthquakes. Only through a better understanding of earthquake hazards can earthquake losses be reduced for all peoples in seismically active regions of the world.The tragic consequences of these earthquakes remind scientists and public officials alike of their urgent responsibilities to understand and mitigate the effects of earthquakes. On behalf of the U.S. Geological Survey, I would like to express appreciation to our Soviet colleagues for their kind invitation to participate in joint scientific and engineering studies. Without their cooperation and generous assistance, the conduct of these studies would not have been possible.This report provides seismologic and geologic data collected during the time period December 21, 1988, through February 2, 1989. These data are presented in their entirety to expedite analysis of the data set for inferences regarding hazard mitigation actions, applicable not only in Armenia but other regions of the world exposed to high seismic risk.

Inclusion or Exclusion? Local Ownership and Security Sector Reform

Directory of Open Access Journals (Sweden)

Timothy Donais

2009-10-01

Full Text Available This paper explores the dynamics of security sector reform (SSR, a term used to refer to efforts made to reform the security structures of states emerging from conflict or authoritarianism. While "local ownership" is increasingly viewed as a necessary element of any sustainable SSR strategy, there remains a significant gap between international policy and practice in this area. In practice, the SSR agenda continues to be driven largely by international actors, with minimal input, let alone ownership, on the part of either governments or civil society within reforming states. Indeed, the notion of local ownership has come to serve as much as a disciplining mechanism as a tool to overcome exclusion in the making and execution of security policy, and the effectiveness and sustainability of SSR programming have suffered as a result. In light of this, the paper will explore both the potential for, and the limits of, rehabilitating the notion of local ownership to enable more participatory forms of SSR, and argues that any practical local ownership strategy requires a dual policy of negotiating with state actors and engaging with non-state actors.

Sequence-based SSR marker development and their application in defining the Introgressions of LA0716 (Solanum pennellii in the background of cv. M82 (Solanum lycopersicum.

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Wenbo Long

Full Text Available The introgression lines (ILs from cv. M82 (Solanum lycopersicum × LA0716 (S. pennellii have been proven to be exceptionally useful for genetic analysis and gene cloning. The introgressions were originally defined by RFLP markers at their development. The objectives of this study are to develop polymorphic SSR markers, and to re-define the DNA introgression from LA0716 in the ILs. Tomato sequence data was scanned by software to generate SSR markers. In total, 829 SSRs, which could be robustly amplified by PCR, were developed. Among them, 658 SSRs were dinucleotide repeats, 162 were trinucleotide repeats, and nine were tetranucleotide repeats. The 829 SSRs together with 96 published RFLPs were integrated into the physical linkage map of S. lycopersicum. Introgressions of DNA fragments from LA0716 were re-defined among the 75 ILs using the newly developed SSRs. A specific introgression of DNA fragment from LA0716 was identified in 72 ILs as described previously by RFLP, whereas the specific DNA introgression described previously were not detected in the ILs LA4035, LA4059 and LA4091. The physical location of each investigated DNA introgression was finely determined by SSR mapping. Among the 72 ILs, eight ILs showed a shorter and three ILs (IL3-2, IL12-3 and IL12-3-1 revealed a longer DNA introgression than that framed by RFLPs. Furthermore, 54 previously undefined segments were found in 21 ILs, ranging from 1 to 11 DNA introgressions per IL. Generally, the newly developed SSRs provide additional markers for genetic studies of tomatoes, and the fine definition of DNA introgressions from LA0716 would facilitate the use of the ILs for genetic analysis and gene cloning.

Development of SSR Markers in Hickory (Carya cathayensis Sarg.) and Their Transferability to Other Species of Carya.

Science.gov (United States)

Li, Juan; Zeng, Yanru; Shen, Dengfeng; Xia, Guohua; Huang, Yinzhi; Huang, Youjun; Chang, Jun; Huang, Jianqin; Wang, Zhengjia

2014-10-01

Hickory (Carya cathayensis Sarg.), an important nut-producing species in Southeastern China, has high economic value, but so far there has been no cultivar bred under species although it is mostly propagated by seeding and some elite individuals have been found. It has been found recently that this species has a certain rate of apomixis and poor knowledge of its genetic background has influenced development of a feasible breeding strategy. Here in this paper we first release SSR (Simple sequence repeat) markers developed in this species and their transferability to other three species of the same genus, Carya. A total of 311 pairs of SSR primers in hickory were developed based on sequenced cDNAs of a fruit development-associated cDNA library and RNA-seq data of developing female floral buds and could be used to distinguish hickory, C. hunanensis Cheng et R. H. Chang ex R. H. Chang et Lu, C. illinoensis K. Koch (pecan) and C. dabieshanensis M. C. Liu et Z. J. Li, but they were monomorphic in both hickory and C. hunanensis although multi-alleles have been identified in all the four species. There is a transferability rate of 63.02% observed between hickory and pecan and the markers can be applied to study genetic diversity of accessions in pecan. When used in C. dabieshanensis, it was revealed that C. dabieshanensis had the number of alleles per locus ranging from 2 to 4, observed heterozygosity from 0 to 0.6667 and expected heterozygosity from 0.333 to 0.8667, respectively, which supports the existence of C. dabieshanensis as a separate species different from hickory and indicates that there is potential for selection and breeding in this species.

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.

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.

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.

25 CFR 15.504 - Who may inspect records and records management practices?

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2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false Who may inspect records and records management practices... Records § 15.504 Who may inspect records and records management practices? (a) You may inspect the probate... Secretary and the Archivist of the United States may inspect records and records management practices and...

The United States digital recording industry

Science.gov (United States)

Simonds, John L.

1993-01-01

The recording industry resembles the semiconductor industry in several aspects. Both are large (greater than $60 Billion/year revenues); both are considered critical technologies supporting national objectives; both are experiencing increased competition from foreign suppliers; they recognize significant opportunities for both technological and market growth in the decade to come; and both realize that a key to this future growth lies in alliances among industry, academia, and government. The semiconductor industry has made significant investments in alliances relating to manufacturing technologies (SEMATECH) and to joint long-term technology research centered in universities (SRC). The federal government has provided funding support of these efforts in recognition of the critical roles semiconductor technologies play in national interests. The recording industry is now also forming critical alliances, but has been slower in starting and in gaining broad recognition by government agencies and legislators that the industry needs federal support. Traditionally, the recording industry has been viewed as mature, stable, and, while critical to national interests, able to chart and fund its own course toward future national needs. That perception is fortunately changing.

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

OpenAIRE

Ziya Motalebipour, Elmira; Kafkas, Salih; Khodaeiaminjan, Mortaza; ?oban, Nergiz; G?zel, Hatice

2016-01-01

Background 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 cha...

Common cause failure data collection and analysis for safety-related components of TRIGA SSR-14MW Pitesti, Romania

International Nuclear Information System (INIS)

Radu, G.; Mladin, D.

2003-01-01

This paper presents a study performed on the set of common cause failures (CCF) of safety-related components of the research reactor TRIGA SSR-14 MW Pitesti. The data collected cover a period of 20 years, from 1979 to 2000. The sources of data are Shift Supervisor Reports, Work Authorizations, and Reactor Log Books. Events collected are analyzed by failure mode and degrees of failure. Qualitative analysis of root causes, coupling factors and corrective actions and quantitative analysis of CCF events are studied. The objective of this work is to develop qualitative insights in the nature of the reported events and to build a site-specific common cause events database. (author)

75 FR 70342 - Privacy Act; System of Records: Equal Employment Opportunity Records

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2010-11-17

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SPADER - Science Planning Analysis and Data Estimation Resource for the NASA Parker Solar Probe Mission

Science.gov (United States)

Rodgers, D. J.; Fox, N. J.; Kusterer, M. B.; Turner, F. S.; Woleslagle, A. B.

2017-12-01

Scheduled to launch in July 2018, the Parker Solar Probe (PSP) will orbit the Sun for seven years, making a total of twenty-four extended encounters inside a solar radial distance of 0.25 AU. During most orbits, there are extended periods of time where PSP-Sun-Earth geometry dramatically reduces PSP-Earth communications via the Deep Space Network (DSN); there is the possibility that multiple orbits will have little to no high-rate downlink available. Science and housekeeping data taken during an encounter may reside on the spacecraft solid state recorder (SSR) for multiple orbits, potentially running the risk of overflowing the SSR in the absence of mitigation. The Science Planning Analysis and Data Estimation Resource (SPADER) has been developed to provide the science and operations teams the ability to plan operations accounting for multiple orbits in order to mitigate the effects caused by the lack of high-rate downlink. Capabilities and visualizations of SPADER are presented; further complications associated with file downlink priority and high-speed data transfers between instrument SSRs and the spacecraft SSR are discussed, as well as the long-term consequences of variations in DSN downlink parameters on the science data downlink.

Security Sector Reform, Local Ownership and Community Engagement

Directory of Open Access Journals (Sweden)

Eleanor Gordon

2014-07-01

Full Text Available Local ownership is widely considered to be one of the core principles of successful Security Sector Reform (SSR programmes. Nonetheless, there remains a gap between policy and practice. This article examines reasons for this gap, including concerns regarding limited capacity and lack of expertise, time and cost constraints, the allure of quantifiable results and quick wins, and the need to ensure that other principles inherent to SSR are not disregarded. In analysing what is meant by local ownership, this article will also argue that, in practice, the concept is narrowly interpreted both in terms of how SSR programmes are controlled and the extent to which those at the level of the community are actively engaged. This is despite policy guidance underscoring the importance of SSR programmes being inclusive and local ownership being meaningful. It will be argued that without ensuring meaningful and inclusive local ownership of SSR programmes, state security and justice sector institutions will not be accountable or responsive to the needs of the people and will, therefore, lack public trust and confidence. The relationship between the state and its people will be weak and people will feel divorced from the decisions that affect their security and their futures. All this will leave the state prone to further outbreaks of conflict. This article will suggest that the requisite public confidence and trust in state security and justice sector institutions, and ultimately, the state itself, could be promoted by SSR programmes incorporating community safety structures.

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides.

Science.gov (United States)

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-09-01

Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

Science.gov (United States)

Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

2015-01-01

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

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Jian-Wei Zong

Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

78 FR 54946 - Privacy Act; System of Records: Digital Outreach and Communications, State-79

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2013-09-06

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Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers.

Science.gov (United States)

Ramakrishnan, M; Antony Ceasar, S; Duraipandiyan, V; Al-Dhabi, N A; Ignacimuthu, S

2016-01-01

We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60-70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard's similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard's similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on

Burn-up determinations and dimensional measurements of TRIGA-HEU fuel elements from the 14 MW steady-state core

International Nuclear Information System (INIS)

Toma, C.; Alexa, Al.; Craciunescu, T.; Pirvan, M.; Dobrin, R.

2008-01-01

In this paper there are presented the results of nondestructive examination in Post Irradiation Examination Laboratory for twenty five fuel rods selected from 14 MW steady state core. Gamma scanning and dimensional measurements were carried out in order to determine burn-up and diametric deflection of the fuel rods. Also, some comparisons with SSR Safety Report estimations for the maximum burn-up pin were made. (authors)

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2010-04-01

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Optimization of synthesis technique and luminescent properties in Eu{sup 3+}-activated NaCaPO{sub 4} phosphor for solid state lighting applications

Energy Technology Data Exchange (ETDEWEB)

Ratnam, B.V. [Department of Physics, Changwon National University, Changwon 51140 (Korea, Republic of); Sahu, Mukesh K.; Vishwakarma, Amit K.; Jha, Kaushal [Luminescent Materials Research Lab (LMRL), Department of Applied Physics, Delhi Technological University, Delhi 110042 (India); Woo, Hyun-Joo [Department of Physics, Changwon National University, Changwon 51140 (Korea, Republic of); Jang, Kiwan, E-mail: kwjang@changwon.ac.kr [Department of Physics, Changwon National University, Changwon 51140 (Korea, Republic of); Jayasimhadri, M., E-mail: jayaphysics@yahoo.com [Luminescent Materials Research Lab (LMRL), Department of Applied Physics, Delhi Technological University, Delhi 110042 (India)

2017-05-15

Europium activated NaCaPO{sub 4} phosphor has been synthesized by various synthesis techniques such as solid-state reaction (SSR), molten salt synthesis (MSS) and sol-gel combustion (SGC) method to optimize the synthesis procedure. The comparative investigations of structural and luminescent properties have been studied to know the best synthesis method. The XRD patterns and Rietveld refinement analysis of the synthesized phosphors confirmed the single phase orthorhombic structure of NaCaPO{sub 4}. Excitation spectra indicate the strong absorption in near ultraviolet (n-UV) region and the emission spectra exhibit strong emission band at 595 nm corresponds to {sup 5}D{sub 0}→{sup 7}F{sub 1} transition under n-UV (λ{sub ex}=392 nm) excitation. The SGC route synthesized phosphor exhibit intense emission than that of the SSR and MSS method. Therefore, the effect of dopant (Eu{sup 3+}) concentration on the emission intensity and concentration quenching mechanism has been discussed in detail for the Eu{sup 3+} doped NaCaPO{sub 4} phosphor synthesized by SGC method. The CIE chromaticity coordinates have been calculated for the phosphors synthesized by SSR, MSS and SGC methods to reveal the emitting color and also to know the utility of this phosphor for white LEDs.

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.

Stages of Formation of the Strategy of Social Responsibility of Business

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Zatieyshchykova Olha O.

2014-02-01

Full Text Available The article studies existing approaches to formulation of stages of the strategy, according to which a list of stages of formation of the strategy of social responsibility (SSR is formed, including: identification of the mission and vision of SSR, formation of the system of goals of SSR, assessment of influence of factors of external environment, assessment of the level of social responsibility, analysis of alternatives and selection of strategies. The article identifies SSR mission for Ukrainian enterprises, which lies in increase of the quality of life of employees, local society and society in general. SSR vision – improvement of effectiveness of business and profitability indicators on the basis of creation of trustworthy relations between business, society and state. The article develops the goals tree of SSR that has goals of three levels. It identifies a list of factors of external environment, including: growing anxiety about the state of environment and demographic situation, level of education and culture, growing intensity of competition, level of income and wellbeing, active participation of the state policy in the use of principles of social responsibility, propaganda of social responsibility within the impact area, fast change of technologies, fair marketing practice, informing and executing agreements. The article offers to assess the level of social responsibility on the basis of calculation of indicators of social investments both by quantitative and qualitative methods and calculation of indicators of voluntary social responsibility of business. It also offers main components of the essence of the SSR strategy.

Genetic Diversity in Jatropha curcas L. Assessed with SSR and SNP Markers

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Juan M. Montes

2014-08-01

Full Text Available Jatropha curcas L. (jatropha is an undomesticated plant that has recently received great attention for its utilization in biofuel production, rehabilitation of wasteland, and rural development. Knowledge of genetic diversity and marker-trait associations is urgently needed for the design of breeding strategies. The main goal of this study was to assess the genetic structure and diversity in jatropha germplasm with co-dominant markers (Simple Sequence Repeats (SSR and Single Nucleotide Polymorphism (SNP in a diverse, worldwide, germplasm panel of 70 accessions. We found a high level of homozygosis in the germplasm that does not correspond to the purely outcrossing mating system assumed to be present in jatropha. We hypothesize that the prevalent mating system of jatropha comprise a high level of self-fertilization and that the outcrossing rate is low. Genetic diversity in accessions from Central America and Mexico was higher than in accession from Africa, Asia, and South America. We identified makers associated with the presence of phorbol esters. We think that the utilization of molecular markers in breeding of jatropha will significantly accelerate the development of improved cultivars.

Solid-state track recorder neutron dosimetry in light water reactor pressure vessel surveillance mockups

International Nuclear Information System (INIS)

Ruddy, F.H.; Roberts, J.H.; Gold, R.; Preston, C.C.

1984-09-01

Solid-State Track Recorder (SSTR) measurements of neutron-induced fission rates have been made in several pressure vessel mockup facilities as part of the US Nuclear Regulatory Commission's (NRC) Light Water Reactor Pressure Vessel Surveillance Dosimetry Improvement Program (LWR-PV-SDIP). The results of extensive physics-dosimetry measurements made at the Pool Critical Assembly (PCA) at Oak Ridge National Laboratory (ORNL) in Oak Ridge, TN are summarized. Included are 235 U, 238 U, 237 Np and 232 Th fission rates in the PCA 12/13, 8/7, and 4/12 SSC configurations. Additional low power measurements have been made in an engineering mockup at the VENUS critical assembly at CEN-SCK, Mol, Belgium. 237 Np and 238 U fission rates were made at selected locations in the VENUS mockup, which models the in-core and near-core regions of a pressurized water reactor (PWR). Absolute core power measurements were made at VENUS by exposing solid-state track recorders (SSTRs) to polished fuel pellets within in-core fuel pins. 8 references, 4 figures, 10 tables

Computational Mining and Genome Wide Distribution of Microsatellite in Fusarium oxysporum f. sp. lycopersici

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Sudheer KUMAR

2012-11-01

Full Text Available Simple sequence repeat (SSR is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Hence, in present study an attempt was made to mine and analyze microsatellite dynamics in whole genome of Fusarium oxysporum f. sp. lycopersici. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of tetra-nucleotide (3837 repeats followed by tri-nucleotide (3367 repeats. Maximum frequency distribution in coding region was shown by mono-nucleotide SSR motifs (34.8%, where as minimum frequency is observed for penta-nucleotide SSR (0.87%. Highest relative abundance (1023 SSR/Mb and density of SSRs (114.46 bp/Mb were observed on chromosome 1, while least density of SSR motifs was recorded on chromosome 11 (7.40 bp/Mb and 12 (7.41 bp/Mb, respectively. Maximum trinucleotide (34.24% motifs code for glutamic acid (GAA while GT/CT were the most frequent repeat of dinucleotide SSRs. Most common and highly repeated SSR motifs were identified as (A64, (T48, (GT24, (GAA31, (TTTC24, (TTTCT28 and (AACCAG27. Overall, the generated information may serve as baseline information for developing SSR markers that could find applications in genomic analysis of F. oxysporum f. sp. lycopersici for better understanding of evolution, diversity analysis, population genetics, race identification and acquisition of new virulence.

Science Planning for the Solar Probe Plus NASA Mission

Science.gov (United States)

Kusterer, M. B.; Fox, N. J.; Turner, F. S.; Vandegriff, J. D.

2015-12-01

With a planned launch in 2018, there are a number of challenges for the Science Planning Team (SPT) of the Solar Probe Plus mission. The geometry of the celestial bodies and the spacecraft during some of the Solar Probe Plus mission orbits cause limited uplink and downlink opportunities. The payload teams must manage the volume of data that they write to the spacecraft solid-state recorders (SSR) for their individual instruments for downlink to the ground. The aim is to write the instrument data to the spacecraft SSR for downlink before a set of data downlink opportunities large enough to get the data to the ground and before the start of another data collection cycle. The SPT also intend to coordinate observations with other spacecraft and ground based systems. To add further complexity, two of the spacecraft payloads have the capability to write a large volumes of data to their internal payload SSR while sending a smaller "survey" portion of the data to the spacecraft SSR for downlink. The instrument scientists would then view the survey data on the ground, determine the most interesting data from their payload SSR, send commands to transfer that data from their payload SSR to the spacecraft SSR for downlink. The timing required for downlink and analysis of the survey data, identifying uplink opportunities for commanding data transfers, and downlink opportunities big enough for the selected data within the data collection period is critical. To solve these challenges, the Solar Probe Plus Science Working Group has designed a orbit-type optimized data file priority downlink scheme to downlink high priority survey data quickly. This file priority scheme would maximize the reaction time that the payload teams have to perform the survey and selected data method on orbits where the downlink and uplink availability will support using this method. An interactive display and analysis science planning tool is being designed for the SPT to use as an aid to planning. The

Radiosynthesis of 7-chloro-N, N-dimethyl-5-[11C] methyl-4-oxo-3-phenyl-3, 5-dihydro-4H pyridazino [4, 5-b]indole-1-acetamide, [11C]SSR180575, a novel radioligand for imaging the TSPO (peripheral benzodiazepine receptor) with PET

International Nuclear Information System (INIS)

Thominiaux, C.; Damont, A.L.; Kuhnast, B.; Demphel, St.; Le Helleix, St.; Chauveau, F.; Boutin, H.; Van Camp, N.; Boisgard, R.; Tavitian, B.; Dolle, F.; Boisnard, S.; Rivron, L.; Roy, S.; Allen, J.; Chauveau, F.; Boutin, H.; Van Camp, N.; Boisgard, R.; Tavitian, B.; Rooney, T.; Benavides, J.; Hantraye, Ph.

2010-01-01

SSR180575 (7-chloro-N, N, 5-trimethyl-4-oxo-3-phenyl-3, 5-dihydro-4H-pyridazino [4, 5-b]indole-1-acetamide) is the lead compound of an original pyridazino-indole series of potent and highly selective TSPO (peripheral benzodiazepine receptor) ligands. Isotopic labeling of SSR180575 with the short-lived positron-emitter carbon-11 (T1/2: 20.38 min) at its 5-methyl-pyridazino[4, 5-b]indole moiety as well as at its N, N-dimethylacetamide function by methylation of the corresponding nor-analogues was investigated. Best results in terms of radiochemical yields and purities were obtained for the preparation of [indole-N-methyl- 11 C]SSR180575, where routine production batches of 4.5-5.0 GBq of radiochemically pure (499%) i.v. injectable solutions (specific radioactivities: 50-90 GBq/μmol) could be prepared within a total synthesis time of 25 min (HPLC purification included) starting from a 55 GBq [ 11 C]CO 2 cyclotron production batch (non decay-corrected overall radiochemical yields: 8-9%). The process comprises (1) trapping at -10 C of [ 11 C]methyl triflate in DMF (300 μl) containing 0.2-0.3 mg of the indole precursor for labeling and 4 mg of K 2 CO 3 (excess); (2) heating at 120 C for 3 min; (3) dilution of the residue with 0.5 ml of the HPLC mobile phase and (4) purification using semi-preparative reversed phase HPLC (Zorbax R SB-C-18). In vivo pharmacological properties of [indole-N-methyl- 11 C]SSR180575 as a candidate for imaging neuro-inflammation with positron emission tomography are currently evaluated. (authors)

75 FR 63253 - State-56, Network User Account Records

Science.gov (United States)

2010-10-14

... to the records covered by this system of records receive cyber security awareness training which... access or inappropriate usage is suspected or detected; and to identify the need for training programs... suspected or detected; and to identify the need for training programs. ROUTINE USES OF RECORDS MAINTAINED IN...

Reptilia, Gymnophthalmidae, Micrablepharus maximiliani (Reinhardt and Lutken, 1861: Distribution extension, new state record and geographic distribution map.

Directory of Open Access Journals (Sweden)

Moura, M. R.

2010-01-01

Full Text Available We provide records for Micrablepharus maximiliani from state of Minas Gerais and present a map representingits distribution. The record of M. maximiliani from municipality of Resplendor, Minas Gerais, represents a distributionextension of 1,050 km southern from the type locality at the municipality of Maruim, Sergipe. Others 57 new recordsare presented based on specimens housed in several Brazilian and Paraguayan herpetological collections, improving theknowledge on geographic distribution of M. maximiliani in South America.

Sympathetic skin responses in patients with hyperthyroidism.

Science.gov (United States)

Gozke, E; Ozyurt, Z; Dortcan, N; Ore, O; Kocer, A; Ozer, E

2007-01-01

The aim of this study was to investigate the disorders of sympathetic nervous system in patients with hyperthyroidism using sympathetic skin response (SSR). Twenty-two newly diagnosed cases with hyperthyroidism were included in the study. The results were compared with those of 20 healthy controls. SSR was recorded with the contralateral electrical stimulation of the median nerve (of the upper extremities) and tibial nerve (of the lower extremities) with active electrodes placed on palms and soles and reference electrodes attached on the dorsal aspects of hands and feet. Ages of the cases with hyperthyroidism and controls ranged between 15-65 years (mean: 46.7 +/- 15.0 years) and 24-62 years (mean: 39.6 +/- 9.8 years) respectively (p > 0.05). In all the control subjects SSR could be obtained, while from the lower extremities of 4 cases with hyperthyroidism (18.0%) SSR could not be elicited. Mean SSR latencies of lower extremities were found significantly longer than control group (p nervous system involvement in cases with hyperthyroidism.

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.

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides1

Science.gov (United States)

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-01-01

Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species. PMID:26421250

Electronic health records to support obesity-related patient care: Results from a survey of United States physicians.

Science.gov (United States)

Bronder, Kayla L; Dooyema, Carrie A; Onufrak, Stephen J; Foltz, Jennifer L

2015-08-01

Obesity-related electronic health record functions increase the rates of measuring Body Mass Index, diagnosing obesity, and providing obesity services. This study describes the prevalence of obesity-related electronic health record functions in clinical practice and analyzes characteristics associated with increased obesity-related electronic health record sophistication. Data were analyzed from DocStyles, a web-based panel survey administered to 1507 primary care providers practicing in the United States in June, 2013. Physicians were asked if their electronic health record has specific obesity-related functions. Logistical regression analyses identified characteristics associated with improved obesity-related electronic health record sophistication. Of the 88% of providers with an electronic health record, 83% of electronic health records calculate Body Mass Index, 52% calculate pediatric Body Mass Index percentile, and 32% flag patients with abnormal Body Mass Index values. Only 36% provide obesity-related decision support and 17% suggest additional resources for obesity-related care. Characteristics associated with having a more sophisticated electronic health record include age ≤45years old, being a pediatrician or family practitioner, and practicing in a larger, outpatient practice. Few electronic health records optimally supported physician's obesity-related clinical care. The low rates of obesity-related electronic health record functions currently in practice highlight areas to improve the clinical health information technology in primary care practice. More work can be done to develop, implement, and promote the effective utilization of obesity-related electronic health record functions to improve obesity treatment and prevention efforts. Published by Elsevier Inc.

Record Keeping Guidelines

Science.gov (United States)

American Psychologist, 2007

2007-01-01

These guidelines are designed to educate psychologists and provide a framework for making decisions regarding professional record keeping. State and federal laws, as well as the American Psychological Association's "Ethical Principles of Psychologists and Code of Conduct," generally require maintenance of appropriate records of psychological…

Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae to develop and characterize new EST-SSR markers and construct an EST-SSR database.

Directory of Open Access Journals (Sweden)

Fang K Du

Full Text Available BACKGROUND: Microsatellite markers or Simple Sequence Repeats (SSRs are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. METHODOLOGY/PRINCIPAL FINDINGS: A total of 94,090 non-redundant Expressed Sequence Tags (ESTs from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37% and hexanucleotides (33% repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs and selected 673 of these pairs at random for further validation. 575 pairs (85% gave successful amplification, of which, 464 (80.7% were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html. CONCLUSIONS: The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.

First records of Casiornis rufus (Vieillot, 1816) (Aves, Tyrannidae) for the state of Rio Grande do Sul, southern Brazil

DEFF Research Database (Denmark)

Vizentin-Bugoni, Jeferson; Bellagamba-Oliveira, Danielle; Bellagamba, Gina

2015-01-01

The Rufous Casiornis, Casiornis rufus (Vielliot, 1916), is widespread in central South America, reaching its southernmost distribution in northern Argentina and Uruguay. Here we present the first nine records of the species for Rio Grande do Sul state, southern Brazil. The records were documented...

CORRELATION BETWEEN RESPECT, RESPONSIBILITY, INTERPERSONAL RELATIONSHIP, SUPERVISION, AND COMPENSATION TO THE PERFORMANCE OF OFFICIAL RECORDER AT STATE HOSPITALS BUKITTINGGI WEST-SUMATRA INDONESIA

Directory of Open Access Journals (Sweden)

Syukra Alhamda

2013-01-01

Full Text Available Objective: Primary survey was conducted on November 10, 2012 at The State Hospitals Bukittinggi, with randomly selected of 100 hospital medical records. There were incomplete contents of 61.66% and 48.33% of late files. This issue is very disturbing process for management of recording medical data, therefore, disrupting functions of medical recorders.Method: This study applied cross-sectionalstudy to determine the correlation between respect, responsibility, interpersonal relations, supervisionand compensation for the performance of official recorders at The State Hospitals Bukittinggi West-Sumatra Indonesia. Questionnaires from the subjects were proceed and computed by applying chisquare test.Results: The results showed that there were significant correlation between the performance of official award recorders (p = 0.003 and OR = 9.208, responsibilities (p = 0.012 and OR = 6.094, interpersonal (p = 0.0025 and OR = 5.417, performance of official (p = 0.012 and OR = 6.094, and compensation of official recorders (p = 0.025 and OR = 5.417 to recorders performance. Conclusion: In this research, we observed that there was a significant correlation between respect, responsibility, interpersonal relations, supervision and compensation to the performance of official recorders. A greater

Imaging of fast-neutron sources using solid-state track-recorder pinhole radiography

International Nuclear Information System (INIS)

Ruddy, F.H.; Gold, R.; Roberts, J.H.; Kaiser, B.J.; Preston, C.C.

1983-08-01

Pinhole imaging methods are being developed and tested for potential future use in imaging the intense neutron source of the Fusion Materials Irradiation Test (FMIT) Facility. Previously reported, extensive calibration measurements of the proton, neutron, and alpha particle response characteristics of CR-39 polymer solid state track recorders (SSTRs) are being used to interpret the results of imaging experiments using both charged particle and neutron pinhole collimators. High resolution, neutron pinhole images of a 252 Cf source have been obtained in the form of neutron induced proton recoil tracks in CR-39 polymer SSTR. These imaging experiments are described as well as their potential future applications to FMIT

First record of Amphisbaena mertensi Strauch, 1881 (Squamata: Amphisbaenidae) in Minas Gerais state, Brazil

OpenAIRE

Silveira, Adriano; Brites, Vera; Valinhas e Valinhas, Raquel

2012-01-01

We present here the first record of Amphisbaena mertensi in Minas Gerais state, southeastern Brazil. Through analysis of scientific collections, we found specimens of A. mertensi from municipalities of Patos de Minas, Uberaba, Indianópolis, Uberlândia and Araguari, in Triângulo Mineiro and Alto Paranaíba regions. These localities are inserted in the Cerrado biome, with Atlantic Forest enclaves, and represent an expansion of the previously known geographic distribution for the species.

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. PMID:25025376

Solid state track recorder measurements in the poolside critical assembly

International Nuclear Information System (INIS)

Ruddy, F.H.; Gold, R.; Roberts, J.H.

1979-01-01

Fission rate measurements using solid state track recorders (SSTR) have been performed at the PCA. A schematic representation of a cross-section of the PCA is shown. Fission rates were measured in the pressure vessel simulator at the T/4, T/2 and 3T/4 positions and in the void box (VB). SSTR measurements were carried out with 232 Th, 235 U (bare and cadmium covered), 238 U and 237 Np fissionable deposits. Midplane only measurements were carried out for 235 U and 237 Np, while 5 axial locations at 1/4T and 1/2T and 3 axial locations at 3/4T and in the VB were sampled for 232 Th and 238 U. The HEDL SSTR fission rate measurements reported herein for both configurations together with NBS and CEN/SCK fission chamber measurements will be used to establish absolute and relative fission reaction rates, and ratios for the PCA pressure vessel Benchmark Facility

Extent of ICT Application in the Management of Administrative and Student Personnel Records in the Public Universities in Enugu State, Nigeria

Science.gov (United States)

Chidobi, Roseline Unoma

2015-01-01

The purpose of the study is to identify the extent of ICT application in management of administrative and student personnel record in the public universities in Enugu state. The study was a survey research the quantitative data were collected through a 20-item questionnaire title "Extent of ICT Application in Record management"…

Efficiently reducing transition curvature in heat-assisted magnetic recording with state-of-the-art write heads

Science.gov (United States)

Vogler, Christoph; Abert, Claas; Bruckner, Florian; Suess, Dieter

2017-05-01

Curvatures of bit transitions on granular media are a serious problem for the read-back process. We address this fundamental issue and propose a possibility to efficiently reduce transition curvatures with state-of-the-art heat-assisted magnetic recording heads. We compare footprints of conventional with those of the proposed head design on different media, consisting of exchange coupled and single phase grains. Additionally, we investigate the impact of various recording parameters, such as the full width at half maximum (FWHM) of the applied heat pulse and the coercivity gradient near the write temperature of the recording grains. The footprints are calculated with a coarse grained model, based on the Landau-Lifshitz-Bloch equation. The presented simulations show a transition curvature reduction of up to 40%, in the case of a medium with exchange coupled grains and a heat pulse with a FWHM of 40 nm. We further give the reason for the straightening of the bit transitions, by means of basic considerations with regard to the effective recording time window of the write process. Besides the transition curvature reduction, the proposed head design yields an improvement of the transition jitter in both down-track and off-track directions.

19 CFR 210.38 - Record.

Science.gov (United States)

2010-04-01

... 19 Customs Duties 3 2010-04-01 2010-04-01 false Record. 210.38 Section 210.38 Customs Duties UNITED STATES INTERNATIONAL TRADE COMMISSION INVESTIGATIONS OF UNFAIR PRACTICES IN IMPORT TRADE ADJUDICATION AND ENFORCEMENT Prehearing Conferences and Hearings § 210.38 Record. (a) Definition of the record...

Making magnetic recording commercial: 1920-1955

Science.gov (United States)

Clark, Mark H.

1999-03-01

Although magnetic recording had been invented in 1898, it was not until the late 1920s that the technology was successfully marketed to the public. Firms in Germany, the United Kingdom, and the United States developed and sold magnetic recorders for specialized markets in broadcasting and telephone systems through the 1930s. The demands of World War II considerably expanded the use of magnetic recording, and with the end of the war, firms in the United States sought to bring magnetic recording to home and professional music recording. Using a combination of captured German technology and American wartime research, American companies such as Ampex, Magnecord, 3M, the Brush Development Company, and others created a vast new industry. By the mid-1950s, magnetic recording was firmly established as a method for recording both sound and data.

Development of a novel set of EST-SSR markers and cross-species amplification in Tamarix africana (Tamaricaceae).

Science.gov (United States)

Terzoli, Serena; Beritognolo, Isacco; Sabatti, Maurizio; Kuzminsky, Elena

2010-06-01

Tamarix plants are resistant to abiotic stresses and have become invasive in North America. Their taxonomy is troublesome, and few molecular makers are available to enable species identification or to track the spread of specific invasive genotypes. Transcriptome sequencing projects offer a potential source for the development of new markers. • Thirteen polymorphic simple sequence repeats (SSRs) markers derived from Expressed Sequence Tags (ESTs) from Tamarix hispida, T. androssowii, T. ramosissima, and T. albiflonum were identified and screened on 24 samples of T. africana to detect polymorphism. The number of alleles per locus ranged from two to eight, with an average of 4.3 alleles per locus, and the mean expected heterozygosity was 0.453. • Amplification products of these 13 loci were also generated for T. gallica. These new EST-SSR markers will be useful in genetic characterization of Tamarix, as additional tools for taxonomic clarification, and for studying invasive populations where they are a threat.

Record Statistics and Dynamics

DEFF Research Database (Denmark)

Sibani, Paolo; Jensen, Henrik J.

2009-01-01

with independent random increments. The term record dynamics covers the rather new idea that records may, in special situations, have measurable dynamical consequences. The approach applies to the aging dynamics of glasses and other systems with multiple metastable states. The basic idea is that record sizes...... fluctuations of e. g. the energy are able to push the system past some sort of ‘edge of stability’, inducing irreversible configurational changes, whose statistics then closely follows the statistics of record fluctuations....

Record of Spot-winged Pigeon Patagioenas maculosa (Aves: Columbidae in Santa Catarina state, southern Brazil.

Directory of Open Access Journals (Sweden)

Felipe Lohmann Arend

2009-06-01

Full Text Available We present the first record of the Spot-winged Pigeon Patagioenas maculosa (Aves: Columbidae for Santa Catarina, southern Brazil. One individual was observed on 10 September 2006 in an open area (cattle pasture and shrubby vegetation in the town of Anita Garibaldi (center-south of the state. We suggest that this punctual encounter is a result of the recent expansion of this species’ distribution due to landscape modification in the region.

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

Directory of Open Access Journals (Sweden)

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

Use of EST-SSR Markers for Evaluating Genetic Diversity and Fingerprinting Celery (Apium graveolens L. Cultivars

Directory of Open Access Journals (Sweden)

Nan Fu

2014-02-01

Full Text Available Celery (Apium graveolens L. is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting celery molecular breeding are quite limited, thus few studies on celery have been conducted so far. In this study we made use of simple sequence repeat (SSR markers generated from previous celery transcriptome sequencing and attempted to detect the genetic diversity and relationships of commonly used celery accessions and explore the efficiency of the primers used for cultivars identification. Analysis of molecular variance (AMOVA of Apium graveolens L. var. dulce showed that approximately 43% of genetic diversity was within accessions, 45% among accessions, and 22% among horticultural types. The neighbor-joining tree generated by unweighted pair group method with arithmetic mean (UPGMA, and population structure analysis, as well as principal components analysis (PCA, separated the cultivars into clusters corresponding to the geographical areas where they originated. Genetic distance analysis suggested that genetic variation within Apium graveolens was quite limited. Genotypic diversity showed any combinations of 55 genic SSRs were able to distinguish the genotypes of all 30 accessions.

Solid State Track Recorder fission rate measurements at high neutron fluence and high temperature

International Nuclear Information System (INIS)

Ruddy, F.H.; Roberts, J.H.; Gold, R.

1985-01-01

Solid State Track Recorder (SSTR) techniques have been used to measure 239-Pu, 235-U, and 237-Np fission rates for total neutron fluences approaching 5 x 10 17 n/cm 2 at temperatures in the range 680 to 830 0 F. Natural quartz crystal SSTRs were used to withstand the high temperature environment and ultra low-mass fissionable deposits of the three isotopes were required to yield scannable track densities at the high neutron fluences. The results of these high temperature, high neutron fluence measurements are reported

Amphibia, Anura, Microhylidae, Chiasmocleis avilapiresae Peloso and Sturaro, 2008: First record from the state of Acre, southwestern Amazonia, Brazil

Directory of Open Access Journals (Sweden)

Sampaio, P. R. M.

2010-01-01

Full Text Available We record for the first time the presence of Chiasmocleis avilapiresae in the state of Acre, Brazil. This microhylidfrog is found throughout Amazon in Brazil and no information about its distribution in the Acre state was reported previously.An increase on sampling efforts, revision of material housed in herpetological collections, and use of diverse herpetofaunasampling methods might reveal additional localities and more information about this species.

Amphibia, Anura, Microhylidae, Chiasmocleis avilapiresae Peloso and Sturaro, 2008: first record for the state of Acre, southwestern Amazonia, Brazil

OpenAIRE

Sampaio, Paulo; da Silva, Talisson; Peloso, Pedro

2016-01-01

We record for the first time the presence of Chiasmocleis avilapiresae in the state of Acre, Brazil. This microhylid frog is found throughout Amazon in Brazil and no information about its distribution in the Acre state was reported previously. An increase on sampling efforts, revision of material housed in herpetological collections, and use of diverse herpetofauna sampling methods might reveal additional localities and more information about this species.

Characterization of expressed sequence tag-derived simple sequence repeat markers for Aspergillus flavus: emphasis on variability of isolates from the southern United States.

Science.gov (United States)

Wang, Xinwang; Wadl, Phillip A; Wood-Jones, Alicia; Windham, Gary; Trigiano, Robert N; Scruggs, Mary; Pilgrim, Candace; Baird, Richard

2012-12-01

Simple sequence repeat (SSR) markers were developed from Aspergillus flavus expressed sequence tag (EST) database to conduct an analysis of genetic relationships of Aspergillus isolates from numerous host species and geographical regions, but primarily from the United States. Twenty-nine primers were designed from 362 tri-nucleotide EST-SSR sequences. Eighteen polymorphic loci were used to genotype 96 Aspergillus species isolates. The number of alleles detected per locus ranged from 2 to 24 with a mean of 8.2 alleles. Haploid diversity ranged from 0.28 to 0.91. Genetic distance matrix was used to perform principal coordinates analysis (PCA) and to generate dendrograms using unweighted pair group method with arithmetic mean (UPGMA). Two principal coordinates explained more than 75 % of the total variation among the isolates. One clade was identified for A. flavus isolates (n = 87) with the other Aspergillus species (n = 7) using PCA, but five distinct clusters were present when the others taxa were excluded from the analysis. Six groups were noted when the EST-SSR data were compared using UPGMA. However, the latter PCA or UPGMA comparison resulted in no direct associations with host species, geographical region or aflatoxin production. Furthermore, there was no direct correlation to visible morphological features such as sclerotial types. The isolates from Mississippi Delta region, which contained the largest percentage of isolates, did not show any unusual clustering except for isolates K32, K55, and 199. Further studies of these three isolates are warranted to evaluate their pathogenicity, aflatoxin production potential, additional gene sequences (e.g., RPB2), and morphological comparisons.

Screening of IR50 x Rathu Heenati F7 RILs and identification of SSR markers linked to brown planthopper (Nilaparvata lugens Stål) resistance in rice (Oryza sativa L.).

Science.gov (United States)

Kumari, Sanju; M Sheba, Jennifer; Marappan, Maheshwaran; Ponnuswamy, Shanmugasunderam; Seetharaman, Suresh; Pothi, Nagarajan; Subbarayalu, Mohankumar; Muthurajan, Raveendran; Natesan, Senthil

2010-09-01

Brown planthopper (Nilaparvata lugens Stål) is one of the major insect pests of rice. A Sri Lankan indica rice cultivar Rathu Heenati was found to be resistant to all biotypes of the brown planthopper. In the present study, a total of 268 F(7) RILs of IR50 and Rathu Heenati were phenotyped for their level of resistance against BPH by the standard seedbox screening test (SSST) in the greenhouse. A total of 53 SSR primers mapped on the chromosome 3 were used to screen the polymorphism between the parents IR50 and Rathu Heenati, out of which eleven were found to be polymorphic between IR50 and Rathu Heenati. The eleven primers that have shown polymorphism between the IR50 and Rathu Heenati parents were genotyped in a set of five resistant RILs and five susceptible RILs along with the parents for co-segregation analysis. Among the eleven primers, two primers namely RM3180 (18.22 Mb) and RM2453 (20.19 Mb) showed complete co-segregation with resistance. The identification of SSR markers linked with BPH resistant could be used for the maker assisted selection (MAS) program in rice breeding and to map the resistant genes on rice chromosomes for further gene cloning.

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

The Development Strategies for the Management Models of the Electronic Documents and Records in the United States, United Kingdom and Australia

Directory of Open Access Journals (Sweden)

Chiu-Yen Lin

2015-06-01

Full Text Available The trend toward electronic government has espoused a large quantity of electronic records, which challenge the existing records management models in the modern countries. This paper describes and compares the development and transition toward electronic records management in the United States, United Kingdom, and Australia to show how the three advanced countries evolved the government records management practices. The analysis emphasized on the holistic policy initiative perspective and compared the directives and regulations, research and development programs and plans, the emerging structures of governance, staffing and professional training, and risk management provisions. The comparison may shed lights on the government electronic management in the other countries. [Article content in Chinese

New record of the mangrove rivulid Kryptolebias hermaphroditus Costa, 2011 (Cyprinodontiformes: Cynolebiidae) in the Pará state, northern Brazil

OpenAIRE

Guimarães-Costa, Auryceia; Schneider, Horacio; Sampaio, Iracilda

2017-01-01

The mangrove killifish Kryptolebias herma­phro­ditus is reported to the southeast and northeast regions of Brazil. Recently, a specimen of K. hermaphroditus was collected in a shallow running seawater stream at Ajuruteua beach, Pará state, northern Brazil. This new record is ca. 1,350 km from the nearest previously known occurrence in Rio Grande do Norte state, Brazil. Morphological, molecular, and ecological aspects of this species are described.

Genetic characterization of autochthonous grapevine cultivars from Eastern Turkey by simple sequence repeats (SSRs

Directory of Open Access Journals (Sweden)

Sadiye Peral Eyduran

2016-01-01

Full Text Available In this research, two well-recognized standard grape cultivars, Cabernet Sauvignon and Merlot, together with eight historical autochthonous grapevine cultivars from Eastern Anatolia in Turkey, were genetically characterized by using 12 pairs of simple sequence repeat (SSR primers in order to evaluate their genetic diversity and relatedness. All of the used SSR primers produced successful amplifications and revealed DNA polymorphisms, which were subsequently utilized to evaluate the genetic relatedness of the grapevine cultivars. Allele richness was implied by the identification of 69 alleles in 8 autochthonous cultivars with a mean value of 5.75 alleles per locus. The average expected heterozygosity and observed heterozygosity were found to be 0.749 and 0.739, respectively. Taking into account the generated alleles, the highest number was recorded in VVC2C3 and VVS2 loci (nine and eight alleles per locus, respectively, whereas the lowest number was recorded in VrZAG83 (three alleles per locus. Two main clusters were produced by using the unweighted pair-group method with arithmetic mean dendrogram constructed on the basis of the SSR data. Only Cabernet Sauvignon and Merlot cultivars were included in the first cluster. The second cluster involved the rest of the autochthonous cultivars. The results obtained during the study illustrated clearly that SSR markers have verified to be an effective tool for fingerprinting grapevine cultivars and carrying out grapevine biodiversity studies. The obtained data are also meaningful references for grapevine domestication.

75 FR 64350 - Notice of Availability of Record of Decision for the NextLight Renewable Power, LLC, Silver State...

Science.gov (United States)

2010-10-19

...Light Renewable Power, LLC, Silver State Solar Project Environmental Impact Statement AGENCY: Bureau of... CONTACT: Gregory Helseth, Renewable Energy Project Manager, phone: (702) 515-5173; address: BLM Southern...) announces the availability of the Record of Decision (ROD) for the NextLight Renewable Power, LLC, Silver...

Inferring introduction history and spread of Falcaria vulgaris Bernh. (Apiaceae) in the United States based on herbarium records

Science.gov (United States)

Sarbottam Piya; Madhav P. Nepal; Achal Neupane; Gary E. Larson; Jack L. Butler

2012-01-01

Herbarium records were studied to infer the introduction history and spread of the exotic Eurasian sickleweed (Falcaria vulgaris Bernh.) in the United States. The spread of the plant was reconstructed using the location of early collections as the possible sites of primary introduction, and the location of subsequent collections as potential pathways along which this...

Electronic Health Records Data and Metadata: Challenges for Big Data in the United States.

Science.gov (United States)

Sweet, Lauren E; Moulaison, Heather Lea

2013-12-01

This article, written by researchers studying metadata and standards, represents a fresh perspective on the challenges of electronic health records (EHRs) and serves as a primer for big data researchers new to health-related issues. Primarily, we argue for the importance of the systematic adoption of standards in EHR data and metadata as a way of promoting big data research and benefiting patients. EHRs have the potential to include a vast amount of longitudinal health data, and metadata provides the formal structures to govern that data. In the United States, electronic medical records (EMRs) are part of the larger EHR. EHR data is submitted by a variety of clinical data providers and potentially by the patients themselves. Because data input practices are not necessarily standardized, and because of the multiplicity of current standards, basic interoperability in EHRs is hindered. Some of the issues with EHR interoperability stem from the complexities of the data they include, which can be both structured and unstructured. A number of controlled vocabularies are available to data providers. The continuity of care document standard will provide interoperability in the United States between the EMR and the larger EHR, potentially making data input by providers directly available to other providers. The data involved is nonetheless messy. In particular, the use of competing vocabularies such as the Systematized Nomenclature of Medicine-Clinical Terms, MEDCIN, and locally created vocabularies inhibits large-scale interoperability for structured portions of the records, and unstructured portions, although potentially not machine readable, remain essential. Once EMRs for patients are brought together as EHRs, the EHRs must be managed and stored. Adequate documentation should be created and maintained to assure the secure and accurate use of EHR data. There are currently a few notable international standards initiatives for EHRs. Organizations such as Health Level Seven

A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat （Triticum aestivum L.）

Institute of Scientific and Technical Information of China (English)

ZHAI Hui-jie; FENG Zhi-yu; LIU Xin-ye; CHENG Xue-jiao; PENG Hui-ru; YAO Ying-yin; SUN Qi-xin; NI Zhong-fu

2015-01-01

The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci （QTLs） controlling agronomically important traits. In this study, simple sequence repeat （SSR） markers and Illumina 9K iSelect single nucleotide polymorphism （SNP） genechip were employed to construct one genetic linkage map of common wheat （Triticum aestivum L.） using 191 recombinant inbred lines （RILs） derived from cross Yu 8679xJing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1,703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 （92.27%） of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 （97.4%） were located on one single chromosome, and the rest 31 （2.6%） were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags （ESTs）, 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

Tales of the Supernatural: A Selected List of Recordings Made in the United States and Placed in the Archive of Folk Culture. Folk Archive Finding Aid.

Science.gov (United States)

Delcambre, Angie C., Comp.; And Others

This finding aid is a selected list of supernatural-related narratives recorded in the United States and held in the Archive of Folk Culture of the Library of Congress. Brief descriptions of the recordings are accompanied by identification numbers. Information about listening to or ordering any of the listed recordings is available from the…

Automation in Records Management in University Libraries in Nigeria

African Journals Online (AJOL)

... State university libraries and less archival record were automated in both Federal and State university libraries, it was recommended that State university libraries should follow the lead of Federal university libraries by automating their records, this will go a long way to make information retrieval and accessibility easier.

Disturbance recording system

International Nuclear Information System (INIS)

Chandra, A.K.; Deshpande, S.V.; Mayya, A.; Vaidya, U.W.; Premraj, M.K.; Patil, N.B.

1994-01-01

A computerized system for disturbance monitoring, recording and display has been developed for use in nuclear power plants and is versatile enough to be used where ever a large number of parameters need to be recorded, e.g. conventional power plants, chemical industry etc. The Disturbance Recording System (DRS) has been designed to continuously monitor a process plant and record crucial parameters. The DRS provides a centralized facility to monitor and continuously record 64 process parameters scanned every 1 sec for 5 days. The system also provides facility for storage of 64 parameters scanned every 200 msec during 2 minutes prior to and 3 minutes after a disturbance. In addition the system can initiate, on demand, the recording of 8 parameters at a fast rate of every 5 msec for a period of 5 sec. and thus act as a visicorder. All this data is recorded in non-volatile memory and can be displayed, printed/plotted and used for subsequent analysis. Since data can be stored densely on floppy disks, the volume of space required for archival storage is also low. As a disturbance recorder, the DRS allows the operator to view the state of the plant prior to occurrence of the disturbance and helps in identifying the root cause. (author). 10 refs., 7 figs

Cluster and principal component analysis based on SSR markers of Amomum tsao-ko in Jinping County of Yunnan Province

Science.gov (United States)

Ma, Mengli; Lei, En; Meng, Hengling; Wang, Tiantao; Xie, Linyan; Shen, Dong; Xianwang, Zhou; Lu, Bingyue

2017-08-01

Amomum tsao-ko is a commercial plant that used for various purposes in medicinal and food industries. For the present investigation, 44 germplasm samples were collected from Jinping County of Yunnan Province. Clusters analysis and 2-dimensional principal component analysis (PCA) was used to represent the genetic relations among Amomum tsao-ko by using simple sequence repeat (SSR) markers. Clustering analysis clearly distinguished the samples groups. Two major clusters were formed; first (Cluster I) consisted of 34 individuals, the second (Cluster II) consisted of 10 individuals, Cluster I as the main group contained multiple sub-clusters. PCA also showed 2 groups: PCA Group 1 included 29 individuals, PCA Group 2 included 12 individuals, consistent with the results of cluster analysis. The purpose of the present investigation was to provide information on genetic relationship of Amomum tsao-ko germplasm resources in main producing areas, also provide a theoretical basis for the protection and utilization of Amomum tsao-ko resources.

Light-water-reactor pressure-vessel surveillance dosimetry using solid-state track recorders

International Nuclear Information System (INIS)

Ruddy, F.H.; Roberts, J.H.; Gold, R.; Preston, C.C.

1983-07-01

The accumulation of neutron dose by the pressure vessel of an operating nuclear power plant results in damage in the form of steel embrittlement. In order to ascertain the safe operating lifetime of the reactor pressure vessel, dosimetric measurements must be made to evaluate the neutron dose to the pressure vessel and relate this dose to the cumulative radiation damage. Advanced dosimetry techniques are being evaluated for surveillance of operating reactors. Solid-state track recorder (SSTR) techniques are included among these advanced dosimetry techniques. Described herein are low neutron fluence calibration and standardization measurements that are being carried out in pressure vessel mockup benchmark neutron fields in the USA, Belgium, and England. In addition, high fluence SSTR dosimetry capsules have been irradiated with metallurgical specimens in a pressure vessel mockup facility. The design and deployment of advances SSTR dosimetry capsules in operating power reactors are also described

Taxonomic key for the genera of Elmidae (Coleoptera, Byrrhoidea occurring in Goiás State, Brazil, including new records and distributional notes

Directory of Open Access Journals (Sweden)

Felipe F. Barbosa

2013-06-01

Full Text Available A taxonomic key for the genera of Elmidae (Coleoptera, Byrrhoidea occurring in Goiás State, Brazil, including new records and distributional notes. Despite their great diversity and high abundance in Neotropical aquatic environments, the fauna of Elmidae remains practically unknown in some areas and even entire biomes in this region. In this work we bring, for the first time, faunistic data for the Elmidae of central Brazil. The aim of this work was to inventory the Elmidae fauna in central, southwestern and southeastern Goiás State, Brazil and to produce a taxonomic key, at genus level, for adults from the studied region. The taxonomic key presented herein offers means for the identification of all the 13 genera known to occur in Goiás, 11 of them being new records for the State. Moreover, the number of named species registered for Goiás increased from one to nine.

28 CFR 16.10 - Preservation of records.

Science.gov (United States)

2010-07-01

... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Preservation of records. 16.10 Section 16.10 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION... title 44 of the United States Code or the National Archives and Records Administration's General Records...

Experimental Analysis of Steady-State Maneuvering Effects on Transmission Vibration Patterns Recorded in an AH-1 Cobra Helicopter

Science.gov (United States)

Huff, Edward M.; Dzwonczyk, Mark; Norvig, Peter (Technical Monitor)

2000-01-01

Flight experiment was designed primarily to determine the extent to which steady-state maneuvers influence characteristic vibration patterns measured at the input pinion and output annulus gear locations of the main transmission. If results were to indicate that maneuvers systematically influence vibration patterns, more extensive studies would be planned to explore the response surface. It was also designed to collect baseline data for comparison with experimental data to be recorded at a later date from test stands at Glenn Research Center. Finally, because this was the first vibration flight study on the Cobra aircraft, considerable energy was invested in developing an in-flight recording apparatus, as well as exploring acceleration mounting methods, and generally learning about the overall vibratory characteristics of the aircraft itself.

Holocene record of precipitation seasonality from lake calcite δ18O in the central Rocky Mountains, United States

Science.gov (United States)

Anderson, Lesleigh

2011-01-01

A context for recent hydroclimatic extremes and variability is provided by a ~10 k.y. sediment carbonate oxygen isotope (??18O) record at 5-100 yr resolution from Bison Lake, 3255 m above sea level, in northwestern Colorado (United States). Winter precipitation is the primary water source for the alpine headwater lake in the Upper Colorado River Basin and lake water ??18O measurements reflect seasonal variations in precipitation ??18O. Holocene lake water ??18O variations are inferred from endogenic sedimentary calcite ??18O based on comparisons with historic watershed discharge records and tree-ring reconstructions. Drought periods (i.e., drier winters and/or a more rain-dominated seasonal precipitation balance) generally correspond with higher calcite ??18O values, and vice-versa. Early to middle Holocene ??18O values are higher, implying a rain-dominated seasonal precipitation balance. Lower, more variable ??18O values after ca. 3500 yr ago indicate a snow-dominated but more seasonally variable precipitation balance. The middle to late Holocene ??18O record corresponds with records of El Ni??o Southern Oscillation intensification that supports a teleconnection between Rocky Mountain climate and North Pacific sea-surface temperatures at decade to century time scales. ?? 2011 Geological Society of America.

27 CFR 24.311 - Taxpaid wine record.

Science.gov (United States)

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Taxpaid wine record. 24..., DEPARTMENT OF THE TREASURY LIQUORS WINE Records and Reports § 24.311 Taxpaid wine record. A proprietor who has taxpaid United States or foreign wine on taxpaid wine premises or on taxpaid wine bottling house...

NRC comprehensive records disposition schedule

International Nuclear Information System (INIS)

1992-03-01

Title 44 United States Code, ''Public Printing and Documents,'' regulations cited in the General Services Administration's (GSA) ''Federal Information Resources Management Regulations'' (FIRMR), Part 201-9, ''Creation, Maintenance, and Use of Records,'' and regulation issued by the National Archives and Records Administration (NARA) in 36 CFR Chapter XII, Subchapter B, ''Records Management,'' require each agency to prepare and issue a comprehensive records disposition schedule that contains the NARA approved records disposition schedules for records unique to the agency and contains the NARA's General Records Schedules for records common to several or all agencies. The approved records disposition schedules specify the appropriate duration of retention and the final disposition for records created or maintained by the NRC. NUREG-0910, Rev. 2, contains ''NRC's Comprehensive Records Disposition Schedule,'' and the original authorized approved citation numbers issued by NARA. Rev. 2 totally reorganizes the records schedules from a functional arrangement to an arrangement by the host office. A subject index and a conversion table have also been developed for the NRC schedules to allow staff to identify the new schedule numbers easily and to improve their ability to locate applicable schedules

DOCUMENTED RECORD OF A MIGRATING EASTERN SLATY THRUSH (Turdus subalaris (TURDIDAE, PASSERIFORMES IN WESTERN MATO GROSSO STATE, BRAZIL

Directory of Open Access Journals (Sweden)

Breno Dias Vitorino

2016-12-01

Full Text Available The Eastern Slaty Thrush (Turdus subalaris occurs in the meridional parts of South America, from Bolivia Southward to Argentina, Paraguay and South and Southeastern Brazil. During the winter on the continent, it performs migration little known toward areas of ecotone between Amazon and Cerrado, with little information on their area of wintering in the Mato Grosso state. In this study we report on a record documenting the species for the Alto Rio Guaporé basin, Western Mato Grosso, based on a mist-netted individual. We present a record until now unpublished of the species in the region of Vila Bela da Santíssima Trindade and contribute to the knowledge of the species’ wintering range and their annual cycle. Keywords: Austral migration; wintering; birds; Vila Bela da Santíssima Trindade.

76 FR 43666 - Privacy Act of 1974; System of Records

Science.gov (United States)

2011-07-21

..., home of record state, sex, race, education level; VA disability payment records; digital signatures... conducting an on-going computer matching program with state Medicaid agencies to determine the extent to... the identity of [[Page 43668

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

Science.gov (United States)

Edwards, J D; Baldo, A M; Mueller, L A

2016-01-01

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

United States Geological Survey (USGS) FM cassette seismic-refraction recording system

International Nuclear Information System (INIS)

Murphy, J.M.

1988-01-01

In this two chapter report, instrumentation used to collect seismic data is described. This data acquisition system has two parts: (1) portable anolog seismic recorders and related ''hand-held-testers'' (HHT) and (2) portable digitizing units. During the anolog recording process, ground motion is sensed by a 2-Hz vertical-component seismometer. The voltage output from the seismometer is split without amplification and sent to three parallel amplifier circuit boards. Each circuit board amplifiers the seismic signal in three stages and then frequency modulates the signal. Amplification at the last two stages can be set by the user. An internal precision clock signal is also frequency modulated. The three data carrier frequencies, the clock carrier frequency, and a tape-speed compensation carrier frequency are summed and recorded on a recorded on a cassette tape. During the digitizing process, the cassette tapes are played back and the signals are demultiplexed and demodulated. An anolog-to-digital converter converts the signals to digital data which are stored on 8-inch floppy disks. 7 refs., 19 figs., 6 tabs

Adoption and Completeness of Documentation Using a Structured Delivery Record in Secondary Care, Subdistrict Government Hospitals of Karnataka State, India

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Prem K. Mony

2016-05-01

Full Text Available Objective: Poor medical record documentation remains a pervasive problem in hospital delivery rooms, hampering efforts aimed at improving the quality of maternal and neonatal care in resource-limited settings. We evaluated the feasibility and completeness of labor room documentation within a quasi-experimental study aimed at improving emergency preparedness for obstetric and neonatal emergencies in 8 nonteaching, subdistrict, secondary care hospitals of Karnataka state, India. Methods: We redesigned the existing open-ended case sheet into a structured, delivery record cum job aide adhering to principles of local clinical relevance, parsimony, and computerizability. Skills and emergency drills training along with supportive supervision were introduced in 4 “intervention arm” hospitals while the new delivery records were used in eight intervention and control hospitals. Results: Introduction of the new delivery record was feasible over a “run-in” period of 4 months. About 92% (6103 of 6634 of women in intervention facilities and 80% (6205 of 7756 in control facilities had their delivery records filled in during the 1-year study period. Completeness of delivery record documentation fell into one of two subsets with one set of parameters being documented with minimal inputs (in both intervention and control sites and another set of parameters requiring more intensive training efforts (and seen more in intervention than in control sites; P < .05. Conclusion: Under the stewardship of the local government, it was possible to institute a robust, reliable, and valid medical record documentation system as part of efforts to improve intrapartum and postpartum maternal and newborn care in hospitals.

A closer looking at dimming and brightening in China during 1961–2005

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X. Xia

2010-05-01

Full Text Available This study investigates dimming and brightening of surface solar radiation (SSR during 1961–2005 in China as well as its relationships to total cloud cover (TCC. This is inferred from daily ground-based observational records at 45 pyranometer stations. A statistical method is introduced to study contributions of changes in the frequency of TCC categories and their atmospheric transparency to the secular SSR trend. The surface records suggest a renewed dimming beyond 2000 in North China after the stabilization in the 1990s; however, a slight brightening appears beyond 2000 in South China. Inter-annual variability of SSR is negatively correlated with that of TCC, but there is a positive correlation between decadal variability of SSR and TCC in most cases. The dimming during 1961–1990 is exclusively attributable to decreased atmospheric transparency, a portion of which is offset by TCC frequency changes in Northeast and Southwest China. The dimming during 1961–1990 in Northwest and Southeast China primarily results from decreased atmospheric transparency under all sky conditions and the percentage of dimming stemming from TCC frequency changes is 11% in Northwest and 2% in Southeast China. Decreased atmospheric transparencies during 1991–2005 in North China in most cases lead to the dimming. TCC frequency changes also contribute to the dimming during this period in North China. This feature is more pronounced in summer and winter when TCC frequency changes can account for more than 80% of dimming. In South China, increased atmospheric transparencies lead to the brightening during 1991–2005. A substantial contribution by TCC frequency changes to the brightening is also evident in spring and autumn.

A closer looking at dimming and brightening in China during 1961-2005

Energy Technology Data Exchange (ETDEWEB)

Xia, X. [Chinese Academy of Sciences, Beijing (China). LAGEO, Inst. of Atmospheric Physics

2010-07-01

This study investigates dimming and brightening of surface solar radiation (SSR) during 1961-2005 in China as well as its relationships to total cloud cover (TCC). This is inferred from daily ground-based observational records at 45 pyranometer stations. A statistical method is introduced to study contributions of changes in the frequency of TCC categories and their atmospheric transparency to the secular SSR trend. The surface records suggest a renewed dimming beyond 2000 in North China after the stabilization in the 1990s; however, a slight brightening appears beyond 2000 in South China. Inter-annual variability of SSR is negatively correlated with that of TCC, but there is a positive correlation between decadal variability of SSR and TCC in most cases. The dimming during 1961-1990 is exclusively attributable to decreased atmospheric transparency, a portion of which is offset by TCC frequency changes in Northeast and Southwest China. The dimming during 1961-1990 in Northwest and Southeast China primarily results from decreased atmospheric transparency under all sky conditions and the percentage of dimming stemming from TCC frequency changes is 11% in Northwest and 2% in Southeast China. Decreased atmospheric transparencies during 1991- 2005 in North China in most cases lead to the dimming. TCC frequency changes also contribute to the dimming during this period in North China. This feature is more pronounced in summer and winter when TCC frequency changes can account for more than 80% of dimming. In South China, increased atmospheric transparencies lead to the brightening during 1991-2005. A substantial contribution by TCC frequency changes to the brightening is also evident in spring and autumn. (orig.)

Host records for Ornithonyssus sylviarum (Mesostigmata: Macronyssidae) from birds of North America (Canada, United States, and Mexico).

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Knee, Wayne; Proctor, Heather

2007-07-01

The northern fowl mite, Ornithonyssus sylviarum (Canestrini and Fanzago, 1877) (Mesostigmata: Macronyssidae) is a broadly distributed blood-feeding parasite that has been collected from many birds of temperate regions. Previously, the most complete host list was published in 1938, and it included 15 North American (Canada, United States, and Mexico) host species. In the process of a general survey of bird-associated mites in Alberta, Canada, we recovered many O. sylviarum specimens. Herein, we update the previous host list with these observations and records published since 1938. We collected mites by washing the bodies of salvaged birds and examining the filtrate. Northern fowl mites were collected from 26 host species, with 16 of these species being the first host records for North America. Including results from the current study, O. sylviarum has been reported from 72 species of North American birds from 26 families. This updated host list will be useful to anyone interested in the role of O. sylviarum in transmission of avian disease.

First record of Chara indica and Chara zeylanica (Charophyceae, Charales, Characeae in the semiarid reservoirs the state of Rio Grande do Norte, Brazil

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Norma Catarina Bueno

2013-09-01

Full Text Available In the present study we present the first record of the macroalgaes Chara indica and Chara zeylanica for the state of Rio Grande do Norte, Brazil, and the semiarid northeastern. Specimens of C. indica and C. zeylanica were collected in Santa Cruz and Umari reservoirs, respectively. Both reservoirs are located in the river basin Apodi-Mossoró (Western State in the Caatinga Biome.

78 FR 54945 - Privacy Act; System of Records: Protocol Records, State-33

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2013-09-06

... and decorations received from foreign governments; donors; guest lists; type of function; sample... authentication and time out function. All Department of State employees and contractors with authorized access...

32 CFR 701.107 - Record access.

Science.gov (United States)

2010-07-01

... copies of “all records pertaining to them,” because they do not have a centralized index that would allow... penalty under the laws of the United States of America that the foregoing is true and correct.” (j... military supervisory personnel concerning subordinates are not systems of records within the meaning of...

Registros nuevos para la avifauna del estado de Hidalgo, México New records for the avifauna of the state of Hidalgo, Mexico

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Raúl Valencia-Herverth

2010-04-01

Full Text Available Se presentan 6 registros nuevos de aves para el estado de Hidalgo que se obtuvieron durante el trabajo de campo realizado de agosto 2006 a octubre 2007 y de registros no publicados de especímenes de la Colección Ornitológica del Instituto Tecnológico de Huejutla.Six new state records of birds for Hidalgo based on field work carried out from August 2006 to October 2007 are presented, and from unpublished records of specimens in the Ornithological Collection of the Instituto Tecnológico de Huejutla.

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.

15 CFR 280.313 - Recordal of additional insignia.

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2010-01-01

... for recordal of its trademark for fasteners if the trademark is the subject of a duly filed application or is registered in the United States Patent and Trademark Office on the Principal Register. Upon recordal, either the alphanumeric designation or the trademark, or both, may be used as recorded insignias...

Personal factors affecting organizational commitment of records ...

African Journals Online (AJOL)

This study investigated personal factors affecting organizational commitment among records management personnel in the state universities in Nigeria. Simple cluster sampling with equal allocation method was used to select 180 records management personnel from the study population. A five item organizational ...

A new species and records of Anacroneuria (Plecoptera: Perlidae) from the Ecological Station, Wenceslau Guimarães, State of Bahia, Brazil.

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Almeida, Lucas Henrique DE; Duarte, Tácio

2017-03-28

We studied specimens of the perlid genus Anacroneuria collected at the Ecological Station, Wenceslau Guimarães, State of Bahia, Brazil. A list of Anacroneuria species is provided including a description of a new species, A. patioba n. sp., and a new record is given for A. paprockii Novaes & Bispo, 2014.

First record of Crypticerya zeteki (Cockerell, 1914 (Monophlebidae in Brazil and Maconellicoccus hirsutus (Green, 1908 (Pseudococcidae in the state of Maranhão

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A. S. J. C. Ramos

2017-06-01

Full Text Available Abstract Crypticerya zeteki (Cockerell, 1914 (Hemiptera: Coccomorpha: Monophlebidae is recorded for the first time from Brazil and Maconellicoccus hirsutus (Green, 1908 (Hemiptera: Coccomorpha: Pseudococcidae is recorded for the first time from the state of Maranhão, Brazil. Both species were collected from branches, leaves and fruits of various fruit trees in the municipalities of São José de Ribamar, São Luís and Paço do Lumiar, Maranhão, Brazil. Crypticerya zeteki was collected on Citrus spp. (Rutaceae, Cocos nucifera (L. (Arecaceae, Cycas revoluta L. (Cycadaceae, Malpighia punicifolia L. (Malpighiaceae, Mangifera indica L. (Anacardiaceae, Musa paradisiaca L. (Musaceae and Theobroma grandiflorum Schum (Malvaceae, all first records for this species. Maconellicoccus hirsutus was collected on Spondias tuberosa Arruda (Anacardiaceae and M. punicifolia L. (Malpighiaceae, both new records for this species.

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers.

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Zhang, Yu; Yan, Haidong; Jiang, Xiaomei; Wang, Xiaoli; Huang, Linkai; Xu, Bin; Zhang, Xinquan; Zhang, Lexin

2016-01-01

To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass ( Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei's gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r 2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 ( P  < 0.01). The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.

Genetic Diversity Among Historical Olive (Olea europaea L.) Genotypes from Southern Anatolia Based on SSR Markers.

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Sakar, Ebru; Unver, Hulya; Ercisli, Sezai

2016-12-01

Olive (Olea europaea) is an ancient and important crop in both olive oil production and table use. It is important to identify the genetic diversity of olive genetic resources for cultivar development and evaluation of olive germplasm. In the study, 14 microsatellite markers (UDO4, UDO8, UDO9, UDO11, UDO12, UDO22, UDO24, UDO26, UDO28, DCA9, DCA11, DCA13, DCA15, and DCA18) were used to assess the genetic variation on 76 olive (Olea europaea L.) genotypes from Mardin province together with 6 well-known Turkish and 4 well-known foreign reference cultivars. All microsatellite markers showed polymorphism and the number of alleles varied between 9 and 22, with an average of 14.57. The most informative loci were DCA 11 (22 alleles) and DCA 9 (21 alleles). Dendrogram based on genetic distances was constructed for the 86 olive genotypes/cultivars, which revealed the existence of different clusters. The high genetic similarity was evident between Bakırkire2 and Zinnar5 (0.74) genotypes, while the most genetically divergent genotypes were Gürmeşe5 and Yedikardeşler2 (0.19). It was concluded that there was abundant SSR polymorphism in olive germplasm in southern Anatolia in Turkey and could be important for future breeding activities.

Synthesis, Characterization and Performance of Cu 2 for Solar Cell Application SnSe 3

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Mostafa Sh. Eraky

2017-12-01

Full Text Available Cu2SnSe3 (CTSe powders were prepared by solvothermal (SR and solid state reactions (SSR using low cost starting materials. The crystal structure, morphology, UV-Vis absorbance, electrochemical and solar energy properties were investigated using X-ray Diffraction (XRD, Field Emission Scanning Electron Microscopy (FESEM, Electrochemical Impedance Spectroscopy (EIS and solar energy applications using I-V characteristics measurements. A single cubic Cu2SnSe3 was obtained for the two methods of preparations. The calculated crystallite size (L values for CTSe prepared by SR and SSR are 24.1 and 30.3 nm, respectively. UV-Vis. spectra for SR and SSR preparations showed maximum absorbencies at 240 nm with band gap (Eg values of 0.9 and 1.4 eV, respectively. The charge transfer resistances (Rct were equal to 3.5 and 24  for photoelectrochemical cells (PEC and the calculated conductivities were equal to 3x10-2 and 2x10-2 S.cm for samples that prepared by SR and SSR methods, respectively. A good photoelectrochemical cell (PCE has accomplished power conversion efficiency per unit area of about 0.84 and 0.64 % for cells prepared by SR and SSR, respectively.

PASSIVE ACOUSTIC MONITORING OF ODONTOCETES IN THE VICINITY OF PUULOA UNDERWATER DETONATION TRAINING RANGE, HAWAII RANGE COMPLEX, OAHU

Science.gov (United States)

2016-09-25

Printed on recycled paper Approved for public release; distribution is unlimited. SITE SPECIFIC REPORT SSR-NAVFAC-EXWC-EV-1702 SEPTEMBER 2016...NOAA’s Coral Reef Ecosystem Division. The EAR is an autonomous underwater recorder controlled by a Persistor CF2 microcontroller that may be

28 CFR 16.48 - Preservation of records.

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2010-07-01

... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Preservation of records. 16.48 Section 16.48 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION... authorized by title 44 of the United States Code or the National Archives and Records Administration's...

Advances and current state of the security and privacy in electronic health records: survey from a social perspective.

Science.gov (United States)

Tejero, Antonio; de la Torre, Isabel

2012-10-01

E-Health systems are experiencing an impulse in these last years, when many medical agencies began to include digital solutions into their platforms. Electronic Health Records (EHRs) are one of the most important improvements, being in its most part a patient-oriented tool. To achieve a completely operational EHR platform, security and privacy problems have to be resolved, due to the importance of the data included within these records. But given all the different methods to address security and privacy, they still remain in most cases as an open issue. This paper studies existing and proposed solutions included in different scenarios, in order to offer an overview of the current state in EHR systems. Bibliographic material has been obtained mainly from MEDLINE and SCOPUS sources, and over 30 publications have been analyzed. Many EHR platforms are being developed, but most of them present weaknesses when they are opened to the public. These architectures gain significance when they cover all the requisites related to security and privacy.