The presence of pubescence on the leaves of cassava confers resistance to mealybug, an important pest of cassava in Africa. We therefore, investigated RAPD markers linked to the pubescent trait in four descendants of cassava clone TMS 4(2)1425, namely, diploid (2X) 4(2)1425 pubescent, diploid (2X) 4(2)1425 ...
Sep 21, 2011 ... Biotechnol. Biotechnol. Equip.14: 16-18. Belaj A, Satovic Z, Cipriani G, Baldoni L, Testolin R, Rallo L, Trujillo I. (2003). Comparative study of the discriminating capacity of RAPD,. AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor. Appl. Genet. 107: 736-744 ...
tolerance in wheat. Waqas Manzoor Bhutta* and Muhammad Hanif. Department of Botany, Government College University Faisalabad, 38040-Pakistan. Accepted 24 August, 2009 ... Key words: Marker, RAPD, root length, salinity, wheat. INTRODUCTION. Salinity is a ..... to leaf rust resistance in barley. Theor. Appl. Genet.
Haley, S D; Miklas, P N; Stavely, J R; Byrum, J; Kelly, J D
Rust in bean (Phaseolus vulgaris L.), caused byUromyces appendiculatus (Pers.) Unger var.appendiculatus [ =U. phaseoli (Reben) Wint.], is a major disease problem and production constraint in many parts of the world. The predominant form of genetic control of the pathogen is a series of major genes which necessitate the development of efficient selection strategies. Our objective was focused on the identification of RAPD (random amplified polymorphic DNA) markers linked to a major bean rust resistance gene block enabling marker-based selection and facilitating resistance gene pyramiding into susceptible bean germplasm. Using pooled DNA samples of genotyped individuals from two segregating populations, we identified two RAPD markers linked to the gene block of interest. One such RAPD, OF10970 (generated by a 5'-GGAAGCTTGG-3' decamer), was found to be closely linked (2.15±1.50 centi Morgans) in coupling with the resistance gene block. The other identified RAPD, OI19460 (generated by a 5'-AATGCGGGAG-3' decamer), was shown to be more tightly linked (also in coupling) than OF10970 as no recombinants were detected among 97 BC6F2 segregating individuals in the mapping population. Analysis of a collection of resistant and susceptible cultivars and experimental lines, of both Mesoamerican and Andean origin, revealed that: (1) recombination between OF10970 and the gene block has occurred as evidenced by the presence of the DNA fragment in several susceptible genotypes, (2) recombination between OI19460 and the gene block has also occurred indicating that the marker is not located within the gene block itself, and (3) marker-facilitated selection using these RAPD markers, and another previously identified, will enable gene pyramiding in Andean germplasm and certain Mesoamerican bean races in which the resistance gene block does not traditionally exist. Observations of variable recombination among Mesoamerican bean races suggested suppression of recombination between
Faleiro Fábio Gelape
Full Text Available Rust, caused by the fungus Uromyces appendiculatus, may cause a significant loss to common bean (Phaseolus vulgaris L. yield. RAPD markers tightly linked to the resistance genes may be used in breeding programs to aid the development of rust-resistant bean cultivars. In this sense, the objective of the present work was to identify RAPD markers linked to a rust resistance gene block present in the cultivar Ouro Negro. Two hundred and fourteen F2 individuals from a cross between the resistant cultivar Ouro Negro and the susceptible cultivar US Pinto 111 were inoculated with a mixture of eight races of U. appendiculatus. The segregation ratio obtained suggested that resistance is monogenic and dominant. Bulked segregant analysis was used in conjunction with the RAPD technique to search for markers linked to rust resistance genes. Two molecular markers flanking the rust resistance gene block were identified, one at 5.8 ± 1.6 cM (OX11(630 and the other at 7.7 ± 1.7 cM (OF10(1,050 of the gene. Simulated indirect selection efficiency in the F2 population using the two markers was 100%. The molecular markers identified in this work are currently being used for the selection of disease-resistant plants in the commom bean breeding program of the Federal University of Viçosa.
Genetic diversity can be measured by a number of ways, including pedigree, phenotype and allelic diversity at loci controlling phenotypes of interest. A DNA marker for root length in wheat (Triticum aestivum L.) was identified. The individual plants from F2 population segregation for salinity tolerance and the parents (S-24 ...
Full Text Available Genetic variability and identification of some molecular markers were studied in twenty promising lines of wheat using agronomic traits, ISSR (inter simple sequences repeats and RAPD (random amplified polymorphic DNA markers. Significant variation was evidenced in all agronomic traits. The lines proved to be superior to the check cultivar Sahel1 in yield and its component traits. Lines L2, L7 and L8 were the best in most yield component traits in both seasons. Moreover, Lines L2, L4, L5, L7 and L8 showed drought tolerance by which they displayed high performance in agronomic traits as well as a low drought susceptibility index. The percentage of polymorphism was 39.3% and 53.2% for ISSRs and RAPDs, respectively. UBC-881 belonged to penta-nucleotide repeat sequences (GGGTG that produced the highest level of polymorphism, while UBC-846 belonged to di-nucleotide repeat sequences (CA that produced the lowest level of polymorphism. Genetic similarities among wheat lines based on ISSR and RAPD markers ranged from 0.81 to 1.00 and from 0.86 to 0.98, respectively. There was a low average of PIC (polymorphism information content values which were 0.10 (ISSR and 0.15 (RAPD. The RAPD technique exhibited a higher marker index (MI = 0.69 compared to ISSR (MI = 0.43. There was insignificant correlation between ISSR and RAPD data (0.168, p > 0.05. There were two markers (UBC-881450bp and OPF-10540bp, on each of which two traits regressed significantly. The associated markers each explained a maximum regression of 18.92–34.95% of the total available variation for individual associated traits.
Ashwath, S K; Sreekumar, S; Toms, J T; Dandin, S B; Kamble, C K
Digestive amylase has been identified as a useful marker for breeding in the silkwrom, Bombyx mori L (Lepidoptera: Bombycidae), due to its wide genetic divergence, its role in better digestibility and robustness. The low yielding indigenous B. mori breeds of tropics like India are characterized by high activity amylase genes controlled by Amy d(iv) or d(v) alleles, while the high yielding breeds of temperate origin are endowed with 'null' type (Amy d(n)) with low activity. For improving the digestibility and survival of temperate breeds of Japanese origin, Near Isogenic Lines (NILs) were developed introgressing the Amy d(iv) and d(v) alleles from the Donor Parents (DPs) into the genetic background of the Recurrent Parents (RPs) with 'null' type of amylase, which showed significant improvement in viability of the NILs. With the objective to know whether the amylase gene itself may confer higher survival by improving digestibility or some other closely linked genes flanking the amylase locus is responsible for better viability of the NILs, RAPD profiles among six B. mori breeds comprising of the DPs, RPs, and NILs developed through introgression of Amy d(iv) or d(v) alleles were analysed using 27 sets of RAPD primers. Out of the 27 primers, six (OPA01, OPA06, OPA09, OPA15, OPAH03, and OPAH05) showed RAPD products linked to the amylase genes of the DPs introgressed in the NILs, which were absent in their respective RPs. Three amplicons of 1584 bp, 1904 bp, and 1232 bp were specific to Amy d(iv) allele and one amplified product of 1776 bp was found to be linked with the Amy d(v) allele. Interestingly, two PCR products of 2628 and 1375 bp were associated with both Amy d(iv) and d(v) alleles. The results are discussed in light of further characterization of these amplified products leading to identification of DNA sequences that may be responsible for better digestibility and higher survival in B. mori.
... the most effective method for disease control. The application of molecular markers is an efficient way to identify host resistance for breeding programs. In this study, bulked segregant analysis (BSA) was used to search for random amplified polymorphic DNA (RAPD) markers linked to the late blight resistance gene Ph-3, ...
Tullu, A; Buchwaldt, L; Warkentin, T; Taran, B; Vandenberg, A
Anthracnose, caused by Colletotrichum truncatum, is a major disease problem and production constraint of lentil in North America. The research was conducted to examine the resistance to anthracnose in PI 320937 lentil and to identify molecular markers linked to the resistance gene in a recombinant inbred line (RIL) population developed from a cross of Eston lentil, the susceptible parent, and PI 320937, the resistant parent. A total of 147 F(5:6) RILs were evaluated for resistance to anthracnose in the greenhouse using isolate 95B36 of C. truncatum. Bulked segregant analysis (BSA) strategy was employed and two contrasting DNA bulks were constructed based on greenhouse inoculation of F(5)-derived F(6) RILs. DNA from the parents and bulks were screened with 700 RAPD primers and seven AFLP primer combinations. Analysis of segregation data indicated that a major dominant gene was responsible for resistance to anthracnose while variations in the resistance level among RILs could be the influences of minor genes. We designate the major gene as LCt-2. MapMaker analysis produced two flanking RAPD markers OPEO6(1250) and UBC-704(700) linked to LCt-2 locus in repulsion (6.4 cM) and in coupling (10.5 cM), respectively. Also, three AFLP markers, EMCTTACA(350) and EMCTTAGG(375) in coupling, and EMCTAAAG(175) in repulsion, were linked to the LCt-2 locus. These markers could be used to tag the LCt-2 locus and facilitate marker-assisted selection for resistance to anthracnose in segregating populations of lentil in which PI 320937 was used as the source of resistance. Also, a broader application of the linked RAPD markers was also demonstrated in Indianhead lentil, widely used as a source of resistance to anthracnose in the breeding program at the Crop Development Centre, University of Saskatchewan. Further selection within the few F(5:6) lines should be effective in pyramiding one or several of the minor genes into the working germplasm of lentil, resulting in a more durable and
RAPD) methods were used to analyze F2 individuals of 82-3041 × Yunyan 84 to screen and characterize the molecular marker linked to brown-spot resistant gene. A total of 800 arbitrary decamer oligonucleotide primers were used for RAPD ...
RAPD markers demonstrate genetic diversity in Pterocarpus angolensis from Zimbabwe and Zambia. E Chisha-Kasumu, S Woodward, A Price. Abstract. Understanding the availability, extent and apportionment of genetic variability in natural populations of the southern African savanna tree Pterocarpus angolensis can ...
Jun 29, 2011 ... between the studied provenances were less than 39%. Key words: Acacia Senegal, provenance variation, random amplified polymorphic DNA (RAPD) marker, salt tolerance, seed germination, seedling growth. INTRODUCTION. Salinity is the major factor limiting plants growth, widely spread and has more ...
Jun 29, 2011 ... bands detected were polymorphic for the provenances of A. senegal and the dissimilarity indices between the studied provenances were less than 39%. Key words: Acacia Senegal, provenance variation, random amplified polymorphic DNA (RAPD) marker, salt tolerance, seed germination, seedling growth ...
Jun 11, 2014 ... The random amplified polymorphic DNA (RAPD) technique has been widely applied to identify different varieties of plants for molecular breeding. However, application of RAPD markers to identify parthenogenesis in plants has not been reported. In this investigation, we used pedigree and RAPD markers ...
The random amplified polymorphic DNA (RAPD) technique has been widely applied to identify different varieties of plants for molecular breeding. However, application of RAPD markers to identify parthenogenesis in plants has not been reported. In this investigation, we used pedigree and RAPD markers to differentiate ...
Analogy of ISSR and RAPD markers for comparative analysis of genetic diversity among different Jatropha curcas genotypes. S Gupta, M Srivastava, GP Mishra, PK Naik, RS Chauhan, SK Tiwari, M Kumar, R Singh ...
Oct 16, 2013 ... 1Indian Agricultural Research Institute- Regional Station, Kalimpong, West Bengal, India- 734 301. 2Central Agricultural Research Institute, Port .... List of selected informative RAPD primers, their sequence and some information about generated bands in this study. DNA marker. Marker sequence. (5' to 3').
Gupta, Mamta; Verma, Bhawna; Kumar, Naresh; Chahota, Rakesh K; Rathour, Rajeev; Sharma, Shyam K; Bhatia, Sabhyata; Sharma, Tilak R
Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n = 2x = 14), cool-season legume crop and is consumed worldwide as a rich source of protein (~24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F(2) plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.
Oliveira Roberto Pedroso de
Full Text Available The objective of this work was to evaluate the processes of selection in a citrus hybrid population using segregation analysis of RAPD markers. The segregation of 123 RAPD markers between 'Cravo' mandarin (Citrus reticulata Blanco and 'Pêra' sweet orange (C. sinensis (L. Osbeck was analysed in a F1 progeny of 94 hybrids. Genetic composition, diversity, heterozygosity, differences in chromosomal structure and the presence of deleterious recessive genes are discussed based on the segregation ratios obtained. A high percentage of markers had a skeweness of the 1:1 expected segregation ratio in the F1 population. Many markers showed a 3:1 segregation ratio in both varieties and 1:3 in 'Pêra' sweet orange, probably due to directional selection processes. The distribution analysis of the frequencies of the segregant markers in a hybrid population is a simple method which allows a better understanding of the genetics of citrus group.
Dec 3, 2008 ... (PCR) technology has offered new marker systems for diagnosis of genetic diversity in large scale studies (Saiki et al., 1988). Over the last 15 years, polymerase chain reaction technology has led to the development of two simple and quick techniques called random amplified polymorphic DNA (RAPD) and ...
Hongwen Huang; Desmond R. Layne; Thomas L. Kubisiak
Thirty-four extant pawpaw [Asimina triloba (L.) Dunal] cultivars and advanced selections representing a large portion of the gene pool of cultivated pawpaws were investigated using 71 randomly amplified polymorphic DNA (RAPD) markers to establish genetic identities and evaluate genetic relatedness. All 34 cultivated pawpaws were uniquely...
Mar 8, 2010 ... The experimental material consisted of two parents Gurjari (white backed plant hopper resistant) and. Jaya (white backed plant hopper susceptible) and their F2 progeny. The purpose of the study was the identification of RAPD (Random Amplified Polymorphic DNA) marker for white backed plant hopper.
The present study evaluated genetic variability of superior bael genotypes collected from different parts of Andaman Islands, India using fruit characters and random amplified polymorphic DNA (RAPD) markers. Genomic DNA extracted from leaf material using cetyl trimethyl ammonium bromide (CTAB) method was ...
Conclusions: This study developed stable SCAR markers for the identification of L. chinensis by the cloning of the improved RAPD fragments. Combining RAPD and SCAR markers provides a simple and reliable tool for the genetic characterization of plant species.
Haley, S D; Afanador, L K; Miklas, P N; Stavely, J R; Kelly, J D
The development and use of RAPD markers for applications in crop improvement has recently generated considerable interest within the plant breeding community. One potential application of RAPDs is their use for "tagging" simply-inherited (monogenic) pest-resistance genes and enabling more efficient identification and selection of genotypes carrying specific combinations of resistance genes. In this report, we propose and describe the use of heterogeneous inbred populations as sources of near-isogenic lines (NILs) for targeting RAPD markers linked to major pest resistance genes. The development of these NILs for RAPD marker analyses involved a sequence of line and mass selection during successive generations of inbreeding. DNA bulks derived from the NILs were used to identify a RAPD marker (designated OK14620, generated by 5'-CCCGCTACAC-3' decamer) that was tightly linked (2.23±1.33 centiMorgans) to an important rust [Uromyces appendiculatus (Pers.) Unger var. appendiculatus] resistance gene (Ur-3) in common bean (Phaseolus vulgaris L.). The efficiency of this approach was demonstrated by a low rate of false-positives identified, the tightness of the linkage identified, and the ability to detect polymorphism between genomic regions that are representative of the same gene pool of common bean. This method of deriving NILs should find application by researchers interested in utilizing marker-assisted selection for one or more major pest resistance genes. The identification of OK14620 should help to facilitate continued use of the Ur-3 resistance source and will now enable marker-assisted pyramiding of three different bean rust resistance sources (two previously tagged) to provide effective and stable resistance to this important pathogen.
Johnson, E; Miklas, P N; Stavely, J R; Martinez-Cruzado, J C
The Guatemalan black bean (Phaseolus vulgaris L.) plant introduction (PI) 181996 is resistant to all known US races of the bean rust fungus Uromyces appendiculatus (Pers. ex Pers.) Unger var. appendiculatus [syn. U. phaseoli (Reben) Wint.]. We report on two random amplified polymorphic DNA (RAPD) markers OAC20490 tightly linked (no recombinants) in coupling phase and OAE19890 linked in repulsion phase (at 6.2±2.8 cM) to PI 181996 rust resistance. These RAPDs, generated by single decamer primers in the polymerase chain reaction, were identified in near-isogenic bulks of non-segregating resistant and susceptible BC4F2 (NX-040*4/PI 181996) lines. Linkage of the RAPD markers was confirmed by screening 19 BC4F2 and 57 BC4F3 individuals segregating for PI 181996 resistance. Utility of the RAPDs OAC20490 and OAE19890 was investigated in a diverse group of common bean cultivars and lines. All cultivars into which the PI 181996 resistance was introgressed had the RAPD OAC20490. A RAPD similar in size to OAC20490, observed in some susceptible common bean lines, was confirmed by Southern blotting to be homologous to the RAPD OAC20490. Use of the RAPDs OAC20490 and OAE19890 in marker-assisted selection (MAS) is proposed. The coupling-phase RAPD is most useful for MAS of resistant BCnF1individuals during traditional backcross breeding. The repulsion-phase RAPD has greatest utility in MAS of homozygous-resistant individuals in F2 or later-segregating generations.
A strong correlation was observed between morphology and molecular marker systems. Identification of specific markers to wild as well as cultivated accessions is yet another important finding in the present study. Such genetic diversity is useful in facilitating the development of large number of new varieties through ...
Oct 26, 2011 ... PCO generated using UPGMA (3D view). et al., 2003). A high degree of correlation between marker systems has also been reported in wheat and safflower (Bohn et al., 1999). However, Powell et al. (1996) observed little correlation between various marker systems in soybean. The incongruity between ...
A bulked segregant analysis was performed using 184 random amplified polymorphic DNA (RAPD) primers in an F1 population of P. maximum segregating for reproductive mode. Four RAPD markers linked to apomixis were identified and mapped in this population. These markers showed good selection efficiency, ranging ...
The genetic relationships among ten types of endod (Phytolacca dodecandra) cultivated by the Institute of Pathobiology of the Addis Ababa University to combat the disease bilharzia in Ethiopia were studied using morphology and molecular markers. A total of 18 morphological characters, 194 amplified fragment length polymorphism (AFLP) and 42 random amplified polymorphic DNA (RAPD) markers were used to determine genetic proximity between types. Genetic distance and cluster analysis of the AFLP data revealed the lack of genetic difference between E47 and E48 but relatively wider genetic difference among the other endod types. Cluster and principal component analyses performed on the AFLP and RAPD markers demonstrated the presence of distinct separation of E56 but not that of E44 from the others. The AFLP and RAPD data, thcrefore, did not support the hypothesis that the superiority of E44 in agronomic traits and molluscicidal potency is linked to its distinct genetic difference from the other endod types. Matrices correspondence tests demonstrated the presence of greater correspondence between AFLP and RAPD data (r = 0.842) but not between the morphology and that of AFLP and RAPD. This indicates the correspondence more between the two DNA markers systems than either of them with morphological traits. The cophenetic correlation coefficients also revealed poor fit for morphology (r = 0.716), good fit for RAPD (r = 0.872) and very good fit for AFLP (r = 0.975), reflecting the hyper-variability and higher resolving power of AFLP.
Sep 11, 2013 ... column of individual fish with the aid of hypodermal needle. The drawn blood were ... Abbreviations: RAPD-DNA, Random amplified polymorphic deoxyribonucleic acid-polymerase chain reaction; PIC, polymorphic information content; RMS ..... lignin degrading Bacteria from the soil. J. Appl. Sci. Res.
Aug 18, 2009 ... Full Length Research Paper. Differentiation of Lactobacillus-probiotic strains by ... Key words: Lactobacillus, RAPD analysis, differentiation. INTRODUCTION. The random amplified polymorphic DNA ..... co-efficient, follow by cluster analysis of the pairwise distance matrix among molecular profiles using the ...
Sharma, Shubhangi; Kumar, Pankaj; Gambhir, Geetika; Kumar, Ramesh; Srivastava, D K
The importance of germplasm characterization is an important link between the conservation and utilization of plant genetic resources in various breeding programmes. In the present study, genetic variability and relationships among 25 Lactuca sativa L. genotypes were tested using random amplified polymorphic DNA (RAPD) molecular markers. A total of 45 random decamer oligonucleotide primers were examined to generate RAPD profiles, out of these reproducible patterns were obtained with 22 primers. A total of 87 amplicon were obtained, out of which all were polymorphic and 7 were unique bands. The level of polymorphism across genotypes was 100% as revealed by RAPD. Genetic similarity matrix, based on Jaccard's coefficients ranged from 13.7 to 84.10% indicating a wide genetic base. Dendrogram was constructed by unweighted pair group method with arithmetic averages method. RAPD technology could be useful for identification of different accessions as well as assessing the genetic similarity among different genotypes of lettuce. The study reveals the limited genetic base and the needs to diversify using new sources from the germplasm.
Faria, V V; Rolim, L S; Vaz, L A L; Furtado-Neto, M A A
We investigated a reported case of stingray Dasyatis americana misidentification not detected in a published study using the random amplified polymorphic DNA (RAPD) technique. If the referred specimen (landed by fisheries in Ceará, northeastern Brazil) was misidentified (as Dasyatis centroura) in the field, why did its RAPD data fail to clarify the mistake? Was it due to limitations of RAPD markers or perhaps to a taxonomic issue? Contrary to our initial expectations, neither of these hindered the detection of the misidentification. After reanalyzing the primary genetic data associated with the misidentified specimen (PCR gel photographs and/or matrices of presence/absence of markers for six RAPD primers), we found that the RAPD markers were sufficient to correctly assign the misidentified specimen to its proper species identity. In the original study, the specimen misidentification was neither noticed by the authors nor apparent in the published article due to how their results were interpreted and presented.
Furman, Burford J.; Grattapaglia, Dario; Dvorak, William S.; O'Malley, David M.
Phylogenetic relationships were inferred for six Central American and Mexican pine species by analysing RAPD marker differences among pooled DNA samples. This population level pooling strategy discounts low-frequency allelic variation within taxa, thus obtaining a ‘cumulative genotype’ to compare among taxa. We used the morphologically based taxonomy of pines as the basis for inference concerning molecular marker divergence. Only RAPD polymorphisms that were repeatable and inte...
PARJANTO; SUPRIYADI; ISMI PUJI RUWAIDA
Ruwaida IP, Supriyadi, Parjanto. 2009. Variability analysis of Sukun durian plant (Durio zibethinus) based on RAPD marker. Nusantara Bioscience 1: 84-91.The purpose of the study is to assess the diversity of the durian varieties of Sukun, Sunan, Kani, Monthong, and Petruk; and Sukun durian variety grown in different regions based on RAPD markers. Materials research is durian leaves of Sukun, Sunan, Kani, Monthong and Petruk from Ranukutri Garden Seeds, Karanganyar, and also Sukun durian leaf ...
The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. Information on genetic diversity and relationships among rice landraces from Bangladesh is currently very limited. Thirty-five rice genotypes including 33 landraces and 01 HYV of Bangladesh and 1 Indian landrace of particular interest to breeding programs were evaluated by means of random amplified polymorphic DNA (RAPD) technique. For molecular characterization, RAPD markers viz., OPC 03...
Wangsomnuk, P P; Khampa, S; Wangsomnuk, P; Jogloy, S; Mornkham, T; Ruttawat, B; Patanothai, A; Fu, Y B
Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement.
Apr 3, 2008 ... 5′-GAC AGG CCA A-3′. RAPD. 8. 650. 5′-AGT ATG CAG C-3′. RAPD. 9. The alleles of identified QTLs of studied traits trans- mitted to F2 plants and F3 families are from both parents based on their negative and positive additive effects. All of identified QTLs had small additive effects and other.
Luciana do Valle Rego Oliveira; Ricardo Tadeu de Faria; Claudete de Fátima Ruas; Paulo Maurício Ruas; Melissa de Oliveira Santos; Carvalho,Valdemar P.
In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95%) were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intra...
Rafael Gustavo Ferreira Morales
Full Text Available Most strawberry (Fragaria × ananassa Duchesne cultivars used in Brazil are developed in other countries, it became clear the need to start the strawberry breeding program in the country. To start a breeding program is necessary the genetic characterization of the germplasm available. Molecular markers are important tools that can be used for this purpose. The objectives of the present study were to assess the genetic similarity among 11 strawberry cultivars using RAPD and ISSR molecular markers and to indicate the possible promising crosses. The DNA of the eleven strawberry cultivars was extracted and amplified by PCR with RAPD and ISSR primers. The DNA fragments were separated in agarose gel for the RAPD markers and in polyacrylamide gel for the ISSR markers. The genetic similarity matrix was estimated by the Jaccard coefficient. Based on this matrix, the cultivars were grouped using the UPGMA method. The dendogram generated by the RAPD markers distributed the cultivars in three groups while the ISSR markers generated two groups. There was no direct relationship between the marker groups when the two types of markers were compared. The grouping proposed by the ISSR markers was more coherent with the origin and the genealogy of the cultivars than that proposed by the RAPD markers, and it can be considered the most efficient method for the study of genetic divergence in strawberry. The most promising crosses, based on the genetic divergence estimated from the RAPD and ISSR molecular data were between the Tudla and Ventana and the Oso Grande and Ventana cultivars, respectively.
Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A
The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.
Patel, Hardik K; Fougat, Ranbir S; Kumar, Sushil; Mistry, Jigar G; Kumar, Mukesh
There is a lack of information on the molecular characterization of Ocimum species and hence, efforts have been made under the present study to characterize 17 Ocimum genotypes belonging to 5 different species (O. basilicum, O. americanum, O. sanctum, O. gratissimum and O. Polystachyon) through random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers. PCR amplification using 20 RAPD primers generated a total of 506 loci, of which 490 (96.47 %) loci were found polymorphic. The PIC value for RAPD ranged from 0.907 (OPF 14) to 0.954 (OPC 11) with an average of 0.937. The ISSR primers generated a total of 238 loci, of them 234 (98.17 %) loci were polymorphic. The PIC value ranged from 0.892 (UBC 808) to 0.943 (ISSR A12) with an average of 0.923. The average Jaccard's similarity coefficient based on RAPD and ISSR analysis was 0.58 and 0.52, respectively. Clustering pattern of dendrogram generated using the pooled RAPD and ISSR data showed all Ocimum genotypes in their respective species groups at a cutoff value of 0.49 and 0.42, respectively. Many unique species-specific alleles were amplified by RAPD and ISSR markers. In both marker systems, a maximum number of unique alleles were observed in O. sanctum. The results of the present investigation provided valid guidelines for collection, conservation and characterization of Ocimum genetic resources.
Full Text Available Olive (Olea europea L. is one of the oldest cultivated plants characteristic in the Mediterranean area, where it is the most important oilproducing crop. The cultivated olive (O. europaea L. var. europaea is propagated by cutting or grafting, whereas wild olive (O. europaea L. var. sylvestris is reproduced from seeds. These two olive types are interfertile and have led to a large number of varieties. Morphological descriptions are not entirely reliable, due to numerous synonyms and homonyms in designations, labelling mistakes, the presence of varietal clones, and the uncertain identification methods thus far applied. Molecular markers, as random amplified polymorphic DNA (RAPD markers, are environment-independent and efficient to identify olive varieties and to detect synonymous and homonymous. In this study, fifteen selected RAPD markers are used for determination of relationships among twenty individuals belonging to four important Turkish olive cultivars. Our results showed that RAPD markers can be used to differentiate olive cultivars
Desai, Parth; Gajera, Bhavesh; Mankad, Mounil; Shah, Shikha; Patel, Armi; Patil, Ghanshyam; Narayanan, Subhash; Kumar, Nitish
Bamboo is one of the important plant for pulp, paper and charcoal industries. After China, India is the second largest bamboo reserve in Asia. Around the globe, wide genetic diversity of bamboo is present which serves as the base for selection and improvement. DNA based molecular markers appears to be a striking substitute for systematic assessment of the genetic diversity in conservation and genetic improvement of plants. DNA based molecular markers such as RAPD and ISSR were used to assess the genetic diversity in 13 bamboo genotypes. Total 120 RAPD and 63 ISSR primers were tested, of which only 42 polymorphic primers (30 RAPD and 12 ISSR), gave reproducible amplification profile and were used in this study. 30 RAPD primers yielded total 645 amplified fragments, of which 623 were polymorphic, and 20.76 polymorphic bands per primer were observed across 13 genotypes. 12 ISSR primers produced 246 amplified fragments, of which 241 were polymorphic, and 20.08 polymorphic bands per primer was observed across 13 different genotypes. The Jaccard's coefficient of RAPD, ISSR and pooled RAPD and ISSR dendrograms ranged from 0.26 to 0.83, 0.23 to 0.86 and 0.26 to 0.84 respectively. The present study found the large genetic diversity present between different elite genotypes of bamboo. Such investigation can deliver a well understanding of the available genotypes, which might be further exploited for the paper industry.
In this study, we report the use of random amplified polymorphic DNA (RAPD) to determine genetic relationships in the genus Crataegus. Five species, including Crataegus monogyna, Crataegus meyeri, Crataegus aronia, Crataegus pentagyna and Crataegus pontica were chosen from northwest forests of Iran and ...
Adrise Medeiros Nunes
Full Text Available O grupo botânico Arecaceae é de extremo interesse por compreender plantas em extinção e por apresentar um grande potencial de exploração econômica. O butiazeiro (Butia capitata (Mart. Becc. ocorre naturalmente no Sul do Brasil. Sua caracterização molecular é de extremo interesse para futuros trabalhos de melhoramento genético. Assim sendo, verificou-se a variabilidade genética existente entre vinte e dois genótipos de butiazeiro da espécie (Butia capitata, pertencentes ao BAG (Banco Ativo de Germoplasma de frutíferas nativas do Centro Agropecuário da Palma - UFPel. Esses genótipos foram analisados usando marcadores do tipo RAPD (Random Amplified Polymorphic DNA. Um total de 136 fragmentos foram obtidos, sendo 77 polimórficos. O primer OPA11 apresentou maior polimorfismo, produzindo 9 perfis diferentes. A análise de agrupamento, realizada pelo método UPGMA, produziu um dendrograma que permitiu a clara separação dos genótipos em dois grupos principais. Verificou-se que, com a técnica de marcadores de RAPD, foi possível obter um perfil molecular único e uma estimativa da variabilidade existente entre os genótipos de butiazeiro avaliados.The study of the botanical group Arecaceae is of extreme interest for evolving several endangered species of plants and for presenting a great potential of economical exploration. The Pindo palm (or wine palm, jelly palm (Butia capitata (Mart. Becc. is natural from the south of Brazil. Its molecular characterization is of extreme interest for future researches of genetic improvement. Since little is known about the variability of the species, the existent genetic variability was verified among twenty-two genotypes of Pindo palm (or wine palm, jelly palm, from BAG (Germoplasm Assets Bank of fruit trees native from the Agricultural Center of the Palma - UFPEL, which were analyzed using markers RAPD (Random Amplified Polymorphic DNA with Operon Technologies' decamers primers. With 21 primers
del Piano L
Full Text Available At present there is no information about the level of genetic variability in N. tabacum and in the Nicotiana genus as revealed by random amplified polymorphic DNA (RAPD. Such knowledge could be useful for taxonomic and breeding purposes. The aim of this paper is to assess the potential application of the DNA polymorphisms generated by RAPD markers within this genus and in tobacco. As rigorously standardized reaction conditions are required to obtain a reproducible RAPD marker, four rapid DNA extraction methods were compared and several parameters of the reaction conditions for the random polymorphic DNA amplification were analysed and optimized. The DNA of six-week-old leaves of N. tabacum var. Samsun was obtained with the following methods differing in the strategy of purification: the cetyltrimethylammonium bromide (CTAB method, that of Edwards, nucleon phytopure system and the method of Goring. Reproducible amplification profiles were obtained with all the methods except for Edwards'. As regards amplification conditions, the effects of primer-template annealing temperature, of a final extension step, of the number of cycles and of the length of extension time in each cycle were analysed. Moreover, the effects on amplification reaction of the DNA amount, of MgCl2, primer and deoxynucleotide triphosphate (dNTP concentration were evaluated. Then DNA of 12 Nicotiana species and Nicotianatabacum was amplified with primers OPA-01 and OPA-13 which revealed a considerable polymorphism. The same primers used to analyse 36 var. of N. tabacum belonging to different types, showed identical amplification profiles. Further amplification experiments were carried out with only 12 of the tobacco lines; three primers among the 12 assayed revealed one polymorphic fragment each.
Quintela-Sabaris, C.; Fraga, M.I. [Dept. of Botany, Univ. of Santiago de Compostela (Spain); Kidd, P.S. [Dept. of Soil Science and Chemical Agronomy, Univ. of Santiago de Compostela (Spain)
The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel's test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures. (orig.)
Quintela-Sabarís, Celestino; Kidd, Petra S; Fraga, María Isabel
The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel's test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures.
Full Text Available RAPD markers were used to investigate the genetic diversity of 31 Brazilian cassava clones. The results were compared with the genetic diversity revealed by botanical descriptors. Both sets of variates revealed identical relationships among the cultivars. Multivariate analysis of genetic similarities placed genotypes destinated for consumption "in nature" in one group, and cultivars useful for flour production in another. Brazil?s abundance of landraces presents a broad dispersion and is consequently an important resource of genetic variability. The botanical descriptors were not able to differentiate thirteen pairs of cultivars compared two-by-two, while only one was not differentiated by RAPD markers. These results showed the power of RAPD markers over botanical descriptors in studying genetic diversity, identifying duplicates, as well as validating, or improving a core collection. The latter is particularly important in this vegetatively propagated crop.
Full Text Available Abstract Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species. Results RAPD analysis using 19 random primers generated 128 discrete markers ranging from 500–3000 bp in size. One-hundred-nineteen of these were polymorphic (92%, with an average of 6.26 markers per primer. Among these were a few putative species-specific amplification products which could be useful for germplasm classification and introgression studies. The ISSR analysis employed six anchored primers, 4 of which generated 93 polymorphic markers with an average of 23.25 markers per primer. Cluster analysis of RAPD and ISSR data using the WINBOOT package to calculate the Dice coefficient resulted into two clusters, one comprising polyploid wild species and the other with domesticated (mostly diploid species. Conclusion These results suggest that RAPD and ISSR markers are useful for mulberry genetic diversity analysis and germplasm characterization, and that putative species-specific markers may be obtained which can be converted to SCARs after further studies.
Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj
The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.
Leal, A A; Mangolin, C A; do Amaral, A T; Gonçalves, L S A; Scapim, C A; Mott, A S; Eloi, I B O; Cordovés, V; da Silva, M F P
Using only one type of marker to quantify genetic diversity generates results that have been questioned in terms of reliability, when compared to the combined use of different markers. To compare the efficiency of the use of single versus multiple markers, we quantified genetic diversity among 10 S(7) inbred popcorn lines using both RAPD and SSR markers, and we evaluated how well these two types of markers discriminated the popcorn genotypes. These popcorn genotypes: "Yellow Pearl Popcorn" (P1-1 and P1-5), "Zélia" (P1-2 and P1-4), "Curagua" (P1-3), "IAC 112" (P9-1 and P9-2), "Avati Pichinga" (P9-3 and P9-5), and "Pisankalla" (P9-4) have different soil and climate adaptations. Using RAPD marker analysis, each primer yielded bands of variable intensities that were easily detected, as well as non-specific bands, which were discarded from the analysis. The nine primers used yielded 126 bands, of which 104 were classified as polymorphic, giving an average of 11.6 polymorphisms per primer. Using SSR procedures, the number of alleles per locus ranged from two to five, giving a total of 47 alleles for the 14 SSR loci. When comparing the groups formed using SSR and RAPD markers, there were similarities in the combinations of genotypes from the same genealogy. Correlation between genetic distances obtained through RAPD and SSR markers was relatively high (0.5453), indicating that both techniques are efficient for evaluating genetic diversity in the genotypes of popcorn that we evaluated, though RAPDs yielded more polymorphisms.
YUYU SURYASARI POERBA
Full Text Available Poerba YS, Ahmad F (2010 Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers. Biodiversitas 11: 118-123. This study was done to assess the molecular diversity of 36 accessions (18 cultivars of the plantain and cooking bananas (Musa acuminata x M. balbisiana, AAB, ABB subgroups based on Random amplified polymorphic DNA (RAPD and and Inter Simple Sequence Repeats (ISSR markers and to determine genetic relationships in the bananas. RAPD and ISSR fingerprinting of these banana varieties was carried out by five primers of RAPDs and two primers of ISSRs. RAPD primers produced 63 amplified fragments varying from 250 to 2500 bp in size. 96.82% of the amplification bands were polymorphic. ISSR primers produced 26 amplified fragments varying from 350 bp to 2000 bp in size. The results showed that 92.86% of the amplification bands were polymorphic. The range of genetic distance of 18 cultivars was from 0.06-0.67.
Al-Khalifah, Nasser S; Shanavaskhan, A E
Ambiguity in the total number of date palm cultivars across the world is pointing toward the necessity for an enumerative study using standard morphological and molecular markers. Among molecular markers, DNA markers are more suitable and ubiquitous to most applications. They are highly polymorphic in nature, frequently occurring in genomes, easy to access, and highly reproducible. Various molecular markers such as restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) markers have been successfully used as efficient tools for analysis of genetic variation in date palm. This chapter explains a stepwise protocol for extracting total genomic DNA from date palm leaves. A user-friendly protocol for RAPD analysis and a table showing the primers used in different molecular techniques that produce polymorphisms in date palm are also provided.
Based on the RAPD markers used in this study, it can be concluded that genetic distance between susceptible and resistant S. nodiflora is higher than that within susceptible samples supporting our previous morphological and protein data, although genetic variation among susceptible individuals seems to be significantly high.
Full Text Available Studies on plants show that populations growing on the stressful environments indicate higher levels of genetic diversity, and that in outcrossing species majority of total genetic variation allocated to within population rather than between populations. We compared the level of genetic variation between populations growing in stressful and normal environments, and measured levels of within- and between population genetic variations in Onobrychis viciifolia L. (Sainfoin, Fabaceae based on RAPDs. Our results show that populations growing on he stressful environment i.e. saline soils indicated either the lowest 0.2466 or highest (0.3186 within-population genetic variation based on Nei’s diversity. That disagrees with Niche-Width Variation Theory, which expects highest genetic diversity within stressful populations. Partitioning the total genetic variation by analysis of molecular variance (AMOVA showed that 89.03% of total genetic diversity allocated to within populations while 10.97% of this variation dedicated to among populations, indicating predominantly outcrossing mode of pollination in sainfoin. The two population pairs growing under similar environmental stresses (cold climate and saline soil showed higher genetic similarity. This may suggest that RAPDs patterns reflex selection rather than random drift.
Arik Arubil Fatinah
Full Text Available Genera of amaranth family tend to have phenotypic variation partly caused by environmental factor. Phenotypic variation was the result of interaction between genetic and environmental factors. One of molecular markers that is widely used for detecting genetic variation is RAPD. RAPD is used for polymorphism detections and is now possible for identifiying a large number of loci and ascribes unambiguous taxonomic and genetic relationships among different taxa. Members of amaranth family found in Indonesia are Amaranthus, Celosia, Aerva, Alternanthera, Achyranthes, Gomphrena, Salsola, and Iresine. Six genera of which (Amaranthus, Celosia, Aerva, Alternanthera, Achyranthes, and Gomphrena were observed in this study. DNA was extracted from fresh young leaves using Doyle and Doyle’s method with modification in the extraction buffer used. RAPD analyses were carried out with 20 decamer primers from Kit A of Operon Technology. DNA was amplified using master cycler gradient Eppendorf with 35 cycles. RAPD products were separated on 1,5 % agarose gels and detected by staining with ethidium bromide. There were 374 bands generated in 18 random primers. The number of monomorphic bands, polymorphic bands, and the percentage of polymorphism were 21 bands, 353 bands, and 94,38 % respectively. The high number and percentage of polymorphic bands revealed genomic DNA variation. This variation is in accordance with phenotypic variation detected in this experiment. Therefore, it can be concluded that, based on DNA polymorphism detected by RAPD, Amaranth family can be classified into two sub families namely Amaranthoideae and Gomphrenoideae.
Full Text Available Knowledge of maize germplasm genetic diversity is important for planning breeding programmes, germplasm conservation per se etc. Genetic variability of maize hybrids grown in the fields is also very important because genetic uniformity implies risks of genetic vulnerability to stress factors and can cause great losts in yield. Early maturing maize hybrids are characterized by shorter vegetation period and they are grown in areas with shorter vegetation season. Because of different climatic conditions in these areas lines and hybrids are developed with different features in respect to drought resistance and disease resistance. The objective of our study was to characterize set of early maturing maize hybrids with protein and RAPD markers and to compare this clasification with their pedigree information. RAPD markers gave significantly higher rate of polymorphism than protein markers. Better corelation was found among pedigree information and protein markers.
Full Text Available Persian walnut (Juglans regia L. belongs to the family Juglandaceae is one of the most important nut crops in Iran. In this research, morphometric and genetic variations among some genotypes of Persian walnut collected from different parts of west Iran were evaluated based on nut characteristics and RAPD markers. In the first experiment, 29 traits related to nut and kernel were used to evaluate genetic potential of 119 walnut genotypes. The primary results of fruit morphometric characteristics showed that there is high variability in the some evaluated traits such as fruit shape, nut diameter and Kernel removal from nut in studied genotypes. Also, in the second experiment, the genetic diversity among 50 genotypes of walnut was evaluated using 13 RAPD markers. A total of 87 alleles were produced in the 13 RAPD markers with their sizes ranging from 140 to 2500 bp. The number of observed alleles for each locus ranged from 4 (OPA-18 and OPA-13 to 11 (OPA-09, with an average of 6.46 alleles per locus. Shannon's information index (I value was observed to be highest (3.20 in the OPA-09 locus, while the OPA-13 locus had the lowest value (0.70 with an average of 1.66 among RAPD locus. The Jaccards’ genetic similarity coefficient ranged from 0.08 to 0.79 among genotypes. Finally, our results demonstrate some of these genotypes have been desirable traits and must be conserved as valuable genetic resources, from the perspective of breeding.
Bianca W. Bertoni
Full Text Available Jacaranda decurrens (Bignoniaceae is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD and amplified fragment length polymorphism (AFLP. Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2% polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA and Pearson's correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006 between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.
Zhao, Ya-E; Wu, Li-Ping
For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.
Marcelo Marchi Costa
Full Text Available Os objetivos deste trabalho foram confirmar a herança da resistência da PI 459025 (Rpp4 à ferrugem-asiática-da-soja e identificar marcadores moleculares do tipo RAPD, ligados a este gene de resistência, em populações de soja. Pelo cruzamento dos genitores contrastantes PI 459025 x Coodetec 208 obteve-se uma população, cujas populações das gerações F2 e F2:3 foram artificialmente infectadas e avaliadas quanto à reação ao fungo Phakopsora pachyrhizi, pelo tipo de lesão (RB - resistente e TAN - suscetível. Com os resultados da avaliação fenotípica, dois "bulks" foram obtidos com DNA de plantas homozigóticas resistentes e suscetíveis, respectivamente, pela análise de "bulks" segregantes. De 600 iniciadores RAPD aleatórios, foram identificados três com fragmentos polimórficos entre os "bulks" e parentais contrastantes quanto à resistência. Pela análise do qui-quadrado, confirmaram-se: a herança monogênica, com dominância completa quanto à resistência ao patógeno, e a segregação 3:1 para a presença de banda dos três marcadores. Os três marcadores são ligados respectivamente a 5,1, 6,3 e 14,7 cM de distância do loco de resistência, em fase de repulsão no grupo de ligação G, o que foi confirmado pela utilização do marcador microssatélite Satt288. Estes marcadores são promissores na seleção assistida para resistência à ferrugem-asiática-da-soja.The objectives of this work were to confirm the PI 459025 inheritance of resistance (Rpp4 to Asian soybean rust pathogen and to detect RAPD markers linked to this resistance gene in soybean populations. Through the cross of the distint parental lines PI 459025 x Coodetec 208, a population was obtained, whose F2 and F2:3 generations had their populations artificially infected and evaluated for the reaction to Phakopsora pachyrhizi, by lesion type classification (RB - resistant and TAN - susceptible. Using the phenotypic results, the bulked segregant analysis
Jin, Xiaofeng; Ding, Bingyang; Gao, Shuqin; Jiang, Weimei
Applying randomly amplified polymorphic DNA (RAPD), the genetic variation of Cabomba caroliniana Gray (cabomba or fanwort), a new alien plant in China, was analyzed in this paper. Total 143 bands, including 47 polymorphic bands, were amplified from 23 primers in 20 samples. The sampling distance was large, but its genetic diversity was low. The main results were that: (1) Cabomba, which grew and dispersed mainly in fragment, was an abundant and dominant species in freshwater, and its main dispersal mechanism was vegetative reproduction (2) Cabomba was originally introduced into China as an aquarium submerged plant. Somehow, those discarded cabomba became invasive species in the areas of Hangzhou, Shanghai, and Meicheng, and other places. (3) Although the level of genetic diversity in cabomba was low, their rapid dispersion and propagation could seriously harm to local aquatic community. Therefore, specific measure should be used to control cabomba from uncontrolled spreading and damage to local vegetation communities.
Full Text Available Modern agriculture, breeding procedures, as well as competition among breeding institutions contribute to further reduction of already narrowed diversity of soybean commercial varieties. The objective of the study was to characterize eighteen soybean cultivars from three different breeding programs for agro-morphological traits and to reveal genetic diversity using molecular markers. Morphological description was performed with 13 qualitative and 9 quantitative traits. The genetic relationships were estimated using 21 RAPD markers. PIC was calculated for RAPD data, while the diversity of qualitative traits was described by Shannon genetic diversity index. Cluster analysis based on qualitative morphological characters showed clear separation of genotypes on the basis of their plant growth type. PC analysis performed for quantitative traits divided genotypes according to their maturity group. Grouping pattern based on molecular marker data was in agreement with pedigree of cultivars. A great similarity was found, primarily between the varieties under the same institution, and then among all examined varieties. Comparison of three methods in the assessment of diversity indicated that morphological markers might provide useful information in breeding process and allow classification by pedigree to some extent, but RAPD markers were found to be superior in assessing differences among genetically very similar genotypes. [Projekat Ministarstva nauke Republike Srbije, br. TR-31068
Khadivi-Khub, Abdollah; Soorni, Aboozar
Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs.
Conversion of the random amplified polymorphic DNA (RAPD) marker UBC#116 linked to Fusarium crown and root rot resistance gene (Frl) into a co-dominant sequence characterized amplified region (SCAR) marker for marker-assisted selection of tomato.
Jiang, Y; Liu, J-P
Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority.
Ahmad, M; McNeil, D L; Fautrier, A G; Armstrong, K F; Paterson, A M
Broadening of the genetic base and systematic exploitation of heterosis in cultivated lentils requires reliable information on genetic diversity in the germplasm. The ability of random amplified polymorphic DNA (RAPD) to distinguish among different taxa of Lens was evaluated for several geographically dispersed accessions/cultivars of four diploid Lens species. This study was carried out to assess whether RAPD data can provide additional evidence about the origin of the cultivated lentil and to measure genetic variability in lentil germplasm. Three cultivars of Lens culinaris ssp. culinaris, including one microsperma, and two macrosperma types, and four wild species (L. culinaris ssp. orientalis, L. odemensis and L. nigricans) were evaluated for genetic variability using a set of 1 11-mer and 14 random 10-mer primers. One hundred and fifty-eight reproducible and scorable DNA bands were observed from these primers. Genetic distances between each of the accessions were calculated from simple matching coefficients. Split decomposition analysis of the RAPD data allowed construction of an unrooted tree. This study revealed that (1) the level of intraspecific genetic variation in cultivated lentils is narrower than that in some wild species. (2) L. culinaris ssp. orientalis is the most likely candidate as a progenitor of the cultivated species, (3) L. nigricans accession W6 3222 (unknown) and L. c. ssp. orientalis W6 3244 (Turkey) can be reclassified as species of L. odemensis and (4) transmission of genetic material in Lens interspecific hybrids is genotypically specific, as identified by the RAPD markers in our study.
May 18, 2009 ... et al., 2003), rice (Wu et al., 2002), Chrysanthemum hybrids (Huang et al., 2000) and SSR markers in maize heterozygous DH lines (Heckenberger et al., 2002). The presence of slower migrating heteroduplex DNA is, there- fore, useful for detection of heterozygous individuals. Maintenance of hybrid seeds ...
accessions and 17 primers were selected (Table 2). Amplification was preformed in a 15 µl reaction volume, containing 50 ng template DNA. 1X PCR buffer, 0.4 ..... excellent assistance. REFERENCES. Bachmann K (1997). Nuclear DNA markers in plant biosystematic. Lalhruaitluanga and Prasad 6061 research. Opera.
S. M. Sarid Ullah
Full Text Available In the present study an efficient and easy method was followed for the isolation of DNA from meristem cylinder in five chewing sugarcane varieties, namely Amrita, Bomaby, Babulal (Co.527, Q83 and Misrimala. The quality and quantity of DNA were assured by visual estimation using agarose gel electrophoresis and UV spectrophotometry. The highest amount of DNA was retrieved from the Amrita (3250 ng/ml and the lowest amount was attained from the variety Q83 (1450 ng/ml. The amount of recovered DNA was enough for PCR amplification and marker studies such as random amplified polymorphic DNA (RAPD. Using RAPD markers, bands obtained from fingerprinting (190 bp to 1200 bp showed 73.5% polymorphism. The dendrogram, based on linkage distance using unweighted pair group method of arithmetic means (UPGMA, indicated segregation of the five chewing varieties of sugarcane into two main clusters. Amrita, Bombay and Misrimala were grouped in cluster 1 (C1 followed by sub-clusters. Babulal and Q83 were grouped in cluster 2 (C2. The results of the present investigation also revealed that the twenty RAPD primers were able to identify and classify the chewing sugarcane varieties based on their genetic relationship.
Full Text Available The aim of this study was to evaluate the genetic diversity of Iranian improved rice varieties. Sixteen rice varieties of particular interest to breeding programs were evaluated by means of random amplified polymorphic DNA (RAPD technique. The number of amplification products generated by each primer varied from 4 (OPB-04 to 11 (OPD-11 with an average of 8.2 bands per primer. Out of 49 bands, 33 (67.35% were found to be polymorphic for one or more cultivars ranging from 4 to 9 fragments per primer. The size of amplified fragments ranged between 350 to 1800 bp. Pair-wise Nei and Li�s (1979 similarity estimated the range of 0.59 to 0.98 between rice cultivars. Results illustrate the potential of RAPD markers to distinguish improved cultivars at DNA level. The information will facilitate selection of genotypes to serve as parents for effective rice breeding programs in Iran.
Full Text Available Saffron (Crocus sativus L. is one of the most valuable medicinal and spice herbs in the world. In spite of the ancient cultivation history in Iran, there are limited breeding studies on the plant due to its vegetative reproduction. In order to evaluation genetic diversity of Iranian saffron germplasm, sixty-five different saffron accessions from the main cultivation areas in Khorasan including Torbat heidarieh, Gonabad, Mahvelat, Ghaenat and Ferdows were collected and were studied by molecular markers. The used RAPD and ISSR primers produced 43 and 122 polymorphic markers loci, respectively, and totally 165 markers with average of 7.5 markers by each primer, totally. Diversity index ranged from 0.36 to 0.7 with average of 0.23. Also, marker index with the average of 0.16 varied in the range of 0.2 to 0.7. The accessions from Ghaenat and Mahvelat had the maximum (83.03% and the minimum (52.73% polymorphism, respectively. Grouping the studied saffron accessions using cluster analysis displayed four distinct groups which had little correspondence to their collection areas, while clustering for the main cultivation areas had relatively good correspondence to their geographical distances. So, it is expected to have nearly approaching improvements of qualitative and quantitative yields via the selection of superior clones of saffron. Key words: Saffron, Molecular variation, Germplasm, RAPD, ISSR, Khorasan region, clustering .
Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.
Full Text Available Moringa peregrina and M. oleifera are the only Moringa species found in Saudi Arabia. Both species are drought resistant and have very high nutritional and medicinal properties. Detection of genetic diversity is of great value for the improvement of nutritional and medicinal value of these plants. The aim of the present study was to characterize a new biotype Moringa observed in Al Bahah Region, Saudi Arabia. We used 11 RAPD and 15 ISSR primers to characterize and compare the new biotype with M. peregrina and M. oleifera. Level of polymorphism generated by each marker was calculated. We also calculate Nei and Li’s coefficient to measure the genetic distance between the studied species. Level of polymorphism generated by RAPD and ISSR was 46% and 57%, respectively. RAPD and ISSR primers revealed that the new biotype shared 55 amplicons (45.08% with both M. peregrina and M. oleifera, 28 amplicons with M. peregrina (22.95%, 21 amplicons (17.21% with M. oleifera, and displayed 18 unshared amplicons (14.75%. Based on RAPD data, genetic distance between M. oleifera and M. peregrina was 0.32, whereas genetic distance between the new biotype and M. oleifera and M. peregrina was 0.21 and 0.29, respectively. For ISSR data, genetic distance between M. oleifera and M. peregrina was 0.5, whereas genetic distance between the new biotype and M. oleifera and M. peregrina was 0.36 and 0.34, respectively. Based on these results we suggested that the new biotype is a hybrid crossbred between M. peregrina and M. oleifera.
Tadeusz Kowalski; Wojciech Kraj
On the basis of morphological features and RAPD markers the strains of Chalara ovoidea found in Poland on planks and on stems of beech trees were identified. As reference strains the cultures taken from CBS Utrecht were employed; they were cultures CBS 354.76 and CBS 136.88. The amplification of genomic DNA was conducted using 10 primers (OPA01-OPA10), 7 of which (OPA01-OPA05, OPA09, OPA10) gave positive results. In total 42 fragment of DNA (bands) were obtained. In case of primers OPA03, OPA...
Ruzicka, Joana; Lukas, Brigitte; Merza, Lina; Göhler, Irina; Abel, Gudrun; Popp, Michael; Novak, Johannes
Verbenae herba is a widely used drug and consists of the aerial parts of Verbena officinalis (Verbenaceae). Until now, the identification has been performed based on morphological and phytochemical analyses, which are not reliable enough to distinguish Verbena officinalis from other relevant species of the genus Verbena. Hence, impurities and adulterants, negatively influencing the therapeutic effect of the drug, may remain undetected. In an attempt to generate an accurate authentication method we used two different DNA-based approaches: comparison of ITS sequences and molecular markers (RAPD). Both approaches generally enabled discrimination of V. officinalis from the rest of the genus despite the intraspecific variation existing within V. officinalis. The application of the two independent methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, however, a SCAR marker and primers for HRM were derived from the RAPD results. The SCAR marker could distinguish V. officinalis from all other verbena species except its closest relative V. hastata, while discrimination of V. officinalis even from V. hastata was unproblematic with HRM.
Zargar, Sajad Majeed; Farhat, Sufia; Mahajan, Reetika; Bhakhri, Ayushi; Sharma, Arjun
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.
Cerqueira-Silva, C B M; Conceição, L D H C S; Santos, E S L; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X
The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.
Basheer-Salimia, R; Shtaya, M; Awad, M; Abdallah, J; Hamdan, Y
Until now, neither phenotypic nor molecular approaches have been used to characterize the landraces of Palestine faba beans (Vicia faba). We used PCR-based RAPD markers to determine the genetic diversity and relatedness among 26 Palestinian faba bean landraces (traditional farmers' varieties) from 8 localities in the West Bank, Palestine. In tests with 37 primers, 14 generated no polymorphic bands, 12 exhibited weak and unclear products, and 11 primers produced good amplification products with high intensity and pattern stability. Ninety-four DNA fragments (loci) were detected, with an average of 8.54 loci per primer and size ranging from 160 to 1370 bp. A minimum of 4 and a maximum of 14 DNA fragments were obtained using (OPA-05 and OPA-09) and (BC-261) primers, respectively. The maximum percentage of polymorphic markers was 71.4 (BC-298) and the minimum was 50.0 (OPA-05, -09, -16). The 11 primers exhibited relatively high collective resolving power (Rp) values of 26.316, and varied from 0.154 for the OPA-09 primer to 5.236 for the BC-261, with an overall mean of 2.392. The primers BC-261, -322, and -298 were found to be the most useful RAPD primers to assess the genetic diversity of Palestinian faba beans, as they revealed relatively high Rp rates (5.236, 3.618, and 3.150, respectively). Based on the Jaccard coefficient, the genetic distance ranged from 0.358 to 0.069, with a mean of 0.213. We conclude that the RAPD technique is useful for determining genetic diversity and for developing suitable fingerprints for faba bean landraces grown in Palestine.
Santos, M F; Damasceno-Silva, K J; Carvalhaes, M A; Lima, P S C
The purpose of this study was to analyze the effects of management on the genetic structure of natural populations of Attalea speciosa in the State of Piauí, Brazil, using random-amplified polymorphic DNA (RAPD) markers. Three babassu populations under different management systems were selected. Polymerase chain reactions were performed for 20 RAPD primers. A total of 146 bands were generated, 141 of which were polymorphic (96.58%), with a variation of 4 and 12 loci and an average of 7 bands per primer. A dendrogram revealed a clear separation between the three populations (0.57). Data reliability and node consistency were verified by bootstrap values and the cophenetic correlation coefficient (88.15%). Coefficients of similarity between pairs of genotypes ranged from 0.26 to 0.86, with a mean of 0.57. Nei's genetic diversity index (HE) value of the population sampled in Teresina was 0.212, of Esperantina it was 0.195, and of José de Freitas it was 0.207. After the HE was decomposed, the complete diversity was found to be 0.3213. Genetic differentiation between populations was 0.362, and the estimation of gene flow between populations was low (0.879). Analysis of molecular variance revealed that 59.52% of the variation was contained within populations, and 40.48% was between populations. RAPD markers were effective for genetic diversity analysis within and between natural babassu populations, and exhibited a high level of polymorphism. Genetic diversity was the highest within populations; variability was lower in the managed populations than in the undisturbed populations.
Maaß, H I; Klaas, M
Garlic (Allium sativum L.) is a sterile species of considerable variability with respect to morphological and physiological features. The crop presumably originated in West to Middle Asia from its progenitor A. longicuspis Regel and was transported from there to the Mediterranean and other areas of cultivation. In order to clarify older classification schemes, often based on small or biased collections, we used isozyme and RAPD markers to analyze and structure a collection of 300 accessions, many of which were gathered in Middle Asia close to the assumed center of origin. All of the accessions were first investigated with isozymes, and 48 were selected for a RAPD analysis. The resulting molecular markers were used to construct neighbor-joining dendrograms to group the accessions and to indicate the genetic distances between them. Based on the dendrograms and in conjunction with some morphological features, we propose an infraspecific classification of garlic with four major groups. In agreement with the results of other workers, A. longicuspis lies within the range of the species A. sativum. Numerous forms with varying degrees of domestication are part of our longicuspis group, from which presumably the more derived cultivar groups originated. The origin and spreading of the crop are discussed with respect to the geographical distribution and the genetic distances of the accessions.
Luciana do Valle Rego Oliveira
Full Text Available In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95% were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intraspecifc genetic similarity varied 88% for the individuals of Catasetum triodon to 93% between the individuals of Catasetum atratum and Catasetum macrocarpum. These results would contribute to understand the genetic relationship in Catasetum, to define the strategies to establish a germplasm core collection for the genus and to provide support for breeding programs.Neste trabalho, marcadores moleculares de RAPD foram utilizados para acessar a variabilidade genética e estudar as relações interespecíficas e intraespecífica em um grupo de 37 espécies, compreendendo 56 plantas individuais. Um total de 15 primers foram selecionados para amplificação do DNA. De um total de 221 bandas analisadas, 209 (95% foram polimórficas. O nível de similaridade genética interespecífica variou de 37% entre Catasetum complanatum e Catasetum laminatums a 83% entre Catasetum triodon e Catasetum uncatum. A similaridade genética intraespecífica variou de 88% entre os indivíduos de Catasetum triodon a 93% entre os indivíduos de Catasetum atratum e Catasetum macrocarpum. Os resultados deste trabalho contribuem para o entendimento das relações interespecíficas no gênero Catasetum, para definir estratégias para o estabelecimento de um banco de germoplasma e para dar suporte a programas de melhoramento.
Full Text Available Hawthorn (Crataegus spp. is an important forest fruit species in Iran. Genetic variability among some genotypes of hawthorn was investigated using morphological traits and random amplified polymorphic DNA (RAPD marker. The collected genotypes belonged to four species of Crataegus genus. High variability among genotypes was found for most of the traits. Results from the principal component analysis (PCA indicated that 85.05% of the observed variability was accounted by the first five components. The first two components explained about 55.24% of the total achieved variability. In PCA, fruit weight, fruit length, fruit diameter, fruit moisture, fruit dry matter, leaf length, leaf area, leaf width, number of leaves per node, seed weight and seed length were predominant in the first two components, indicating that they were useful for the assessment of hawthorn germplasm characterization. A total of 58 polymorphic bands were produced with 10 RAPD primers. The bands' sizes ranged from 180 to 2700 bp. The number of the observed polymorphic bands for each primer ranged from 4 to 8, with an average of 5.8 alleles per locus. The polymorphism information content was observed to be the highest (0.79 in the Oligo_32 locus, whereas the Oligo_339 locus had the lowest value of 0.64, with an average of 0.72, among the RAPD primers. The Jaccard's genetic similarity coefficient ranged from 0.12 to 0.95 among the genotypes. At a similarity coefficient of 0.46, the unweighted pair group method with arithmetic mean (UPGMA cluster analysis divided the genotypes into three major groups.
Mansour, Hassan; Mekki, Laila E; Hussein, Mohammed A
DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes.
Huo, J; Yang, G; Zhang, Y; Li, F
We developed a new approach using RAPD fingerprints to distinguish 37 currant cultivars from northeastern China based on optimization of RAPD by choosing 11 nucleotide primers and strict screening PCR annealing temperature. We found that the manual cultivar identification diagram (MCID) approach clearly developed fingerprints from 8 different primers that were useful for cultivar identification; a cultivar identification diagram (CID) was readily constructed. This CID allows efficient currant cultivar identification, providing information to separate all the currant cultivars from each other, based on the detail polymorphic bands from the corresponding primers, which were marked in the correct positions on the currant CID. According to the CID, 10 currant cultivars in 5 groups were randomly selected for the referable and workable identification of this strategy. The results proved the workability and efficiency of the MCID method, facilitating the identification of fruit cultivars with DNA markers. This MCID approach will be useful for early identification of seedlings in the nursery industry and protection of cultivar rights.
Full Text Available Bemisia tabaci (Genn. was considered a secondary pest in Brazil until 1990, despite being an efficient geminivirus vector in beans and soybean. In 1991, a new biotype, known as B. tabaci B biotype (=B. argentifolii was detected attacking weed plants and causing phytotoxic problems in Cucurbitaceae. Nowadays, B. tabaci is considered one of the most damaging whitefly pests in agricultural systems worldwide that transmits more than 60 different plant viruses. Little is known about the genetic variability of these populations in Brazil. Knowledge of the genetic variation within whitefly populations is necessary for their efficient control and management. The objectives of the present study were to use RAPD markers (1 to estimate the genetic diversity of B. tabaci populations, (2 to study the genetic relationships among B. tabaci biotypes and two other whitefly species and (3 to discriminate between B. tabaci biotypes. A sample of 109 B. tabaci female individuals obtained from 12 populations in Brazil were analyzed and compared to the A biotype from Arizona (USA and B biotype from California (USA and Paraguay. Trialeurodes vaporariorum and Aleurodicus cocois samples were also included. A total of 72 markers were generated by five RAPD primers and used in the analysis. All primers produced RAPD patterns that clearly distinguished the Bemisia biotypes and the two other whitefly species. Results also showed that populations of the B biotype have considerable genetic variability. An average Jaccard similarity of 0.73 was observed among the B biotype individuals analyzed. Cluster analysis demonstrated that, in general, Brazilian biotype B individuals are scattered independently in the localities where samples were collected. Nevertheless, some clusters were evident, joining individuals according to the host plants. AMOVA showed that most of the total genetic variation is found within populations (56.70%, but a significant portion of the variation is found
Full Text Available Phyllanthus emblica Linn. is the most important medicinally useful tree crop in Asian Subcontinent and is severely infested by Betousa stylophora Swinhoe, known as shoot gall maker (SGM. This pest tunnels the shoots of seedlings and actively growing branches of trees and develops gall, leading to stunted growth, unusual branching and death of actively growing shoots. Our study revealed that trees possessing smooth bark were free from the attack of this pest than those with rough bark surface. Unfortunately, this character is not detectable either at seedling stage or during early growth of trees in the orchard. RAPD genetic fingerprinting of trees possessing smooth and rough bark revealed distinguishable and highly reproducible DNA banding pattern between the two genotypes. Of the 20 RAPD primers tested, five of them produced distinguishable RAPD bands between rough and smooth barked genotypes of P. emblica. Trees with smooth bark produced five unique RAPD bands with molecular weight ranging from 350 bp to 1500 bp and those with rough bark produced six RAPD bands (350 bp–650 bp to utilize these DNA bands as potential DNA marker for screening tolerant genotypes of this crop against SGM. The utility of this finding in genetic improvement of this tree crop against SGM is discussed.
Full Text Available Variasi genetik ikan kancra yang dikoleksi dari daerah Kuningan (Pesawahan, Gandasoli, dan Ragawacana dan Sumedang di Jawa Barat telah diteliti dengan menggunakan polimorfisme Mitokondria DNA D-loop dan Random Amplified Polymorphism DNA (RAPD. Berdasarkan analisis Mt DNA tidak terdapat perbedaan yang nyata antara ras ikan kancra dari empat lokasi tersebut. Sedangkan analisis RAPD menunjukkan perbedaan yang nyata. Panjang daerah Mt DNA D-loop ikan kancra berkisar antara 700--800 bp. Satu komposit haplotype terdeteksi dengan menggunakan 4 enzim restriksi yaitu Rsa I, Nde II, Taq I, dan Sac I pada sekuens D-loop. Dua dari 20 primer RAPD menunjukkan perbedaan yang nyata di antara keempat populasi ikan kancra. Jarak genetik berdasarkan polimorfisme dua primer tersebut adalah 0,349. The aim of this research was to evaluate genetic variability of Tor soro. The genetic variability of Tor soro collected from Kuningan (Pesawahan, Gandasoli, and Ragawacana and Sumedang, West Java were examined using polymorphism of the mitochondria DNA (MtDNA D-loop and RAPD markers. Based on MtDNA D-loop analysis, there was no significant different among collection. The length size of MtDNA D-loop region was approximately 700--800 bp. A composite haplotype was detected using four endonuclease i.e. Rsa I, Nde II, Taq I, and Sac I. Two of 20 RAPD primers showed significantly different among collections. Average genetic distance based on the polymorphism of two primers was 0.349.
Full Text Available Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.
Frello, S.; Hansen, K.R.; Jensen, J.
We have examined the inheritance of 20 rapeseed (Brassica napus)-specific RAPD (randomly amplified polymorphic DNA) markers from transgenic, herbicide-tolerant rapeseed in 54 plants of the BC1 generation from the cross B. juncea x (B. juncea x B. napus). Hybridization between B. juncea and B. napus......, with B. juncea as the female parent, was successful both in controlled crosses and spontaneously in the field. The controlled backcrossing of selected hybrids to B. juncea, again with B. juncea as the female parent, also resulted in many seeds. The BC1 plants contained from 0 to 20 of the rapeseed RAPD...... markers, and the frequency of inheritance of individual RAPD markers ranged from 19% to 93%. The transgene was found in 52% of the plants analyzed. Five synteny groups of RAPD markers were identified. In the hybrids pollen fertility was 0-28%. The hybrids with the highest pollen fertility were selected...
Lamare, Animos; Rao, Satyawada Rama
North east India is considered as one of the major biodiversity hotspots worldwide and centre of origin of several plant species including Musa. Musa acuminata Colla is known to be one of the wild progenitors of cultivated bananas and plantains. Three single primer based DNA marker techniques viz., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and directed amplification of minisatellites DNA (DAMD) were used for diversity diagnostics among 25 genotypes of wild M. acuminata collected from Meghalaya province of north east India. A total of 58 primers (26-RAPD, 21-ISSR, and11-DAMD) yielded 451 DNA fragments, of which 395 (87.58 %) were found to be polymorphic in nature. The polymorphic information content (PIC) values were almost identical for each marker system. The resolving power of the marker system was found to be highest in RAPD (3.96) whereas ISSR resolved highest marker index (16.39) in the study. Selected amplicon data obtained through single primer amplification reactions were utilized for determination of diversity within and among the populations of M. acuminata. Nei's genetic differentiation (Gst) value (0.451) indicated higher proportion of the genetic variation within the populations which is supported by the AMOVA analysis (88 %). The study provides insight into the efficacy of RAPD, ISSR and DAMD to analyse the genetic variation existing in the wild Musa germplasm, which can further be exploited for quality trait improvement and domestication of such important horticultural crops. The genetic diversity based population structure may shed light on the genetic basis of speciation and evolution of various species within the genus Musa.
Full Text Available The purpose of the present study was to determine the level of genetic diversity within and among Ciuc basin, Romania (populations from Mohos and Luci raised bogs in Harghita Mountain and Sumuleu in Ciuc Mountain Pinus sylvestris populations using molecular markers. Two of populations (Mohos and Luci seems to be the descendants that survived the continental glaciation. Genetic diversity was analyzed by RAPD (Random Amplified Polymorphic DNA. Nine primers were selected for analysis, which generated reproducible bands. On base of presence or absence of homologues bands Nei’s gene diversity, the percentage of polymorphic loci and Nei’s unbiased genetic distance were calculated. The level of genetic variation among populations was found to be low. For both populations the variation values among populations were higher than within populations. The fossil records and geological historical data explain the extremely low genetic diversity of this species. Pinus sylvestris experienced strong bottlenecks during its evolutionary history, which caused the loss of genetic variation. Genetic drift and breeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity and genetic differentiation of populations. Human activities may have accelerated the loss of genetic diversity in Pinus sylvestris.
Danuza Araújo de Souza
Full Text Available The purpose of this work was to identify hybrids in intraspecific crosses between sugar apple accessions and interspecific crosses between sugar apple and atemoya accessions by using RAPD markers. Four sugar apple accessions were selected: Seedless P1, P2, P3 and P4 and the atemoya cultivar Gefner (G1. In the pre-female phase the flowers were adequately protected and reciprocal crosses were performed. In crosses where the sugar apple accession Seedless P1 was used as the male parent, the fruits contained seeds, indicating that the pollen grains of Seedless P1 are viable. The fruits of reciprocal crosses where Seedless P1 was used as a female parent contained no seeds. The percentage of true hybrids in the crosses P4 x Seedless P1, P3 x Seedless P1, P2 x Seedless P1, and G1 x Seedless P1 were, respectively, 100%, 95.55%, 82.86%, and 44.44%. Primer OPF10 was efficient in obtaining polymorphic bands in all Annonaceae hybrid populations.
Md. Shariful Islam
Full Text Available Genetic diversity and relationships among six rice genotypes were investigated using five random amplified polymorphic DNA (RAPD markers. A total of 69 alleles were amplified, of which 66 were polymorphic. The size of the amplified alleles was between 0.25 and 2.35 kbp. The number of polymorphic alleles detected with each primer ranged from 7 to 24 with an average of 13.2 per primer and the polymorphism information content (PIC values varied from 0.8672 to 0.9471. Pair-wise similarity estimated the range of 0.308 to 0.718 among all the genotypes and the highest genetic similarity was found between Maloti and BRRI dhan53. Cluster analysis using UPGMA (unweighted pair group method with arithmetic averages revealed three clusters at genetic similarity of 46%. A moderately drought tolerant landrace, Boalia, formed a single cluster and the remaining genotypes grouped into distinct clusters based on their relatedness. The results showed a high level of genetic diversity among studied genotypes and this information will assist in conservation as well as selection of parents during breeding programs for the development of drought tolerant rice varieties in near future.
Julieta Torres Jaramillo
Full Text Available Se utilizó la técnica RAPD (amplificación al azar de ADN polimórfico para el estudio de la diversidad genética de Oreochromis sp. (tilapia roja en cinco piscícolas del Valle del Cauca (Colombia y en la determinación del nivel de introgresión de las especies parentales Oreochromis mosambicus, O. niloticus y O. aureus. Se evaluaron 25 cebadores, ocho fueron polimórficos y se obtuvieron 109 bandas. Los valores de heterocigosidad esperada (0.196 a 0.256 y la estructura genética (Gst = 0.22 para Oreochromis sp. indicaron un elevado grado de polimorfismo y alta estructuración genética. Estos resultados fueron consistente con el Fst = 0.268 (P Random amplified polymorphic DNA (RAPD markers were used to study genetic diversity on red Tilapia (Oreochromis sp. species collected from five fish farms located in the Valle del Cauca, Colombia and to determine the level of introgression from three parental species O. mosambicus, O. niloticus and O. aureus into local Oreochromis populations. from the 25 RAPD primers evaluated, eight were polymorphic and 109 banding patterns were observed, any of them were specific. The expected levels of heterozygosis (0.1964 to 0.2561 and genetic structure (Gst = 0.22 funded for Oreochrosmis sp. indicate high grade of polymorphism and genetic structuring. This results were observed following the analysis of molecular variance [AMOVA] (Fst = 0.268 (P <0.0001 and Multiple correspondence analysis (Gst = 0.040. The values of genetic similarity, the analysis of group, the analysis of multiple correspondence and the level of introgression, indicated that the differences in the introgression levels(P=0.0001 were significant. The low level of observed genetic differentiation among populations, could be the result of fish with the same genetic origin, whereas the high variation within populations can be displayed by handling practices and the pressure of selection to favor commercial phenotypes. The level of introgression
Maki Cristina Sayuri
Full Text Available The growth of thirty-four Lentinula edodes strains submitted to different mycelial cultivation conditions (pH and temperature was evaluated and strain variability was assessed by RAPD molecular markers. The growth at three pH values (5, 6 and 7 and four different temperatures (16, 25, 28 and 37ºC was measured using the in vitro mycelial development rate and water retention as parameters. Mycelial cultivation was successful at all pH tested, while the ideal temperature for mycelial cultivation ranged between 25 and 28ºC. The water content was lower in strains grown at 37ºC. Among 20 OPA primers (Operon Technologies, Inc. used for the RAPD analyses, seventeen presented good polymorphism (OPA01 to OPA05, OPA07 to OPA14, OPA17 to OPA20. The clustering based on similarity coefficients allowed the separation of strain in two groups with different geographic origins.
Full Text Available The objective of this research was to determine genetic variability of the soursop (Annona muricata L. populations from Central Java and East Java based on RAPD markers. Leaves of 40 individuals were collected from 4 soursop populations in Central Java and East Java, include : Sukoharjo, Karanganyar (Central Java, and Ngawi, Pacitan (East Java. Genomic DNA was extracted from the leaves by the CTAB extraction procedure with some modifications. A total of 15 RAPD primers were purchased from commercial source and tested to find specific diagnostic markers for each individuals by RAPD-PCR. The measurement of soursop population genetic distance was based on similarity coefficient using method of Group Average Clustering and Unweight Pair Group Method Arithmetic (UPGMA of NTSYS program version 2.02i. Results showed that each soursop population collected from different localities seemed have variability in RAPD profiles by using different primers. Four RAPD polymorphic primer was selected from 15 RAPD primers, namely A18, A20, P10 and P11. A total of 58 bands produced, varying from 9 to 20 bands per primer. The selected four RAPD primers produced 57 polymorphic bands, whereas polymorphism for each primer ranged from 95 % to 100 %. Dendrogram indicated that four soursop populations tend to segregate form two separated clade. The sample collected from Sukoharjo formed a separate cluster while the sample collected from Ngawi, Pacitan and Karanganyar grouped together in other cluster and diverged from population Sukoharjo.
Ranjekar Prabhakar K
Full Text Available Abstract Background Various species of genus Trigonella are important from medical and culinary aspect. Among these, Trigonella foenum-graecum is commonly grown as a vegetable. This anti-diabetic herb can lower blood glucose and cholesterol levels. Another species, Trigonella caerulea is used as food in the form of young seedlings. This herb is also used in cheese making. However, little is known about the genetic variation present in these species. In this report we describe the use of ISSR and RAPD markers to study genetic diversity in both, Trigonella foenum-graecum and Trigonella caerulea. Results Seventeen accessions of Trigonella foenum-graecum and nine accessions of Trigonella caerulea representing various countries were analyzed using ISSR and RAPD markers. Genetic diversity parameters (average number of alleles per polymorphic locus, percent polymorphism, average heterozygosity and marker index were calculated for ISSR, RAPD and ISSR+RAPD approaches in both the species. Dendrograms were constructed using UPGMA algorithm based on the similarity index values for both Trigonella foenum-graecum and Trigonella caerulea. The UPGMA analysis showed that plants from different geographical regions were distributed in different groups in both the species. In Trigonella foenum-graecum accessions from Pakistan and Afghanistan were grouped together in one cluster but accessions from India and Nepal were grouped together in another cluster. However, in both the species accessions from Turkey did not group together and fell in different clusters. Conclusions Based on genetic similarity indices, higher diversity was observed in Trigonella caerulea as compared to Trigonella foenum-graecum. The genetic similarity matrices generated by ISSR and RAPD markers in both species were highly correlated (r = 0.78 at p = 0.001 for Trigonella foenum-graecum and r = 0.98 at p = 0.001 for Trigonella caerulea indicating congruence between these two systems
Masuzaki, S.; Miyazaki, T.; McCallum, J.; Heusden, van A.W.; Kik, C.; Yamashita, K.; Tashiro, Y.
Integration of previously developed Allium cepa linkage maps requires the availability of anchor markers for each of the eight chromosomes of shallot (A. cepa L. common group Aggregatum). To this end, eight RAPD markers originating from our previous research were converted into SCAR markers via
Full Text Available On the basis of morphological features and RAPD markers the strains of Chalara ovoidea found in Poland on planks and on stems of beech trees were identified. As reference strains the cultures taken from CBS Utrecht were employed; they were cultures CBS 354.76 and CBS 136.88. The amplification of genomic DNA was conducted using 10 primers (OPA01-OPA10, 7 of which (OPA01-OPA05, OPA09, OPA10 gave positive results. In total 42 fragment of DNA (bands were obtained. In case of primers OPA03, OPA04, OPA05, and OPA09 all obtained fragments for analyzed strains were fully monomorphic. This means, that no genetic variability was found using the above mentioned primers. Low genetic variability was ascertained in the analysis of frequency of occurrence of DNA fragments using other primers, namely OPA01, OPA02, and OPA10. The matrix and dendrogram of genetic affinities among different strains of Chalara, calculated using the Jaccard’s similarity coefficient suggested, that the most similar strains are the ones coming from Poland (HMIPC 16136 and HMIPC16664 as well as the strain CBS 136.88, while somewhat different from them is the strain CBS 354.76. To determine, how exactly did the dendrogram reflect genetic affinity among analyzed strains, the Mantel’s test was employed. The correlation coefficient amounted to 0.78, suggesting that the strains under study had been grouped properly. The results showed, that the fungal strains found in southern Poland represent the species Chalara ovoidea.
Cristina Sayuri Maki; Flavia França Teixeira; Edilson Paiva; Luzia Doretto Paccola-Meirelles
The growth of thirty-four Lentinula edodes strains submitted to different mycelial cultivation conditions (pH and temperature) was evaluated and strain variability was assessed by RAPD molecular markers. The growth at three pH values (5, 6 and 7) and four different temperatures (16, 25, 28 and 37ºC) was measured using the in vitro mycelial development rate and water retention as parameters. Mycelial cultivation was successful at all pH tested, while the ideal temperature for mycelial cultivat...
Maria do Socorro Padilha de Oliveira
Full Text Available Caracterizou-se a diversidade genética entre acessos de açaizeiro por meio de marcadores RAPD. Foram analisados 116 acessos conservados na coleção de germoplasma da Embrapa Amazônia Oriental, Belém, PA com base em 28 primers. A matriz binária foi utilizada para a obtenção das dissimilaridades genéticas, pelo complemento artimético do coeficiente de similaridade de Dice, e também para a análise de bootstrap. As dissimilaridades genéticas foram representadas em um dendrograma gerado pelo método UPGMA. Os primers revelaram 263 bandas polimórficas e apresentaram ampla diversidade genética entre os acessos, variando de 0,06 a 0,67, sendo dois acessos de Chaves, PA, os mais divergentes. Mas, alguns acessos da mesma procedência apresentaram baixas dissimilaridades. O dendrograma permitiu a formação de oito grupos, delimitados pela dissimilaridade genética média (dg m: 0,40: dois formados por um único acesso; dois constituídos por dois acessos e os demais por vários subgrupos com acessos de diferentes locais. O número ideal de bandas para a estimativa da diversidade genética entre os 116 acessos foi de 180. Logo, o número de bandas empregado neste estudo foi eficiente para caracterizar com precisão as relações genéticas entre os acessos de açaizeiro. Os acessos divergentes devem ser úteis na formação de coleções nucleares e em programas de melhoramento genético.One characterized the genetic diversity among accessions of assai palm using RAPD markers. One hundred and sixteen accessions conserved in the Embrapa Eastern Amazon germplasm collection, in Belém, PA, were analyzed using 28 primers. The data of the binary matrix were used to estimate the genetic dissimilarities using the arithmetical complement of Dice similarity coefficient and also for the bootstrap analysis. The genetic dissimilarities were represented in a dendrogram generated by the UPGMA method. The primers revealed 263 polymorphic RAPD loci
ROBERTO PEDROSO DE OLIVEIRA
Full Text Available Os marcadores moleculares apresentam várias aplicações no melhoramento de plantas, permitindo uma série de análises genéticas. Este trabalho foi realizado com o objetivo de estabelecer marcadores RAPD para serem utilizados em estudos de mapeamento genético e na seleção de híbridos entre tangerina-'Cravo' (Citrus reticulata Blanco e laranja-'Pêra' (C. sinensis (L. Osbeck. Extraiu-se DNA de folhas dos parentais e de seis híbridos F1. As reações de amplificação foram preparadas em 13 uL de solução, constituída por tampão 1x GIBCO BRL; soluções 1,54 mM de MgCl2 e 0,2 mM de cada dNTP; 15 ng de cada 'primer'; 1,5 unidade de 'Taq DNA Polymerase' e 15 ng de DNA genômico. As reações foram realizadas em termocicladores programados para 36 ciclos de 1 min a 92ºC, 1 min a 36ºC, 2 min a 72ºC e 10 min de extensão a 72ºC. Foram testados 'primers' decâmeros arbitrários dos 'kits' A, AB, AT, AV, B, C, D, E, G, H, M, N, P, Q, R e U da Operon, sendo selecionados 113 por apresentarem polimorfismo, com número de marcadores variando de 1 a 6 por 'primer'. Esses 'primers' amplificaram 201 (23,13% bandas polimórficas, aplicáveis no mapeamento genético e seleção de híbridos. A freqüência de 'primers' com 1; 2; 3; 4; 5 e 6 bandas polimórficas foi de 49,5%, 33,6%, 9,7%, 4,4%, 1,8% e 1,0%, respectivamente.Molecular markers have many applications in plant breeding, enabling some types of genetic analyses. The aim of this work was to establish RAPD markers to be used to genetic mapping studies and selection of hybrids between 'Cravo' tangerine (Citrus reticulata Blanco and 'Pêra' orange (C. sinensis (L. Osbeck. DNA of the parents and six hybrids F1 was isolated from the leaves. The amplification reactions were performed in volumes of 13 µL, composed by GIBCO BRL 1x buffer, 1,54 mM MgCl2, 0,2 mM of each dNTP, 15 ng of each primer, 1,5 unit of Taq DNA Polymerase and 15 ng of genomic DNA. These reactions were carried out in
Korsunenko, Anna; Chrisanfova, Galina; Lopatkin, Anton; Beer, Sergey A; Voronin, Mikhail; Ryskov, Alexey P; Semyenova, Seraphima K
Avian schistosome Trichobilharzia szidati is a member of the largest genus within the family Schistosomatidae (Trematoda). Population genetic structure of Trichobilharzia spp. schistosomes, causative agents of cercarial dermatitis in humans, has not been studied yet. The knowledge of the genetic structure of trichobilharzian populations is essential for understanding the host-parasite coevolutionary dynamics and epidemiology strategies. Here we examined genetic diversity in three geographically isolated local populations of T. szidati cercariae inhabiting Russia based on nuclear (randomly amplified polymorphic DNA, RAPD) and mt (cox1) markers. We analyzed T. szidati cercariae shed from seven naturally infected snails of Lymnaea stagnalis. Using three random primers, we demonstrated genetic variation among populations, thus posing genetic structure across geographic sites. Moreover, T. szidati cercariae have been genetically structured among hosts (infrapopulations). Molecular variance analysis was performed to test the significance of genetic differentiation within and between local populations. Of total parasitic diversity, 18.8% was partitioned between populations, whereas the higher contribution (48.9%) corresponds to the differences among individual cercariae within infrapopulations. In contrast to RAPD markers, a 1,125-bp fragment of cox1 mt gene failed to provide any significant within-species structure. The lack of geographic structuring was detected using unique haplotypes which were determined in the current work for Moscow and Western Siberian local populations as well as obtained previously for European isolates (Czech Republic and Germany). All T. szidati/Trichobilharzia ocellata haplotypes were found to be mixed across their geographical origin.
Maria do Socorro Maués Albuquerque
Full Text Available O objetivo deste trabalho foi caracterizar, por meio de marcadores RAPD, dois grupos genéticos de búfalos, Carabao e tipo Baio, que estão sendo conservados in situ, assim como verificar as relações genéticas entre eles e os outros três grupos genéticos de búfalos existentes no Brasil, Murrah, Jafarabadi e Mediterrâneo, considerados raças comerciais. Foram estudados 48 animais de cada grupo, com exceção dos grupos Murrah e Mediterrâneo, com 47 e 42 animais, respectivamente, compreendendo um total de 233 animais. Os 21 iniciadores polimórficos geraram 98 marcadores. A variabilidade genética entre e dentro dos grupos foi estimada em 26,5 e 73,5%, respectivamente, sugerindo divergência significativa entre os cinco grupos genéticos. Na análise entre pares de grupos, foi verificado que a maior e a menor divergência estavam em torno de 40 e 18%, quando se compararam os grupos Carabao x Mediterrâneo e Murrah x Jafarabadi, respectivamente. Entre os grupos Baio e Murrah, a análise revelou divergência genética de 20,42%, indicando que esses grupos são distintos. Os cinco grupos são geneticamente distintos, o que reforça a necessidade de conservação dos grupos genéticos Carabao e Baio, ameaçados de extinção no Brasil.The objective of this work was to characterize genetically, using RAPD markers, two genetic groups of buffalos, Carabao and Baio, which are being conserved in situ, as well as to verify the genetic relationship among them and the other three genetic groups of buffalos raised in Brazil, considered as commercial breeds: Murrah, Jaffarabadi and Mediterrâneo. Forty eight animals of each group were studied, with the exception of the Murrah and Mediterrâneo, in which 47 and 42 animals, respectively, were sampled, comprising a total of 233 animals. The 21 polymorphic primers produced 98 markers. Genetic variability within and between groups was estimated in 26.5 and 73.5%, respectively, suggesting a significant
ROSSELLÓ, JOSEP A.; CEBRIÁN, M. CARMEN; MAYOL, MARIA
Analyses of RAPD profiles from 17 populations of the Hippocrepis balearica complex revealed a highly structured geographic pattern, not only among continental–insular areas but also within the eastern Balearic islands. In marked contrast to previous morphometric results, a clear separation between continental and insular samples was found, and intermediates between H. balearica and H. valentina samples were not detected. Molecular data indicated that western and eastern Balearic populations of the complex (H. grosii and H. balearica) were more closely related to each other than to continental populations (H. valentina). Multivariate analyses of the RAPD data clearly indicated that the similarities between continental and eastern Balearic samples of the H. balearica complex recovered by morphometric methods are due either to parallel evolution or to retention of plesiomorphic features. PMID:12096744
Ahsyee Salem R.
Full Text Available Alfalfa (Medicago sativa L. is an important forage legume in Libya. The genetic diversity of nine alfalfa domesticated varietal populations was studied using thirteen RAPD primer combinations. The number of polymorphic fragments detected per primer combination ranged from 8 to 46 bands with an average of 24 bands. The number of polymorphic bands detected was from 6 (Atalia population to 37 (Gabsia population. The lowest genetic distance was 0.058 and the highest was 0.655. The average genetic distance was (0.356. The dendrogram based on Ward’s minimum variance clustering method grouped the nine populations into the two main clusters. The first group included Fazania, Atalia, Masratia, Zawia, Denamo Ferade and Arezona. The second group was composed of Tagoria, Gabsia and Wade Alrabeh. The simplicity of RAPD assays for detection of genetic polymorphisms is confirmed in our study, and results can be utilized in breeding practice.
The aim of the present study was to determine the effect of nickel on shoot regeneration in tissue culture as well as to identify polymorphisms induced in leaf explants exposed to nickel through random amplified polymorphic DNA (RAPD). In vitro leaf explants of Jatropha curcas were grown in nickel amended Murashige and Skoog (MS) medium at four different concentrations (0, 0.01, 0.1, 1 mM) for 3 weeks. Percent regeneration, number of shoots produced and genotoxic effects were evaluated by RAPD using leaf explants obtained from the first three treatments following 5 weeks of their subsequent subculture in metal free MS medium. Percent regeneration decreased with increase in addition of nickel to the medium up to 14 days from 42.31% in control to zero in 1.0 mM. The number of shoot buds scored after 5 weeks was higher in control as compared to all other treatments except in one of the metal free subculture medium wherein the shoot number was higher in 0.01 mM treatment (mean = 7.80) than control (mean = 7.60). RAPD analysis produced only 5 polymorphic bands (3.225%) out of a total of 155 bands from 18 selected primers. Only three primers OPK-19, OPP-2, OPN-08 produced polymorphic bands. The dendrogram showed three groups A, B, and C. Group A samples showed 100% genetic similarity within them. Samples between groups B and C were more genetically distant from each other as compared to samples between groups A and B as well as groups A and C. Cluster analysis based on RAPD data correlated with treatments. © 2010 Springer Science+Business Media, LLC.
Karine Cristina Bicalho
Full Text Available A seringueira [Hevea brasiliensis (Willd. ex. Adr. de Juss Muell.-Arg.] é uma espécie nativa da região amazônica e compreende a maior fonte produtora de borracha natural do mundo. Na busca de condições mais favoráveis ao cultivo, além da busca pela auto-suficiência na produção de borracha natural, o cultivo da seringueira migrou para outras regiões do país. Objetivou-se, com o presente trabalho, estimar a similaridade genética de genótipos de seringueira, provenientes de regiões distintas do país, Lavras-MG (UFLA e Campinas-SP (IAC, por meio de marcadores moleculares RAPD. A análise foi efetuada em 41 indivíduos, representados por 17 genótipos diferentes, com base em 19 primers, que geraram 121 fragmentos polimórficos. Os dados foram analisados utilizando o software NTSYS-pc - 2.1, por meio do coeficiente de Dice e pelo método das médias (UPGMA. A similaridade genética entre o material analisado variou de 0,56 a 1,00. Na análise do dendrograma, foram observados 18 grupos. Os clones (RRIM600, GT1, PB235, PL PIM e FX2261, utilizados em diferentes repetições, foram idênticos, quando comparados entre si, entretanto o mesmo não foi observado para os clones identificados como RRIM 701. Os resultados obtidos sugerem que o material avaliado na UFLA é o mesmo implantado no IAC, exceto o RRIM 701, mostrando uma ampla variabilidade genética, disponível para estudos e propagação da cultura.The rubber tree [Hevea brasiliensis (Willd. ex. Adr. de Juss Muell.-Arg.] is a native species from Amazon region, and represents the biggest source of natural rubber in the world.. However, the rubber tree culture has had an expansion to other brazilian regions, in search of more favorable conditions for its cultivation and self-sufficiency in natural rubber. The aim of this work was to estimate genetic similarity among rubber tree clones, from different Brazilian regions, Lavras (UFLA and Campinas (IAC, by using RAPD molecular markers
Andréa Alves do Egito
Full Text Available Blood samples were collected from Pantaneiro Horses in five regions of Mato Grosso do Sul and Mato Grosso States. Arabian, Mangalarga Marchador and Thoroughbred were also included to estimate genetic distances and the existing variability among and within these breeds by RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction molecular markers. From 146 primers, 13 were chosen for amplification and 44 polymorphic bands were generated. The analysis of molecular variance (AMOVA indicated that the greatest portion of detected variability was due to differences between individuals within populations (75.47%. Analysis of the genetic variability between pairs of populations presented higher estimates for the five Pantaneiro populations with the Arabian breed, while lowest estimates were presented by pairs formed among the Pantaneiro populations with the Mangalarga Marchador. Highest genic diversity was shown by the Pantaneiro (0.3396, which also showed highest genetic distance with the Arabian and lowest with Mangalarga Marchador breed. UPGMA dendrogram showed distinct differences between naturalized (Pantaneiro and Mangalarga Marchador and exotic (Arabian and Thoroughbred breeds. In the dendrogram generated by UPGMA method, the similarity matrix generated by the Jaccard coefficient showed distinction between the naturalised breeds, Pantaneiro and Mangalarga Marchador, and the exotic breeds, Árab and English Thoroughbred. Results suggest that the Pantaneiro presents a higher genetic variability than the other studied breeds and has a close relationship with the Mangalarga Marchador.Amostras de sangue foram coletadas de cavalos Pantaneiros de cinco regiões dos estados de Mato Grosso do Sul e Mato Grosso. As raças Mangalarga Marchador, Árabe e Puro-Sangue Inglês (PSI usando marcadores moleculares RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction foram incluídas no intuito de se calcular as distâncias gen
Kelly Y. C. Lam
Full Text Available Cordyceps sinensis is an endoparasitic fungus widely used as a tonic and medicinal food in the practice of traditional Chinese medicine (TCM. In historical usage, Cordyceps specifically is referring to the species of C. sinensis. However, a number of closely related species are named themselves as Cordyceps, and they are sold commonly as C. sinensis. The substitutes and adulterants of C. sinensis are often introduced either intentionally or accidentally in the herbal market, which seriously affects the therapeutic effects or even leads to life-threatening poisoning. Here, we aim to identify Cordyceps by DNA sequencing technology. Two different DNA-based approaches were compared. The internal transcribed spacer (ITS sequences and the random amplified polymorphic DNA (RAPD-sequence characterized amplified region (SCAR were developed here to authenticate different species of Cordyceps. Both approaches generally enabled discrimination of C. sinensis from others. The application of the two methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, the SCAR markers derived from the RAPD results provide a new method for quick authentication of Cordyceps.
Verma, Kumar Sambhav; Ul Haq, Shamshad; Kachhwaha, Sumita; Kothari, S L
Citrullus colocynthis (L.) Schrad. (Cucurbitaceae) shows high levels of variation in fruit color, fruit stripe pattern, seed coat color, and size. Thirty-eight accessions of C. colocynthis plants from different parts of semi-arid Rajasthan were collected and genetic diversity was assessed using random-amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 65 RAPD decamer primers, 50 primers produced 549 scorable bands of which 318 were polymorphic. Polymorphic banding patterns with the number of amplified fragments varied from 5 (OPA-08 and OPF-9) to 19 (OPT-20) in the molecular size range of 150-6000 bp. Percent polymorphism ranged from 22.2% (OPA-09) to 83.3% (OPE-12) with 55.14% polymorphism. Out of the 20 ISSR primers screened, 13 primers produced 166 amplification products, of which 99 were polymorphic. The number of bands amplified per primer varied between 9 (UBC-807, 802) and 16 (UBC-803, 812) with average band size between 250 and 4000 bp. Percent polymorphism ranged from 45.4% (UBC-815) to 73.3% (UBC-814) with 65.05% polymorphism. Dendrogram constructed on the basis of RAPD + ISSR polymorphism separated the accessions into four distinct clusters at 72% variation with Jaccard's similarity coefficient ranging from minimum 0.64 to 0.95. The matrices for RAPD and ISSR were also compared using Mantel's test and obtained correlation value (r = 0.7947). Discriminating power of RAPD and ISSR markers was assessed by calculating polymorphic information content, multiplex ratio, marker index, and resolving power. Approx. 50% RAPD and ISSR markers showed PIC value and heterozygosity (H) ≥ 0.50, indicating marker as informative. The primers that showed higher polymorphism had higher RP, MR, and MI values.
Full Text Available In 1991, the poinsettia strain, silverleaf whitefly or B biotype of Bemisia tabaci was detected in Brazil. This variant is a far more serious agricultural pest than the previously prevalent non-B (BR biotype. The correct identification of B. tabaci is problematic since it is highly polymorphic with extreme plasticity in key morphological characters that vary according to the host. RAPD-PCR was used to survey the B biotype and other biotypes of B. tabaci in Brazil. Whiteflies were collected from cultivated plants and weeds from 57 different localities and on 27 distinct crops. RAPD analyses using two selected 10-mer primers reliably identified the BR biotype and the B biotype of B. tabaci and also differentiated other whitefly species. The presence of the B biotype was confirmed in 20 Brazilian states. The BR and B biotypes of B. tabaci were found to coexist in the whitefly populations of three different localities: Jaboticabal, SP; Rondonópolis and Cuiabá, MT, and Goiânia, GO.Em 1991, um novo biótipo de Bemisia tabaci denominado de raça B, mosca branca da poinsétia ou mosca da folha prateada foi detectado no Brasil. Esta praga trouxe muitos prejuízos e danos à agricultura nacional, por ser mais agressiva do que a existente anteriormente, conhecida como B. tabaci ou B. tabaci biótipo BR (não B. A relação taxonômica entre B. tabaci e B. tabaci biótipo B não é clara e não existem evidências morfológicas consistentes que possam distinguir esses dois biótipos. RAPD-PCR tem sido utilizada para identificação de biótipos presentes nas populações, utilizando-se, como padrões de referência, adultos de Bemisia tabaci das raças A e B provenientes dos Estados Unidos. As coletas de mosca branca foram feitas em 27 culturas e plantas daninhas em 57 localidades do país. As populações foram então analisadas, observando-se que a população predominante em 20 estados brasileiros é de B. tabaci biótipo B. Os biótipos BR e B foram
Full Text Available Many factors have contributed to the destruction of fish habitats. Hydroelectric dams, water pollution and other environmental changes have resulted in the eradication of natural stocks. The aim of this study was to detect the genetic variation in Prochilodus marggravii from three collection sites in the area of influence of the Três Marias dam (MG on the São Francisco river (Brazil, using the RAPD technique. The results obtained revealed that the fish in the downstream region nearest the dam have a higher similarity coefficient than those from the other sampling sites that may be related to differences in environmental characteristics in these regions. Additionaly, significant differences in the band frequencies were observed from one collection site to another. These both findings suggest the occurrence of a structured population and have important implications for the conservation of the genetic variability of distinct natural P. marggravii stocks.
Maria do Desterro M dos Santos
Full Text Available Onion is a crop of significant socioeconomic importance to Brazil. Onion germplasm with adaptation to tropical and sub-tropical conditions has played an important role in the development of this crop in the country. In this context, we studied the genetic diversity in a germplasm collection potentially useful for the development of cultivars for tropical and subtropical regions. The genetic variability of 21 accessions/cultivars that have been used as germplasm and/or were developed by onion breeding programs in Brazil was evaluated via RAPD markers. The following accessions were included in the study :'Red Creole', 'Roxa IPA-3', 'Valenciana 14', 'Beta Cristal', 'Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Alfa Tropical', 'Pêra IPA-4', 'Primavera', 'Belém IPA-9', 'Crioula Alto Vale', 'Conquista', 'Pira-Ouro', 'Vale-Ouro IPA-11', 'Franciscana IPA-10', 'Serrana', 'CNPH 6400', 'Petroline', and 'Baia Periforme'. From the 520 primers used in the initial screening only 38 displayed stable polymorphisms. They produced 624 amplicons, of which 522 (83.7% were monomorphic and 102 (16.3% were polymorphic. An average similarity coefficient of 0.72 was calculated among accessions based upon this subgroup of polymorphic amplicons. This allowed the discrimination of this germplasm collection into six groups with only one of them comprising more than one accession. The main group was formed by 16 accessions ('Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Conquista', 'Pira-Ouro', 'Serrana', 'Vale-Ouro IPA-11', 'Baia Periforme', 'Primavera', 'Franciscana IPA-10', 'Belém IPA-9', 'Crioula Alto Vale', 'Petroline', 'Pêra IPA-4' and 'Alfa Tropical', for which the genetic origin (with few exceptions can be traced back to the variety 'Baia Periforme'. The populations 'Red Creole', 'Roxa IPA-3', 'Beta Cristal', 'CNPH 6400', and 'Valenciana 14' comprised a set of five isolated groups, showing genetic divergence among them and in
Full Text Available Analysis of karyotype, nuclear DNA content and RAPD markers were performed in four species of Bruguiera (Rhizophoraceae of Bhitarkanika mangrove forests, Orissa, India. Detailed karyotype analysis revealing 2n=34 in B. cylindrica and 2n=36 in B. gymnorrhiza was reported for the first time and 2n=34 in B. parviflora and B. sexangula was confirmed. On the basis of the common types of chromosomes present among Bruguiera, two distinct groups were found; one consists of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula. The symmetrical karyotype with same chromosome types grouped B. cylindrica and B. parviflora together and presence of Type E chromosomes placed B. gymnorrhiza and B. sexangula in a separate group, suggesting their closer affinity in their respective group. Analysis of chromosome length, volume, INV and 4C DNA content confirmed this division. Nuclear DNA content was two-fold higher (~17.0 pg in the second group than in the first (~8.0 pg. The amplification products generated through RAPD revealed 1-9 amplicons with size variations from 600 bp to 2 500 bp with 49.31% genetic similarity between B. gymnorrhiza and B. sexangula and 47.10% in between B. cylindrica and B. parviflora. The high copy number marker band (~ 1 100 bp yielded in OPN-15 primer in B. parviflora the characteristic DNA marker, which was cloned and used as probes for assessment of genetic diversity, and demonstrated its close genetic affinity to B. cylindrica. B. gymnorrhiza and B. sexangula also produced similar marker bands of ~600 bp and ~2 200 bp in the same primer. All of the cytological, 4C DNA content and RAPD data confirmed the existence of two taxonomically distinct groups of Bruguiera: one consisting of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula as placed earlier (1862 in the tribe Rhizophoreae by Bentham and Hooker, on the basis of the flowering habits of Bruguiera. Genetically, the B
Ilczuk, Agnieszka; Jacygrad, Ewelina
Cornus alba L. (white dogwood) is an important ornamental shrub having a wide range of applications such as reforestation programs and soil retention systems. The vegetative propagation of dogwood by cuttings may be slow, difficult, and cultivar dependent; therefore, an improved micropropagation method was developed. Nodal stem segments of C. alba cultivars 'Aurea' and 'Elegantissima' were cultured on media enriched with six different sources of macronutrients. Media were supplemented with either N6-benzyladenine (BA) or thidiazuron (TDZ) in combination with 1-naphthaleneacetic acid (NAA). Regardless of the cultivar, the best shoot proliferation was observed on Lloyd and McCown medium (woody plant medium (WPM)) at pH 6.2, containing 1.0 mg L-1 BA, 0.1 mg L-1 NAA, and 20-30 g L-1 sucrose. Rooting of regenerated shoots was achieved by an in vitro method when different concentrations of NAA or indole-3-butyric acid (IBA) were tested. Microcuttings were rooted for 8 wk on medium enriched with 0.25 mg L-1 NAA and potted into P9 containers in the greenhouse. The final survival rate of the plants after 20 wk was 80% for 'Aurea' and 90% for 'Elegantissima'. Genetic stability of the micropropagated plants was confirmed by using two DNA-based molecular marker techniques. A total of 30 random amplified polymorphic DNA (RAPD) and 20 inter-simple sequence repeat (ISSR) primers resulted in 197-199 and 184-187 distinct and reproducible band classes, respectively, in 'Aurea' and 'Elegantissima' plantlets. All of the RAPD and ISSR profiles were monomorphic and comparable with the mother plant.
May 28, 2014 ... Apomixia, genética e melhoramento de plantas. Rev. Bras. Agrosci. 11:127-133. Ebina M, Nakagawa H, Yamamoto T, Araya H, Tsuruta I, Takahara M,. Nakajima K (2005). Co-segregation of AFLP and RAPD markers to apospory in guineagrass (Panicum maximum Jacq.).Grassland Sci. 51:71-78. Gualtieri ...
Kenia Gracielle da Fonseca
Full Text Available O Brasil é o maior produtor mundial de maracujá, entretanto tem-se observado redução na produtividade do maracujazeiro nos últimos anos, devido, principalmente, a fatores fitossanitários. Na Embrapa Cerrados, a transferência de genes de resistência de espécies silvestres para as comerciais de maracujazeiro tem sido feita por meio de hibridações interespecíficas seguidas de um programa de retrocruzamentos auxiliados por marcadores moleculares. Este trabalho teve por objetivo verificar a recuperação do genoma recorrente nas plantas RC4 e RC5 [(Passiflora edulis x Passiflora setacea x Passiflora edulis ] com base em marcadores RAPD. O estudo foi desenvolvido no Laboratório de Genética e Biologia Molecular da Embrapa Cerrados. Amostras de DNA de cada material genético (17 plantas RC4, 16 plantas RC5, Passiflora edulis e Passiflora setacea foram amplificadas para obtenção de marcadores RAPD. Foram utilizados 12 primers decâmeros para as plantas RC4 e 14 primers decâmeros para as plantas RC5. Os marcadores RAPD gerados foram convertidos em matriz de dados binários. Verificou-se alta porcentagem de marcadores polimórficos em consequência do cruzamento-base interespecífico. A menor similaridade genética foi observada entre as espécies P. edulis e P. setacea, evidenciando a grande distância genética dessas espécies.Brazil is the largest world producer of passion fruit, however, it has been observed a reduction in the productivity in recent years due, mainly, to phytosanitary factors. At Embrapa Cerrados, the transfer of resistance genes from wild to commercial species of passion fruit has been made through interspecific hybridations, followed by a backcrossing molecular marker-assisted program. The objective this work was to verify the recovery of recurrent genome at the plants RC4 and RC5 [(Passiflora edulis x Passiflora setacea x Passiflora edulis] based on RAPD markers. The study was developed at Embrapa Cerrados
Newton Alex Mayer
Full Text Available Um projeto de pesquisa visando à utilização de clones de umezeiro (Prunus mume Sieb. et Zucc. como porta-enxertos para pessegueiro [Prunus persica (L. Batsch] está sendo conduzido na FCAV/UNESP, Câmpus de Jaboticabal-SP, com promissoras perspectivas de sucesso. Três genótipos de umezeiro foram selecionados de acordo com características agronômicas desejáveis para esta finalidade. A distinção dos três genótipos entre si, baseada exclusivamente em características morfológicas, apresenta limitações. Dessa forma, o objetivo do presente trabalho foi identificar marcadores RAPD capazes de diferenciar e caracterizar os Clones 05, 15 e a cv. Rigitano (Clone 10 de umezeiro, utilizando-se das cultivares Aurora-1 e Okinawa de pessegueiro como outgroup. Dos 220 primers testados, foram selecionados 42, que amplificaram todos os cinco genótipos. Verificou-se que os marcadores RAPD permitiram a distinção entre o Clone 05, o Clone 15 e a cv. Rigitano de umezeiro, demonstrando a existência de variabilidade genética entre os mesmos. Dentre os três genótipos de umezeiro estudados, constatou-se que a similaridade genética é maior entre o Clone 05 e o Clone 15.A research project with the objective do develop mume clones (Prunus mume Sieb. et Zucc., to be used as rootstocks for peach tree [Prunus persica (L. Batsch] is been carried out at the Faculdade de Ciências Agrárias e Veterinárias (FCAV/UNESP, Jaboticabal Campus, São Paulo State, Brazil. These project showed promising perspectives of success, with three clones that were selected according to their characteristics for peach rootstock. But the distinction of the three clones among them, based only in morphologic characteristics, has presented limitations. The objective of the present research was to identify RAPD markers able to characterize and differentiate the 05 and 15 Clones and Rigitano mume cultivar, using Aurora-1 and Okinawa peach tree as outgroup. Among the 220 tested
Investigation of genetic variation and phylogenetic relationships among date palm (Phoenix dactylifera L.) cultivars is useful for their conservation and genetic improvement. Various molecular markers such as restriction fragment length polymorphisms (RFLPs), simple sequence repeat (SSR), representational difference analysis (RDA), and amplified fragment length polymorphism (AFLP) have been developed to molecularly characterize date palm cultivars. PCR-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) are powerful tools to determine the relatedness of date palm cultivars that are difficult to distinguish morphologically. In this chapter, the principles, materials, and methods of RAPD and ISSR techniques are presented. Analysis of data generated from these two techniques and the use of these data to reveal phylogenetic relationships among date palm cultivars are also discussed.
Siril, E A; Joseph, Nisha
An in vitro propagation technique based on axillary bud proliferation was developed for the first time to mature annatto (Bixa orellana L.) tree. Nodal segments cultured on Murashige and Skoog (MS) medium supplemented with 1.0 μM benzyl adenine (BA) and tender coconut water (10 %) showed significantly high (P < 0.05) explant response (67.0 %), development of elongated shoots (3.36), shoot buds (8.9) and shoot elongation (3.53 cm). Cytokinins like zeatin, isopentenyl adenine (2-iP), kinetin, or thidiazuron (TDZ) were inferior to BA to induce multiple shoots. Seasonal variations significantly affected the in vitro response of nodal explants. In vitro rooting experiments have showed 55.6 % rooting on MS medium containing 15 μM indole-3-butyric acid (IBA). Alternatively, in vitro raised shoots were rooted (61.1 %) ex vitro, by 10 mM indole-3-butyric acid (IBA) for 30 s. The results of the RAPD marker system revealed the genetic stability among the micropropagated plants. The present protocol in brief, can be used for the clonal propagation of the superior genotype and preservation of germplasm.
BISWAS MD. SANAULLAH
Full Text Available RAPD marker was used to evaluate genetic relationships among 11 genotypes of country bean, including first three genotypes were photo-insensitive and the rests were sensitive. The genotypes were grouped into two major clusters where photo-insensitive genotypes remain in cluster I and sensitive genotypes remain in cluster II. A total of 26 bands were detected, of which 57.69% were polymorphic and the remaining were monomorphic across all genotypes. A highest level of genetic distance was observed between CB04 and CB06 while the lowest level of genetic distance showed between CB01 and CB03. The highest similarity index between the genotypes CB01 and CB03 indicated less divergence between them. Low similarity indices were observed between CB04 and CB06, which indicated more divergence. Crossing between the genotypes with low similarity coefficient will manifest high heterosis. The identified genetically distinct cultivars could be potentially important source of germplasm for further improvement of country bean.
RONAN XAVIER CORRÊA
Full Text Available Four methods were applied to determine pairwise genetic distances among five soybean genotypes which are potential genitors for a mapping population. Additionally, individual plants from the most divergent pair of genotypes were evaluated by the RAPD technique to determine their degree of homozygosity. Genetic distances based on RAPD data were calculated by the modified Rogers' distance, and also by the following arithmetical complements of similarity: simple match, Nei and Li, and Gower. These genetic distances were similar, presenting a correlation coefficient ranging from 0.99 to 1.00. In all four methods lines UFV 91-717 and Ichigowase were the most divergent ones (4.53 to 21.43%. DNA samples from five plants from each of the two most divergent genotypes were amplified with 28 different primers. Among the amplified products, only five were polymorphic in each group (2.10%, demonstrating their high intragroup degree of homozygosity. These homozygosity were maintained when DNA samples from 12 plants from each of the two most divergent genotypes were amplified. These parameters were extremely useful for the confirmation of the chosen pair of genitors to generate a mapping population.Aplicaram-se quatro métodos para determinar as distâncias genéticas entre cinco cultivares de soja, que são genitores potenciais para uma população de mapeamento genético. Adicionalmente, o grau de homozigose do par de genótipos mais divergente foi avaliado por meio da técnica de RAPD. Calcularam-se as distâncias genéticas fundadas em dados obtidos pela técnica de RAPD pela distância modificada de Rogers e pelos seguintes complementos aritméticos de similaridade: distância simples; Nei e Li, e Gower. As distâncias genéticas foram similares, apresentando valores de coeficiente de correlação de 0,99 a 1,00. Nos quatro métodos, as linhagens UFV 91-717 e Ichigowase foram as mais divergentes (4,53 to 21,43%. Amostras de DNA de cinco plantas de cada
Jones, C.J.; Edwards, K.J.; Castiglione, S.; Winfield, M.O.; Sala, F.; Wiel, van de C.C.M.; Bredemeijer, G.M.M.; Vosman, B.; Matthes, M.; Daly, A.; Brettschneider, R.; Bettini, P.; Buiatti, M.; Maestri, E.; Malcevschi, A.; Marmiroli, N.; Aert, R.; Volckaert, G.; Ru, J.; eda,; Linacero, R.; Vazquez, A.; Karp, A.
A number of PCR-based techniques can be used to detect polymorphisms in plants. For their wide-scale usage in germplasm characterisation and breeding it is important that these marker technologies can be exchanged between laboratories, which in turn requires that they can be standardised to yield
Ana Paula de Andrade Aukar
Full Text Available It has been evaluated the genetic variability through the use of RAPD molecular markers on the following passionflower species: Passiflora amethystina, P. caerulea, P. cincinnata, P. coccinea, P. serrato digitata, P. foetida, P. maliformis, P. alata, P. giberti, P. laurifolia, P. macrocarpa, P. nitida, P. setacea, P. suberosa, P. ligularis, P. capsularis, P. edulis Sims and its botanical variety P. edulis Sims f. flavicarpa Deg. In this research work, the analyses of the random amplified polymorphic DNA products (RAPD were employed to estimate the genetic diversity and the taxonomic linkage within the species above. The total of 21 primers were used in this study which generated 270 different polymorphic products. It was possible to detect that the Passiflora species had shown a similarity of 17,3%, and between Passiflora edulis Sims and Passiflora edulis Sims f. flavicarpa a similarity of 34,35% has been found. The rate of similarity within edulis specie is low, making it clear that a large variability between the yellow and the purple forms exists.Foram avaliadas as variações genéticas através de marcadores moleculares RAPD, as seguintes espécies de maracujá: Passiflora amethystina, P. caerulea, P. cincinnata, P. coccinea, P. serrato digitata, P. foetida, P. maliformis, P. alata, P. giberti, P. laurifolia, P. macrocarpa, P. nitida, P. setacea, P. suberosa, P. ligularis, P. capsularis, P. edulis Sims e sua variedade botânica P. edulis Sims f. flavicarpa Deg. Neste estudo, a análise dos produtos da amplificação ao acaso do DNA polimórfico (RAPD foi usada para estimar a diversidade genética e as relações taxonômicas entre as espécies. Foram utilizados 21 "primers", que produziram um total de 270 bandas polimórficas. Verificou-se que as espécies de Passiflora apresentaram uma média de similaridade de 17,3%, e entre Passiflora edulis Sims e Passiflora edulis Sims f. flavicarpa, de 34,35%. Pode-se perceber que o valor de
Full Text Available A study was carried out to improve anther culture ability of the non-responsive cultivated oat, Avena sativa L. cv. Puhti by introgressing favourable alleles from the responsive wild red oat, Avena sterilis L. acc. CAV 2648. Anther culture ability of these parental lines and F2 progenies of their cross and two backcrosses was tested. Genotype effects were significant on all anther culture traits measured. The number of anther culture derived embryo-like structures was highest in acc. CAV 2648, and the number of green regenerants from the Puhti × CAV 2648 progeny. Anther culture response was greatly reduced in backcross progeny and was least in cv. Puhti. Random amplified polymorphic DNA (RAPD was used to test for marker associations with oat anther culture traits in a population of 38 F2 progenies. Two RAPD markers were putatively associated with improved production of green regenerants (one derived from acc. CAV 2648 and the other from cv. Puhti. One marker putatively associated with decreased albino plant regeneration (derived from acc. CAV 2648. These markers might be useful for selecting alleles for better anther culture ability among progeny of planned crosses. In addition, three markers, derived from acc. CAV 2648, were putatively associated with decreased anther culture response rates.;
Mikkelsen, T.R.; Jensen, J.; Bagger Jørgensen, Rikke
Different cultivars/transgenic lines of oilseed rape (Brassica napus) were crossed (as females) with different cultivars/populations of Brassica campestris. All cross combinations produced seed, with an average seed set per pollination of 9.8. Backcrossing of selected interspecific hybrids (as...... markers could be assigned to six linkage groups, most probably reflecting six B. napus C-chromosomes. The presence of backcross plants with recombinant genotypes suggests that complex genetic processes can take place during the interspecific hybridisation and backcrossing in these Brassica species....... The implications of our results for the possible choice nf integration sites of transgenes in oilseed rape are discussed....
Variabilidade genética de acessos silvestres e comerciais de Passiflora edulis Sims. com base em marcadores RAPD Genetic variability of wild and commercial passion fruit (Passiflora edulis Sims. accessions using RAPD markers
Full Text Available No Cerrado brasileiro, há uma grande diversidade de cores, tamanhos e aromas de frutos em acessos silvestres de P. edulis. Estes acessos também são importantes fontes de resistência a doenças, podendo ser incorporados em programas de melhoramento genético do maracujazeiro azedo. Neste trabalho, objetivou-se estimar a variabilidade genética existente em acessos silvestres e comerciais de P. edulis utilizando-se de marcadores RAPD. O DNA genômico de cada acesso foi extraído e amplificado com treze iniciadores decâmeros (OPD-04, OPD-07, OPD-08, OPD-16, OPE-18, OPE-20, OPF-01, OPF-14, OPG-05, OPG-08, OPH-04, OPH-12 e OPH-16 para a obtenção dos marcadores RAPD. Os marcadores obtidos foram convertidos em uma matriz de dados binários, a partir da qual foram estimadas as distâncias genéticas entre os acessos e realizadas análises de agrupamento e de dispersão gráfica. Um total de 187 marcadores foi gerado, sendo que apenas 28 (14,97% deles foram monomórficos. As distâncias genéticas entre os 15 acessos de maracujazeiro variaram de 0,091 a 0,496. Os marcadores moleculares demonstraram a alta variabilidade genética dos acessos de P. edulis, sendo que os acessos de frutos amarelos apresentaram maior distanciamento em relação aos de frutos roxos. Menores distâncias genéticas foram verificadas entre os acessos de mesma origem geográfica.There are a great diversity of colors, sizes and aromas of fruits in wild accessions of P. edulis in Brazilian Savannah. These accessions are also important resistance sources against illness which can be incorpored in passionfruit breeding programs. In this work, the objetive was to evaluate the genetic variability in wild and commercial P. edulis accessions using RAPD markers. The genomic DNA of each accession was extracted and amplified using thirteen decamer primers (OPD-04, OPD-07, OPD-08, OPD-16, OPE-18, OPE-20, OPF-01, OPF-14, OPG-05, OPG-08, OPH-04, OPH-12 and OPH-16 to obtain RAPD markers
Keize Pereira Junqueira
naturally vegetate on solid rocky sandstone or quartzite, tree trunks and on rocky fields sand soils at Minas Gerais, Goiás, Distrito Federal, Tocantins, Rio de Janeiro and Bahia, with strong evidences that Brazil central region is the biggest pitayas dispersion center, because of wide phenotypic diversity observed in collected accesses. We had the objective to realize genetic diversity study of 13 pitaya accesses maintained at Embrapa Cerrados germoplasm collection through RAPD (Random Amplified Polymorphic DNA molecular markers. Each access genomic DNA were extracted and fourteen decamer initiators were used to obtain RAPD molecular markers, that were converted in a binary data matrix, from where we estimate genetic distances between accesses and realize grouping and graphic dispersion analysis. 162 RAPD markers were obtained, making 11,57 markers medium per primer. From markers total, 154 (95,06% were polymorphic. Genetic distances varied within 0,088 and 0,848, biggest values observed refer to distance between Unaí, MG access and Seleção Embrapa Cerrados access. The most different access was "Unaí, MG", that showed 0,675 of genetic distance avarege in relation to others accessions. The high genetic distance verified is due to the fact that the referred accesses do not belong to the same species. Pitaya accesses groups had little relation to their geographic origin. The genetic diversity found at brazilian savannas allow to include this biome at pitaya species diversity center, showing good perspectives to studies about this fruit potential.
Egeland, Thore; Sheehan, Nuala
This paper considers identification problems based on DNA marker data. The topics we discuss are general, but we will exemplify them in a simple context. There is DNA available from two persons. There is uncertainty about the relationship between the two individuals and a number of hypotheses describing the possible relationship is available. The task is to determine the most likely pedigree. This problem is fairly standard. However, there are some problems that cannot be solved using DNA from independently segregating loci. For example, the likelihoods for (i) grandparent-grandchild, (ii) uncle-niece and (iii) half-sibs coincide for such DNA data and so these relations cannot be distinguished on the basis of markers normally used for forensic identification problems: the likelihood ratio comparing any pair of hypotheses will be unity. Sometimes, but not in the examples we consider, other sources of DNA like mtDNA or sex chromosomes can help to distinguish between such equally likely possibilities. Prior information can likewise be of use. For instance, age information can exclude alternative (i) above and also indicate that alternative (iii) is apriori more likely than alternative (ii). More generally, the above problems can be solved using linked autosomal markers. To study the problem in detail and understand how linkage works in this regard, we derive an explicit formula for a pair of linked markers. The formula extends to independent pairs of linked markers. While this approach adds to the understanding of the problem, more markers are required to obtain satisfactory results and then the Lander-Green algorithm is needed. Simulation experiments are presented based on a range of scenarios and we conclude that useful results can be obtained using available freeware (MERLIN and R). The main message of this paper is that linked autosomal markers deserve greater attention in forensic genetics and that the required laboratory and statistical analyses can be performed
, Andhra Pradesh and Tamil Nadu in India was studied using randomly amplified polymorphic DNA (RAPD) markers. Five selective primers provided distinct and consistent RAPD profiles in all the four populations. The bands in the range 400 ...
Galina-Pantoja, L.; Siggens, K.; Schriek, M.G.; Heuven, H.C.M.|info:eu-repo/dai/nl/314417818
Anim Genet. 2009 Jun 3. [Epub ahead of print] Mapping markers linked to porcine salmonellosis susceptibility. Galina-Pantoja L, Siggens K, van Schriek MG, Heuven HC. PIC/Genus, 100 Bluegrass Commons Blvd, Hendersonville, TN 37075, USA. The goal of this study was to identify pig chromosomal regions
Full Text Available Em programas de melhoramento de citros, a caracterização adequada dos recursos genéticos disponíveis é de grande importância, principalmente devido às características biológicas da cultura, como a heterozigosidade, a embrionia nucelar e o longo ciclo reprodutivo. A facilidade com que ocorrem hibridações (interespecíficas e intergenéricas e a embrionia nucelar favoreceram a formação e a preservação de novas combinações, classificadas como espécies. Neste estudo, marcadores RAPDs foram utilizados para analisar 15 acessos de Citrus spp., sendo quatro variedades de laranjeiras doce (C. sinensis Osbeck, quatro tangerineiras (C. reticulata Blanco, C. nobilis Loureiro, C. sunki Loureiro e C. deliciosa Tenore, uma laranjeira azeda (C. aurantium L., um pomeleiro (C. paradisi Macf., uma torangeira (C. grandis Osbeck, uma cidreira (C. medica L., uma limeira ácida (C. latifolia e dois híbridos (Citrus clementina T. x (C. tangerina T. x C. paradisi Macf.. Doze sequências iniciadoras aleatórias foram utilizadas para estudar os 15 genótipos, encontrando-se um grau de similaridade mínimio de 0,81 ("Simple Matching" entre as tangerineiras. Os menores graus de similaridade foram encontrados entre as espécies de Citrus menos aparentadas (C. medica, C. grandis e C. latifolia. As quatro cultivares de laranjeiras doces não puderam ser diferenciadas pelos marcadores RAPD utilizados, apresentando similaridade máxima.In citrus improvement programs the characterization of the available genetic resources is of great importance, mainly concerning biological characteristics of the culture, as the heterozigosity, nucellar the embriony and long reproductive cycle. Favored by nucellar embriony interespecific and intergeneric hybridizations and genotypes preservation happen easily. RAPDs markers were used to analyze 15 Citrus spp., four sweet orange (C. sinensis Osbeck, (C. medica, C. grandis e C. latifolia, four mandarins (C. reticulata Blanco, C
S.M. Zakiur Rahman
Full Text Available Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822 in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001 departure from homogeneity and the F ST values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.
Dhakshanamoorthy, Dharman; Selvaraj, Radhakrishnan; Chidambaram, Alagappan
The presence of important chemical and physical properties in Jatropha curcas makes it a valuable raw material for numerous industrial applications, including the production of biofuel. Hence, the researcher's interest is diversified to develop more and better varieties with outstanding agronomic characteristics using conventional breeding. Among these, mutation breeding is one of the best approaches to bring genetic changes in plant species. The aim of this study is to evaluate the diversity and genetic relationship among J. curcas mutants, which were obtained from different doses of gamma rays (control, 5 Kr, 10 Kr, 15 Kr, 20 Kr and 25 Kr) and EMS (1%, 2%, 3% and 4%), using RAPD marker. Among the 21 random primers, 20 produced polymorphic bands. The primers, OPM-14 and OPAW-13, produced a minimum number of bands (3) each across the ten mutants, while the primer OPF-13 produced the maximum number of bands (10), followed by the primers OPU-13, OPAM-06, OPAW-09 and OPD-05, which produced 9 bands each. The number of amplicons varied from 3 to 10, with an average of 7 bands, out of which 4.57 were polymorphic. The percentage of polymorphism ranged from 0.00 to 100 with an average of 57%. In the present study, RAPD markers were found most polymorphic, with an average polymorphism information content (PIC) value of 0.347, effective multiplex ratio (EMR) of 35.14, marker index (MI) of 14.19, resolution power (Rp) of 11.19, effective marker index (EMI) of 8.21 and genotype index (GI) of 0.36, indicating that random primers are useful in studies of genetic characterization in J. curcas mutant plants. In a dendrogram constructed based on Jaccard's similarity coefficients, the mutants were grouped into three main clusters viz., (a) control, 10 Kr, 15 Kr, 20 Kr, 2% EMS, and 3% EMS, (b) 5 Kr and 1% EMS, and (c) 25 Kr and 4% EMS mutants. Based on the attributes of the random primers and polymorphism studied, it is concluded that RAPD analysis offers a useful molecular marker
Full Text Available The Random Amplified Polymorphic DNA (RAPD technique was used to study the genetic diversity of four Elops machnata populations in South India. Elops machnata is considered as a least concern species (LC, categorized by the International Union for Conservation and Nature (IUCN. The population trends are currently stable in Indian Ocean, Eastern Africa, but are unknown throughout the rest of its expansive range, especially in Indian estuaries. Among the ten RAPD primers tested, eight primers got amplified and gave scorable bands. In total, 119 scorable bands were observed in all populations. The overall observed and effective number of alleles was found to be 2.000 ± 0.000 and 1.5307 ± 0.2503 respectively for the entire population. The overall polymorphic loci were 61.00% and the overall gene flow among the four populations was predicted to 0.1032. The genetic distance and geographic distance between the four populations showed a positive correlation. The highest genetic similarity (0.6824 was found between Parangipettai and Muthupettai population, which reflected the geographical relationship between them. Tow main clusters were obtained based on UPGMA dendrogram. This study proves that RAPD analysis has the ability to discriminate E. machnata populations in South Indian coastal waters.
Mohammed H. Abass
Full Text Available Genetic stability and uniformity of in vitro-derived date palm plants has a major importance to ascertain true-to-typeness of produced plants. The goal of present study was to evaluate the genetic toxicity of different plant growth regulators on date palm callus at initiation stages using protein patterns and RAPD analysis. Date palm offshoots of Hillawii cultivar were dissected, apical meristems were divided into four segments and cultured on callus induction medium containing the plant growth regulators as 2,4-D at 50 and 100 mg/L; NAA at 30 mg/L and Dicamba at 10 mg/L. The changes occurred in protein profile of callus when treated with high concentration of 2,4-D (100 mg/L, including loss of normal fragments (19 and 66 KDa polypeptides in control, as well as, appearance of new fragments, while at low concentration of 2,4-D (50 mg/L and Dicamba treatment, the protein patterns showed no changes compared to control profile. Similar trends of polymorphisms were obtained with RAPD marker. The high concentration of 2,4-D produced more polymorphic fragments in comparison to control treatment. The DNA profile was identical between 2,4-D at low concentration and control. Dendrograms were generated using similarity indices of protein and RAPD results, and revealed that genetic similarity index was high between 2,4-D treatment at low concentration and control, as separated in one subcluster, followed by Dicamba and NAA, while, the highest genetic distance was obtained between 2,4-D at high concentration and control treatment and separated alone in one cluster.
Analysis of the genetic diversity in Metopolophium dirhodum (Walker (Hemiptera, Aphididae by RAPD markers Análise da diversidade genética de Metopolophium dirhodum (Walker (Hemiptera, Aphididae por meio de marcadores RAPD
Full Text Available The emergence of host-races within aphids may constitute an obstacle to pest management by means of plant resistance. There are examples of host-races within cereals aphids, but their occurrence in Rose Grain Aphid, Metopolophium dirhodum (Walker, 1849, has not been reported yet. In this work, RAPD markers were used to assess effects of the hosts and geographic distance on the genetic diversity of M. dirhodum lineages. Twenty-three clones were collected on oats and wheat in twelve localitites of southern Brazil. From twenty-seven primers tested, only four primers showed polymorphisms. Fourteen different genotypes were revealed by cluster analysis. Five genotypes were collected only on wheat; seven only on oats and two were collected in both hosts. Genetic and geographical distances among all clonal lineages were not correlated. Analysis of molecular variance showed that some molecular markers are not randomly distributed among clonal lineages collected on oats and on wheat. These results suggest the existence of host-races within M. dirhodum, which should be further investigated using a combination of ecological and genetic data.A emergência de raças hospedeiro-especialistas em afídeos pode constituir um obstáculo ao manejo de pragas por meio de plantas resistentes. Existem exemplos de raças hospedeiro-especialistas em afídeos de cereais, embora a ocorrência de raça hospedeiro-especialista no pulgão-verde-pálido-do-trigo Metopolophium dirhodum (Walker, 1849 (Hemiptera, Aphididae não tenha sido relatada ainda. Marcadores RAPD foram utilizados para avaliar os efeitos da distância geográfica e do hospedeiro sobre a diversidade genética de linhas clonais de M. dirhodum. Vinte e três clones foram coletados em aveia e trigo em doze localidades do sul do Brasil. De vinte e sete iniciadores usados para a análise, apenas quatro iniciadores mostraram polimorfismos. A análise de agrupamento por similaridade genética revelou haver quatorze
Genetic divergence among elephantgrass cultivars assessed by RAPD markers in composit samples Divergência genética entre cultivares de capim-elefante avaliada por marcadores RAPD em amostras compostas
Rogério Figueiredo Daher
Full Text Available Elephantgrass (Pennisetum purpureum Schum. is native to regions of tropical Africa and was introduced in Brazil around 1920 through plantings imported from Cuba. It is currently one of the most widespread forage plants throughout the country. At first, there were two cultivars, Napier and Mercker, with well defined characteristics. New genotypes arose and it is believed that the large number of cultivars existing today in germplasm bank is due to duplicates. DNA markers for cultivar characterization are a very valuable tool, especially in situations where morphological and isoenzymatic markers have already been used as in the case of elephantgrass. Thus RAPD markers were used to estimate the genetic divergence among the Napier group elephantgrass cultivars from the elephantgrass Active Germplasm Bank at EMBRAPA Dairy Cattle. The polymerase chain reaction with 37 arbitrary primers from the OPERON Technologies series supplied 94 polymorphic and 73 monomorphic bands. From the matrix of complement of the Nei index, cluster analysis by the Tocher optimization method formed three clusters. Pearson correlation among genetic distance estimates obtained from the DNA markers and the isoenzymatic markers showed the consistency of both the methods in assessing genetic divergence among elephantgrass cultivars. No duplicates were found in the treatments assessed.O capim-elefante (Pennisetum purpureum Schum. é nativo de regiões da África Tropical e foi introduzido no Brasil por volta de 1920, por meio de mudas provenientes de Cuba, e é, atualmente, uma das forrageiras mais difundidas em todo o país. No início de sua utilização, existiam praticamente dois cultivares com características bem definidas, Napier e Mercker. Com o decorrer do tempo, surgiram novos genótipos e acredita-se que o grande número de cultivares existentes atualmente no Banco de Germoplasma da espécie se deva à ocorrência de duplicatas. O uso de marcadores de DNA na caracteriza
Genetic diversity evaluations among 10 canola (Brassica napus) genotypes were determined using RAPD and ISSR markers. The RAPD and ISSR primers with the highest degree of polymorphism were selected. A total of 67 bands of polymorphic RAPD bands were detected out of 77 bands, with an average of 13.4 ...
Arias, Alberto; Fernández-Moreno, Mercedes; Fernández-Tajes, Juan; Gaspar, Miguel B.; Méndez, Josefina
The sword razor shell Ensis siliqua (Linnaeus, 1758) is a bivalve with a high commercial value being appreciated in fresh and processed markets. However, the genetic studies carried out in populations of E. siliqua are scarce. In this work, the genetic variability and differentiation of the sword razor shell was assessed using PCR-RFLPs of a fragment of the 16S rRNA mitochondrial gene and random amplified polymorphic loci (RAPD) in nine localities from Ireland, Spain, and Portugal. In the 314 individuals examined for the mitochondrial fragment, 12 composite haplotypes were observed; meanwhile, a unique phenotype was observed for each of the 242 individuals analyzed with 61 RAPD loci. Two of the mitochondrial composite haplotypes accounted for the majority of individuals (89.81%) and showed a remarkably disjoint distribution between Irish and Iberian samples, with the exception of Aveiro which exhibited as the most frequent haplotype the same found in Ireland. The level of variability observed for each sample was generally correlated with both types of markers and the results obtained suggest the existence of a strong population differentiation between Irish and Iberian localities, except for the Portuguese sample from Aveiro which is surprisingly closer to Irish individuals, although it is probably highly differentiated.
Divergência genética em tomate estimada por marcadores RAPD em comparação com descritores multicategóricos Genetic divergence among tomato accessions using RAPD markers and its comparison with multicategoric descriptors
Leandro SA Gonçalves
Full Text Available A estimativa da variabilidade genética existente em um banco de germoplasma é importante não só para a conservação dos recursos genéticos, mas também para aplicações no melhoramento de plantas. O presente trabalho teve como objetivo estudar a divergência genética entre 78 acessos de uma coleção de germoplasma de tomateiro, com base em 74 marcadores RAPD e correlacionar esses resultados àqueles da caracterização morfoagronômica realizada para 27 descritores. Foi utilizado o agrupamento hierárquico UPGMA para analisar os dados, observando-se a formação de 13 grupos. Esses grupos foram correlacionados a cinco descritores (hábito de crescimento, tipo de folha, cor do fruto, número de lóculos e formato do fruto. Alguns grupos apresentaram peculiaridades, a exemplo do grupo IV, que reuniu acessos com frutos no formato de pêra; o grupo VII com acessos resistentes a murcha-bacteriana e o grupo IX, que englobou acessos com folhas do tipo batata. As análises por bootstrap revelaram poucos agrupamentos consistentes. Houve correlação positiva e altamente significativa entre as matrizes geradas pelos 27 descritores qualitativos e pelos marcadores RAPD (t = 14,02. A correlação de Mantel (r = 0,39 foi altamente significativa, porém de baixa magnitude. O baixo valor verificado para esta correlação sugere que ambas as etapas de caracterização (morfoagronômica e molecular são importantes para um conhecimento mais amplo e melhor discriminação entre os acessos de tomate.The estimation of genetic variability in a germplasm bank is important not only for the conservation of the genetic resources, but also for applications in plant breeding. The genetic divergence among 78 tomato accessions was studied, based on 74 RAPD markers. Also, a correlation between the molecular profile and 27 morphological and agronomic data was performed. Cluster analysis (UPGMA, used to study the data, resulted in 13 groups that were correlated with
Full Text Available Although intraspecies researches within the black pine (Pinus nigra Arnold have a long tradition, the intraspecies taxonomy, classification and chorology are still unclear. Among the numerous reasons that have caused this situation the most important are: the absence of a study that would completely cover the whole range of this species, the impossibility of connection of results of the existing detailed studies of certain areas, and the high variability of traits which have been used so far. Since the characteristics of the molecular systematic techniques could make possible the research free of the mentioned shortages, the intention of this study was to determine the relationships among nine populations of black pine using the random amplified polymorphic DNA (RAPD. The obtained results were compared to the recent results of the morphological and anatomical analysis of the leaves of the same populations. The RAPD results clearly divided the Croatian populations from populations of Austria (subsp. nigra and Turkey (subsp. pallasiana, while among Croatian populations, as in previous study, the existence of several groups (subsp. illyrica, subsp. dalmatica and transitional population between them was noticed. It is assumed that the optimisations conducted in this study will finally make possible estimating the relationships on the level of the whole range of the black pine and the classification based on molecular traits that are probably less dependent on environmental influences than it has been the case with the characteristics mostly used so far.
CAGATCCTTTGCCACACTGA-3') and Udtg4 (5'- CGTACCTGCCAA CATA ACAG - 3') were successfully designed and could be applied as a diagnostic marker in detection of catechin content production of gambier plant. Keywords: Gambier, RAPD, specific ...
Muravenko, Olga V; Yurkevich, Olga Yu; Bolsheva, Nadezhda L; Samatadze, Tatiana E; Nosova, Inna V; Zelenina, Daria A; Volkov, Alexander A; Popov, Konstantin V; Zelenin, Alexander V
Karyotypes of species sects. Linum and Adenolinum have been studied using C/DAPI-banding, Ag-NOR staining, FISH with 5S and 26S rDNA and RAPD analysis. C/DAPI-banding patterns enabled identification of all homologous chromosome pairs in the studied karyotypes. The revealed high similarity between species L. grandiflorum (2n = 16) and L. decumbens by chromosome and molecular markers proved their close genome relationship and identified the chromosome number in L. decumbens as 2n = 16. The similarity found for C/DAPI-banding patterns between species with the same chromosome numbers corresponds with the results obtained by RAPD-analysis, showing clusterization of 16-, 18- and 30-chromosome species into three separate groups. 5S rDNA and 26S rDNA were co-localized in NOR-chromosome 1 in the genomes of all species investigated. In 30-chromosome species, there were three separate 5S rDNA sites in chromosomes 3, 8 and 13. In 16-chromosome species, a separate 5S rDNA site was also located in chromosome 3, whereas in 18-chromosome species it was found in the long arm of NOR-chromosome 1. Thus, the difference in localization of rDNA sites in species with 2n = 16, 2n = 30 and 2n = 18 confirms taxonomists opinion, who attributed these species to different sects. Linum and Adenolinum, respectively. The obtained results suggest that species with 2n = 16, 2n = 18 and 2n = 30 originated from a 16-chromosome ancestor.
Thakur, Julie; Dwivedi, Mayank D.; Sourabh, Pragya; Uniyal, Prem L.; Pandey, Arun K.
Pittosporum eriocarpum Royle, a medicinally important taxon, is endemic to Uttarakhand region of Himalaya. It has become endangered due to over-collection and the loss of habitats. As raising plants through seeds in this plant is problematic, a reliable protocol for micropropagation using nodal explants has been developed. High shoot regeneration (95%) occurred in MS medium augmented with BA 0.4mg/l in combination IBA 0.6mg/l. In vitro regenerated shoots were rooted in MS medium supplemented with three auxins, of which 0.6 mg/l indole butyric acid proved to be the best for rooting (90%) with maximum number of roots per shoot. Thereafter, rooted plants were hardened and nearly 73% of rooted shoots were successfully acclimatized and established in the field. Start codon targeted (SCoT), inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers were used to validate the genetic homogeneity amongst nine in vitro raised plantlets with mother plant. DNA fingerprints of in vitro regenerated plantlets displayed monomorphic bands similar to mother plant, indicating homogeneity among the micropropagated plants with donor mother plant. The similarity values were calculated based on SCoT, ISSR and RAPD profiles which ranged from 0.89 to 1.00, 0.91 to 1.00 and 0.95 to 1.00 respectively. The dendrograms generated through Unweighted Pair Group Method with arithmetic mean (UPGMA) analysis revealed 97% similarity amongst micropropagated plants with donor mother plant, thus confirming genetic homogeneity of micropropagated clones. This is the first report on micropropagation and genetic homogeneity assessment of P. eriocarpum. The protocol would be useful for the conservation and large scale production of P. eriocarpum to meet the demand for medicinal formulations and also for the re-introduction of in vitro grown plants in the suitable natural habitats to restore the populations. PMID:27434060
Diversidade genética de Enterolobium contortisiliquum (Vell. Morong. no Baixo Rio São Francisco, por meio de marcadores RAPD Genetic diversity of Enterolobium contortisiliquum (Vell. Morong. in the low San Francisco river by RAPD markers
Georgea da Cruz Santana
Full Text Available Enterolobium contortisiliquum Vell. Morong (Leguminosae-Mimosoideae é uma espécie muito utilizada em programas de recuperação de matas ciliares no Baixo Rio São Francisco, devido ao seu rápido crescimento inicial. Assim, o objetivo deste trabalho foi avaliar, por meio de marcadores moleculares RAPD, a diversidade genética de oito indivíduos de uma população remanescente dessa espécie, visando contribuir para a definição de estratégias de coleta de sementes. Os indivíduos estão situados em uma área de 100 ha de mata ciliar do Baixo Rio São Francisco. Para a extração do DNA, pelo método CTAB 2%, foram utilizadas folhas tenras dos indivíduos. Testaram-se 20 oligonucleotídios de 10 bases de seqüência arbitrária, cujos produtos foram separados em gel de agarose 0,8%, submetidos à eletroforese horizontal, corados com brometo-de-etídio e visualizados em luz ultravioleta. A similaridade genética entre os indivíduos foi calculada pelo Coeficiente de Similaridade de Jaccard e a construção do dendrograma, realizada utilizando-se o método UPGMA. O valor médio de diversidade genética entre as matrizes foi de 49%, variando de 33 a 85%. Os indivíduos 6 e 7 apresentaram relativa proximidade genética (67%, não sendo indicado o plantio de suas mudas ou semeadura direta para recuperação de área ciliar em locais muito próximos. A partir dos resultados observados, podem-se desenvolver estratégias para a coleta de sementes e produção de mudas, auxiliando, assim, programas de restauração ambiental.Enterolobium contortisiliquum Vell. Morong (Leguminosae-Mimosoideae is very much used in riparian forest restoration programs in the Low San Francisco River because of its fast initial growth. The objective of this work was to evaluate by RAPD molecular markers the genetic diversity of eight individuals of a remaining population of this species, in order to contribute for the definition of strategies for seed production. The
Palacios, C; González-Candelas, F
Limonium dufourii (Plumbaginaceae) is a triploid species, with apomictic reproduction, endemic to the east mediterranean coast of Spain, where it is present in only six populations with a few individuals in most of them. L. dufourii is included in the Red List of Endangered Species by the IUCN. Genetic variation and population structure in this species has been studied using RAPDs. Twelve different primers provided 124 reliable bands of which 33 were polymorphic among the 165 individuals analysed. Those polymorphic bands were able to define 44 different patterns, of which all but six were present in only one population. Several methods for statistical evaluation have been used for intra- and interpopulation analysis of genetic variability. Relationships among patterns have led to the identification of four main clusters. Two of them show a perfect correspondence to the population of origin of those individuals that present them (Cullera and Torreblanca), and the other two (Groups A and B) include patterns found in individuals coexisting in the same populations (Marjal del Moro populations) and in El Saler. Most of the variation found in this species is due to differences among populations as shown by the analysis of molecular variance. This agrees with the expectation for an apomictic species such as L. dufourii. The analysis of homogeneity of variance shows that substantial differences in the amount of genetic variability present in the six populations exist. These results have been used to understand the evolutionary and demographic history of L. dufourii, which is a requisite in order to establish efficient conservation measures for this species.
Sánchez, M Concepción; Martínez, M Teresa; Valladares, Silvia; Ferro, Enrique; Viéitez, Ana M
Experiments were performed to determine the influence of maturation medium carbohydrate content on the rates of germination and plantlet conversion (root and shoot growth) of somatic embryos from four embryogenic lines derived from leaf or internode explants of Quercus robur L. seedlings. The conversion rate was favoured by high carbohydrate content as long as the maturation medium contained at least 2% sucrose, which was necessary for healthy embryo development. Given this, sorbitol and mannitol favoured the conversion rate more efficiently than sucrose, the highest rate, 32%, being achieved by medium with 6% sorbitol and 3% sucrose. Maturation treatment did not affect the root or shoot lengths of converted embryos. In supplementary experiments, 2 weeks of gibberellic acid treatment between maturation and germination treatments did not improve germination rates, but did reduce root length and the number of leaves per regenerated plantlet. In the four embryogenic lines tested, plant recovery rate was enhanced by inclusion of benzyladenine into the germination medium following culture of the embryos on maturation medium with 6% sorbitol and 2-3% sucrose. In embryogenic systems it is important to assess the uniformity of the regenerants. Random amplified polymorphic DNA (RAPD) analysis using 32 arbitrary oligonucleotide primers was performed to study variability in DNA sequences within and between four embryogenic lines. No intraclonal nor interclonal polymorphism was detected between embryogenic lines originating from different types of explant from the same seedling, but every one of the primers detected enough polymorphism among clones originating from different plants to allow these three origins to be distinguished. No differences in DNA sequences between regenerated plantlets and their somatic embryos of origin were detected, but a nodular callus line that had lost its embryogenic capacity was found to be mutant with respect to three other clones originating
Genetic Diversity Evaluation of Moringa Oleifera, Lam From East Flores Regency Using Marker Random Amplified Polymorphic DNA (RAPD) and Its Relationship to Chemical Composition and in Vitro Gas Production
Kleden, Markus Miten; Soetanto, Hendrawan; Kusmartono, Kusmartono; Kuswanto, Kuswanto
The research objective was to evaluate the genetic diversity of Moringa oleifera, Lam (MO) and its relationship to chemical composition and in vitro gas production (IVGP). Fresh MO leaves were kept frozen in ice gels pack until laboratory analysis. Four methods applied: RAPD marker for measuring DNA concentration and purification; Kjeldhal and HPLC for analysing proximate and amino acid (AA) composition; and IVGP. MO's four distinct morphology found: green, red, reddish green and aromatic gre...
Diversidade genética entre híbridos de laranja-doce e tangor 'Murcott' avaliada por fAFLP e RAPD Genetic diversity among hybrids of sweet orange and 'Murcott' tangor evaluated by fAFLP and RAPD markers
Full Text Available O objetivo deste trabalho foi avaliar a diversidade genética em uma população de 148 híbridos de tangor 'Murcott' (Citrus reticulata Blanco x C. sinensis L. Osbeck e laranja 'Pêra' (C. sinensis L. Osbeck obtidos por polinização controlada, pelo uso de marcadores fAFLP e RAPD. Marcadores polimórficos (416 marcadores fAFLP e 33 RAPD foram utilizados para avaliar a similaridade genética entre os híbridos, calculada com o coeficiente Jaccard pelo método UPGMA. A consistência de cada agrupamento foi determinada pelo programa BOOD. Houve alta similaridade genética entre os parentais. A laranja 'Pêra' apresentou maior número (132 de loci em heterozigose em relação ao tangor 'Murcott' (105, corroborando a teoria de origem híbrida para a laranja-doce. Observaram-se dois grupos distintos de plantas, e um deles abrangeu 80% dos híbridos com maior similaridade com a laranja 'Pêra'. A análise bootstrap não revelou consistência estatística entre esses grupos. Marcadores fAFLP são mais eficientes na avaliação do polimorfismo, sendo indicados para seleção de indivíduos híbridos mais próximos a um dos parentais.The objective of this work was to evaluate the genetic diversity in a population of 148 hybrids of 'Murcott' tangor (Citrus reticulata Blanco x C. sinensis L. Osbeck and 'Pêra' sweet orange (C. sinensis L. Osbeck, obtained by controlled polination, using fAFLP and RAPD markers. Polymorphic markers (416 fAFLP and 33 RAPD markers were used to evaluate genetic similarity among the hybrids, calculated by the coefficient of Jaccard, using the UPGMA method. The consistency of each group was determined by software BOOD. There was high genetic similarity within the parents. 'Pêra' sweet orange had a higher number of loci in heterozygosis (132 compared to 'Murcott' tangor (105, supporting the theory of hybrid origin for sweet oranges. Two distinct groups of plants were observed: one group had 80% of the hybrids that displayed
Prioli Sônia M.A.P.
Full Text Available Astyanax fishes are among the most important food-web components of South America rivers. In the Iguaçu River basin, the Astyanax genus is represented mainly by endemic species. For millions of years, that hydrographic basin has been geographically isolated from the Paraná River basin by the Iguaçu Falls. Recently, a species from the Upper Paraná River basin identified as Astyanax bimaculatus was revised and described as a new species named Astyanax altiparanae Garutti & Britski, 2000. Fauna endemism and geographic isolation triggered interest in investigations to evaluate the identification and genetic relatedness among two A. altiparanae populations from the Upper Paraná River basin and the population identified as A. bimaculatus in the Iguaçu River, upstream from the Iguaçu Falls. Mitochondrial DNA sequences and RAPD markers revealed high genetic diversity within each population, as well as low genetic distance, high gene flow, and high mitochondrial DNA similarity among all three populations. In conjunction with morphological similarities, these results demonstrated that the population presently known as Astyanax bimaculatus in the Iguaçu River should actually be stated as Astyanax altiparanae. Furthermore, it could be inferred that the A. altiparanae population is not endemic and most likely it was recently introduced in the Iguaçu River basin, maintaining the ancestral genetic identity.
Pereira, J C; Lino, P G; Leitão, A; Joaquim, S; Chaves, R; Pousão-Ferreira, P; Guedes-Pinto, H; dos Santos, M Neves
Restocking and stock enhancement programs are now recognized as an important tool for the management of fishery resources. It is important, however, to have an adequate knowledge on the genetic population structure of both the released stock and the wild population before carrying out such programs. In this study, random amplified polymorphic DNA (RAPD) markers were applied to assess genetic diversity and population structure of wild and hatchery populations of the white seabream Diplodus sargus and the common two-banded seabream D. vulgaris (Sparidae). The estimated values for intrapopulation genetic variation, measured using the percentage of polymorphic loci (%P), Shannon index (H'), and Nei's gene diversity (h), showed high values for all populations. The percentage of genetic variation within D. sargus and D. vulgaris populations, based on coefficient of gene differentiation, reached 82.5% and 90% of the total genetic variation, respectively. An undeniable decrease in genetic variation was found in both hatchery populations, particularly in D. sargus, compared to the wild ones. However, the high values of variation within all populations and the low levels of genetic variation among populations did not indicate inbreeding or depression effects, thus indicating a fairly proper hatchery management. Nevertheless, the results of this study highlight the importance of monitoring the genetic variation of hatchery populations, particularly those to be used in restocking programs. The creation of a genetic baseline database will contribute to a more efficient conservation management and to the design of genetically sustainable restocking programs.
Diversidade genética de Chenopodium ambrosioides da região cacaueira da Bahia com base em marcadores RAPD Genetic diversity based on RAPD markers of Chenopodium ambrosioides from the cocoa region of Bahia State, Brazil
Simone Gualberto Santos
Full Text Available Chenopodium ambrosioides L., conhecida no Brasil por suas propriedades medicinais e usada principalmente para o controle de verminoses intestinais, é pouco estudada quanto à diversidade genética. O objetivo deste trabalho foi avaliar a diversidade genética de 16 indivíduos de C. ambrosioides, provenientes de diferentes municípios da região cacaueira da Bahia, pela técnica de RAPD (DNA polimórfico amplificado ao acaso. Apenas 6,9% das 216 bandas RAPD amplificadas foram polimórficas e a análise de agrupamento evidenciou que não há formação de grupos por área de coleta. Portanto, há pequena variabilidade entre os materiais e esta variabilidade encontra-se distribuída entre as regiões amostradas.Chenopodium ambrosioides L. is known in many parts of Brazil for its medicinal properties, mainly used to control intestinal worms. Its genetic diversity is little studied. The objective of this work was to evaluate the genetic variability of 16 accessions of C. ambrosioides from the cocoa region of Bahia State, Brazil, by the RAPD technique (Random Amplified Polymorphic DNA. Only 6.9% of the 216 amplified RAPD bands were polymorphic and the pattern of dispersion of individuals showed no clustering related to sample site. Therefore, there is low variability among accessions and it is distributed among the accessions from the entire sampled region.
Daniela Cristina Bruel
Full Text Available The objective of this work was to evaluate the genetic diversity of 16 maize inbred lines, and to determine the correlation between genetic distance and hybrid performance, using random amplified polymorphic DNA (RAPD molecular markers. Twenty-two different random primers were used, which resulted in the amplification of 265 fragments, 237 (84.44% of them being polymorphic. A genetic similarity matrix was created from the RAPD data, using Jaccard coefficient, and a dendrogram was constructed. Hybrid analyses were carried out using random block design and Griffing method VI for diallel crossings. The genetic associations showed five distinct heterotic groups. Correlations between genetic divergences detected by RAPD, as well as the means observed in the diallel crossings were positive and significant for plant height, ear height, prolificacy, and grain weight. The correlation of genetic divergences, detected by RAPD, and the specific combining ability between heterotic group associations, showed significance in all characteristics under study, except prolificacy. A direct relationship between genetic divergence and productivity was found in 79.2% of the 120 hybrids confirming the hypothesis that genetic divergence is directly related to the performance of hybrids and is efficient in predicting it.Este trabalho teve por objetivo utilizar marcadores moleculares de DNA (RAPD, para analisar a diversidade genética entre 16 linhagens elite de milho e estimar a correlação entre a distância e o desempenho de híbridos. Vinte e dois primers aleatórios resultaram na amplificação de 265 fragmentos, dos quais 237 (84,44% foram polimórficos. A partir dos marcadores RAPD, uma matriz de similaridade genética foi gerada, tendo-se usado o coeficiente de Jaccard, e um dendrograma foi construído. Para a avaliação dos híbridos resultantes dos dialelos, utilizaram-se blocos ao acaso e o método IV de Griffing. As associações genéticas obtidas
Marcadores moleculares RAPD e descritores morfológicos na avaliação da diversidade genética de goiabeiras (Psidium guajava L. = RAPD molecular markers and morphological descriptors in the evaluation of genetic diversity of guava (Psidium guajava L.
Aroldo Gomes Filho
Full Text Available O conhecimento da variabilidade genética e fenotípica entre diferentes acessos de goiabeiras é importante para se apoiar programas de melhoramento dessa espécie na região Norte Fluminense que carece de novas culturas capazes de gerar renda aos produtores locais. O objetivo deste trabalho foi avaliar a divergência genética entre seis cultivares e 19 acessos de goiabeiras, por meio de marcadores moleculares RAPD e características morfoagronômicas. Foram obtidas 117 marcas polimórficas, utilizando-se 28 iniciadores. Os resultados mostraram uma concordância parcial entre os métodos de agrupamentos estudados, com a formação de 12 grupos. O acesso Vita 3 e o acesso 6 foram os mais divergentes, apresentando distância genética de 0,663. A análise comparativa dos agrupamentos revelou que os marcadores RAPD e os descritores morfológicos foram eficientes para discriminação dos acessos e que houve variabilidade genética potencial para uso em Programa de Melhoramento Genético.The knowledge of the genetic and phenotypic variability among different accessions of guava is important for supporting improvement programs of this specie in northern Rio de Janeiro state, which needs new cultivars able to generate income for local farmers. This work aimed to evaluate the genetic divergence among six cultivars and 19 accessions of guava via RAPD molecular markers and morphologicalcharacteristics. One hundred and seventeen polymorphic markers were obtained from 28 primers. The results showed a partial agreement between the methods of studied groupings, with the formation of 12 groups. The accessions ‘Vita 3’and ‘6’ were the most divergent, showing genetic distance of 0.663. The comparative analysis of groupings showed that RAPD markers and morphological descriptors were effective in discriminating the accessions and to show potentialgenetic variability useful in genetic improvement programs.
Sep 15, 2009 ... ginseng (Um et al., 2001). Naugzemys et al. (2007) analyzed Lonicera caerulea germplasm accessions using. RAPD markers and found that RAPD analysis is efficient for genotyping of accessions. DNA polymorphism signifi- cantly exceeds the morphological diversity of the sam- ples. A total of 105 bands ...
[Panwar P., Nath M., Yadav V. K. and Kumar A. 2010 Comparative evaluation of genetic diversity using RAPD, SSR and cytochome P450 gene based markers ... sity analysis, the present study aimed to evaluate the relative usefulness of RAPD .... primer ranged from 3 to 15, and size of the products ranged from 300 bp to ...
Jun 6, 2011 ... of polymorphic bands, average number of alleles per locus, effective .... Materials for DNA isolation were obtained from a set of 5 to 7 plants ..... Among factors that might have contributed to ... Inheritance of RAPDs in F1 hybrids of corn. ... by using cluster analysis of RAPD molecular marker, phenotype and.
Singh, Reetika; Kashyap, Sarvesh Pratap; Kumari, Nishi; Singh, Major
Somatic embryogenic system was developed in Sapindus mukorossi Gaertn. using rachis as explants from a mature tree. Explants showed callus initiation on Murashige and Skoog medium supplemented with TDZ (1-Phenyl-3-(1, 2, 3-thiadiazol-5-yl) urea), zeatin or 6-benzylaminopurine. Induction of somatic embryogenesis was achieved on both MS basal medium and MS medium supplemented with 8.88 µM 6-benzylaminopurine. Hundred percent embryogenesis was observed on MS medium supplemented with 8.88 µM 6-benzylaminopurine with maximum intensity of embryogenesis (51.92 ± 0.40 a). Maximum maturation of somatic embryos (92.86 ± 0.34 a) was observed on induction medium supplemented with 0.0378 µM abscisic and treated for 21 days. Germination of somatic embryos was maximum (77.33 ± 0.58 a) on MS medium supplemented with 8.88 µM 6-benzylaminopurine. In vitro raised plantlets were hardened, acclimatized and transferred to the field. Survival frequency of plantlets was 80 % in field conditions. The genetic fidelity of in vitro regenerated plants was also evaluated and compared with mother plant using random amplified polymorphic DNA and inter simple sequence repeat. Both markers showed similarity in molecular profile of mother plant and in vitro regenerated plants.
Wang, Ting; Su, Ying-juan; Li, Xue-Yan; Zheng, Bo; Chen, Guo-Pei; Zeng, Qing-Lu
RAPD markers and sequences of chloroplast DNA (cpDNA) atpB-rbcL intergenic spacers were used to characterize the pattern of genetic variation and the phylogenetic relationships of the relict populations of Alsophila spinulosa located in Jian Feng Ling (JFL) and Diao Luo Shan (DLS), Hainan, and Tang Lang Shan (TLS), Ding Hu Shan (DHS), and Da Xi Shan (DXS), Guangdong, of southern China. 28 random primers generated 118 bands, out of which 26 (22.03%) were polymorphic loci, distinguishing 17 different RAPD phenotypes. Percentage of polymorphic loci, Shannon phenotypic diversity and Nei's gene diversity comprehensively indicated that JFL possessed the highest diversity, TLS and DHS in intermediate and DLS or DXS the least; the corresponding values of the population appeared correlated with the population size. Differentiation was detected among populations of A. spinulosa (1-Hpop/Hsp=0.7453, GST=0.7763, and phist=0.8145). AMOVA showed that 47.44% of the variance was partitioned among regions (Hainan and Guangdong), 34.01% attributed among populations within regions, whereas only 18.55% occurring within populations. Low level of intra-specific diversity was maintained in A. spinulosa with Shannon diversity and gene diversity merely 0.0560 and 0.0590, repectively. Sequence length of atpB-rbcL intergenic spacer varied from 724 bp to 730 bp. Base composition was with A+T content between 63.17% and 63.70%. 13 haplotypes of atpB-rbcL noncoding spacers were identified. UPGMA dendrogram of RAPD phenotypes, principal components analysis based on RAPD patterns, minimum spanning network and neighbour-joining (NJ) tree established on atpB-rbcL haplotypes consistently suggested the geographical subdivision of populations of A. spinulosa between Hainan and Guangdong. Breeding system and conservation strategy of A. spinulosa was discussed based on the information of population genetic structure and variation.
DGGE-RAPD) was used to overcome the main drawbacks of RAPD (i.e., the low levels of reproducibility and polymorphism). As a model, six barley cultivars of known origin were tested for RAPD markers using DGGE methodology with 29 ...
Correlação entre heterose e divergência genética estimadas por cruzamentos dialélicos e marcadores moleculares rapd em populações de milho-pipoca Correlation between heterosis and genetic divergence estimated of diallel crosses and rapd molecular markers in populations of popcorn
Danilo Antonio Rinaldi
Full Text Available Com o objetivo de correlacionar a heterose, estimada através de cruzamentos dialélicos, com a divergência genética obtida pelo uso de marcadores moleculares RAPD, oito populações de milho-pipoca (1-PASHA, 2-PAPA, 3-PAAPC, 4-PO, 5-ZL, 6-CMS 042, 7-RS 20 e 8-CMS 43 foram intercruzadas em esquema dialélico completo, sem recíprocos, no ano agrícola de 2002/2003, gerando 28 híbridos. A avaliação dos híbridos foi realizada no ano agrícola de 2003/2004, em Londrina e Ponta Grossa, PR, em um ensaio com trinta e oito tratamentos, constituídos de vinte e oito combinações híbridas, oito parentais e duas testemunhas (IAC 112 e IAC TC01. O delineamento experimental utilizado foi o de blocos casualizados com três repetições. Foram avaliados seis caracteres: massa de grãos, capacidade de expansão, altura de planta, altura de espiga, prolificidade e florescimento feminino. Foi utilizada a técnica de RAPD para a obtenção das estimativas de distâncias genéticas entre as populações. Os resultados inferem em correlações positivas e significativas entre a divergência genética detectada pelos marcadores RAPD e massa de grãos, altura de plantas, altura de espiga e prolificidade, dos vinte e oito híbridos avaliados no dialelo em estudo. Para capacidade de expansão, florescimento e heterose percentual não foi detectada correlação significativa com a divergência genética.The objective of this study was to correlate the heterosis evaluated by diallel complete design with the genetic divergence estimated through the use of RAPD markers. Eight popcorn populations (1-PASHA, 2-PAPA, 3-PAAPC, 4-PO, 5-ZL, 6-CMS 42, 7-RS 20 and 8-CMS 43 were intercrossed on a complete diallel scheme, without reciprocal crosses, during 2002/2003 summer season, resulting in 28 hybrids. Hybrid evaluations were accomplished in the 2003/2004 summer season, at Londrina and Ponta Grossa, PR, in a trial with thirty-eight treatments, including all hybrid
The sequence of this fragment was used to design a new combination of primers that developed a second SCAR marker, designated as 61R-M2. Subsequent analysis of the three markers, E-ACT/M-CAA524, 61R and 61M2 showed that they are linked to each other by 0.6 centimorgans (cM). The utility of these SCARs in ...
Oct 10, 2011 ... Both RAPD markers and PPO genes data were scored as binary system where 1 and 0 indicated the presence or absence of a particular band respectively. Data were analyzed using NT-SYS-pc. (Numerical taxonomy and multivariate analysis system) program. Both AFLP and protein gels were scored as ...
A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt ...
May 28, 2014 ... Panicum maximum Jacq. is an important forage grass of African origin largely used in the tropics. The genetic breeding of this species is based on the hybridization of sexual and apomictic genotypes and selection of apomictic F1 hybrids. The objective of this work was to identify molecular markers linked to.
Ross, K. G.; Shoemaker, D. D.; Krieger, M. J.; DeHeer, C. J.; Keller, L.
We used 30 genetic markers of 6 different classes to describe hierarchical genetic structure in introduced populations of the fire ant Solenopsis invicta. These included four classes of presumably neutral nuclear loci (allozymes, codominant random amplified polymorphic DNAs (RAPDs), microsatellites, and dominant RAPDs), a class comprising two linked protein-coding nuclear loci under selection, and a marker of the mitochondrial DNA (mtDNA). Patterns of structure revealed by F statistics and ex...
Freqüência de híbridos em cruzamento entre tangerina 'cravo' e laranja 'pêra': análise de marcadores morfológicos e RAPD Hybrid frequency between tangerine 'cravo' and orange 'pêra' crossing: analysis of morphological and RAPD markers
ROBERTO PEDROSO DE OLIVEIRA
Full Text Available Os objetivos deste trabalho foram avaliar a freqüência de híbridos de cruzamento entre tangerina 'Cravo' (Citrus reticulata Blanco e laranja 'Pêra' (Citrus sinensis (L. Osbeck, o uso de marcadores morfológicos e moleculares (RAPD na identificação precoce de plantas zigóticas, e a variabilidade dos híbridos. A porcentagem de híbridos foi maior na população germinada em placas de Petri (19,4%. Verificou-se que quanto maior a competição entre os "seedlings" por espaço e nutrientes, menor a freqüência de plantas híbridas. A identificação dos híbridos não foi possível apenas com o uso de marcadores morfológicos. A análise morfológica dos híbridos revelou elevada variabilidade.The objectives of this work were to evaluate the hybrid frequency from the cross between tangerine 'Cravo' (Citrus reticulata Blanco and sweet orange 'Pêra' (Citrus sinensis (L. Osbeck, the use of morphological and RAPD markers for early identification of zygotic plants between parents with similar phenotype, and the morphological variability among the hybrids. Plants germinated on Petri dishes showed the higher hybrid percentage (19.4%. Hybrid plant frequency was inversely proportional to the competition level for space and nutrients among the hybrids. Accurate hybrid identification is not possible using morphological markers alone. The hybrids selected showed high morphological variability.
Full Text Available As an aim in sustainable agriculture, biological control of plant diseases has received intensive attention mainly as a response to public concern about the use of chemical fungicides in the environment. Soil Actinomycetes particularly Streptomyces spp. enhance soil fertility and have antagonistic activity against wide range of plant pathogens. To investigate for biocontrol means against the pathogen, 30 isolates of Actinomycetes have been isolated from agricultural soils of Kerman province of Iran and assayed for antagonistic activity against Botrytis allii, the agent of onion gray mold. RAPD DNA analysis has been used to determine the relatedness of active and non-active isolates based on their RAPD-PCR fingerprints. PCR amplifiable DNA samples have been isolated using the CTAB method and amplified fragments have been obtained from 5 random 10-mer primers. Different DNA fingerprinting patterns have been obtained for all of the isolates. Electrophoretic and cluster analysis of the amplification products has revealed incidence of polymorphism among the isolates. A total of 138 bands, ranging in size from 150-2800 bp, have been amplified from primers which 63.7% of the observed bands have been polymorphic. Genetic distances among different varieties have been analyzed with a UPGMA (Unweighted pair-group method, arithmetic average-derived dendrogram. Resulting dendrogram has showed from 0.65 to 0.91 similarities among varieties and divided the isolates into five major groups. Isolates which haven’t had any antagonistic activity against B. allii have been separated into a group and other isolates classified into four groups. The results indicate that RAPD is an efficient method for discriminating and studying genetic diversity of Streptomyces isolates.
Felipe Oliveira Vilela
Full Text Available The aim of this research was to study the effects of recurrent selection on the genetic variability of UNB-2U popcorn population after three cycles of recurrent selection (mass selection, full-sib selection and S1 families based on RAPD markers in 30 progenies from each selection cycle. There was no significant variation between the C0 and C2 cycles based on RAPD, showing that the use of different recurrent selection strategies in the cycles did not decrease genetic variability, due to the size of the population selected in the different cycles. The significant difference observed between mean values of C1 and C2 cycles was attributed to the smaller population size in C1 generation. Individuals were distributed into three large clusters and 20% of the individuals were placed in a groupdifferent from their original cycle. This can be explained by alleles’ transference from one generation to another and by the relationship between cycles.Com o objetivo de averiguar o impacto da seleção recorrente navariabilidade genética de progênies da população de milho pipoca UNB-2U, após 3 ciclos de seleção recorrente por diferentes métodos (massal, irmãos completos e famílias S1, 30 progênies de cada ciclo foram avaliadas por marcadores RAPD. Constatou-se que não houve variação molecular significativa entre os ciclos C0 e C2, revelando que o uso de diferentes estratégias de seleção recorrente não promoveu estreitamento genético, em razão do tamanho populacional selecionado nos ciclos. A diferença significativa na média entre osciclos C1 e C2 é atribuída ao menor tamanho populacional da geração C1. A distribuição dendrogrâmica dos indivíduos revelou a formação de 3 grandes grupos, sendo que 20% dos indivíduos foram alocados em grupo distinto do ciclo a que pertenciam, em razão da transferência de alelos nas subseqüentes gerações, bem como da própria semelhança entre os ciclos.
Marcadores RAPD e caracteres morfoagronômicos na determinação da diversidade genética entre acessos de pimentas e pimentões RAPD markers and morphoagronomic traits in determining genetic diversity among chili peppers and sweet peppers
Fabiane Rabelo da Costa
Full Text Available A diversidade genética existente em coleções e bancos de germoplasma pode ser estimada por meio de diversos métodos, sendo que a escolha destes depende da disponibilidade dos recursos e da precisão desejada pelo pesquisador. Neste trabalho, marcadores RAPD e caracteres morfoagronômicos foram usados para estimar a divergência genética entre 52 acessos de Capsicum spp. Um total de 57 variáveis binárias geradas pela caracterização morfoagronômica e 84 bandas polimórficas obtidas a partir da análise por RAPD foram analisadas separadamente e em conjunto, permitindo a construção de três dendrogramas. Observou-se a formação de dois grupos principais, tanto na análise morfoagronômica e molecular separadamente, quanto na análise conjunta dos dados. O agrupamento dos acessos pela análise conjunta seguiu o mesmo padrão verificado para a análise molecular, que se constituiu em um grupo formado por acessos de C. baccatum e outro grupo formado pelos acessos de C. chinense, C. frutescens e C. annuum. Esse agrupamento segue a proposta vigente para a classificação de Capsicum spp. em complexos gênicos. A associação dos métodos permitiu uma melhor distinção entre os acessos, o agrupamento desses em nível de espécie e a conclusão de que não há duplicatas na coleção, demonstrando a importância do uso de diferentes técnicas na caracterização de um banco de germoplasma.The genetic diversity within collections and banks of germplasm can be estimated by different methods and their choice is dependent of the available resources and the desired precision from the researcher. In the present work, RAPD markers and morph-agronomic traits were used to estimate the genetic divergence among 52 Capsicum spp. accessions. Fifty-seven binary variables from morph-agronomic characterization and 84 polymorphic markers from RAPD analysis were both separately and jointly evaluated and three dendrograms were generated. Two major groups were
Maria Cristina Rocha Cordeiro
Full Text Available Actually mango (Mangifera indica, L. is considered one of the largest Brazilian fruitbusiness for the export market. Cultivar selection having high fruit quality is a fundamental step to obtain excellent results in this business. A mango breeding program based on intervarietal hybridization may produce new improved cultivars for mango growers. Mango hybrids have been obtained by controlled or open crosses. In the last one, it is important to identify the male parent because it is useful for the genetic cultivar history, thus it is important for planning further improvements. This work presents a parentage test using among others parameters RAPD (Random amplified Polymorphic DNA markers to estimate the male parent of the selected hybrids in an open cross plot by using five mango cultivars densely planted in a latin square design.Atualmente, o cultivo da mangueira (Mangifera indica, L. é considerado um dos maiores agronegócios frutícolas brasileiros para o mercado externo. A seleção de cultivares com elevada qualidade de frutos é uma etapa fundamental para o sucesso deste negócio. O melhoramento genético da mangueira, baseado em hibridações intervarietais, pode originar cultivares superiores aos padrões disponíveis no mercado, ofertando uma nova alternativa ao produtor. Híbridos de mangueira têm sido obtidos por meio de cruzamentos controlados ou abertos. Neste último, é importante identificar o genitor masculino visando a obter a história genética da cultivar além de ser importante no planejamento do melhoramento subseqüente. Este trabalho apresenta um teste de paternidade, utilizando, entre outros parâmetros, marcadores RAPD (Random Amplified Polymorphic DNA, para estimar o genitor masculino de híbridos selecionados em uma área de cruzamento aberto contendo cinco cultivares de manga plantadas em alta densidade, no delineamento experimental do quadrado latino.
Nadezhda L Bolsheva
Full Text Available The wide variation in chromosome number found in species of the genus Linum (2n = 16, 18, 20, 26, 28, 30, 32, 36, 42, 72, 84 indicates that chromosomal mutations have played an important role in the speciation of this taxon. To contribute to a better understanding of the genetic diversity and species relationships in this genus, comparative studies of karyotypes and genomes of species within section Syllinum Griseb. (2n = 26, 28 were carried out. Elongated with 9-aminoacridine chromosomes of 10 species of section Syllinum were investigated by C- and DAPI/С-banding, CMA and Ag-NOR-staining, FISH with probes of rDNA and of telomere repeats. RAPD analysis was also performed. All the chromosome pairs in karyotypes of the studied species were identified. Chromosome DAPI/C-banding patterns of 28-chromosomal species were highly similar. Two of the species differed from the others in chromosomal location of rDNA sites. B chromosomes were revealed in all the 28-chromosomal species. Chromosomes of Linum nodiflorum L. (2n = 26 and the 28-chromosomal species were similar in DAPI/C-banding pattern and localization of several rDNA sites, but they differed in chromosomal size and number. The karyotype of L. nodiflorum was characterized by an intercalary site of telomere repeat, one additional 26S rDNA site and also by the absence of B chromosomes. Structural similarities between different chromosome pairs in karyotypes of the studied species were found indicating their tetraploid origin. RAPD analysis did not distinguish the species except L. nodiflorum. The species of section Syllinum probably originated from a common tetraploid ancestor. The 28-chromosomal species were closely related, but L. nodiflorum diverged significantly from the rest of the species probably due to chromosomal rearrangements occurring during evolution.
Variabilidade genética de acessos obtidos de populações cultivadas e silvestres de maracujazeiro-doce com base em marcadores rapd Genetic diversity obtained from cultivated population and native accesses of seewt passion fruit based on rapd markers
Full Text Available O maracujazeiro-doce (Passiflora alata Curtis, devido a preços diferenciados, vem ganhando importância dentro do mercado de frutas in natura. O melhoramento genético é fundamental para elevar a qualidade e a produtividade da cultura. Os marcadores moleculares do DNA têm sido muito úteis por permitirem a obtenção de um número praticamente ilimitado de polimorfismo genético sem influência do ambiente. Objetivou-se, neste trabalho, estudar a variabilidade genética de 17 acessos de maracujá-doce, com base em marcadores moleculares RAPD. Um acesso de P. quadrangularis e um de P. edulis foram utilizados como outgroups. Amostras de DNA genômico de cada acesso foram extraídas e 11 iniciadores decâmeros (OPD 04; 07; 08 e16; OPE 18 e 20; OPF 01 e 14; OPG 08; OPH 12 e 16 foram utilizados para a obtenção dos marcadores. Os marcadores obtidos foram convertidos em uma matriz de dados binários, a partir da qual foram estimadas as distâncias genéticas entre os acessos e realizadas análises de agrupamento e de dispersão gráfica. Do total de marcadores, considerando-se apenas os acessos de P. alata, observaram-se 87 (62,12% bandas polimórficas, evidenciando a grande variabilidade intraespecífica. A análise de agrupamento realizada com base nas distâncias genéticas permitiu subdividir os 17 acessos de P. alata em, pelo menos, cinco grupos de similaridade genética. Os acessos silvestres foram os que mais contribuíram para a ampliação da base genética dos materiais estudados, abrindo perspectivas para o uso desses materiais em programas de melhoramento.Sweet passion fruit (Passiflora alata Curtis is gaining importance in the in natura fruit market due to differential value. Genetic breeding is crucial to improve crop quality and productivity. Molecular markers of DNA have been very useful by allowing obtaining a virtually unlimited number of genetic polymorphism without environment influence. This work's objective was to study the
Avaliação da fidelidade genotípica por marcadores RAPDs de brotações de pereira (Pyrus communis L. cv. Carrick, regeneradas in vitro Evaluation of the genotypic fidelity by RAPD markers of pear shoots (Pyrus communis L. cv. Carrick, in vitro regenerated
Alan Cristiano Erig
Full Text Available O objetivo deste trabalho foi avaliar a fidelidade genotípica de brotações de pereira (Pyrus communis L. cultivar Carrick, regeneradas in vitro, utilizando marcadores RAPDs. O DNA genômico foi extraído de folhas oriundas das brotações de pereira regeneradas a partir de diferentes tratamentos e de plantas matrizes micropropagadas (planta controle, utilizando-se o protocolo descrito por FERREIRA & GRATTAPAGLIA (1996. Para triagem dos primers foram utilizados os kits OPAN, OPA e OPF (Operon Technologies, Inc. e, destes, foram escolhidos sete primers: OPAN-03, OPAN-14, OPAN-15, OPAN-16, OPA-02, OPA-08 e OPF-04. A separação dos produtos da amplificação foi realizada através de eletroforese horizontal em gel de agarose 1,2%, corado com brometo de etídio. Após a corrida, os géis foram visualizados sobre um transiluminador de luz ultravioleta e fotografados com câmara Polaroid para registro dos dados. A ausência ou adição de uma ou mais bandas comparativamente ao padrão da planta matriz (planta controle foi considerado variação somaclonal. Dos 66 fragmentos produzidos pelos sete primers, observou-se 100% de bandas monomórficas, indicando que nenhum dos primers utilizados detectou variação somaclonal nas brotações regeneradas.The aim of this work was to evaluate the genotypic fidelity of pear shoots (Pyrus communis L. cultivar Carrick regenerated in vitro, using RAPD markers. Genomic DNA was extracted from leaves regenerated from pear shoots submitted to different treatments and from micropropagated matrix plants (control plant, using the protocol descripted by FERREIRA & GRATTAPAGLIA (1996. For primer selection, the Kits OPAN, OPA, and OPF (Operon Technologies, Inc. were used. Seven primers were chosen: OPAN-03, OPAN-14, OPAN-15, OPAN-16, OPA-02, OPA-08 and OPF-04. Amplified products were submitted to horizontal electrophoresis in 1.2% agarose gel, stained with ethidium bromide and visualized under UV light. The result was
Awan, Faisal Saeed; Maryam; Jaskani, Muhammad J; Sadia, Bushra
Breeding of date palm is complicated because of its long life cycle and heterozygous nature. Sexual propagation of date palm does not produce true-to-type plants. Sex of date palms cannot be identified until the first flowering stage. Molecular markers such as random amplified polymorphic DNA (RAPD), sequence-characterized amplified regions (SCAR), and simple sequence repeats (SSR) have successfully been used to identify the sex-linked loci in the plant genome and to isolate the corresponding genes. This chapter highlights the use of three molecular markers including RAPD, SCAR, and SSR to identify the gender of date palm seedlings.
V. M. Shinde
Full Text Available In this study, the RAPD (Random Amplified Polymorphic DNA technique was employed for determination of the components in an Ayurvedic herbal prescription, Rasayana Churna. One-hundred-and-twenty decamer oligonucleotide primers were screened in the RAPD analysis to identify three Ayurvedic medicines, dried stem of Tinospora cordifolia, dried fruit of Emblica officinalis and dried fruit of Tribulus terestris, the Ayurvedic prescription. Primer OPC-6 simultaneously generated three distinct amplicons, each specific to one component. The marker with 600 bp is specific to Tinospora cordifolia; the marker 500 bp is specific to Emblica officinalis and the remaining marker >1000 bp was present in Tribulus terestris. Presence of three herbal medicines was determined when RAPD reaction with OPC-6 was performed. The technique was proved to contribute to the identification of components in Ayurvedic herbal preparation and thus helping to serve as a complementary tool for quality control.
Ana Paulina Velasco-Ramírez
Conclusion: This indicates an important level of genetic differences despite the fact that the plant is asexually propagated. Based on the diversity statistics, any marker tested in present work can be recommended for use in large-scale genetic studies of populations. However, the low correlations among different molecular marker systems show the importance of the complementarity of the information that is generated by different markers for genetic studies involving estimation of polymorphism and relationships.
K.D. Jermstad; D.L. Bassoni; N.C. Wheeler; D.B. Neale
We have constructed a sex-averaged genetic linkage map in coastal Douglas-fir ( Pseudotsuga menziesii [Mirb.] Franco var menziesii) using a three-generation outcrossed pedigree and molecular markers. Our research objectives are to learn about genome organization and to identify markers associated with adaptive traits. The map...
Jul 6, 2011 ... to downy mildew resistance in lettuce. RAPD analysis has also been used to develop DNA markers that are linked to disease and insect resistance in several crops. (Williams et al., 1990; Mutengwa et al., 2005). This is yet to be achieved in Sigatoka leaf spot disease complex. Sigatoka leaf spot otherwise ...
Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.
This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.
Wang, Wei; Hu, Yulin; Sun, Dequan; Staehelin, Christian; Xin, Dawei; Xie, Jianghui
Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. cubense race 4 (FOC4) results in vascular tissue damage and ultimately death of banana (Musa spp.) plants. Somaclonal variants of in vitro micropropagated banana can hamper success in propagation of genotypes resistant to FOC4. Early identification of FOC4 resistance in micropropagated banana plantlets is difficult, however. In this study, we identified sequence-characterized amplified region (SCAR) markers of banana associated with resistance to FOC4. Using pooled DNA from resistant or susceptible genotypes and 500 arbitrary 10-mer oligonucleotide primers, 24 random amplified polymorphic DNA (RAPD) products were identified. Two of these RAPD markers were successfully converted to SCAR markers, called ScaU1001 (GenBank accession number HQ613949) and ScaS0901 (GenBank accession number HQ613950). ScaS0901 and ScaU1001 could be amplified in FOC4-resistant banana genotypes ("Williams 8818-1" and Goldfinger), but not in five tested banana cultivars susceptible to FOC4. The two SCAR markers were then used to identify a somaclonal variant of the genotype "Williams 8818-1", which lost resistance to FOC4. Hence, the identified SCAR markers can be applied for a rapid quality control of FOC4-resistant banana plantlets immediately after the in vitro micropropagation stage. Furthermore, ScaU1001 and ScaS0901 will facilitate marker-assisted selection of new banana cultivars resistant to FOC4.
Caracterização da diversidade genética entre acessos crioulos de feijão (Phaseolus vulgaris L. coletados em Santa Catarina por marcadores RAPD Characterization of the genetic diversity of landraces of common bean (Phaseolus vulgaris L. collected in Santa Catarina State by RAPD markers
Márcio Fonseca de Carvalho
, and of three cultivars ('Pérola', 'SCS 202-Guará' e 'BRS Valente', using RAPD markers. 21 decamer-primers that allowed the visualization of 96 bands were used, and 41 (42.7% presented polymorphism among the studied accesses, resulting in a band range of 650 to 2000pb. The dissimilarity was calculated using the Sorensen-Dice coefficient and the grouping analyses were derived from UPGMA. The accesses were separated in two main groups, with wide dissimilarity when compared with the divergence inside each group. These two groups indicate the possible center of domestication, Middle-American or Andean, of the accesses in this study. The dissimilarity among the cultivars evaluated ('SCS 202-Guará', 'BRS Valente' e 'Pérola' was small (0.15, if compared with the divergence among the accesses of the germplasm bank (0.65. The smaller dissimilarity among the studied accesses (BAF63 and BAF04 was 0.02. The results reinforce the need of new collection expeditions, which will increase the representation of the genetic variability of the remaining bean landraces in Santa Catarina State.
Hongwen Huang; Zuozhou Li; Jianqiang Li; Thomas L. Kubiisiak; Desmond R. Lavne
Phylogenetic relationships within the Actinidia were investigated using randomly amplified polymorphic DNA (RAPD) markers. DNAs from 10 taxa, including31 species encompassing all four sections and four series of the traditional subdivisions within the genus, were amplified using 22 preselected 10-mer oligonucieotide primers. A total 204 DNA bands...
Random amplified polymorphic DNA (RAPD) markers were used to evaluate genetic stability of regenerants of cucumber plants obtained through somatic embryogenesis. Somatic embryo plants and plants of F1 hybrids, from which they were derived, were compared during weaning, early growth, flowering, fruiting and at ...
Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...isition method The information of markers was collected from other databases and/or papers. Data analysis me...Database Site Policy | Contact Us Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...
Oct 19, 2009 ... Key word: Eggplant, bacterial wilt-resistance, molecular marker, inheritance. ... hundreds of plant species, including many crops such as tomato, potato ... rotation, adjusting the date of planting, cultural methods and soil ...
Brotman, Yariv; Kovalski, Irina; Dogimont, Catherine; Pitrat, Michel; Portnoy, Vitaly; Katzir, Nurit; Perl-Treves, Rafael
In melon, the Fom-1 gene confers monogenic resistance against the soil-borne fungus Fusarium oxysporum f. sp. melonis, races 0 and 2, while the closely linked Prv gene specifies resistance against the papaya ring spot virus. Markers linked to these resistance (R) genes were identified using two recombinant inbred line populations, derived from crosses between Cucumis melo Vedrantais and C. melo PI 161375, and between C. melo Vedrantais and C. melo PI 414723, respectively. Using bulked segregant analysis, as well as systematic scoring of the mapping populations, we developed two amplified fragment length polymorphism markers, two random amplified polymorphic DNA markers and five restriction fragment length polymorphism (RFLP) markers linked to this locus. Four of the RFLP sequences bear homology to nucleotide-binding site-leucine-rich repeat R genes, indicating the presence of a significant R-gene cluster in this locus. Our study provides the most closely linked markers published so far for these important traits. It also improves the resolution of the whole linkage group IX, which was difficult to order in our previous studies. Two of the markers were converted to cleaved amplified polymorphic sequence markers to facilitate their application in marker-assisted selection. Testing these two markers in several melon lines revealed different marker haplotypes in the melon germplasm and supported multiple, independent origin of the Fusarium races 0 and 2 resistance trait.
; Paran and Michelmore 1993) markers were introduced to overcome the disadvantages of RAPD. It is easy to design SCAR primers if the target sequence is known. SCAR primers are longer (18–25 bases) than RAPD.
Full Text Available Finding association between molecular markers and agronomic traits provide an excellent tool for indirect selection of a trait of interest in the population. In this study, stepwise regression analysis was used to estimate associations between ISSR and RAPD markers with some agronomic traits in lemon balm ecotypes. The analysis of results revealed significant associations between the traits and some of the studied loci. For all the traits, more than one informative marker was detected. Totally,90informative markers, including 48 ISSR loci and 42 RAPD loci, were identified. The SA-R-10, UBC826-1, UBC812-9, UBC813-10, UBC825-4, OPA-01-15, OPC-04-7 and CS-56-8 markers or fragment showed a significant correlation with Essential oil percentage and controlled 99.8% of the phenotypic variation. These markers are relatively more reliable. Among the RAPD primers, special attention should be drawn to primer SA-R, which had the highest associated fragments with the traits including days for 50% flowering, number of branches per plant, fresh weight and dry weight. Some of ISSR and RAPD markers were associated with more than one trait in multiple regression analysis that may be due to pleiotropic effect of the linked quantitative trait locus on different traits or its linkage to different genes. These primers have been found useful for improved lemon balm.
DNA markers used in assisting selection method is a safe method in breeding process, due to deletion of environmental conditions, and it is an important tool in preparing linkage map and QTLs mapping. In mulberry silkworm that is, foundation of world sericulture, its major production-economic characteristics are polygenic.
Oct 19, 2009 ... resistance in eggplant was controlled by a single dominant gene showing Mendelian inheritance model. In addition, a 762 bp molecular marker ... solarization, to change soil pH and reduce survival and activity of plant pathogens ..... hence to better understanding of the genetic control of the resistance(s).
Ramya R Mishra
Full Text Available The mode of gene action governing resistance to plume moth (Exelastis atomosa Walsingham 1886 derived from pigeon-pea (Cajanus scarabaeoides (L. Thouars accession ICPW-94 has been determined and the resistance alleles have been designated as PPM1. The progenies of F2 population and F3 families derived from an interspecific cross C. cajan (L. Huth ('ICP-26' x C. scarabaeoides (accession ICPW-94 revealed monogenic gene action for resistance to plume moth, and the dominant control by single locus or cluster of tightly linked alleles. Bulked segregant analysis (BSA of 116 F2 progenies by using 143 parental polymorphic RAPD primers could identify a fragment OPA09(910 associated with plume moth resistance in coupling phase of linkage. Further single plant analysis of the 116 F2 mapping population revealed OPA09(910 was linked to PPMi locus conferring host resistance to plume moth with recombination fraction (rf value of 0.125 (12.7 cM of Kosambi function. The resistance specific fragment OPA09(910 was cloned, sequenced and converted into a sequence characterized amplified region (SCAR marker, SCOPA09(942, which was also closely associated (10.3 cM with the locus PPMl with rf value 0.102. BLAST analysis with pigeon-pea genome sequence also confirmed its occurrence in CcLG02 (Scafseq.LG_V5.0fa and contig 01597 (AFSP01.fsa1. This SCAR marker showed reasonable screening efficiency in the F2, F3, and BC1F1 lines, thus it can be used as genetic handle in marker-assisted introgression of the genomic fragment conferring plume moth resistance and screening of breeding lines in pigeon-pea.
Hedden, Trey; Schultz, Aaron P.; Rieckmann, Anna; Mormino, Elizabeth C.; Johnson, Keith A.; Sperling, Reisa A.; Buckner, Randy L.
Age-related alterations in brain structure and function have been challenging to link to cognition due to potential overlapping influences of multiple neurobiological cascades. We examined multiple brain markers associated with age-related variation in cognition. Clinically normal older humans aged 65–90 from the Harvard Aging Brain Study (N = 186) were characterized on a priori magnetic resonance imaging markers of gray matter thickness and volume, white matter hyperintensities, fractional anisotropy (FA), resting-state functional connectivity, positron emission tomography markers of glucose metabolism and amyloid burden, and cognitive factors of processing speed, executive function, and episodic memory. Partial correlation and mediation analyses estimated age-related variance in cognition shared with individual brain markers and unique to each marker. The largest relationships linked FA and striatum volume to processing speed and executive function, and hippocampal volume to episodic memory. Of the age-related variance in cognition, 70–80% was accounted for by combining all brain markers (but only ∼20% of total variance). Age had significant indirect effects on cognition via brain markers, with significant markers varying across cognitive domains. These results suggest that most age-related variation in cognition is shared among multiple brain markers, but potential specificity between some brain markers and cognitive domains motivates additional study of age-related markers of neural health. PMID:25316342
A.M. AI-Moshileh; M.I. Motawei; A. AI-Wasel; T. Abdel-Latif
The suitability of randomly amplified polymorphic DNA (RAPD) fingerprints as genetic markers in date palms was tested. Five date palm cultivars (Barbi, Nabtet Ali. Rothanah, Ajwa, and Sokkari) from Saudi well- known dates were subject to DNA fingerprint analysis. From 20 primers tested, only 12 were selected as reproducible, giving 64 bands. The RAPD profiles obtained were successfully used to differentiate the genotypes. Based on the pair-wise comparison of amplification products, the geneti...
Seed germination was significantly reduced in all provenances with the increase in NaCl concentrations. Provenance Al Feel (FE, clay+ high rainfall) from Eastern Sudan was more tolerant than the other provenances at seed emergence stage. Greenhouse experiment examined the growth response of 8 provenances A.
Jan 19, 2009 ... Aydin is on the fault line and there were countless devastating earthquakes in the past. (Altunel, 1998). In Ilica location of Imamlar Village, there was a big earthquake in the past and samples used in this study were collected from crushed fault base. Earthquakes might induce geographic isolations between.
Mar 20, 2009 ... The rhizobia, Sinorhizobium meliloti and Rhizobium sullae, which fix nitrogen in root nodules of alfalfa. (Medicago sativa L.) and sulla (Hedysarum sp.) forage legumes, respectively, were isolated from root nodules and soils from Morocco. We used three PCR-based techniques namely, rep-PCR, RAPD and.
Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...tabases were collected by web-search. Data analysis method - Number of data entri...e Site Policy | Contact Us Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...
Bernardo, Amy; Wang, Shan; St Amand, Paul; Bai, Guihua
With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat (Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat.
Full Text Available With the advent of next generation sequencing (NGS technologies, single nucleotide polymorphisms (SNPs have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat (Triticum aestivum L. that can be effectively used in marker-assisted selection (MAS is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP and sequence tagged site (STS markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat.
Full Text Available Allozyme and random amplified polymorphic DNA (RAPD techniques have been compared for their usefulness for genetic and taxonomic studies in Prosopis glandulosa and P. velutina populations. Isozymes and RAPDs yielded similarly high estimates of genetic variability. Genetic structure and differentiation were analyzed through non-hierarchical Wright's F DT. For all populations considered, both markers produced low gene flow (Nm 1, in agreement with that expected for conspecific populations. However, in RAPD data the expected reduction in F DT and the increase in Nm were not observed. Correlation between F DT and geographical distance matrices (Mantel test for all populations was significant (P = 0.02 when based on isozymes, but not so (P = 0.33 when based on RAPDs. No significant associations among genetic and geographical or climatic variables were observed. Two isoenzyme systems (GOT and PRX enabled us to distinguish between P. glandulosa and P. velutina, but no diagnostic band for recognition of populations or species studied here were detected by RAPD. However, RAPD markers showed higher values for genetic differentiation among conspecific populations of P. glandulosa and a lower coefficient of variation than those obtained from isozymes.
Apr 1, 2015 ... markers were employed (1) to detect the genetic diversity and polymorphism among different isolates of. Pseudomonas collected from rhizospheric soil of different locations and (2) to estimate the relative efficiencies of both RAPD and ISSR markers. MATERIALS AND METHODS. Bacterial isolates and ...
Mienie, C M S; Liebenberg, M M; Pretorius, Z A; Miklas, P N
Rust in common bean (Phaseolus vulgaris L.) is caused by Uromyces appendiculatus Pers.:Pers. (Unger) which exhibits a high level of pathogenic diversity. Resistance to this disease is conditioned by a considerable number of genes. Pyramiding resistance genes is desirable and could be simplified by the use of molecular markers closely linked to the genes. The resistance gene Ur-13, present in the South African large seeded cultivar Kranskop, has been used extensively in the local breeding program. The purpose of this study was the development of a molecular marker linked to Ur-13. An F(2) population derived from a cross between Kranskop and a susceptible (South African) cultivar Bonus was used in combination with bulked segregant analysis utilizing the amplified fragment length polymorphism (AFLP) technique. Seven AFLP fragments linked significantly to the rust resistance and five were successfully converted to sequence characterized amplified region (SCAR) markers. The co-dominant SCAR markers derived from a 405 bp EAACMACC fragment, KB 126, was located 1.6 cM from the gene. Two additional SCAR markers and one cleaved amplified polymorphic sequence marker were located further from the gene. The gene was mapped to linkage group B8 on the BAT 93/Jalo EEP 558 core map (chromosome 3).
Jing WANG,Chen CHENG,Yanru ZHOU,Yong YANG,Qiong MEI,Junmin LI,Ye CHENG,Chengqi YAN,Jianping CHEN
Full Text Available Y73 is a progeny of asymmetric somatic hybridization between Oryza sativa cv. Dalixiang and the wild rice species Oryza meyeriana. Inoculation with a range of strains of Xanthomonas oryzae pv. oryzae showed that Y73 had inherited a high level of resistance to rice bacterial blight (BB from its wild parent. An F2 population of 7125 individuals was constructed from the cross between Y73 and a BB-susceptible cultivar IR24. After testing 615 SSR and STS markers covering the 12 rice chromosomes, 186 markers were selected that showed polymorphism between Y73 and IR24. Molecular markers linked to the BB resistance genes in Y73 were scanned using the F2 population and the polymorphic markers. The SSR marker RM128 on chromosome 1, the STS marker R03D159 on chromosome 3 and the STS marker R05D104 on chromosome 5 were found to be linked to the rice BB resistance genes in Y73.
Jun 3, 2009 ... are a very powerful tool for characterization and genetic diversity estimation. Many molecular marker techniques have been successfully used in identification and genetic diversity analysis in mulberry, such as RAPD (Xiang et al., 1995; Feng et al., 1996; Zhao and Pan, 2004),. AFLP (Sharma and Sharma, ...
G. M. Tabor; Thomas L. Kubisiak; N. B. Klopfenstein; R. B. Hall; Henry S. McNabb
In the north central United States, leaf rust caused by Melampsora medusae is a major disease problem on Populus deltoides. In this study we identified molecular markers linked to a M. medusae resistance locus (Lrd1) that was segregating 1:1 within an intraspecific P. deltoides...
To verify the molecular markers linked to the genic multiple-allele male-sterile gene Ms, an F1 plant, which was generated by crossing the inbred line a20 and the male-sterile plant of the genic multipleallele male-sterile AB line, was backcrossed with an a20 plant to develop BC4 and BC5 populations.
Bulk segregant analysis (BSA) and randomly amplified microsatellite polymorphism (RAMP) were employed to analyze F2 individuals of the Yunyan 317×Hubei 517 to screen and characterize molecular markers linked to black shank resistant gene. A total of 800 arbitrary decamer oligonucleotide primerpairs were used for ...
Jun 3, 2009 ... Pak-choi is one of the most important vegetable crops in China. Turnip mosaic virus (TuMV) is one of its main pathogen. Screening the molecular marker linked to the TuMV resistance gene is an efficient method to improve pak-choi breeding. In this paper, a dominant gene, TuRBCH01, has been mapped.
The objectives of this investigation were to study the inheritance or low germination stimulant (lgs) production in cultivar SAR 29 and to identify molecular markers that are linked to this trait. Low germination stimulant production is one of the recognised mechanisms of witchweed resistance. A segregating F2 population ...
Wang, Tiegu; Huang, Qunce; Feng, Weisen
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.
Achar, Devaraja; Awati, Mallikarjuana G; Udayakumar, M; Prasad, T G
Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection.
Ashraf, Kamran; Ahmad, Altaf; Chaudhary, Anis; Mujeeb, Mohd; Ahmad, Sayeed; Amir, Mohd; Mallick, N
The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccard's similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program.
Khoodoo, M H R; Issack, M I; Jaufeerally-Fakim, Y
The genus Salmonella is a common agent of gastroenteritis in Mauritius, generating more cases of the disease during summer than during winter. The aims of this study were to assess the genetic diversity of isolates of Salmonella enterica by RAPD fingerprinting, and to establish the relationship between human and chicken isolates. Twenty-six isolates were obtained from hospital laboratories and commercial poultry producers locally. The RAPD profiles, biochemical and serological analyses showed that two of the chicken isolates were mistakenly identified as Salmonella. The genetic diversity of the remaining 24 isolates (five chicken and 19 human), confirmed as Salmonella, was analysed using four arbitrary primers, OPA-10, OPR-03, OPI-06 and OPJ-09, chosen from an initial set of 10 decamers. Seventy RAPD markers were generated in four individual DNA profiles. Cluster analysis (UPGMA) performed using the NTSYS-pc V 1.8 computer software, confirmed that some strains of Salmonella isolated from chicken were genetically similar to those isolated from humans. Furthermore, a 1 kbp band amplified using primer OPA-10 was specific for the Salmonella genus as it was not amplified in any of the control bacteria.
Pak-choi is one of the most important vegetable crops in China. Turnip mosaic virus (TuMV) is one of its main pathogen. Screening the molecular marker linked to the TuMV resistance gene is an efficient method to improve pak-choi breeding. In this paper, a dominant gene, TuRBCH01, has been mapped. 180 F2 individuals ...
Full Text Available The amplified fragment length polymorphism (AFLP assay is an efficient method for the identification of molecular markers, useful in the improvement of numerous crop species. Bulked Segregant Analysis (BSA was used to identify AFLP markers associated with water-stress tolerance in barley, as this would permit rapid selection of water-stress tolerant genotypes in breeding programs. AFLP markers linked to water-stress tolerance was identified in two DNA pools (tolerant and sensitive, which were established using selected F2 individuals resulting from a cross between water-stress-tolerant and sensitive barley parental genotypes, based on their paraquat (PQ tolerance, leaf size, and relative water content (RWC. All these three traits were previously shown to be associated with water-stress tolerance in segregating F2 progeny of the barley cross used in a previous study. AFLP analysis was then performed on these DNA pools, using 40 primer pairs to detect AFLP fragments that are present/absent, respectively, in the two pools and their parental lines. One separate AFLP fragment, which was present in the tolerant parent and in the tolerant bulk, but absent in the sensitive parent and in the sensitive bulk, was identified. Polymorphism of the AFLP marker was tested among tolerant and sensitive F2 individuals. The presence of this marker that is associated with water-stress tolerance will greatly enhance selection for paraquat and water-stress tolerant genotypes in future breeding programs.
Feb 15, 2010 ... (Aegean Union of Olive and Olive Oil Exporters, 2007). Turkey also has a significant position among countries cultivating olives. The total number of ..... Collins G, Sedgley MA (2004). Molecular linkage map of olive. (Olea europea L.) based on RAPD, microsatellites and SCAR markers. Genome, 47: 26-35.
Maria Lúcia Crochemore; Liliane Moreira Nunes; Giselly Aparecida Andrade; Hugo Bruno Correa Molinari; Maria Elizabeth Vasconcellos
This study aimed the identification of cultivars and/or lines of Coffea arabica of commercial interest, using PCR-RAPD markers. The DNA of ground seeds lots of 12 cultivars and/or lines were evaluated with five primers (Operon OPA 01, OPA 04, OPG 11, OPY 16, and OPX 09) were obtained from a selection of 56 primers. The electrophoretic profiles allowed distinction among eight cultivars and/or lines as well as heterogeneity between and within lots of IAPAR59.Classicamente, a identificação de cu...
Feb 7, 2011 ... albicans isolates obtained from oral cavity of patients was carried out using random amplified polymorphic DNA ... the skin and mucosal surfaces of the genital and intest- inal tracts as well as the .... isoamyl alcohol (24:24:1).
Mar 20, 2009 ... The cultures used in the study were obtained from cyanobacterial culture collection of CAS in Botany, University of Madras. Eight strains of non heterocystous, filamentous Oscillatoria spp. and four strains of Lyngbya spp. were used. The details of the cultures used as sources of DNA are presented in Table ...
Khadeeva, N V; Goriunova, S V; Kochumova, A A; Iakovleva, E Iu; Mel'nikova, N V; Zholobova, O O; Korotkov, O I; Kudriavtsev, A M
The possibility of using RAPD and AFLP methods for genetic monitoring of populations of Matthiola fragrans (Bunge), a species included in the Red Book of the USSR, was shown for the first time. An analysis of inter- and intrapopulation and interspecies genome polymorphism was performed. Differences in the genetic structure of Matthiola populations from various geographical collection points were revealed. A simple method of performing RAPD analysis and the great number of unique markers found in each population compared with the AFLP analysis, as well as the good division of populations under statistical treatment, allow us to draw the conclusion that using the RAPD method in genetic monitoring of rare and insufficiently studied species is well founded.
Full Text Available Abstract For population case-control association studies, the false-positive rates can be high due to inappropriate controls, which can occur if there is population admixture or stratification. Moreover, it is not always clear how to choose appropriate controls. Alternatively, the parents or normal sibs can be used as controls of affected sibs. For late-onset complex diseases, parental data are not usually available. One way to study late-onset disorders is to perform sib-pair or sibship analyses. This paper proposes sibship-based Hotelling's T2 test statistics for high-resolution linkage disequilibrium mapping of complex diseases. For a sample of sibships, suppose that each sibship consists of at least one affected sib and at least one normal sib. Assume that genotype data of multiple tightly linked markers/haplotypes are available for each individual in the sample. Paired Hotelling's T2 test statistics are proposed for high-resolution association studies using normal sibs as controls for affected sibs, based on two coding methods: 'haplotype/allele coding' and 'genotype coding'. The paired Hotelling's T2 tests take into account not only the correlation among the markers, but also take the correlation within each sib-pair. The validity of the proposed method is justified by rigorous mathematical and statistical proofs under the large sample theory. The non-centrality parameter approximations of the test statistics are calculated for power and sample size calculations. By carrying out power and simulation studies, it was found that the non-centrality parameter approximations of the test statistics were accurate. By power and type I error analysis, the test statistics based on the 'haplotype/allele coding' method were found to be advantageous in comparison to the test statistics based on the 'genotype coding' method. The test statistics based on multiple markers can have higher power than those based on a single marker. The test statistics can be
Mutlu, Nedim; Demirelli, Aylin; Ilbi, Hülya; Ikten, Cengiz
We developed highly reliable co-dominant SCAR markers linked to the Frl gene. FORL testing is difficult. The marker is expected to be quickly adapted for MAS by tomato breeders. Fusarium oxysporum f. sp. radicis-lycopersici causes Fusarium crown and root rot (FCR), an economically important soil-borne disease of tomato. The resistance against FCR is conferred by a single dominant gene (Frl) located on chromosome 9. The aim of this study was to develop molecular markers linked to the Frl gene for use in marker-assisted breeding (MAS) programs. The FCR-resistant 'Fla. 7781' and susceptible 'B560' lines were crossed, and F1 was both selfed and backcrossed to 'B560' to generate segregating F2 and BC1 populations. The two conserved set II (COSII) markers were found linked to the Frl gene, one co-segregated with FCR resistance in both F2 and BC1 populations and the other was 8.5 cM away. Both COSII markers were converted into co-dominant SCAR markers. SCARFrl marker produced a 950 and a 1000 bp fragments for resistant and susceptible alleles, respectively. The linkage of SCARFrl marker was confirmed in BC2F3 populations developed by backcrossing the resistant 'Fla. 7781' to five different susceptible lines. The SCARFrl marker has been in use in the tomato breeding programs in BATEM, Antalya, Turkey, since 2012 and has proved highly reliable. The SCARFrl marker is expected to aid in the development of FCR-resistant lines via marker-assisted selection (MAS).
RAPD) profiles of Streptococcus thermophilus strains by using the polymerase chain reaction (PCR). Several factors can cause the amplification of false and non reproducible bands in the RAPD profiles. We tested three primers, OPI-02 MOD, ...
Tanhuanpää, Pirjo; Kalendar, Ruslan; Laurila, Jaana; Schulman, Alan H; Manninen, Outi; Kiviharju, Elina
Short straw is a desired trait in oat germplasm (Avena sativa L.). Marker-assisted selection, a key tool for achieving this objective, is limited by the presence and number of available markers. Here, we have attempted to develop markers sufficiently linked to a gene specifying short straw so that marker-assisted selection could be applied. Bulked-segregant analysis was used to identify anonymous PCR-based markers associated with the dwarfing gene Dw6 in an F2 population from the cross between A. sativa "Aslak" and A. sativa "Kontant". One random amplified polymorphic DNA (RAPD) and 1 retrotransposon-microsatellite amplified polymorphism (REMAP) marker were found to be associated with height. These were converted into codominant single-nucleotide polymorphism (SNP) markers. The SNP-REMAP and the SNP-RAPD markers were located 5.2 and 12.6 cM from Dw6, respectively. They can be used in future efforts both to enhance oat germplasm by application of molecular markers and to determine the nature of the gene through positional cloning.
Redmond, Sean M
The empirical record regarding the expected co-occurrence of attention-deficit/hyperactivity disorder (ADHD) and specific language impairment is confusing and contradictory. A research plan is presented that has the potential to untangle links between these 2 common neurodevelopmental disorders. Data from completed and ongoing research projects examining the relative value of different clinical markers for separating cases of specific language impairment from ADHD are presented. The best option for measuring core language impairments in a manner that does not potentially penalize individuals with ADHD is to focus assessment on key grammatical and verbal memory skills. Likewise, assessment of ADHD symptoms through standardized informant rating scales is optimized when they are adjusted for overlapping language and academic symptoms. As a collection, these clinical metrics set the stage for further examination of potential linkages between attention deficits and language impairments.
Skibsted, U.; Baggesen, Dorte Lau; Dessau, R.
Isolates of Salmonella Enteritidis from 81 patients from Herlev Hospital or from Copenhagen County were analysed by random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) and phage-typing. Fourteen polymorphic markers from five decamer primers unambiguously placed...... that RAPD is useful as a tool in investigations of microbial outbreaks in its own right, or to supplement phage-typing and PFGE of Salmonella Enteritidis....
Zhang, G F; Guan, J M; Lai, X P; Lin, J; Liu, J M; Xu, H H
Mesona chinensis is an economically important agricultural crop, primarily cultivated for making grass jelly. It was originally discovered in South China. We examined 18 cultivars, including cultivars from Guangdong, Fujian, and Guangxi, China, Taiwan, and Indonesia, and a hybrid (a cross between cultivars from Indonesia and Guangdong), based on RAPD markers. The genetic similarity coefficient was calculated by NTSYS 2.10 and the clustering analysis was made by UPGMA. PCR amplification with 10 primers produced 163 bands; 94% of the amplified loci were polymorphic. The primers S208, S206, and S253 could completely distinguish all 19 samples by constructing a DNA fingerprint. Cluster analysis divided the 19 cultivars into five groups, with an overall genetic similarity coefficient of 0.68. Correlations were found among regional distributions, parental sources, and RAPD markers, demonstrating the rich genetic diversity of these 19 cultivars of M. chinensis. This study provides useful information for the classification, identification, and breeding of M. chinensis.
Farooqui, N; Ranade, S A; Sane, P V
Neem, described as a tree for solving global problems, is an evergreen, long-lived, multipurpose tree of the tropics with a wide distribution range in India. It is believed to be highly cross-pollinated. Inter-provenance variations have been reported in neem in case of morphological and physiological characters. Yet no reports about the genetic determinism for these variations are available to our knowledge. In order to have an idea about the extent and/or nature of genetic (DNA) variation in neem, the powerful RAPD technique has been employed. RAPD profiles of 34 accessions/provenances of neem were generated with 200 decamer random primers, of which the data from the 49 primers, that resulted in reproducible amplification products, were considered for analysis. Based on the presence/absence of bands, a similarity matrix was computed. Dendrogram was constructed by UPGMA method based on the pairwise similarities amongst the RAPD profiles. The similarities in RAPD profiles amongst the different DNAs was more than that expected due to the cross-pollinated nature of the tree and furthermore, these more-than-expected similarities were not due to random chance. These results suggest that neem may have a narrow genetic base.
Berg, van den R.G.; Bryan, G.J.; Rio, del A.; Spooner, D.M.
Species boundaries were assessed with three molecular markers [AFLPs, RAPDs and chloroplast simple sequence repeats (cpSSRs)] for all six species of wild potatoes (Solanum section Petota) assigned to ser. Longipedicellata: Solanum fendleri, S. hjertingii, S. matehualae, S. papita, S. polytrichon and
Full Text Available Random amplified polymorphic DNA (RAPD markers were used to characterize a part of a sea buckthorn gene bank collected for plant breeding purposes. Molecular markers were generated in 55 cultivars and accessions, representing five subspecies of Hippophae rhamnoides L. and intraspecific hybrids between different subspecies. Sixty-three markers were used to generate a Dice's similarity coefficient matrix of pairwise comparisons between individual RAPD profiles. Cluster (UPGMA and principal co-ordinate analyses, based on this matrix, revealed clustering of plants into groups which generally correspond to their taxonomic classification or geographic origin. The analysis of molecular variance (AMOVA was found useful for estimating components of genetic variation between and within taxonomic and geographic groups of accessions and cultivars. Whereas both alternatives for grouping the material (taxonomic or geographic origin resulted in significant between-group variation, the major part of molecular variance (approximately 75% was still attributed to variation within groups. We conclude that the RAPD analysis is useful for clarification of taxonomic and geographic origin of accessions and cultivars of sea buckthorn.
Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t_db_link_en.zip (36.3 KB) - 6 Genome analysis methods pgdbj_dna_marker_linkage_map_genome_analysis_methods_... of This Database Site Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...
Arens, P.F.P.; Mansilla, C.; Deinum, D.; Cavellini, L.; Moretti, A.; Rolland, S.; Schoot, van der H.; Calvache, D.; Ponz, F.; Collonnier, C.; Mathis, R.; Smilde, D.; Caranta, C.; Vosman, B.
Molecular markers linked to phenotypically important traits are of great interest especially when traits are difficult and/or costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance genes, resistance traits have become important
Full Text Available Numerous studies using single nucleotide polymorphisms (SNPs have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes, biological process (96 genes, and cellular component (96 genes. A total of 693 SNP markers, including 145 SNP markers [BRH--developed from the B. rapa genome for high-resolution melt (HRM analysis], 425 SNP markers (BRP--based on the B. rapa genome that could be applied to B. oleracea, and 123 new SNP markers (BRS--derived from BRP and designed for HRM analysis, were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome, selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%, 415 of 425 BRP (97.6%, and 118 of 123 BRS (95.9% showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.
Cho, Young-Il; Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Lee, Hye-Eun; Kim, Do-Sun
Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species. PMID:25790283
Cho, Young-Il; Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Lee, Hye-Eun; Kim, Do-Sun
Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH--developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP--based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS--derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.
Shirin, Ghadami; Maryam, Abiri; Farideh, Zonozi Rishsefid; Javad, Tavakkoly-Bazzaz; Sirous, Zeinali
Non-syndromic autosomal recessive intellectual disability (NS-ARID) is a heterogeneous neurodevelopmental disease. More research is needed to study the NS-ARID genes. Using STR markers linked to a specific gene, we can perform homozygosity mapping and prenatal diagnosis. One approach to investigate the NS-ARID genes in large families is homozygosity mapping. In this study, we surveyed allele frequency and allele heterozygosity of 17 NS-ARID STR markers linked to the six NS-ARID genes in Iranian population. The test group consisted of 120 unrelated healthy individuals. STR markers were designed using SERV software. Also, genotyping was done using multiplex PCR. Data was analyzed by Gene Mapper software. Allele frequency and observed heterozygosity rates were estimated using PowerStatV12. Deviation from the Hardy-Weinberg equilibrium (HWE) was performed based on the Exact test. Out of 17 STR loci, 11 were novel. In total, 166 alleles were detected for the 17 markers. According to our study, the D9MAN1B1SD7.4, D19S872, D6GRIK2SI1.7, D19TECRSDI.8, D1ST3GAL3SIO.5, and D14ZC3H14SD5.3 STR loci were found to be the most informative and polymorphic STR markers for MAN1B1, ZNF526, GRIK2, TECR, ST3GAL3, and ZC3H14 genes, respectively. We also performed other statistical analyses on these STR markers and found that all of the 17 STRs were polymorphic and met the Hardy-Weinberg equilibrium. Finding novel STRs, with high allele heterozygosity, is one of the most significant outcomes of the present study. These findings can be useful for homozygosity mapping, PGD, and PND practices for the NS-ARID.
Full Text Available Wood splitting is a defect in eucalyptus which results in considerable losses when converting logs to solid wood products. Commonly in forestry, molecular markers are identified through studying pedigrees from a single cross. This limits...
Houshang NOSRATI; Mohammad Ali Hosseinpour FEIZI; Sona Seyed TARRAH; Ahmad Razban HAGHIGHI
Studies on plants show that populations growing on the stressful environments indicate higher levels of genetic diversity, and that in outcrossing species majority of total genetic variation allocated to within population rather than between populations. We compared the level of genetic variation between populations growing in stressful and normal environments, and measured levels of within- and between population genetic variations in Onobrychis viciifolia L. (Sainfoin, Fabaceae) based on RA...
bolting gene is presented. MATERIALS AND METHODS. P-28 (P1) was used as the early-bolting parent and P-27 (P2) was used as the late-bolting parent. The F2 (255 individuals) population was constructed by the progeny ...
Nov 16, 2006 ... Genetic analysis of resistance to L. maculans was carried out with 15 accessions from the USDA Brassica germplasm collections, representing diploids (A, C), and tetraploid (AC) genomes, respectively; and 9 cultivars from the National Winter Canola Variety Trials (NWCVT) all carrying AC genomes. All.
Apr 15, 2015 ... propagation via seed and vegetative means. The amenability of the species to tissue ..... followed by 35 cycles consisting of 30 s denaturation at 94°C, 45 s annealing at 35°C, 60 s extension at 72°C and ..... ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum) germplasm. Euphytica 13:135-144.
Blackleg, caused by Leptosphaeria maculans, is a serious disease of Brassica species. Genetic analysis of resistance to L. maculans was carried out with 15 accessions from the USDA Brassica germplasm collections, representing diploids (A, C), and tetraploid (AC) genomes, respectively; and 9 cultivars from the National ...
Aug 4, 2008 ... Random amplified DNA polymorphism of Nicotiana tabacum L. cultivars. Biologia Plantarum. 49: 605-607. Zhang HY, Liu XZ, Li TS, Yang YM (2006). Genetic diversity among flue- cured tobacco (Nicotiana tabacum L.) revealed by amplified fragment length polymorphism. Botanical Studies. 47: 223-229.
Rust diseases are the major cause of low yield of wheat in Pakistan. Wheat breeders all over the world as well as in Pakistan are deriving rust resistance genes from alien species like Triticum ventricosum and introducing them in common wheat (Triticum aestivum). One such example is the introgression of rust resistance ...
Jul 20, 2011 ... Genetica. 97: 313-320. Tamura K, Dudley J, Nei M, Kumar S (2007). MEGA 4: Molecular. Evolutionary Genetics Analysis (MEGA) Software version 4.0. Mol. Biol. Evol. 24: 1596-1599. Zhao B (2005). Natural antioxidants for neurodegenerative diseases. Mol. Neurobiol. 31: 283-293. Zuo Z, Zhang L, Zhou L, ...
Apr 3, 2008 ... of QTL Cartographer software. Putative QTL were chosen based on. LOD score of 3.0 or above. RESULTS. The winter survival and related traits of the susceptible parent, Quantum, the resistant parent, SLMO46, and the minimum and maximum values of these traits in F3 families were shown in Table 1 and ...
Identification of “Saccharum officinarum × Erianthus fulvus” F1 hybrids was performed with random amplified polymorphic DNA (RAPD) analysis. Of 280 RAPD primers used, two primers, OPA-19 and OPN-11, were found to be the most suitable for identification of the hybrids. And the hybrids facticitycheck-out rate was 70.6 ...
Random Amplified Polymorphic DNAs (RAPDs) is a DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. Despite the fact that the RAPD technique has become a very powerful tool and has found use in numerous applications, yet, the nature of ...
Dergam Jorge A.
Full Text Available In the Rio Doce basin of southeastern Brazil, the freshwater fish Hoplias malabaricus (trahira is a widespread predatory characin and one of the few resilient native fishes in a highly impacted lake system. In order to test for genetic differentiation in populations within this basin and for biogeographic relationships among populations of this species in other basins, a study was conducted using RAPD-PCR analysis of Rio Doce samples (N = 63 and phylogeographic analyses with mitochondrial DNA (mtDNA haplotypes, including the Rio Grande and Macacu river basins. In the Rio Doce basin, the patterns of genetic similarity of RAPD-PCR markers (individual fingerprinting and Nei?s genetic distance suggest the existence of two genetically different groups, one composed of the lacustrine populations Carioca and Dom Helvécio, and the other of riverine and the remaining lacustrine populations. The differences in the RAPD-PCR patterns may be explained by the existence of sub-basins within this lacustrine system. A maximum parsimony tree of cytochrome b fragment (383 base pairs supports the view that trahiras of the Rio Doce share a complex biogeographic history with those of neighboring basins. The phylogeographic patterns may be explained by a common history of the watersheds of the Rio Doce, Paraíba do Sul, and Rio Grande basins, corroborating the hypothesis of a Plio-Pleistocene separation of these drainage systems, forming the Mantiqueira "divortium aquarium".
Sharaf-Eldin, M A; Al-Tamimi, A; Alam, P; Elkholy, S F; Jordan, J R
The artichoke (Cynara scolymus L.) is an important food and medicinal crop that is cultivated in Mediterranean countries. Morphological characteristics, such as head shape and diameter, leaf shape, and bract shape, are mainly affected by environmental conditions. A molecular marker approach was used to analyze the degree of polymorphism between artichoke hybrid lines. The degree of genetic difference among three artichoke hybrids was evaluated using random amplified polymorphic DNA-PCR (RAPD-PCR). In this study, the DNA fingerprints of three artichoke lines (A13-010, A11-018, and A12-179) were generated, and a total of 10 decamer primers were applied for RAPD-PCR analyses. Polymorphism (16.66 to 62.50%) was identified using eight arbitrary decamers and total genomic DNA extracted from the hybrids. Of the 59 loci detected, there were 25 polymorphic and 34 monomorphic loci. Jaccard's similarity index (JSI) ranged between 1.0 and 0.84. Based on the unweighted pair group method with arithmetic mean (UPGMA) similarity matrix and dendrogram, the results indicated that two hybrids (A13-010 and A11-018) were closely related to each other, and the A12-179 line showed more divergence. When identifying correct accessions, consideration of the genetic variation and genetic relationships among the genotypes are required. The RAPD-PCR fingerprinting of artichoke lines clearly showed that it is possible to analyze the RAPD patterns for correlation between genetic means and differences or resemblance between close accessions (A13-010 and A11- 018) at the genomic level.
Herbicide drift (unintentional physical movement from target to off-target plants) is a cause of crop loss in US. Low-dose, high-potency herbicides that have short environmental persistence times constrain efforts to develop or identify metabolite or biochemical markers of exposu...
Polima cytoplasmic male sterility (pol CMS) has been widely used for exploiting heterosis in rapeseed breeding. The dominant restorer gene of pol CMS (Rfp) is found in the nucleus and is a key component of hybrid production by achieving F1 progeny with complete fertility restoration. To identify the molecular markers ...
Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius).
Yang, Huaan; Jian, Jianbo; Li, Xuan; Renshaw, Daniel; Clements, Jonathan; Sweetingham, Mark W; Tan, Cong; Li, Chengdao
Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding. We demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome
Matilla, T; Corral, J; Miranda, M; Troyano, J; Morrison, K; Volpini, V; Estivill, X
We present a case of prenatal diagnosis of Werdnig-Hoffmann disease, the most severe type of spinal muscular atrophy (SMA). DNA obtained from a mummified umbilical cord of a decreased affected brother of the index case was analysed with four closely linked microsatellite markers [EF1/2a and EF13/14 (D5S125), MAP1B, and JK53CA (D5S112)], flanking the SMA gene, on chromosome 5q11.2-13.3. The fetus was diagnosed as homozygous for the deleterious SMA gene.
Pedersen, C; Lindhardt, B O; Lauritzen, E
A total of 228 stored serum samples from 140 high risk individuals was examined for serological markers of human immunodeficiency virus (HIV) infection by second generation enzyme-linked immunosorbent assay, immunoblot, and HIV antigen assay. All the samples were negative in first generation enzyme...... are common in high risk individuals seronegative by first generation ELISA. However, HIV infection do occur in subjects negative by first generation ELISA, which emphasises the need for more sensitive screening assays and/or the use of antigen detection as part of screening in high risk individuals...
Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...es and/or papers. Data analysis method - Number of data entries 1,767 entries Data item Description Scientif... Data acquisition method The information of QTLs was collected from other databas
Full Text Available Random amplified polymorphic DNA (RAPD analysis is a simple and reliable method used to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of the assay. In this study, we analyzed the effects of different concentrations of primer, magnesium chloride, template DNA and Taq DNA polymerase to develop and standardize a RAPD protocol for Centaurium species. The optimized PCR reaction mixture included: 50 ng of DNA extracted using a CTbased protocol, 2.5 mM MgCl2, 7.5 pmol primer and 2 U of Taq polymerase in a final volume of 25 μl. Each of the five primers used in experiments (OPB11, OPB15, OPB18, OPF05 and OPH02 generated reproducible and distinguishable fingerprinting patterns of four Centaurium species. The obtained optimized RAPD protocol and the selected primers are useful for our further work in the genetic diversity studies of Centaurium species.
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Rodriguez-Echeverria, S.; Freitas, H.; Putten, van der W.H.
Ammophila arenaria (L.) Link (marram grass) is the most important sand-fixing plant species along the northwestern European and Mediterranean coast, and it is also planted worldwide for sand dune stabilization. In spite of the intense use of this species in foredune restoration and stabilization
Redmond, Sean M.
Purpose: The empirical record regarding the expected co-occurrence of attention-deficit/hyperactivity disorder (ADHD) and specific language impairment is confusing and contradictory. A research plan is presented that has the potential to untangle links between these 2 common neurodevelopmental disorders. Method: Data from completed and ongoing…
Ruan, Yuan; Mo, Rong-Hao; Li, Min; Huang, Liu-Qing; Luo, Yu; Li, Xiong-Ying; Zhou, Juan; Wu, Yao-Sheng
To analyze the DNA molecular characters of Centella asiatica with RAPD technology. With the genomic DNA as templates extracted from various source of Centella asiatica samples, optimized RAPD PCR reaction systems had been used. The random promers had been screened to amplify the specific molecular fragments of Centella asiatica. The specific genetic bands of Centella asiatica species from various habitats were established which were highly stable and repeatable and obviously different from those of other families, genuses of plants such as Gynostemma pentaphylum, Tobacco, Cayratia japonica. The developed method of RAPD analysis for the genetic character bands of Centella asiatica could be applied to identify real Centella asiatica from its spurious breed plants. The genetic character bands of Centella asiatica amplified with the RAPD method show high homogeneous in several samples from different habitats.
Fatih Mehmet Tok
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.
Ana Paula Cazerta FARRO
Full Text Available Flowering time is an important trait for tree breeding because it determines the speed of generation turnover and therefore the rapidity of genetic gains, and it is of particular interest in Eucalyptus species. In this work, we used simple sequence repeats (SSRs, random amplified polymorphic DNA (RAPD analysis and specific markers for flowering to evaluate early flowering segregation in a full-sibling family of Eucalyptus grandis and to identify molecular markers associated with the control of flowering time. A cross between a normal flowering tree (wild-type and early flowering tree resulted in 118 progeny with a 1:1 Mendelian segregation ratio for flowering time (χ2 = 0.5424, P > 0.05, which suggested the action of one main gene in a locus named Early flowering in Eucalyptus grandis (PFEg. The SSR marker EMBRA 02 was related to the QTL PFEg, and identified this region as a candidate for trait control. These maps may be used as the basis for a study in which can be inserted new markers in an attempt to find more loci related to early flowering characteristic on eucalyptus. O tempo de florescimento é uma importante característica para o melhoramento genético de árvores, pois este determina o prazo para o surgimento de uma nova geração e a rapidez para o ganho genético de uma determinada espécie, como por exemplo, Eucalyptusgrandis. Neste estudo foram utilizados marcadores moleculares do tipo microssatélites, Random Amplified Polymorphism DNA – RAPD, além de marcadores específicos para avaliar a segregação do florescimento precoce em uma família de irmãos-germanos de E. grandis. Foi também verificado se esses marcadores estão associados ao controle do tempo de florescimento na espécie. A progênie de 118 indivíduos avaliada foi originada do cruzamento entre uma árvore de florescimento normal e outra de florescimento precoce. A segregação da característica de florescimento precoce apresentou uma razão de 1:1 (χ2 = 0
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The ultimate use of DNA markers would be to identify quantitative trait loci (QTL) in order to practice genotypic selection. This paper reviews DNA markers (RAPD, DFP, RFLP AFLP, minisatellites, microsatellites, SNP) and provides a brief overview of the current application of these markers in animal breeding.
May 22, 2013 ... this study to characterize drought tolerance in six wheat genotypes with developed marker assisted drought tolerance. Four of ..... Abdel-Tawab FM, Eman MF, Bahieledin A, Asmhan AM, Moselihy. (2003). Marker RAPD and ISSR marker related to drought tolerance in Rice. Egypt. J. Genet. Cytol. 36:195- ...
Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...tabases and/or the genomic analysis information. Data file File name: pgdbj_dna_marker_linkage_map_plant_spe...ion method The information related to each organism was collected from databases, papers, and/or reveiews. Data analysis...the Plant DB link list in simple search page) Genome analysis methods Presence or absence of Genome analys...is methods information in this DB (link to the Genome analysis methods information
Houston Ross D
Full Text Available Abstract Background Restriction site-associated DNA sequencing (RAD-Seq is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools. Results Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified. Conclusions We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD
Lee, Junghee; Ryu, Hoon
Alzheimer's disease (AD) is the most common age-dependent neurodegenerative disorder and shows progressive memory loss and cognitive decline. Intraneuronal filaments composed of aggregated hyperphosphorylated tau protein, called neurofibrillary tangles, along with extracellular accumulations of amyloid ß protein (Aß), called senile plaques, are known to be the neuropathological hallmarks of AD. In light of recent studies, epigenetic modification has emerged as one of the pathogenic mechanisms of AD. Epigenetic changes encompass an array of molecular modifications to both DNA and chromatin, including transcription factors and cofactors. In this review, we summarize how DNA methylation and changes to DNA chromatin packaging by post-translational histone modification are involved in AD. In addition, we describe the role of SIRTs, histone deacetylases, and the effect of SIRT-modulating drugs on AD. Lastly, we discuss how amyloid precursor protein (APP) intracellular domain (AICD) regulates neuronal transcription. Our understanding of the epigenomes and transcriptomes of AD may warrant future identification of novel biological markers and beneficial therapeutic targets for AD.
E, Guang-Xin; Huang, Yong-Fu; Zhao, Yong-Ju; Ma, Yue-Hui; Na, Ri-Su; Zhang, Jia-Hua; Gao, Hui-Jiang; Wu, Xin
In this study, the genetic variability of Chinese indigenous goat breeds (Capra hircus) was analyzed using the MHC-associated microsatellite markers BF1, BM1818, BM1258, and DYMS1. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from 5.50±3.70 in Enshi black goats (EB) to 11.50±3.70 in the Jianyang big ear (JE) breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.25±0.04 in Jining Qing goats (JQ) to 0.54±0.05 in Chuannan black goats (CN) and from 0.49±0.18 in Hechuan white goats (HW) to 0.78±0.05 in JE, respectively. The mean FIS values ranged from 0.23 in HW to 0.51 in JQ. In addition, the genetic variation among populations and geographic location did indicate a correlation of genetic differences with geographic distance, which was revealed by the phylogenetic network. In conclusion, the high variability and population structure among Chinese native goats in the Major Histocompatibility Complex would be caused by co-evolution between MHC alleles and the epidemic history or pathogens in different agro-ecological zones. Copyright © 2015 Elsevier B.V. All rights reserved.
Full Text Available Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3 verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4% and (15.5–19.9, respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.
Matoba, Hideyuki; Inaba, Kazufumi; Nagano, Katsuya; Uchiyama, Hiroshi
Polemonium kiushianum is a critically endangered species of which only eight populations exist in semi-natural grasslands of the Mt. Aso area of Kyushu, Japan. Habitat modification and the risk of hybridization with non-indigenous horticultural congeners, such as P. caeruleum subsp. caeruleum and P. caeruleum subsp. yezoense var. yezoense, pose increasing threats to P. kiushianum. To develop a DNA marker that distinguishes P. kiushianum from other Polemonium species, we performed random amplified polymorphic DNA (RAPD) analysis and selected an approximately 500-bp fragment generated by the OPB06 RAPD primer. In addition, we designed a primer pair, H11F/R, based on the nucleotide sequences of the fragments derived from P. caeruleum subsp. caeruleum and P. caeruleum subsp. yezoense var. yezoense. The results with the H11F/R primers indicated that most extant P. kiushianum plants in natural populations are not genetically contaminated by hybridization with non-indigenous horticultural species.
Chester, Karishma; Tamboli, Ennus Tajuddin; Parveen, Rabea; Ahmad, Sayeed
Stevia rebaudiana Bertoni (Asteraceae) is an important medicinal plant and is much used due to its zero calories sweetening property. Stevia leaves as well as its extracts and pure compounds are currently used in the preparation of several medicines, food products and neutraceuticals. To study the genetic and metabolic variability in S. rebaudiana among accessions of different geographical regions of India using random amplified polymorphic DNA (RAPD) markers and high-performance thin layer chromatography (HPTLC) analysis. The RAPD analysis of Stevia rebaudiana (11 accessions) was carried out using 20 random operon primers. Dendrogram was constructed for cluster analysis based on the unweighted pair group method with arithmetic means (UPGMA) using Winboot. The HPTLC analysis of all samples was carried out on silica using acetone:ethyl acetate:water (5:4:1, v/v/v) for fingerprinting and quantification of stevioside and rebaudioside A at 360 nm after spraying with anisaldehyde sulphuric acid. Ten out of 20 primers screened were found most informative; amplification products of the genotypes yielded a total of 87 scorable bands (67 polymorphic), whereas genetic similarity (GS) coefficient (0.01-0.08) and polymorphism (67.24-92.40%) showed huge variability. Similarly, HPTLC analysis showed large variation among different samples with respect to their presence or absence of metabolite and their concentration. Out of the 11 Stevia accessions, Delhi and Mohali varieties showed much relatedness with each other and were concluded to be the superior genotype in context to RAPD and HPTLC analysis. The information obtained here could be valuable for devising strategies for cultivating this medicinal plant.
Miklas, P N; Stavely, J R; Kelly, J D
The Up 2 gene of common bean (Phaseolus Vulgaris L.) is an important source of dominant genetic resistance to the bean rust pathogen [Uromyces appendiculatus (Pers. ex Pers.) Unger var 'appendiculatus' [syn U. Phaseoli (Reben) Wint.]. Up 2 in combination with other rust resistance genes may be used to obtain potentially stable genetic resistance. It is difficult, however, to combine rust resistance genes effective against a single race due to epistatic interactions that frequently occur between them. A strategy that employed bulked DNA samples formed separately from the DNA of three BC6F2 individuals with Up 2 and three without Up 2 as contrasting near-isogenic lines (NILs) was used to identify random amplified polymorphic DNA fragments (RAPDs) tightly linked to the Up 2 locus. Only 1 of 931 fragments amplified by 167 10-mer primers of arbitrary sequence in the polymerase chain reaction (PCR) was polymorphic. The RAPD marker (OA141100) amplified by the 5'-TCTGTGCTGG-3' primer was repeatable and its presence and absence easy to score. No recombination was observed between OA141100 and the dominant Up 2 allele within a segregating BC6F2 population of 84 individuals. This result suggests that OA141100 and Up 2 are tightly linked. Andean and Mesoamerican bean germ plasm, with and without the Up 2 allele, were assayed for the presence of OA141100. Apparently, the marker is of Andean origin because all Andean lines, with or without the Up 2 allele, contained the marker, and the marker was absent in all Mesoamerican germ plasm except the lines to which Up-2 had been purposely transferred. These results suggest that OA141100 will be most useful for pyramiding Up 2 with other rust resistance genes into germ plasm of Mesoamerican origin where the marker does not traditionally exist. The use of bulked DNA samples may have concentrated resources toward the identification of RAPDs that were tightly linked to the target locus. Marker-based selection may provide an alternative to
Full Text Available Identification of DNA polymorphisms in teak is important. It is a first step to determine the presence of genetic varia-tion in teak. The information of genetic variation is needed for teak breeding development. RAPD is one of method which can be used for identification of DNA polymorphism. This study aim to get the RAPD primer which can detect the DNA polymorphism in teak. Benefits of this study are provide information about primer which can detect the DNA polymorphism in teak, DNA polymorphism data can be used for genetic variation analysis which needed for teak breeding development. The primers which used in this study shown the DNA polymorphism in teak. The primer are OPF6 (5'-GGGAATTCGG-3 ', OPF8 (5'-GGGATATCGC-3', and OPF11 (5'-TTGGTACCCC-3 '. The highest DNA poly-morphism is shown in DNA which amplified with OPF-8 primer. Keywords: RAPD, Primer, Polymorphism, DNA, Tectona grandis
Full Text Available Background and objectives: The genus Ephedra (Ephedraceae consists of about 40 species of mostly shrubs and rarely small trees around the world. In the present study, the essential oil (EO diversity and genetic relationships were investigated in six Ephedra species from Iran using Random Amplified Polymorphic DNA (RAPD markers. Methods: Theplants were collected from two different provinces; Azarbayjan (north-west and Khorasan (north-east of Iran. The EOs were obtained by hydro-distillation and analyzed by GC and GC/MS. The DNA was extracted from the aerial parts of the plants using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using decamer RAPD primers. Results: A total of 187 bands were scored and used for the analysis of genetic distances. Genetic distance values ranged from 0.25 to 0.95.The analysis showed the highest genetic diversity (25% between E. foliata with other species. Ephedra foliata formed a distinct group. Ephedra strobilacea was found to be the most similar to E. sarcocarpa (male.Conclusion: High genetic and EO diversity was demonstrated in this genus which should be further studied in order to make more efficient use of the species and considering relevant conservation programs.
Full Text Available The genetic variability and phylogenetic relationships in oil palm (Elaeis guineensis Jacq. were studied using RAPD (Random Amplified Polymorphic DNA. Leaf samples of 151 plants were collected from different areas in southern Thailand. DNA from the leaf samples was isolated using CTAB buffer and screened by decamer oligonucleotide primers. Among the total of 160 primers screened, 7 primers (OPB-08, OPR-11, OPT-06, OPT-19, OPAB-01, OPAB-09 and OPAB-14 were chosen to analyse for genetic variation in 151 individuals representing 52 dura, 60 tenera and 39 pisifera. Two hundred and nine amplified fragments were obtained from 7 primers with an average of 29.85 RAPD markers per primer. A dendrogram showing genetic similarities among oil palm was constructed based on polymorphic bands using UPGMA (Unweighted Pair-Group Method Using Arithmetic Average. Cluster analysis was performed using the SPSS program, which revealed four major clusters: 1 dura, tenera and pisifera from Paorong Oil Palm Company, Oil Palm Research Center, dura and tenera from private plantation in Krabi, and dura from Thepa Research Station;2 dura and tenera from Thai Boonthong Company, pisifera and tenera from Thepa Research Station, dura, tenera and pisifera from Klong Hoi Khong Research Station; 3 and 4 dura and tenera from Univanit Company, respectively. In general, a similarity index showed relatively high levels of 0.6 or greater.
Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding.
Yang, Huaan; Tao, Ye; Zheng, Zequn; Shao, Di; Li, Zhenzhong; Sweetingham, Mark W; Buirchell, Bevan J; Li, Chengdao
Selection for phomopsis stem blight disease (PSB) resistance is one of the key objectives in lupin (Lupinus angustifolius L.) breeding programs. A cross was made between cultivar Tanjil (resistant to PSB) and Unicrop (susceptible). The progeny was advanced into F(8) recombinant inbred lines (RILs). The RIL population was phenotyped for PSB disease resistance. Twenty plants from the RIL population representing disease resistance and susceptibility was subjected to next-generation sequencing (NGS)-based restriction site-associated DNA sequencing on the NGS platform Solexa HiSeq2000, which generated 7,241 single nucleotide polymorphisms (SNPs). Thirty-three SNP markers showed the correlation between the marker genotypes and the PSB disease phenotype on the 20 representative plants, which were considered as candidate markers linked to a putative R gene for PSB resistance. Seven candidate markers were converted into sequence-specific PCR markers, which were designated as PhtjM1, PhtjM2, PhtjM3, PhtjM4, PhtjM5, PhtjM6 and PhtjM7. Linkage analysis of the disease phenotyping data and marker genotyping data on a F(8) population containing 187 RILs confirmed that all the seven converted markers were associated with the putative R gene within the genetic distance of 2.1 CentiMorgan (cM). One of the PCR markers, PhtjM3, co-segregated with the R gene. The seven established PCR markers were tested in the 26 historical and current commercial cultivars released in Australia. The numbers of "false positives" (showing the resistance marker allele band but lack of the putative R gene) for each of the seven PCR markers ranged from nil to eight. Markers PhtjM4 and PhtjM7 are recommended in marker-assisted selection for PSB resistance in the Australian national lupin breeding program due to its wide applicability on breeding germplasm and close linkage to the putative R gene. The results demonstrated that application of NGS technology is a rapid and cost-effective approach in
Nov 8, 2010 ... Genetic diversity for restriction fragment length polymorphisms and heterosis for two diallel sets of maize inbreds. Theor. Appl. Genet. 80: 488-496. Mezeneer N, Ghesquire A, Marmey P, Combes MC, Guideror E (1997). Assessment of RAPD markers to detect genetic change in protoplast derived rice plants.
techniques have been developed, a wealth of new DNA marker technologies has arisen enabling the generation of high-density molecular maps for all the major crop species. Molecular markers have also been extensively used to analyze the genetic diversity in crop plants. Based on the data obtained by RAPD analysis, ...
Tobacco (Nicotiana spp.) is one of the most important commercial crops in the world. During the last two decades, molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The principles and characteristics of several molecular markers such as RFLP, RAPD, AFLP, ...
Feb 28, 2011 ... In tomato breeding, the identification of the root-knot nematodes resistance gene, Mi is mainly by ... limited application of MAS in tomato breeding in Ghana. In this work, a co-dominant SCAR marker .... Using RAPD markers to analyze genetic diversity in Portuguese potato cyst nematode populations. J.
Lian, Mulias; Zhao, Mingjue; Lee, Caroline G; Chong, Samuel S
Preimplantation genetic diagnosis (PGD) of myotonic dystrophy type 1 (DM1) currently uses conventional PCR to detect nonexpanded dystrophia myotonica protein kinase ( DMPK ) alleles or triplet-primed PCR to detect the CTG-expanded alleles, coupled with analysis of linked microsatellite markers to increase diagnostic accuracy. We aimed to simplify the process of identification and selection of informative linked markers for application to DM1 PGD. An in silico search was performed to identify all markers within 1-1.5 Mb flanking the DMPK gene. Five previously known (D19S559, APOC2, D19S543, D19S112, and BV209569) and 7 novel (DM45050, DM45178, DM45209, DM45958, DM46513, DM46892, and DM47004.1) markers with potentially high heterozygosity values and polymorphism information content were selected and optimized in a single-tube multiplex PCR panel. Analysis of 184 DNA samples of Chinese and Caucasian individuals (91 from unrelated, anonymized cord blood of Chinese babies born at the National University Hospital, Singapore, and 93 Caucasian DNA samples from the Human Variation Panel HD100CAU) confirmed the high polymorphism indices of all markers (polymorphism information content >0.5), with observed heterozygosity values ranging from 0.62-0.93. All individuals were heterozygous for at least 6 markers, with 99.5% of individuals heterozygous for at least 2 markers on either side of the DMPK CTG repeat. The dodecaplex marker assay was successfully validated on 42 single cells and 12 whole genome amplified single cells. The DM1 multiplex PCR panel is suitable for use in DM1 PGD either as a standalone linkage-based assay or as a complement to DMPK CTG repeat expansion-mutation detection. © 2017 American Association for Clinical Chemistry.
Jeffrey G. Boersma
Full Text Available Wild types of narrow-leaf lupin (Lupinus angustifolius L. have seed pods that shatter upon maturity, leading to the loss of their seeds before or during the harvest process. Two recessive genes have been incorporated into domesticated cultivars of this species to maximize harvest-ability of the produce. One of these genes is called lentus (le. Two microsatellite - anchored fragment length polymorphism (MFLP candidate markers were identified as closely linked to the le gene in a recombinant inbred line (RIL population derived from a domesticated x wild type cross. The candidate MFLP markers were isolated from the gel, re-amplified by PCR, cloned and sequenced. The MFLP polymorphisms were converted into sequence-specific PCR-based markers. Linkage analysis by MapManager indicated that one of the markers, LeM1, was 2.6 centiMorgans (cM and the other, LeM2, was 1.3 cM from the gene, with both being on the same side. The correlation between the marker genotype and the plant phenotype for the le gene is 95% for the Australian cultivars, and approximately 36% on wild types tested. These markers may be useful in marker assisted selection for the le gene when introgressing wild material into lupin breeding programs.
Full Text Available Taxonomic considerations among and within some Egyptian taxa of Capparis and related genera (Capparaceae as revealed by RAPD fingerprinting.- This investigation was carried out to assess the taxonomic relationships among eight taxa of the Egyptian members of Capparaceae based on random amplified polymorphic DNA markers, and to compare the results with those obtained from morphological studies. A total of 46 bands were scored for three RAPD primers corresponding to an average of 15.3 bands per primer. The three primers (A03, A07 and A09 revealed eight polymorphic RAPD markers among the studied taxa ranging in size from 200 bp to 1000 bp. Jaccard’s coefficient of similarity varied from 0.28 to 0.84, indicative of high level of genetic variation among the genotypes studied. UPGMA cluster analysis indicated three distinct clusters, one comprised Cleome amblyocarpa and Gynandropsis gynandra, while another included two clusters at 0.74 phenon line; one for Capparis decidua, and the other for Capparis sinaica and all varieties of Capparis spinosa. The four varieties of Capparis spinosa were segregated at 0.84 phenon line. However, one of these varieties was more closely related to Capparis sinaica than to the other three varieties of C. spinosa. The RAPD analysis reported here confirms previous studies based on morphological markers.Consideraciones taxonómicas sobre algunos taxones egipcios de Capparis y géneros relacionados (Capparaceae a partir de RAPDs.- El objetivo de este trabajo es investigar las relaciones taxonómicas entre ocho taxones pertenecientes a las Capparaceae en base a marcadores de tipo RAPD, y comparar los resultados con los obtenidos previamente en estudios morfológicos. Se han contabilizado un total de 46 bandas para tres pares de cebadores, con una media de 15,3 bandas por cebador. Los tres pares de cebadores (A03, A07 y A09 revelan ocho marcadores polimórficos entre los taxones estudiados, de entre 200 y 1000 pares de
Valmor João Bianchi
Full Text Available Marcadores moleculares têm sido amplamente utilizados nas mais variadas espécies frutíferas para análise de "fingerprinting", para o processo de certificação de material vegetal e como ferramenta auxiliar em programas de melhoramento genético, para acessar a variabilidade genética entre genótipos. Dado a importância da cultura da ameixeira para a região Sul do Brasil, o presente trabalho teve por finalidade contribuir para a caracterização genético-molecular de 17 cultivares. As cultivares foram analisadas com 12 marcadores RAPD, que produziram 187 polimorfismos. O marcador OP A20 foi o mais polimórfico, produzindo 26 perfis diferentes. A análise de agrupamento, realizada com o método UPGMA, produziu um dendrograma que permitiu uma clara separação das cultivares em três grupos, correspondentes às suas respectivas espécies, Prunus salicina, Prunus domestica e Prunus cerasifera. O alto grau de polimorfismo detectado pelos marcadores RAPD confirma o potencial da técnica na análise de "fingerprinting" e sua utilidade na estimativa da variabilidade genética entre cultivares de ameixeira.Molecular markers have been used thoroughly in many fruit crops species for fingerprinting analysis during the vegetal material certification process, and as an auxiliary tool in breeding programs to access genetic variability among genotypes. The plum is an important crop in Southern Brazil. The present paper aims to contribute for the genetic-molecular characterization of 17 plum cultivars, which were analyzed with 12 RAPD markers that produced 187 polymorphisms. The OP A20 marker was the most polymorphic, producing 26 different profiles. The cluster analysis was represented by a dendrogram using the UPGMA method, and showed a clear cultivar separation in to three groups corresponding to the species, Prunus salicina, Prunus domestica and Prunus cerasifera, respectively. A high degree of polymorphism was detected by the RAPD markers in the
Pamela E. Akin-Idowu
Full Text Available Efficient utilization of plant genetic resources for nutrition and crop improvement requires systematic understanding of the important traits. Amaranthus species are distributed worldwide with an interesting diversity of landraces and cultivars whose leaves and seeds are consumed. Despite their potential to enhance food security and economic livelihoods, grain amaranth breeding to improve nutritional quality and adoption by farmers in sub-Saharan Africa is scanty. This study assessed the variation among 29 grain amaranth accessions using 27 phenotypic (10 morphological and 17 nutritional characters and 16 random amplified polymorphic DNA (RAPD primers. Multivariate analysis of phenotypic characters showed the first four principal components contributing 57.53% of observed variability, while cluster analysis yielded five groups at 87.5% similarity coefficient. RAPD primers generated a total of 193 amplicons with an average of 12.06 amplicons per primer, 81% of which were polymorphic. Genetic similarities based on Jaccard’s coefficient ranged from 0.61 to 0.88. The RAPD-based unweighted pair group method with arithmetic mean dendrogram grouped the accessions into nine clusters, with the same species clustering together. RAPD primers distinguished the accessions more effectively than phenotypic markers. Accessions in the different clusters as obtained can be exploited for heterotic gain in desired nutritional traits.
Leila Garcês de Araújo
Full Text Available A doubled-haploid (DH population, obtained by anther culture of F1 plants from a cross between a highlysusceptible rice cultivar Lijiangxintuanheigu and the resistant somaclone (SC09, of the cultivar Araguaia, was used to identifyRAPD markers linked to the blast resistance gene Pi-ar. The 86 DH plants, inoculated with the race IB-9 of Magnaportheoryzae, segregated in 1:1 ratio of resistant and susceptible plants. Of the 67 primers used 31 produced DNA profiles thatdifferentiated resistant and susceptible bulks as well as the parental cultivars. The resistance gene was found linked to theprimer OPS162072 (‘AGGGGGTTCC’ at a distance of 3.6 cM. The selection efficiency of this primer was assessed in a BC3 F1population derived from another cross between a susceptible cultivar IAC 201 and SC09. The marker OPS16 showedefficiency of 86.9%, when six resistant and two susceptible plants were considered as negatives in RAPD analysis.
Genetic analysis of plants relies on high yields of pure DNA samples. Here we present the optimization of DNA isolation and PCR conditions for RAPD analysis of selected medicinal and aromatic plants of conservation concern from Peninsular India containing high levels of polysaccharides, polyphenols and secondary ...
Five species, including: Quercus robur, Quercus macranthera, Quercus infectoria, Quercus magnosquamata and Quercus libani were collected from Northwest forests of Iran and analyzed. Each tree was judged as a genuine type of each species according to the morphological structures. 10 RAPD primers reproducibly and ...
Jun 5, 2012 ... Quercus is one of the most important woody genera of the Northern hemisphere and considered as one of the main forest tree species in Iran. In this study, genetic relationships in the genus Quercus, using random amplified polymorphic DNA (RAPD) was examined. Five species, including: Quercus robur,.
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Aug 14, 2012 ... RAPD primers GLC-07 and GLB-11. PCR amplification using primer GLC-07 produced single band of ... PCR amplification profile of the two genetic stocks of common wheat,. NT2A2B and NT1D1B using .... Isolation of recombinants involving barley arms 3HL and 6HL. Theor. Appl. Genet. 83:489-494.
Jun 17, 2009 ... Nine soil rhizobia isolated from different field locations were subjected to RAPD analysis to study the diversity. It was found that Rhizobium isolates from Agricultural Research Station - Aliyar Nagar (ALN 7),. Department of Agricultural Microbiology (SOB 1), isolates from TNAU Eastern block field No.36 (EB ...
Nine soil rhizobia isolated from different field locations were subjected to RAPD analysis to study the diversity. It was found that Rhizobium isolates from Agricultural Research Station - Aliyar Nagar (ALN 7), Department of Agricultural Microbiology (SOB 1), isolates from TNAU Eastern block field No.36 (EB 36) and Millet ...
of DNA isolation and PCR conditions for RAPD analysis of selected medicinal and aromatic plants of conservation concern from Peninsular ... The technique is ideal for isolation of DNA from different plant species and the DNA isolated was used for ..... showed a reading of between 1.6 to 1.7 after calculating the 260/280 nm ...
Jul 20, 2009 ... RAPD-based detection of genomic instability in cucumber plants derived from somatic embryogenesis. Khaled M. Suliman Elmeer1*, Thomas F. Gallagher2 and Michael J. Hennerty2. 1Plant Tissue Culture Laboratory. Department of Water Research and Agriculture Doha-Qatar. 2School of biology and ...
The highest variation was obtained in regenerates treated with 25 mg/L colchicine, which also exhibited reduced regeneration rates from plbs and mean plantlet fresh weight. RAPD analysis also showed high polymorphism between the mutated regenerant DSB V, and 13 species of the Dendrobium genera, and 13 orchids ...
Hassager, C; Jensen, L T; Pødenphant, J
Carboxy-terminal pyridinoline cross-linked telopeptide of type I collagen (ICTP) in serum has recently been proposed as a new biochemical marker of bone resorption. In the present study we compared serum ICTP with radiopharmaceutical and histomorphometric measurements of bone turnover...... conclude that serum ICTP does reflect bone metabolism in postmenopausal osteoporosis, but it is not a sensitive marker of the changes in bone resorption induced by hormone replacement therapy, and it does not correspond with other measures of bone resorption during anabolic steroid therapy....
Wang, Y S; Liu, Z Y; Li, Y F; Zhang, Y; Yang, X F; Feng, H
Artistic diversiform leaf color is an important agronomic trait that affects the market value of ornamental kale. In the present study, genetic analysis showed that a single-dominant gene, Re (red leaf), determines the red leaf trait in ornamental kale. An F2 population consisting of 500 individuals from the cross of a red leaf double-haploid line 'D05' with a white leaf double-haploid line 'D10' was analyzed for the red leaf trait. By combining bulked segregant analysis and sequence-related amplified polymorphism technology, we identified 3 markers linked to the Re/re locus. A genetic map of the Re locus was constructed using these sequence-related amplified polymorphism markers. Two of the markers, Me8Em4 and Me8Em17, were located on one side of Re/re at distances of 2.2 and 6.4 cM, whereas the other marker, Me9Em11, was located on the other side of Re/re at a distance of 3.7 cM. These markers could be helpful for the subsequent cloning of the red trait gene and marker-assisted selection in ornamental kale breeding programs.
Sep 26, 2011 ... Cotton is cultivated in Iran with diploid and tetraploid forms and hybridization is a means to increase the genetic diversity ... diversity in ISSR markers were obtained in Mehr X Sindose and Mehr X Belilzovar hybrids. Key words: Cotton ..... analysis of F1 and F2 progenies of the interspecific cross between ...
Saxena, Raghvendra; Chandra, Amaresh
Genetic analysis of 30 accessions of marvel grass (Dichanthium annulatum Forsk.), a tropical range grass collected from grasslands and open fields of drier regions, was carried out with the objectives of identifying unique materials that could be used in developing the core germplasm for such regions as well as to explore gene (s) for drought tolerance. Five inter-simple sequence repeat (ISSR) primers [(CA)4, (AGAC), (GACA) 4; 27 random amplified polymorphic DNA (RAPD) and four enzyme systems were employed in the present study. In total, ISSR yielded 61 (52 polymorphic), RAPD 269 (253 polymorphic) and enzyme 55 isozymes (44 polymorphic) bands. The average polymorphic information content (PIC) and marker index (MI) across all polymorphic bands of 3 markers systems ranged from 0.419 to 0.480 and 4.34 to 5.25 respectively Dendrogram analysis revealed three main clusters with all three markers. Four enzymes namely esterase (EST), polyphenoloxidase (PPO), peroxidase (PRX) and superoxide dismutase (SOD) revealed 55 alleles from a total of 16 enzyme-coding loci. Of these, 14 loci and 44 alleles were polymorphic. The mean number of alleles per locus was 3.43. Mean heterozygosity observed among the polymorphic loci ranged from 0.406 (SOD) to 0.836 (EST) and accession wise from 0.679 (1G3108) to 0.743 (IGKMD-10). Though there was intermixing of few accessions of one agro-climatic region to another largely groupings of accessions were with their regions of collections. Bootstrap analysis at 1000 iterations also showed large numbers of nodes (11 to 17) having strong clustering (> 50 bootstrap values) in all three marker systems. The accessions of the arid and drier regions forming one cluster are assigned as distinct core collection of Dichanthium and can be targeted for isolation of gene (s) for drought tolerance. Variations in isozyme allele numbers and high PIC (0.48) and MI (4.98) as observed with ISSR markers indicated their usefulness for germplasm characterization.
Full Text Available Abstract Background Mastitis is the most important disease in dairy cows and it causes significant lost of profit to producers. Identification of the genes, and their variants, involved in innate immune responses is essential for the understanding of this inflammatory disease and to identify potential genetic markers for resistance to mastitis. The progeny of dairy cows would benefit from receiving favourable alleles that support greater resistance to infection, thus reducing antibiotic use. This study aims to identify a key gene in the innate immune response to mastitis, led us to evaluate its genetic association with somatic cell score (SCS, which is an indicator of clinical mastitis, and to evaluate its impact on other traits related to milk production. Results The osteopontin transcript (SPP1 was identified in the somatic cells from cows experimentally infected with Escherichia coli. By selecting bulls with extreme estimated breeding values (EBVs for SCS, which is an indicator of mammary gland health, four DNA polymorphisms in the SPP1 genomic sequence were found. Statistical analysis revealed that the SNP SPP1c.-1301G>A has an impact on EBV for SCS (P SPP1c.-1251C>T, SPP1c.-430G>A, and SPP1c.*40A>C have an impact on SCS whereas SPP1c.-1301G>A has an effect on the EBVs for milk yield (second and third lactations, fat and protein percentages (all three lactations. Analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with sire EBVS for SCS for the first (P = 0.012, second (P P Conclusion This study reports the link between DNA polymorphisms of SPP1, the number of milk immune cells and, potentially, the susceptibility to mastitis. These SNPs were identified by in silico search to be located in transcription factor recognition sites which factors are presumably involved in the Th1 immune response and in the Th2 regulation pathway. Indeed, one SNP abolished the SP1 recognition site, whereas
Full Text Available Optimization and application of RAPD (random amplified polymorphic DNA in a recurrent selection programme of cotton (Gossypium spp..Using DNA extracted from différent wild and cultivated species of cotton, we analyzed and optimized the parameters for the random amplification of polymorphic DNA (RAPD. All the parameters have an effect on the final result but the concentrations of template DNA, magnésium chloride, deoxynucleoside triphosphates, and the température of dénaturation seem to be the most important factors. The optimization was performed by successive adjustements of the standard RAPD conditions and by taking into accourir the manufacturera' recommendations for each reagent. The optimized conditions were then used to assist an interspecific hybridization programme involving two allotetraploid trispecific hybrids [(Gossypium thurberi Tod. x G. sturtianum Will. doubled x G. hirsutum L., designated by G405] and [(G. hirsutum x G. raimondii Ulbr. doubled x G. sturtianum, designated by G376]. Both trispecific hybrids were backcrossed with three varieties (LPB5, NC8 and C2 of the cultivated upland cotton G. hirsutum. In RAPD analysis, thirty random decamer primera generated 375 RAPD markers. Analysis of genetic similarity from the RAPD data with UPGMA and Jaccard's distance revealed 78.3-78.7% similarity between the three varieties of G. hirsutum and 31.3-39.2% similarity between G. hirsutum and the wild diploid species (G. thurberi, G. raimondii and G. sturtianum. The genetic similarity within backcross 1 progenies showed values ranging between 63.2-78.0% for the cross G405 x LPB5, 75.0-80.4% for G405 x NC8, 63.9-82.2% for G405 x C2, 76.3-83% for G376 x C2 and 64.9-79.8% for the cross G376 x LPB5. This study allowed to choose within the first backcross progenies having the searched trait, those sharing the highest genetic similarity with the cultivated parent G. hirsutum. Résulta indicate that RAPD analysis can be used to accelerate the
Full Text Available Leaf rust (LR, caused by Puccinia triticina, is one of the most widespread diseases of common wheat (Triticum aestivum L. worldwide. The LR resistance gene LrBi16 has been mapped on chromosome arm 7BL in Chinese wheat cultivar Bimai 16 and was closely linked to SSR loci Xcfa2257 and Xgwm344 with genetic distances of 2.8 cM and 2.9 cM, respectively. In the present study, a total of 304 AFLP primer pairs were used to screen Bimai 16 and Thatcher and resistant and susceptible DNA bulks. The polymorphic AFLP marker P-ATT/M-CGC173 bp was used to genotype F2 and F3 populations to identify markers more closely linked to LrBi16. Marker P-ATT/M-CGC173 bp was tightly linked to LrBi16 with a genetic distance of 0.5 cM. As LrBi16 was mapped near the Lr14a locus, 809 F2 plants from the Bimai 16/RL6013 (Lr14a cross were inoculated with the Pt pathotype FHNQ to test the allelism of Lr14a and LrBi16. All of the F2 plants were resistant to FHNQ (IT between; and 2, suggesting that Lr14a and LrBi16 are allelic.
Iqbal, M J; Rayburn, A L
The introgression of rye DNA into the wheat genome was studied using random decamer and specific primers with the polymerase chain reaction (PCR). DNA from paired near-isolines in Chisholm and Arkan backgrounds differing with respect to the presence of a 1 RS.1 BL translocation was amplified with 120 arbitrary sequence primers. Two of the primers (OPR 19 and OPJ07) amplified rye-specific DNA fragments. The OPR19 primer amplified a 1.35-kb fragment that appeared to be specific to the 1 RS.1 BL translocation, based on its presence only in lines carrying the 1 RS. 1 BL translocation. A fragment of the same size was also amplified in 1 RS.1 AL translocation lines. This 1 RS. 1 BL marker locus was designated Ximc 1. The other primer, OPJ07, amplified a 1.2-kb DNA sequence, that was designated Ximc 2, specific to the wheat-rye translocation in various wheat backgrounds. The sequences of the two marker loci were found to be different from each other. The Ximc 1 locus was a low-copy sequence which was also present in Balboa rye genomic DNA. Through the use of specific primers, the presence of the rye-specific marker was confirmed in hexaploid as well as in tetraploid wheat backgrounds. The use of RAPDs for the study of smaller alien introgressions into wheat is discussed.
Full Text Available The present study deals with authenticating existing knowledge about 21 Bougainvillea cultivars comprisingof 9 hybrids and their parents through RAPD analysis. The 19 degenerate primer sets generated 234 bands from which 158(67.5% were polymorphic. The UPGMA based dendrogram divided 21 cultivars into two major groups with Jaccard’ssimilarity coefficient ranging from 0.51 to 0.942. Group A had three cultivars namely Trinidad, Formosa and Dr. H. B. Singhin which Dr. H.B. Singh was confirmed as a hybrid of other two cultivars. Group B was sub divided into 8 clusters. Theparentages of 7 out of 8 hybirds have been confirmed based on clusters. The study concluded that the RAPD technique issuitable for confirmation of parent-hybrid relationship.
Medhi, K; Sarmah, D K; Deka, M; Bhau, B S
The genetic diversity in Zanthoxylum species viz. Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612).
Amina A. Aly
Full Text Available BackgroundIn recent years, several plant species have been used as bioindicators to evaluate the toxicity of environmental contaminants on vegetal organisms. In this study, Egyptian clover and Sudan grass seedlings were grown in four cadmium (Cd concentration levels (0.0, 25, 50 and 100 µM in MS media to analyze growth responses, Cd accumulation in the shoots and roots of plantlets, proline contents, chlorophylls content and MDA levels of both plantlets. As well as RAPD analysis and leaves ultrastructure were detected.ResultsThe results showed that there was a significant decrease in root and shoot lengths, Chl a, Chl b, total Chl and carotenoids contents for both Egyptian clover and Sudan grass. However, there was a significant increase in Cd accumulation, proline and malondialdehyde (MDA levels. The genetic variation between Egyptian clover and Sudan grass were evaluated using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR markers to establish specific DNA markers associated with Cd stress. The results of transimssion electron microscopy (TEM showed a clear disorder in the Cd treated Egyptian clover and Sudan grass seedlings.ConclusionIn conclusion, biochemical, molecular and ultrastructure changes in Egyptian clover and Sudan grass could be used as a useful biomarker assay for the detection of genotoxic effects of Cd stress on plants. However, it is necessary to be further confirmed and optimized in the future research.
David C Broadway
The 'swinging light test' is used to detect a relative afferent pupil defect (RAPD): a means of detecting differences between the two eyes in how they respond to a light shone in one eye at a time. The test can be very useful for detecting unilateral or asymmetrical disease of the retina or optic nerve (but only optic nerve disease that occurs in front of the optic chiasm).
David C Broadway
Full Text Available The 'swinging light test' is used to detect a relative afferent pupil defect (RAPD: a means of detecting differences between the two eyes in how they respond to a light shone in one eye at a time. The test can be very useful for detecting unilateral or asymmetrical disease of the retina or optic nerve (but only optic nerve disease that occurs in front of the optic chiasm.
Qu, Fan; Zhou, Jue; Zhou, Zhou; Li, Huiyu; Burrows, Elizabeth
In the research, genetic analysis of Aralia cordata Thunb. (Araliaceae) was conducted using randomly amplified polymorphism DNA (RAPD). 161 loci were detected with 12 RAPD primers. Percentage of Polymorphic Band (PPB) varied from 34.78% to 63.35%. All the samples were respectively collected from the eight provinces richest in Aralia cordata Thunb resources in China, including Hunan, Yunnan, Zhejiang, Sichuan, Jiangxi, Anhui, Shanxi and Gansu. The results showed that Hunan Province enjoyed the highest level of genetic differentiation and Gansu was the lowest. The total genetic diversity (H(T)) of RAPD, intraspecific genetic diversity (H(S)) and genetic diversity (D(ST)) of the various places was respectively 26.33%, 11.14%, and 49.36%. The differentiation among the species accounted for 98.76% of total genetic diversity (G(ST)). Based on the cluster results of genetic distance, the 8 samples were classified into three groups. It is concluded that Hunan Province enjoyed the highest level of genetic differentiation of Aralia cordata Thunb and Gansu was the lowest, which provides a basis for the taxonomic identification and germplasm resource research of Aralia cordata Thunb in the future.
Lisowski, Mirosław; Slawinska, Anna; Dluzniewska, Paulina; Mazanowski, Adam; Bednarczyk, Marek
Commercial geese breeding in Poland is based on two strains of White Italian geese (W11 and W33). The crossbreeds W33 (paternal line) and W11 (maternal line) are distributed in Poland under the commercial brand of White Kołuda goose. However, there are several breeds which are covered by the animal genetic resources conservation program and kept as conservative flocks. These breeds proved invaluable to commercial geese breeding to stabilize body weight, improve muscling and decrease the amount of fat in the carcass of the crossbreeds. Therefore, this study analyzed the reciprocal crossbreeds of White Kołuda geese with the individuals from conservative flocks. DNA polymorphism (RAPD-PCR) of the crossbreeds as well as the phenotypic effect of crossbreeding was evaluated. PCR amplification of five RAPD markers resulted in obtaining 14.25 band/crossbreed group. The genetic similarity of the crossbreeds expressed as band sharing frequency (BS) ranged from 0.44 to 0.97. The direction of crossing of the W33 goose with one of the individuals from the conservative flock strongly affected the genetic similarity estimates. The body weight in the 17th or 24th week of life and the percentage of leg muscle weight in the 24th week of life differed significantly depending on the crossbreed genotype. A similar relationship was demonstrated for egg fertilization and number of nestlings per goose. As the lines were differentiated only by origin of the Z chromosome, the background of the differences in genetic polymorphism and the phenotypic records is hypothesized as (i) the linkage of some production traits with sex chromosomes; (ii) the impact of selection on W33 individuals resulting in lower performance of geese with a W33-derived Z chromosome; (iii) genetic imprinting displayed as the effect of either maternal or paternal origin of the Z chromosome.
Zakharov, E V
Genetic evidence for interspecific hybridization between Parnassius nomion and Parnassius bremeri in nature is presented. To demonstrate hybridization between these species, RAPD analysis was used. By testing 25 decamer primers, three and two diagnostic markers were revealed for P. nomion and P. bremeri, respectively. Out of 28 animals examined, 4 were shown to be interspecific hybrids. According to the distribution of diagnostic markers, the interspecific hybrids were intermediate with regard to the parental species. Ecological and biological characteristics of two swallowtail species that promote their hybridization in nature are discussed.
are expected to have more relevance to obesity -related cancers, such as colon, renal, pancreas, and post- menopausal breast cancer. My studies...highlight novel mechanisms linking obesity and aggressive cancer progression and provide therapeutic strategies for these obesity - related cancers...Adipocyte-Derived Factor Endotrophin Links Obesity with Malignant Tumor Progression Park J. and P.E. Scherer, (2012) Journal of Clinical Investigation
Michael E. Devey; Annette Delfino-Mix1; Bohun B. Kinloch; David B. NEALEt
We have genetically mapped a gene for resistance to white pine blister rust (Cronartium ribicola Fisch.) in sugar pine (Pinus lambertiana Dougl.) by using an approach which relies on three factors: (i) the ability to assay for genetic markers in the haploid stage of the host's life cycle, using...
Patra, K P; Ramu, Thangadurai; Hoti, S L; Pragasam, G Siva; Das, P K
In India, Mass Drug Administration is on going towards elimination of lymphatic filariasis in many areas, which might lead to intense selection pressure on the parasite populations and their genetic restructuring. This calls for molecular finger printing of Wuchereria bancrofti parasite populations at national level and monitoring genetic changes in the future. For this purpose a reliable, less expensive, rapid, and reproducible molecular tool is necessary, which is not available for W. bancrofti at this time. We identified robust molecular markers based on the comparison of random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) profiles and the genetic data generated from parasite populations collected from areas in Northern (Varanasi, Uttar Pradesh state), Southern (Kozhikode, Kerala State) and Central regions (Jagdalpur, Chattisgarh state) of India, where lymphatic filariasis is endemic for many decades. RAPD profiles for these parasite populations were generated using three different primers and the dendrograms constructed using the profiles were all different. In order to identify appropriate RAPD primer(s), we compared the results of RAPD with the fingerprint profile and genetic data obtained by the more reliable AFLP technique, using the parasite populations from the same areas. RAPD marker (OP8) primer produced phylogenetic data almost similar to that of AFLP analysis. The marker was able to reveal variations between the parasite populations collected from Varanasi, Kozhikode, and Jagdalpur. Most importantly, RAPD primer OP8 produced reproducible results, when tested in three different trials. In view of the limited availability of W. bancrofti parasite DNA, along with a lower cost and ease of performance, RAPD appears to be more suitable compared to AFLP at the present juncture, since complete genome information of this parasite is still not available. Thus, RAPD primer OP8 can be a very useful molecular maker for DNA
El Sharabasy, Sherif F; Soliman, Khaled A
The date palm is an ancient domesticated plant with great diversity and has been cultivated in the Middle East and North Africa for at last 5000 years. Date palm cultivars are classified based on the fruit moisture content, as dry, semidry, and soft dates. There are a number of biochemical and molecular techniques available for characterization of the date palm variation. This chapter focuses on the DNA-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) techniques, in addition to biochemical markers based on isozyme analysis. These techniques coupled with appropriate statistical tools proved useful for determining phylogenetic relationships among date palm cultivars and provide information resources for date palm gene banks.
Kim, Jin-Hyun; Lee, Chaeyoung; Hyung, Daejin; Jo, Ye-Jin; Park, Joo-Seok; Cook, Douglas R; Choi, Hong-Kyu
Genetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species. Here we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations. CSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding.
Full Text Available Background Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. Methods The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA. Results The low value of Dice’s coefficient (0.369 along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. Discussion The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.
Guerra, A L; Lima, A V B; Taddei, F G; Castiglioni, L
The prawn genus Macrobrachium belongs to the family Palaemonidae. Its species are widely distributed in lakes, reservoirs, floodplains, and rivers in tropical and subtropical regions of South America. Globally, the genus Macrobrachium includes nearly 210 known species, many of which have economic and ecological importance. We analyzed three species of this genus (M. jelskii, M. amazonicum and M. brasiliense) using RAPD-PCR to assess their genetic variability, genetic structure and the phylogenetic relationship between them and to look for molecular markers that enable separation of M. jelskii and M. amazonicum, which are closely related syntopic species. Ten different random decamer primers were used for DNA amplification, yielding 182 fragments. Three of these fragments were monomorphic and exclusive to M. amazonicum or M. jelskii and can be used as specific molecular markers to identify and separate these two species. Similarity indices and a phylogenetic tree showed that M. amazonicum and M. jelskii are closest to each other, while M. brasiliense was the most differentiated species among them; this may be attributed to the different habitat conditions to which these species have been submitted. This information will be useful for further studies on these important crustacean species.
Keats, B.J.B.; Nouri, N.; Pelias, M.Z.; Deininger, P.L. (Louisiana State Univ., New Orleans, LA (United States)); Litt, M. (Oregon Health Sciences Univ., Portland, OR (United States))
Usher syndrome type I is an autosomal recessive disease characterized by profound congenital hearing impairment and vestibular dysfunction followed by the onset of progressive pigmentary retinopathy in childhood or early adolescence. A locus (USH1C) for one form of this disease was previously assigned to the short arm of chromosome 11 through linkage studies in the Acadian population of southwestern Louisiana. Linkage analyses of a set of microsatellite markers in 27 Acadian families provide evidence that USH1C lies between D11S861 and D11S928. Three markers (D11S419, D11S921, and D11S899) that lie between the flanking markers show no recombination with USH1C, and all 54 chromosomes with the abnormal allele at the disease locus have identical alleles for D11S419 and D11S921. This haplotype was found on only 10 of 50 chromosomes with the normal allele at the disease locus, suggesting a strong founder effect. Of the 54 chromosomes with the abnormal allele, 12 had a divergent allele at D11S899. These results suggest that USH1C is in the 2-3-cM interval between D11S861 and D11S899. 16 refs., 2 figs., 3 tabs.
Random amplified polymorphic DNA (RAPD) primers associated with drought tolerance was used in this study to characterize drought tolerance in six wheat genotypes with developed marker assisted drought tolerance. Four of them were tolerant and two were drought sensitive genotypes. The results indicate that tolerant ...
Roche, P.; Arkel, van G.; Heusden, van A.W.
This report describes the conversion of a restriction fragment length polymorphism (RFLP) marker (the 2B12a locus), linked to the Sd1 aphid resistance gene, to a polymerase chain reaction (PCR) based marker. A section of the 2B12 probe was sequenced and two primers were designed to amplify this
Isolates of Bipolaris oryzae were analysed by RAPD techniques to determine the amount of intraspecific genetic variability. In order to do RAPD-PCR, seven primers were applied. At first, DNA of all isolates was isolated, and then DNA was amplified in thermocycler by using seven primers at a thermal program. As the result ...
Kappe, A.L.; van de Zande, L.; Vedder, E.J.; Bijlsma, R.; van Delden, Wilke
Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands.
Martins-Lopes, Paula; Gomes, Sónia; Santos, Elisabete; Guedes-Pinto, Henrique
The certification of olive oil has led to the definition of Protected Denomination of Origin (PDO) producing regions in European countries. PDO products should be protected, and a solution could be by using DNA fingerprinting. In this work we evaluate the efficiency of RAPD, ISSR, and SSR molecular markers for olive oil varietal identification and their possible use in certification purposes. Twenty-three Portuguese olive oil samples (11 obtained monovarietal and 12 purchased commercial oils) were screened by means of two RAPD, four ISSR, and four SSR markers. The quality of amplified products was used to evaluate the reproducibility and the level of polymorphism. Principal component analysis was performed with DCENTER using unweighted pair group mathematical average (UPGMA) that allowed group formation according to olive oil varietal geographic origin.
Meulen, van der J.J.M.; Oeveren, van J.C.; Sandbrink, J.M.; Tuyl, van J.M.
Segregation of flower longevity in two lily populations was studied and the genetic linkage of morphological markers and RAPD markers with loci involved in flower longevity was investigated. A large variation in flower longevity was found within the two populations tested at individual plant level.
Full Text Available In this present study, we have described the diversity of nine Ocimum genotypes naturally grown in the Dakshin Dinajpur district of West Bengal, India. Their diversity was determined on the basis of morphological, chemical and randomly amplified polymorphic DNA (RAPD to determine the level of variation present in the genus Ocimum. Among nine Ocimum genotypes six (O. americanum, O. × africanum, O. basilicum, O. gratissimum, O. kilimandscharicum and O. tenuiflorum are found to be different Ocimum species and the rest are as varieties. A total of 18 qualitative and 17 quantitative morphological traits and chemical compositions were evaluated. Significant variations were observed in the morphological traits except O. × africanum and O. basilicum species. Cluster generated from the morphological data showed two different groups viz. basilicum group and sanctum group. Chemical analysis did not show much variation between morphologically similar species viz. O. × africanum and O. basilicum. However, RAPD analyses clearly showed that O. × africanum and O. basilicum are different species. Thus the combined analyses of morphological traits, chemical and molecular markers represent the best possible approach to confirm taxonomic delineation. Moreover, we are reporting O. × africanum for the first time from this region as well as from West Bengal, India.
Full Text Available Yulianti, Siregar IZ, Wijayanto N, Tapa Darma IGK, Syamsuwida D (2011 Genetic variation of Melia azedarach in community forests of West Java assessed by RAPD. Biodiversitas 12: 64-69. Melia azedarach L. or mindi (local name is one of the widely planted exotic species in Indonesia, mostly found in community forests in West Java. However, improving and increasing the productivity of mindi commmunity plantation in West Java requires information on patterns of existing genetic diversity. The present work was aimed at estimating the genetic variation of mindi by using RAPD markers. Outcome of the activities was to propose appropriate conservation and management strategies of genetic resources in order to support the establishment of seed sources. Six populations of mindi plantation in the community forests were chosen for this research, i.e Sukaraja (Bogor-1, Megamendung (Bogor-2, Bandung, Purwakarta, Sumedang and Kuningan. Five primers (OPA-07, OPY-13, OPY-16, OPA-09 and OPO-05 producing reproducible bands were analysed for 120 selected mother trees in total, in which 20 trees per locality were sampled. Data were analysed using Popgene ver 1.31, NTSYS 2.02 and GenAlEx 6.3. Based on the analysis, the observed number of alleles per locus ranging from 1.43 to 1.60, and percentage of polymorphic loci (PPL ranging from 43.33 to 60.00.%. The levels of genetic variation were considered as moderate for all populations (He range from 0.1603 to 0.1956 and the the mean level of genetic diversity between population (Gst was 0.3005. Cluster analysis and Principal Coordinates showed three main groups, the first group consists of 4 populations i.e Bandung, Kuningan, Purwakarta and Megamendung, the second was Sukaraja and the third was Sumedang. Based on Analysis of Molecular Variance (AMOVA, the Percentages of Molecular Variance within population (69% is higher than that of between populations (31%. The moderate level of genetic variation in the community
Yadav, P; Koul, K K; Shrivastava, N; Mendaki, M J; Bhagyawant, S S
Chickpea is a food legume which is alleged to be a preferred source of protein next only to milk. Germplasm of cultivated chickpea available is deficient in desired genetic variation. Genetic manipulations therefore, necessitate the genetic exploitation of its related annual and wild species. 42 RAPD and 41 ISSR markers were employed to ascertain polymorphism across 20 genotypes which were collected from 10 different geographical areas of the world. RAPD marker detected 51% genetic polymorphisms while ISSR marker detected 54 %. With an average of 6.5 each RAPD primer amplified 5—8 bands. Similarly with an average of 7.9 each ISSR primer amplified 4—12 bands. The cluster dendrogram demonstrated a similarity coefficient range from 0.80 to 0.92 due to RAPD markers, whereas with ISSR primers the cluster dendrogram showed similarity coefficient of 0.60 to 1.00. Accessions from same geographical area seem to be genetically similar than those from geographically distant and isolated ones. When however compared, interestingly the ISSR dendrogram showed more correlation with pedigree data than the RAPD dendrogram. The variability index worked out in the present study ranges from 0.79 to 0.96. Since the ultimate reason for such studies is selection of diverse genetic accessions for their recommendation to breeding programmers, the accessions like ICC6263, ICC6306 and ICC17160 can be recommended as parents. Further breeding programmes can therefore be planned to procure additional variation complexes in chickpea genetic stocks.
Full Text Available Half-smooth tongue sole (Cynoglossus semilaevis is one of the most important flatfish species for aquaculture in China. To produce a monosex population, we attempted to develop a marker-assisted sex control technique in this sexually size dimorphic fish. In this study, we identified a co-dominant sex-linked marker (i.e., CyseSLM by screening genomic microsatellites and further developed a novel molecular method for sex identification in the tongue sole. CyseSLM has a sequence similarity of 73%–75% with stickleback, medaka, Fugu and Tetraodon. At this locus, two alleles (i.e., A244 and A234 were amplified from 119 tongue sole individuals with primer pairs CyseSLM-F1 and CyseSLM-R. Allele A244 was present in all individuals, while allele A234 (female-associated allele, FAA was mostly present in females with exceptions in four male individuals. Compared with the sequence of A244, A234 has a 10-bp deletion and 28 SNPs. A specific primer (CyseSLM-F2 was then designed based on the A234 sequence, which amplified a 204 bp fragment in all females and four males with primer CyseSLM-R. A time-efficient multiplex PCR program was developed using primers CyseSLM-F2, CyseSLM-R and the newly designed primer CyseSLM-F3. The multiplex PCR products with co-dominant pattern could be detected by agarose gel electrophoresis, which accurately identified the genetic sex of the tongue sole. Therefore, we have developed a rapid and reliable method for sex identification in tongue sole with a newly identified sex-linked microsatellite marker.
Gutierrez, N; Avila, C M; Duc, G; Marget, P; Suso, M J; Moreno, M T; Torres, A M
The antinutritional factors (ANFs) present in Vicia spp. seeds are a major constraint to the wider utilization of these crops as grain legumes. In the case of faba bean (Vicia faba L.), a breeding priority is the absence vicine and convicine (v-c); responsible for favism in humans and for the reduced animal performance or low egg production in laying hens. The discovery of a spontaneous mutant allele named vc-, which induces a 10-20 fold reduction of v-c contents, may facilitate the process. However, the high cost and difficulty of the chemical detection of v-c seriously restricts the advances in breeding-selection. To identify random amplified polymorphic DNA (RAPD) markers linked to this gene, we have analysed an F(2 )population derived from a cross between a line with high v-c content (Vf6) and the vc- genotype (line 1268). Quantification of v-c was done by spectrophotometry on the parents and the F(2 )population (n = 136). By using bulked segregant analysis (BSA), two RAPD markers linked in coupling and repulsion phase to the allele vc- were identified and further converted into sequence characterized amplified regions (SCARs). Amplification of SCARS was more consistent, although the initial polymorphism between pools was lost. To recover the polymorphisms several approaches were explored. Restriction digestion with HhaI (for SCAR SCH01(620)) and RsaI (for SCAR SCAB12(850)) revealed clear differences between the parental lines. The simultaneous use of the two cleavage amplified polymorphism (CAP) markers will allow the correct fingerprinting of faba bean plants and can be efficiently used in breeding selection to track the introgression of the vc- allele to develop cultivars with low v-c content and improved nutritional value.
Full Text Available Abstract Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR, Restriction Enzyme Fragment Polymorphism (RFLP and/or Sequence Tagged Site (STS markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci, with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM. More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in
Karina dos Santos Paduan
Full Text Available The tropical mosquito, Aedes aegypti is the most important domestic vector of urban yellow fever and dengue. Genetic population studies on this vector are important because they may lead to new tools for surveillance. An analysis of genetic structure was conducted among populations of A. aegypti from 11 localities in four demographic regions within six Brazilian federal states. Markers included 21 random amplified polymorphic DNA (RAPD loci. RAPD markers were detected among populations and cluster analysis revealed two main groups. We found high genetic polymorphism (H S = 0.224 and high levels of genetic differentiation between populations from different states (G ST = 0.430, as well as in populations from cities in the same state (G ST = 0.410. These results indicate significant differentiation in A. aegypti populations in Brazil. Regression analyses of geographic distances and pairwise F ST values estimated from RAPD markers showed that there is a correlation between genetic structure and geographic localization.
Yazidi, Rihab; Bettaieb, Jihene; Ghawar, Wissem; Jaouadi, Kaouther; Châabane, Sana; Zaatour, Amor; Ben Salah, Afif
Zoonotic cutaneous leishmaniasis caused by Leishmania (L.) major is endemoepidemic in the Center and South of Tunisia. The clinical course of the disease varies widely among different patients and geographic regions. Although genetic diversity in L. major parasites has been suggested as a potential factor influencing their pathogenic variability, little information on genetic polymorphism among L. major strains is available in the literature. This work aimed to estimate the genetic variability within different isolates of L. major. Our sample comprised 39 isolates (confirmed as L. major by restriction fragment length polymorphism typing) from patients experiencing the same clinical manifestations but living in different regions of Tunisia where L. major is endemic. Random amplified polymorphic DNA (RAPD) PCR marker polymorphism was estimated by calculating Nei and Li's genetic distances and by an analysis of molecular variance (AMOVA). Analysis of the genetic diversity among the isolates revealed a high level of polymorphism (43 %) among them. AMOVA indicated that the highest variability (99 %) existed within the study regions. Our results revealed a heterogeneous genetic profile for L. major with similar clinical manifestations occurring within the different geographical regions. Additional L. major isolates from patients, insect vectors, and reservoir hosts from different endemic foci should be collected for further analysis.
Kjølner, S; Såstad, S M; Taberlet, P; Brochmann, C
Random amplified polymorphic DNA (RAPD) markers are sensitive to changes in reaction conditions and may express polymorphisms of nongenetic origin. Taxa with variable chromosome numbers are particularly challenging cases, as differences in DNA content may also influence marker reproducibility. We addressed these problems by comparing RAPD and amplified fragment length polymorphism (AFLP) analyses of clonal identity and relationships in a chromosomally variable arctic plant, the polyploid Saxifraga cernua, which has been thought to be monoclonal over large geographical distances. Fifty-seven plants from four Greenland populations were analysed using a conservative scoring approach. In total, 26 AFLP and 32 RAPD multilocus phenotypes (putative clones) were identified, of which 21 were identical and each of the remaining five AFLP clones was split into two to three very similar RAPD clones. This minor difference can be explained by sampling error and stochastic variation. The pattern observed in Greenland corroborates our previous results from Svalbard, suggesting that rare sexual events in S. cernua are sufficient to maintain high levels of clonal diversity even at small spatial scales. We conclude that although AFLP analysis is superior in terms of efficiency, RAPDs may still be used as reliable markers in small low-tech laboratories.
Full Text Available Early seedling vigor (ESV is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS. It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM and mixed linear model (MLM approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.
Li, Chao; Gowan, Spencer; Anil, Ammu; Beck, Benjamin H; Thongda, Wilawan; Kucuktas, Huseyin; Kaltenboeck, Ludmilla; Peatman, Eric
Efforts to improve recreational fisheries have included widespread stocking of Micropterus floridanus outside its native range of peninsular Florida. Hybridization of Florida bass (M. floridanus) with largemouth bass (Micropterus salmoides) has now dramatically expanded beyond a naturally occurring intergrade zone in the southeast U.S. In recent years, there has been growing interest in protecting the genetic integrity of native basses and assessing the impact and nature of M. salmoides/M. floridanus introgression from the standpoint of hatchery and sport-fishery managers, fish biologists, ecologists and evolutionary biologists. Here, we conducted RNA-seq-based sequencing of the transcriptomes of M. salmoides, M. floridanus and their F1 hybrid and identified a set of 3674 SNP markers with fixed-allelic differences from 2112 unique genes. We then developed a subset of 25 of these markers into a single diagnostic multiplex assay and validated its capacity for assessing integrity and hybridization in hatchery and wild populations of largemouth and Florida bass. The availability of this resource, high-quality transcriptomes and a large set of gene-linked SNPs, should greatly facilitate functional and population genomics studies in these key species and allow the identification of traits and processes under selection during introgressive hybridization. © 2014 John Wiley & Sons Ltd.
Héctor Aníbal Campos
Full Text Available En el presente estudio, mostramos los primeros resultados moleculares de formas colombianas de Cavia. Claramente, la población silvestre de C. anolaimae fue genéticamente diferenciada de la forma doméstica, C. porcellus, tal como ha sido demostrado por otros autores utilizando resultados morfométricos, osteológicos y cariotípicos. Ambas especies mostraron un considerable nivel de diversidad genética, aunque el segundo taxon mostró niveles mayores de esta diversidad. Los niveles de heterogeneidad genética también fueron mayores entre las poblaciones de C. porcellus (F ST = 0.254 que entre las poblaciones de C. anolaimae (F ST = 0.118. Esos niveles significativos de heterogeneidad genética, y los consiguientes bajos niveles de flujo génico, fueron discutidos comparativamente con los resultados por otros autores analizando otros marcadores moleculares (citocromo-b mitocondrial. Los resultados aquí mostrados son coherentes con un complejo proceso de domesticación en Cavia porcellus.Population genetics of Colombian Guinea Pigs, Cavia spp. (Rodentia: Caviidae with RAPD molecular markers. The genus Cavia occurs in South America, mainly in grasslands.. We collected blood samples from 97 individuals in six field populations and analyzed them with RAPD molecular markers. One wild type (C. anolaimae was differentiated from the domestic form (C. porcellus, in agreement with other authors who used morphological, osteological and karyotipic results. Genetic diversity was considerable in both species, but higher in C. porcellus. The levels of genetic heterogeneity were also higher among the populations of C. porcellus (F ST = 0.254 than among the populations of C. anolaimae (F ST = 0.118. These significant levels of genetic heterogeneity, and the low levels of gene flow, were consistent with a complex domestication process for Cavia porcellus. Rev. Biol. Trop. 56 (3: 1481-1501. Epub 2008 September 30.
Genetic variability of Brazilian isolates of Alternaria alternata detected by AFLP and RAPD techniques Variabilidade genética de isolados Brasileiros de Alternaria alternata por meio de marcadores moleculares de AFLP e RAPD
Full Text Available The Alternaria brown spot (ABS is a disease caused in tangerine plants and its hybrids by the fungus Alternaria alternata f. sp. citri which has been found in Brazil since 2001. Due to the recent occurrence in Brazilian orchards, the epidemiology and genetic variability of this pathogen is still an issue to be addressed. Here it is presented a survey about the genetic variability of this fungus by the characterization of twenty four pathogenic isolates of A. alternata f. sp. citri from citrus plants and four endophytic isolates from mango (one Alternaria tenuissima and three Alternaria arborescens. The application of two molecular markers Random Amplified Polymorphic DNA (RAPD and Amplified Fragment Length Polymorphism (AFLP had revealed the isolates clustering in distinct groups when fingerprintings were analyzed by Principal Components Analysis (PCA. Despite the better assessment of the genetic variability through the AFLP, significant modifications in clusters components were not observed, and only slight shifts in the positioning of isolates LRS 39/3 and 25M were observed in PCA plots. Furthermore, in both analyses, only the isolates from lemon plants revealed to be clustered, differently from the absence of clustering for other hosts or plant tissues. Summarizing, both RAPD and AFLP analyses were both efficient to detect the genetic variability within the population of the pathogenic fungus Alternaria spp., supplying information on the genetic variability of this species as a basis for further studies aiming the disease control.A mancha marrom ou mancha de Alternaria é uma doença causada pelo fungo Alternaria alternata f. sp. citri, encontrada no Brasil desde 2001 em plantas de tangerina e seus híbridos. Por se tratar de uma doença recente no Brasil, a epidemiologia e variabilidade genética deste patógeno compõem importantes pontos a serem estudados. Este trabalho teve como objetivo avaliar a variabilidade genética deste pat
Alain, Karin; Karrow, Niel A; Thibault, Catherine; St-Pierre, Jessika; Lessard, Martin; Bissonnette, Nathalie
Background Mastitis is the most important disease in dairy cows and it causes significant lost of profit to producers. Identification of the genes, and their variants, involved in innate immune responses is essential for the understanding of this inflammatory disease and to identify potential genetic markers for resistance to mastitis. The progeny of dairy cows would benefit from receiving favourable alleles that support greater resistance to infection, thus reducing antibiotic use. This study aims to identify a key gene in the innate immune response to mastitis, led us to evaluate its genetic association with somatic cell score (SCS), which is an indicator of clinical mastitis, and to evaluate its impact on other traits related to milk production. Results The osteopontin transcript (SPP1) was identified in the somatic cells from cows experimentally infected with Escherichia coli. By selecting bulls with extreme estimated breeding values (EBVs) for SCS, which is an indicator of mammary gland health, four DNA polymorphisms in the SPP1 genomic sequence were found. Statistical analysis revealed that the SNP SPP1c.-1301G>A has an impact on EBV for SCS (P T, SPP1c.-430G>A, and SPP1c.*40A>C have an impact on SCS whereas SPP1c.-1301G>A has an effect on the EBVs for milk yield (second and third lactations), fat and protein percentages (all three lactations). Analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with sire EBVS for SCS for the first (P = 0.012), second (P milk immune cells and, potentially, the susceptibility to mastitis. These SNPs were identified by in silico search to be located in transcription factor recognition sites which factors are presumably involved in the Th1 immune response and in the Th2 regulation pathway. Indeed, one SNP abolished the SP1 recognition site, whereas another SNP affected the transcription binding factor IKAROS. All together, these findings support the genetic potential of
Conclusion: The hospital sources for the Aspergillus clinical isolates included air condition and walls. RAPD-PCR analysis can play a trivial role to find the hospital sources of Aspergillus clinical isolates.
Ranjan Kumar Shaw
Full Text Available Genetic diversity was evaluated among 14 cultivars of Catharanthus roseus using RAPD and ISSR markers.The RAPD primers resulted in the amplification of 56 bands, among which 46 (82% bands were polymorphic Four ISSRprimers amplified 31 loci out of which 17 were polymorphic and 14 are monomorphic. The Jaccard's similarity derived fromthe combined marker system showed that the varieties First Kiss Coral and Cooler Orchid were the most closely relatedcultivars, with 98% similarity. In the dendrogram constructed on the basis of both RAPD and ISSR data two clear clusterswere obtained. The smaller cluster included C. roseus Cv Blue Pearl and C. roseus Cv. Patricia White and the larger clusterwas subdivided into two sub clusters with C. roseus Cv. First Kiss Polka Dot isolated from the rest of the cultivars. This maybe useful for breeding for improved quality.
Liu, Wan; Yang, Y S; Li, P J; Zhou, Q X; Xie, L J; Han, Y P
Impact assessment of contaminants in soil is an important issue in environmental quality study and remediation of contaminated land. A random amplified polymorphic DNA (RAPD) 'fingerprinting' technique was exhibited to detect genotoxin-induced DNA damage of plants from heavy metal contaminated soil. This study compared the effects occurring at molecular and population levels in barley seedlings exposed to cadmium (Cd) contamination in soil. Results indicate that reduction of root growth and increase of total soluble protein level in the root tips of barley seedlings occurred with the ascending Cd concentrations. For the RAPD analyses, nine 10-base pair (bp) random RAPD primers (decamers) with 60-70% GC content were found to produce unique polymorphic band patterns and subsequently were used to produce a total of 129 RAPD fragments of 144-2639 base pair in molecular size in the root tips of control seedlings. Results produced from nine primers indicate that the changes occurring in RAPD profiles of the root tips following Cd treatment included alterations in band intensity as well as gain or loss of bands compared with the control seedlings. New amplified fragments at molecular size from approximately 154 to 2245 bp appeared almost for 10, 20 and 40 mg L(-1) Cd with 9 primers (one-four new polymerase chain reaction, (PCR) products), and the number of missing bands enhanced with the increasing Cd concentration for nine primers. These results suggest that genomic template stability reflecting changes in RAPD profiles were significantly affected and it compared favourably with the traditional indices such as growth and soluble protein level at the above Cd concentrations. The DNA polymorphisms detected by RAPD can be applied as a suitable biomarker assay for detection of the genotoxic effects of Cd stress in soil on plants. As a tool in risk assessment the RAPD assay can be used in characterisation of Cd hazard in soil.
A mixture of oleic, erucic and conjugated linoleic acids modulates cerebrospinal fluid inflammatory markers and improve somatosensorial evoked potential in X-linked adrenoleukodystrophy female carriers.
Cappa, Marco; Bizzarri, Carla; Petroni, Anna; Carta, Gianfranca; Cordeddu, Lina; Valeriani, Massimiliano; Vollono, Catello; De Pasquale, Loredana; Blasevich, Milena; Banni, Sebastiano
X-linked adrenoleukodystrophy is a rare inherited demyelinating disorder characterized by an abnormal accumulation of very long chain fatty acids, mainly hexacosanoic acid (26:0), due to a mutation of the gene encoding for a peroxisomal membrane protein. The only available, and partially effective, therapeutic treatment consists of dietary intake of a 4:1 mixture of triolein and trierucin, called Lorenzo's oil (LO), targeted to inhibit the elongation of docosanoic acid (22:0) to 26:0. In this study we tested whether, besides inhibiting elongation, an enhancement of peroxisomal beta oxidation induced by conjugated linoleic acid (CLA), will improve somatosensory evoked potentials and modify inflammatory markers in adrenoleukodystrophy females carriers. We enrolled five heterozygous women. They received a mixture of LO (40 g/day) with CLA (5 g/day) for 2 months. The therapeutic efficacy was evaluated by the means of plasma levels of 26:0, 26:0/22:0 ratio, modification of cerebrospinal fluid (CSF) inflammatory markers and somatosensory evoked potentials. Changes of fatty acid profile, and in particular CLA incorporation, were also evaluated in CSF and plasma. The results showed that CLA promptly passes the blood brain barrier and the mixture was able to lower both 26:0 and 26:0/22:0 ratio in plasma. The mixture improved somatosensory evoked potentials, which were previously found unchanged or worsened with dietary LO alone, and reduced IL-6 levels in CSF in three out of five patients. Our data suggest that the synergic activity of CLA and LO, by enhancing peroxisomal beta-oxidation and preventing 26:0 formation, improves the somatosensory evoked potentials and reduces neuroinflammation.
Full Text Available GWAS discoveries on the X-chromosome are underrepresented in the literature primarily because the analytical tools that have been applied were originally designed for autosomal markers. Our objective here is to employ a new robust and flexible tool for chromosome-wide analysis of X-linked markers in complex traits. Orofacial clefts are good candidates for such analysis because of the consistently observed excess of females with cleft palate only (CPO and excess of males with cleft lip with or without cleft palate (CL/P.Genotypes for 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European isolated cleft triads were available from a previously published GWAS. The R-package HAPLIN enables genome-wide-level analyses as well as statistical power simulations for a range of biologic scenarios. We analyzed isolated CL/P and isolated CPO for each ethnicity in HAPLIN, using a sliding-window approach to haplotype analysis and two different statistical models, with and without X-inactivation in females.There was a larger number of associations in the Asian versus the European sample, and similar to previous reports that have analyzed the same GWAS dataset using different methods, we identified associations with EFNB1/PJA1 and DMD. In addition, new associations were detected with several other genes, among which KLHL4, TBX22, CPXCR1 and BCOR were noteworthy because of their roles in clefting syndromes. A few of the associations were only detected by one particular X-inactivation model, whereas a few others were only detected in one sex.We found new support for the involvement of X-linked variants in isolated clefts. The associations were specific for ethnicity, sex and model parameterization, highlighting the need for flexible tools that are capable of detecting and estimating such effects. Further efforts are needed to verify and elucidate the potential roles of EFNB1/PJA1, KLHL4, TBX22, CPXCR1 and BCOR in isolated clefts.
Full Text Available ABSTRACT An efficient in vitro regeneration protocol for medicinally important herb Swertia chirayita was developed and the genetic fidelity was assessed using RAPD and ISSR markers. The best shoot regeneration was observed on MS basal supplemented with 1.0 mg/L Benzyl amino purine (BAP in combination with Indole-3-acetic acid (IAA (0.5 mg/L that resulted in the increase by multiplication rate (7.65 with an average of 33.33 numbers of shoots and average shoot length of 2.70 cm. It was further enhanced by the addition of adenine sulfate (0.007% that resulted in an average of 42 shoots per clum with 4.13 cm of average shoot length and the increase in multiplication fold to 9.75 that further resulted in the reduced use of other cytokinins and auxins. The rooting was nearly 100 % on 1/4 MS augmented with 1.0 mg/L Indole butyric acid with maximum average root length of 5.1cm. Plantlets were successfully acclimatized with 85-90 % survival rate. Ascorbate peroxidase activity increased with the maximum activity during the shoot multiplication. Clonal fidelity has been checked by two marker systems ISSR and RAPD and regenerated plants showed high clonal fidelity.
Full Text Available The genus of Oligoryzomys includes species of small size, morphologically similar, which may impede taxonomic identification, mainly between O. flavescens (Waterhouse, 1837 and O. nigripes (Olfers, 1818. The main objective of this work was to investigate whether the RAPD markers are capable of genetically differentiating the specimens O. nigripes and O. flavescens, coming from Rio Grande do Sul (RS and Santa Catarina (SC states, and also to estimate the genetic variability among populations of O. nigripes, with the Uruguay River as a geographical barrier. For this purpose, samples were collected in fragments of forests situated in the North of RS, at FLONA (Floresta Nacional de Passo Fundo and in fragments from SC, close to the Uruguay River. The karyotyping of two samples for each species was carried out and compared using the RAPD technique together with non- karyotyped individuals. Samples of O. nigripes presented 2n = 62; NA = 82, with submetacentric arms on the largest chromosomes, while samples of O. flavescens showed 2n = 64; NA = 66, with the largest chromosomes presenting acrocentric morphology, making such a result the main difference between the species. The analysis was able to detect two distinct groups, being the first one with karyotyped O. flavescens and the second with karyotyped O. nigripes. Identification afforded 211 loci, among them 181 (85.78% polymorphic. The Jaccard similarity coefficient was in the range of 0.45 to 0.87. The UPGMA and Main Coordinate Analysis techniques demonstrated the existence of heterogeneous genetics among populations, but did not separate them completely in terms of geographical standards, and they are not influenced by the Uruguay River, which did not act as an efficient barrier.
Full Text Available Advanced techniques of molecular biology have provided the opportunity to study genetic diversity within and among breeds at the single gene level. Many DNA markers, either of genomic DNA or cytoplasmic DNA, have been generated recently by utilizing molecular techniques, such as RFLP, microsatellites, PCR-RFLP, RAPD, sequencing etc. PCR-based techniques have recently progressed rapidly for the detection of both known- and unknown-mutation detections that may be applied in locating gene marker for economically important traits. There are basically two different approaches of locating quantitative trait loci (QTLs, candidate gene and random approaches. The first approach is based on prior supporting knowledge of physiological and biochemical evidence, showing that the gene is involved in the trait(s of interest, while the random marker approach attempts to locate gene markers by measuring genotypes at a large number of loci with unknown phenotypic effects, in the hope that the loci are linked to a QTL influencing the trait of interest.
Thomas L. Kubisiak; James H. Roberds
Microsatellite and RAPD markers suggest that American chestnut exists as a highly variable species. Even at the margins of its natural range, with a large proportion of its genetic variability occurring within populations (~95%). A statistically significant proportion also exists among population. Although genetic differentiation among populations has taken place, no...
Craig S. Echt; Surya Saha; Konstantin V. Krutovsky; Kokulapalan Wimalanathan; John E. Erpelding; Chun Liang; C Dana Nelson
Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety...
Skoda, S R; Skoda, S R; Pornkulwat, S; Foster, J E
The screwworm, Cochliomyia hominivorax (Coquerel), is one of the most important pests of livestock in the Western Hemisphere. During early immature stages it is morphologically very similar (first instars are virtually indistinguishable) to the secondary screwworm, C. macellaria (Fabricius). Here, the utility of the random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) was explored as a technique for developing molecular genetic markers for these two species. Of the 120 arbitrary primers screened, 21 primers produced markers that were further investigated. Seven of the 21 primers produced clear and reproducible markers that were tested with DNA of five individuals from four populations of each species; five of these primers showed 12 RAPD markers that differentiated the species in all populations. Analyses of data from these seven primers also suggested that intraspecific polymorphisms exist that could be useful in distinguishing populations of screwworms. Some population genetic tools, such as genetic distance, cluster analysis and bootstrapping, were used to statistically explore these polymorphisms. The resulting statistics showed 100% support for the ability of RAPD-PCR to discriminate between the two species. Bootstrapping with data from one of the genetic distance calculations produced a tree with all individual screwworms in the correct populations, indicating that RAPD-PCR has promise for displaying intraspecific genetic variation that could be used in establishing the general geographic origin of screwworm samples.
DNA isolation. Individual larvae or adults were ground with a strong diagnostic bands and simple patterns. Primers pro- plastic pestle in...V. (1988) Com- peninsular Malaysia and Thailand (Diptera: Culicidae). Mosq parison of DNA probe and cytogenic methods for identifying field Syst 20
Zhang, X; Dong, Y; Wang, R R
Genomic in situ hybridization (GISH) and Southern hybridization of genome-specific RAPD markers were used to demonstrate that the E genome (including Ee and Eb from Thinopyrum elongatum and Thinopyrum bessarabicum, respectively) and the St genome (from Pseudoroegneria species) were the two basic genomes in Thinopyrum ponticum. GISH also revealed that the centromeric region may be the critical area that discriminates the St genome from the E genome in Th. ponticum. Of the seven partial amphiploids isolated from backcrossed progenies of Triticum aestivum x Thinopyrum ponticum hybrids, two (lines 693 and 7631) have eight pairs of chromosomes from the Ee and (or) Eb genomes. Four partial amphiploids (lines 784, 68, 7430, and 40767-1) have an incomplete St genome, i.e., six pairs of chromosomes of St and one pair of chromosomes from Ee or Eb. In a heptaploid individual of the partial amphiploid 40767-2, there were four pairs of St chromosomes, one pair of St/1B Robertsonian translocation chromosomes, one pair of St/E translocation chromosomes, and one pair of Ee or Eb chromosomes. The isoelectric focusing of Est-5, Est-4, β-Amy-1, α-Amy-1, and α-Amy-2 and the RAPD data generated with 24 decamer primers on five partial amphiploids (lines 784, 693, 7631, 68, and 7430) indicated that lines 693 and 7631 had identical genomes from Th. ponticum. The partial amphiploid 784 probably had a set of chromosomes completely different from those of 693 and 7631. These results indicate that genome recombination usually occurred during the formation of new polyploid lines. Key words : Thinopyrum ponticum, wheat, partial amphiploid, GISH, isozyme, RAPD.
Full Text Available Abstract Background High-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS. MAS is quite challenging in conifers because of their large, complex, and poorly-characterized genomes. Our goal was to construct a high-density linkage map to facilitate the identification of markers that are tightly linked to a major recessive male-sterile gene (ms1 for MAS in C. japonica, a species that is important in Japanese afforestation but which causes serious social pollinosis problems. Results We constructed a high-density saturated genetic linkage map for C. japonica using expressed sequence-derived co-dominant single nucleotide polymorphism (SNP markers, most of which were genotyped using the GoldenGate genotyping assay. A total of 1261 markers were assigned to 11 linkage groups with an observed map length of 1405.2 cM and a mean distance between two adjacent markers of 1.1 cM; the number of linkage groups matched the basic chromosome number in C. japonica. Using this map, we located ms1 on the 9th linkage group and constructed a partial linkage map around the ms1 locus. This enabled us to identify a marker (hrmSNP970_sf that is closely linked to the ms1 gene, being separated from it by only 0.5 cM. Conclusions Using the high-density map, we located the ms1 gene on the 9th linkage group and constructed a partial linkage map around the ms1 locus. The map distance between the ms1 gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the ms1 gene will facilitate the early selection of male-sterile trees, which should expedite C. japonica breeding programs aimed at alleviating pollinosis problems without harming productivity.
Deputy, J C; Ming, R; Ma, H; Liu, Z; Fitch, M M M; Wang, M; Manshardt, R; Stiles, J I
We have developed molecular markers tightly linked to Sex1, the gene that determines plant sex in papaya ( Carica papaya L.). Three RAPD products have been cloned and a portion of their DNA sequenced. Based on these sequences SCAR primers were synthesized. SCAR T12 and SCAR W11 produce products in hermaphrodite and male plants and only rarely in females. SCAR T1 produces a product in all papayas regardless of plant sex. SCAR T12 and SCAR W11 showed no recombination in a population of 182 F2 plants from a 'SunUp' by 'Kapoho' cross. Based on these results a PCR-based technique for rapidly and accurately determining the sex of papaya plants was developed using either W11 or T12 to detect the hermaphrodite or male allele and T1, which amplifies a product regardless of sex type, as a positive control. The sexing technique, using SCAR T12 and SCAR T1 as a positive control, was used to correctly predict hermaphrodite papaya plants in a population of seedlings with an overall accuracy of 99.2%.
Hryncewicz-Gwóźdź, A; Jagielski, T; Dobrowolska, A; Szepietowski, J C; Baran, E
Trichophyton rubrum represents the most frequently isolated causative agent of superficial dermatophyte infections. Several genotyping methods have recently been introduced to improve the delineation between pathogenic fungi at both the species and the strain levels. The purpose of this study was to apply selected DNA fingerprinting methods to the identification and strain discrimination of T. rubrum clinical isolates. Fifty-seven isolates from as many tinea patients were subjected to species identification by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis and strain differentiation using a randomly amplified polymorphic DNA (RAPD) method, with two primers designated 1 and 6. Using PCR-RFLP, 55 of the isolates studied were confirmed to be T. rubrum. Among those, a total of 40 and five distinct profiles were obtained by RAPD with primers 1 and 6, respectively. The combination of profiles from both RAPD assays resulted in 47 genotypes and an overall genotypic diversity rate of 85.4%. A dendrogram analysis performed on the profiles generated by RAPD with primer 1 showed most of the isolates (87.3%) to be genetically related. PCR-RFLP serves as a rapid and reliable method for the identification of T. rubrum species, while the RAPD analysis is rather a disadvantageous tool for T. rubrum strain typing.
Qi, Yunpeng; Jiang, Changtao; Cheng, Jie; Krausz, Kristopher W; Li, Tiangang; Ferrell, Jessica M; Gonzalez, Frank J; Chiang, John Y L
Bile acid synthesis is the major pathway for catabolism of cholesterol. Cholesterol 7α-hydroxylase (CYP7A1) is the rate-limiting enzyme in the bile acid biosynthetic pathway in the liver and plays an important role in regulating lipid, glucose and energy metabolism. Transgenic mice overexpressing CYP7A1 (CYP7A1-tg mice) were resistant to high-fat diet (HFD)-induced obesity, fatty liver, and diabetes. However the mechanism of resistance to HFD-induced obesity of CYP7A1-tg mice has not been determined. In this study, metabolomic and lipidomic profiles of CYP7A1-tg mice were analyzed to explore the metabolic alterations in CYP7A1-tg mice that govern the protection against obesity and insulin resistance by using ultra-performance liquid chromatography-coupled with electrospray ionization quadrupole time-of-flight mass spectrometry combined with multivariate analyses. Lipidomics analysis identified seven lipid markers including lysophosphatidylcholines, phosphatidylcholines, sphingomyelins and ceramides that were significantly decreased in serum of HFD-fed CYP7A1-tg mice. Metabolomics analysis identified 13 metabolites in bile acid synthesis including taurochenodeoxycholic acid, taurodeoxycholic acid, tauroursodeoxycholic acid, taurocholic acid, and tauro-β-muricholic acid (T-β-MCA) that differed between CYP7A1-tg and wild-type mice. Notably, T-β-MCA, an antagonist of the farnesoid X receptor (FXR) was significantly increased in intestine of CYP7A1-tg mice. This study suggests that reducing 12α-hydroxylated bile acids and increasing intestinal T-β-MCA may reduce high fat diet-induced increase of phospholipids, sphingomyelins and ceramides, and ameliorate diabetes and obesity. This article is part of a Special Issue entitled Linking transcription to physiology in lipodomics. Copyright © 2014 Elsevier B.V. All rights reserved.
Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for
Full Text Available Abstract Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM, and are now replacing the markers previously developed by a traditional DNA
Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S
Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.
New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.
Oliver, R E; Jellen, E N; Ladizinsky, G; Korol, A B; Kilian, A; Beard, J L; Dumlupinar, Z; Wisniewski-Morehead, N H; Svedin, E; Coon, M; Redman, R R; Maughan, P J; Obert, D E; Jackson, E W
Nutritional benefits of cultivated oat (Avena sativa L., 2n = 6x = 42, AACCDD) are well recognized; however, seed protein levels are modest and resources for genetic improvement are scarce. The wild tetraploid, A. magna Murphy et Terrell (syn A. maroccana Gdgr., 2n = 4x = 28, CCDD), which contains approximately 31% seed protein, was hybridized with cultivated oat to produce a domesticated A. magna. Wild and cultivated accessions were crossed to generate a recombinant inbred line (RIL) population. Although these materials could be used to develop domesticated, high-protein oat, mapping and quantitative trait loci introgression is hindered by a near absence of genetic markers. Objectives of this study were to develop high-throughput, A. magna-specific markers; generate a genetic linkage map based on the A. magna RIL population; and map genes controlling oat domestication. A Diversity Arrays Technology (DArT) array derived from 10 A. magna genotypes was used to generate 2,688 genome-specific probes. These, with 12,672 additional oat clones, produced 2,349 polymorphic markers, including 498 (21.2%) from A. magna arrays and 1,851 (78.8%) from other Avena libraries. Linkage analysis included 974 DArT markers, 26 microsatellites, 13 SNPs, and 4 phenotypic markers, and resulted in a 14-linkage-group map. Marker-to-marker correlation coefficient analysis allowed classification of shared markers as unique or redundant, and putative linkage-group-to-genome anchoring. Results of this study provide for the first time a collection of high-throughput tetraploid oat markers and a comprehensive map of the genome, providing insights to the genome ancestry of oat and affording a resource for study of oat domestication, gene transfer, and comparative genomics.
Ali, A. M.
Full Text Available The routine identification of mycobacterial strains isolated from patients in different locations in Egypt was confirmed by specific DNA fragment amplification. The susceptibilities of 72 Mycobacterium tuberculosis strains against the four antibiotics used in tuberculosis treatment (Isoniazid, INH; Rifampicin, Rif; Streptomycin, St and Ethambutol, E were examined. Our results indicated that, multi drug resistant tuberculosis (MDR-TB represents about 19.5% of the tested strains, whereas sensitive strains represented 26.4%. The genetic polymorphism of the tested strains was examined using RAPD analysis. Six selected strains represent the different antibiotic susceptibility groups were examined using RAPD fingerprinting. No difference between the strains was recorded using the RFLP analysis of amplified specific fragment. The discrimination power of RAPD analysis was inadequate to clarify the genetic correlation between the tested strains. MDR-TB was approximately double time in 2008 compared with the value in 2007. Most of the new MDRTB was correlated with resident dense population regions.
Sharma, Shivani; Khanna, Pardeep Kumar; Kapoor, Shammi
The molecular phylogeny in seven strains of Lentinus edodes was studied based on RAPD and their internal transcribed spacers (ITS) regions. The strains were analyzed by RAPD with 20 arbitrary primers. Fifteen primers were found efficient for the amplification of the genomic DNA. The size of the polymorphic bands were in the range of 100-1000 bp. However, the size of ITS1-2 and ITS1-4 regions varied among the strains from 278 to 575 bp and from 410 to 616 bp, respectively. The higher alignment score of the ITS 1-2 region indicated more variability in the ITS 1-4 region. Thus, on the basis of RAPD-PCR and ITS sequencing it was found that strains LeC and LeI showed a high degree of divergence from all other strains.
Zhang, He-Cai; Liu, Tong-Yi; Shi, Chang-Ying; Chen, Guang-Wen; Liu, De-Zeng
The aim of this study was to evaluate the genotoxic potential of an urban river - the Wei River in Xinxiang, China using randomly amplified polymorphic DNA (RAPD) assay in planarians. The results showed that the total number of polymorphic bands and varied bands in RAPD patterns of treated planarians decreased with the water sample site far away from the sewage outlet of a factory. In addition, the genome template stability of treated groups decreased and the degree of the decline was negatively related to the distance between the sample site and the sewage outlet, suggesting that the Wei River water had genotoxicity effects on planarians and strengthening the management of the Wei River was necessary. Furthermore, this work also indicated that RAPD assay in planarians was a very promising test for environmental monitoring studies.
Gang, D R; Weber, D J
We describe a method for isolating genomic DNA from teliospores of Tilletia caries (DC) Tul., T. controversa Kuhn and T. foetida (T. laevis) (Wallr.) Liro. for random-amplified polymorphic DNA (RAPD) analysis. DNA analysis of teliospores of covered smut or bunt has been difficult because of the thick wall and the high lipid content of the spores. This method overcomes these problems and yields sufficient quantities of DNA from the three species' teliospores for RAPDs. DNA quality appears to be good with very little degradation. RAPD amplifications of the extracted DNAs are reproducible and produce numerous large molecular weight bands from each individual. This procedure should permit the use of DNA analysis techniques to study species and races of Tilletia as well as fungi with similar spore structure.
Koh, M C; Lim, C H; Chua, S B; Chew, S T; Phang, S T
The random amplified polymorphic DNA (RAPD) method was used to generate fingerprint patterns for 10 meat species: wild boar, pig, horse, buffalo, beef, venison, dog, cat, rabbit and kangaroo. A total of 29 10-nucleotide primers, with GC contents ranging from 50-80%, were evaluated for their specificity and efficiency. The fingerprint patterns that were generated were found in some cases to be species-specific, i.e. one species could be differentiated from another. The advantages and disadvantages of using RAPD-PCR for the identification of red meat species are also discussed.
Wen, G Q; Li, J; Liu, X H; Zhang, Y S; Wen, S S
Dioscorea opposita Thunb. has been used as health food and herbal medicinal ingredients in traditional Chinese medicine. In this study, the total DNA of D. opposita Thunb. was extracted using an improved cetyltrimethylammonium bromide (CTAB) method, and the extracted DNA was further used for random amplified polymorphic DNA (RAPD) reaction system by design of the L16 (4(4)) orthogonal diagram. The results showed that the improved CTAB method can be used to isolate high-quality and high-concentration DNA, and the optimized protocol can overcome the instability of RAPD reaction system. The knowledge stated here can be used to study the genetic diversity of D. opposita Thunb.
Mostafa, M. G.; Ishtiaq Ahmed, A. S.; M. G. Mustafa; M.G. Rabbane; Islam, M. N.; Rafiquzzaman, S. M.
Genetska raznolikost dvaju divljih kalibausa, Labeo calbasu, i jedne mrjestilišne populacije proučavana je pomoću random amplified polymorphic DNA (RAPD) metode. Tri 10–mer nasumična primera (OPA01, OPB02 and OPC03) postigla su ukupno 26 ponovljivih i dosljedno prebrojivih RAPD traka, od kojih je 15 (57,69%) bilo polimorfično (P95), upućujući na visoku razinu genetske varijacije u svim proučavanim populacijama. Od triju populacija, Padma populacija je pokazala relativno nižu razinu genetske r...
Guill N-Nepita, A L; Vazquez-Marrufo, G; Blanco-Guillot, F T; Figueroa-Aguilar, G A; Vazquez-Garciduenas, M S
Random amplified polymorphism DNA (RAPD) is an easy, inexpensive technique for the characterization of pathogens in low-income countries. In this study we used RAPD to assess the genetic diversity of a small collection of isolates of mycobacteria from the Mexican state of Michoacan. In contrast with the low annual tuberculosis incidence in Michoacan relative to the national average, we found a high molecular diversity value suggesting high population diversity of M. tuberculosis in the studied region. Our findings justify further typing efforts with other molecular tools such as MIRU-VNTR and spoligotyping.
Damodar R. Kethidi; David B. Roden; Tim R. Ladd; Peter J. Krell; Arthur Ratnakaran; Qili Feng
DNA markers were identified for the molecular detection of the Asian long-horned beetle (ALB), Anoplophora glabripennis (Mot.), based on sequence charaterized amplified regions (SCARS) derived from random amplified polymorphic DNA (RAPD) fragments. A 2,740-bp DNA fragment that was present only in ALB and not in other Cerambycids was identified after...
vibriosis in hatchery reared and commercially farmed pe- naeid shrimps resulting in severe economic losses to shrimp industry in Asia (Lavilla-Pitogo et al. ..... with amplicon sizes ranging from 0.2 to 4.0 kb. Cluster analysis of primers CRA25 and PM3 generated RAPD pro- files separated the isolates at an average similarity ...
Aug 4, 2009 ... clustering lactic acid bacteria isolated from traditional ... shaped isolates formed five clusters based on numerical analysis of the RAPD-PCR profiles. ..... these isolates are of value in improving the nutritive con- tents and controlling the growth of spoilage and pathogen in diary industry. REFERENCES.
ARIFIN NOOR SUGIHARTO
Full Text Available RAPD-PCR method and isozyme analysis were used to obtain information of genetic relationship among cucumber varieties. Such information is urgently utilized to support plant breeding program of cucumber. Research was done at the Biotechnology Laboratory of Plant Pest and Diseases, Faculty of Agriculture of Brawijaya University, Malang and Molecular Biology Laboratory, Faculty of Matemathic and Natural Sciences of Brawijaya University, Malang. DNA isolation was done using CTAB method by additional NaCl modification. Sixteen primers from operon were employed to amplify DNA genome by RAPD-PCR. Two enzymes, Esterase and AAT were chosen for isozyme analysis. Clad 97 Program was used for analyzing the data and results in data grouping based on proximity value. Cluster analysis based on isozyme data indicated that there was an adequate lower genetic variation in cucumber, where seven of nine tested varieties showed proximity value of 1.00. Eleven of sixteen primers in RAPD-PCR analysis produced DNA bands. Relativity analysis by using RAPD-PCR method showed high enough of genetic variation. Relativity analysis by using both methods showed that variety 07 was the furthermost. The proximity value between varieties 01 and 02 was 0.916667, these varieties have the higest proximity value among all varieties.
The aim of this study was to detect genetic similarities and distances among cultured type olive trees by RAPD-PCR technique. Olives are raised in a high range from the Aegean, Mediterranean, Marmara and Black Sea to Southeast Anatolia regions of Turkey. Olive breeding had a rapid increase in Turkey during recent ...
Conclusions: This study indicated that improved RAPD and ISSR methods are useful tools for evaluating the genetic diversity and characterizing P. chinense. Our findings can provide the theoretical basis for cultivar identification, standardization, and molecular-assisted breeding of P. chinense for medicinal use.
In this study, samples were obtained from the Olive Production Research Institute (Manzanilla, Domat, Gemlik and Memecik) and sapling producers in Manisa, Akhisar (Uslu, Edremit). Genomic DNA's were extracted from young leaves and PCR was used generate RAPD bands. Sixty random primers obtained from Operon ...
Yan, Boqian; Li, Zuozhou; Huang, Hongwen; Qin, Ling
Seventeen Cryphonectria parasitica populations sampled from six regions in China were investigated using RAPD. Across all 169 isolates from the 17 populations evaluated, 52 of the 71 markers (73%) were polymorphic, total genetic diversity (h) was 0.1463, and Shannon's index was 0.2312. Diversity within populations accounted for 74% of total genetic diversity, and genetic differentiation among populations was 0.26 (G (ST) = 0.26). Gene flow was 1.4 among the populations; higher gene flow was found among populations within regions and among regions [N (m) (G (SR)) = 2.8 and N (m) (G (RT)) = 3.5]. The unweighted pair group mean analysis (UPGMA) dendrogram revealed two distinct clusters: the northern China group and the southern China group. The spatial autocorrelation analysis revealed that the variation at most loci was randomly distributed and lacked spatial structure, but several loci and closer distances were spatially structured. Human activity and habitat could also be important factors affecting genetic structure among C. parasitica populations in China. Genetic diversity was highest in Southwest China, descending in an orderly fashion to Northeast China. This pattern indicated that Southwest China might be the center of origin of C. parasitica in China. The present study provides useful information for understanding the origin and spread of chestnut blight fungus in China and valuable data for formulating relevant strategies for controlling the disease in China.
Konstanze Ursula Behrmann
Full Text Available Saithe (Pollachius virens is a commercially important fish species; the annual catch quota in the Northeast Atlantic exceeds 100.000 t. Despite that saithe is underexplored from a fish population genetically view. Because saithe is a highly migratory species, which undergoes a long larval drift, the population structure of saithe within the Northeast Atlantic is not fully understood. Models used as a basis for the management plan are based on tagging studies, which have been carried out in the 1960th. But still there are doubts regarding the numbers of stocks living in the Northeast Atlantic. Migration routes are affected by salmon farming, growing steadily from the 1990th. In the last years a hyperstability of the saithe stock in the North Sea had been detected underlining the need to have a closer look on the saithe stocks in the Northeast Atlantic. Random amplified polymorphic DNA (RAPD - PCR is a DNA fingerprinting technique often used in species identification and population genetic research for species, whose genome has not been sequenced very extensive as being the case for most of the food fishes. We applied RAPD-PCR in a study of saithe populations from the North Atlantic. The suitability of RAPD-PCR was improved by optimisations for enhanced reproducibility. The “classical” protocol for RAPD-PCR was modified by increasing the annealing temperature and shortening the time of annealing, providing a much better reproducibility. Thus, RAPD-PCR was found to be a straightforward and low-cost way, compared to other population genetic tools, to get a first insight into the population structure of less sequenced fish species within a very short time, being useful for preliminary studies or laboratories without large capacities for DNA sequencing.
Full Text Available RAPDs, ISJs, ISSRs, ITS and katGs were applied to determine genetic relationships between common Sphagnum species of the section Acutifolia. Twenty populations were genotyped using ten ISJ primers, 12 pairs of katG primers, 10 ISSR and 10 RAPD primers, and a restriction analysis of ITS1 and ITS2. ISSR and katG markers revealed the greatest number of species-specific bands. An analysis of ITS1 and ITS2 regions with restriction enzymes also proved to be a highly effective tool for species identification.
Eduardo Alano Vieira
Full Text Available Annual ryegrass is a temperate climate annual foraging grass, grown mostly in the South of Brazil, especially in the state of Rio Grande do Sul. Despite its importance, little is known about its genetic diversity, both within and among the populations cultivated. This knowledge is of fundamental importance for developing breeding and conservation strategies. The aim of this study was to characterize the genetic diversity and structure of four populations of annual ryegrass. Three of the populations were located in Rio Grande do Sul and the fourth in Uruguay. RAPD markers were used to study the genetic diversity and structure of these populations. Analysis of 375 individuals sampled from the populations, using six RAPD primers, generated a total of 82 amplified bands. They included 73 polymorphic bands (89,02%. The value of the total genetic diversity index obtained, (0,71 was high, indicating the presence of wide genetic diversity in the four populations. Genetic structure analysis revealed that 98% of total diversity is intrapopulational, whereas interpopulational genetic diversity was only 2%. These results suggest that before these populations separated, they had gone through a period of gene exchange and, even after the separation event, gene frequency stayed at levels similar to the original levels, with no differential selection for these genes in the different cultivation areas.O azevém anual é a gramínea anual forrageira de clima temperado de maior utilização no sul do Brasil, particularmente no Estado do Rio Grande do Sul. Apesar de toda a importância que a espécie apresenta, pouco se conhece a respeito da diversidade genética presente entre e dentro das populações cultivadas. Este conhecimento é de fundamental importância para o estabelecimento das estratégias de melhoramento genético e de conservação destes materiais. O objetivo deste estudo foi caracterizar a diversidade genética e a estrutura genética de quatro
Full Text Available Implementation of Taguchi method to optimize RAPD-PCR Markers for determining the genetic diversity: an example the loggerhead turtle, Caretta caretta (Testudines:Cheloniidae. DNA was isolated from Caretta caretta two zone of the Colombian Caribbean (Don Diego N=5 and Rosario Islands N=3 and quantified it. Was applied a Taguchi orthogonal matriz of four variables to standardize RAPD-PCR reaction. The data were analyzed with the program PopGen. The conditions were standardized to 7.85 ng/ml of DNA, 3.5 mM MgCl2, 200 mM dNTP's, 0.5 mM oligonucleotide and one unit of Taq DNA polymerase in a final reaction volume of 20 ml. Thermocycling conditions initiated at 94°C for 5 min, followed by 40 cycles of: 94°C for 40 s, 37°C for 40 s and 72°C for 90 s. The markers were recorded in a binary matrix of presence (1 and absence (0, and as a model example of genetic diversity was determined using the Shannon index (H '= 0.44 + / -0.27 individuals and Don Diego H '= 0.25 + / -0.32 for Isla del Rosario, the average rate of genetic structure (Gst=0.27 and the effective migration rate (Nm=1.28. Methodology was standardized using Taguchi method that produces bands of light, legible and reproducible that can be used as a reliable alternative for studies of genetic diversity in the loggerhead turtle and other species, and further, integrate them into the curriculum of molecular biology and/or biochemistry for undergraduate and graduate students.
Genotype characterization of Haematobia irritans from different Brazilian geographic regions based on randomly amplified polymorphic DNA (RAPD analysis Caracterização genotípica de Haematobia irritans procedentes de diferentes regiões geográficas brasileiras baseada na análise do DNA polimórfico amplificado ao acaso (RAPD-PCR
Luciana G. Brito
Full Text Available Blood-sucking diptera are important parasites in bovine production systems, especially regarding confinement conditions. Haematobia irritans, the horn fly, is one of the most troublesome species within bovine production systems, due to the intense stress imposed to the animals. An important aspect while studying the variability within a species is the study of the geographic structure of its populations and, attempting to find out the genetic flow of Brazilian populations of horn fly, the RAPD technique, which is suited for this purpose, has been used. The use of molecular markers generated from RAPD made it possible to identify the geographic origin of samples from different Brazilian geographic regions, as well as to estimate the genotypic flow among the different Brazilian populations of the horn fly.Dípteras hematófagos são importantes parasitas dentro de sistemas de produção de bovinos, especialmente em confinamento. Haematobia irritans, a mosca-dos-chifres, é uma das espécies que maiores problemas causa em sistemas de produção de bovinos, dado ao intenso estresse que impõe aos animais. Um importante aspecto quando se estuda a variabilidade genética dentro das espécies é o estudo da estrutura geográfica destas populações. Buscando-se estimar a similaridade genotípica das diferentes populações brasileiras da mosca do chifre utilizou-se a técnica do DNA polimórfico amplificado ao acaso (RAPD-PCR, que mostrou-se eficiente para tal propósito. A utilização dos marcadores moleculares gerados através da técnica de RAPD-PCR tornou possível a identificação da origem geográfica das amostras das diferentes regiões geográficas brasileiras, assim como, estimar o fluxo genotípico entre as diferentes populações brasileiras da mosca-dos-chifres.
Jin, Shuangxia; Mushke, Ramesh; Zhu, Huaguo; Tu, Lili; Lin, Zhongxu; Zhang, Yanxin; Zhang, Xianlong
Two protocols of plant regeneration for cotton were adopted in this study, namely, 2, 4-D and kinetin hormone combination and IBA and kinetin hormone combination. Twenty-eight embryogenic cell lines via somatic embryogenesis and 67 regenerated plants from these embryogenic calli were selected and used for random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), chromosomal number counting, and flow cytometric analysis. The roles of RAPD and SSR markers in detecting somaclonal variation of cotton (Gossypium hirsutum L.) were evaluated. Two cluster analyses were performed to express, in the form of dendrograms, the relationships among the hormone combinations and the genetic variability. Both DNA-based techniques were able to amplify all of the cell clones and regenerated plantlets genomes and relative higher genetic variation could be detected in the culture type with 2, 4-D and kinetin hormone combination. The result suggested that 2, 4-D and kinetin hormone combination could induce relative high somaclonal variation and RAPD and SSR markers are useful in detecting somaclonal variation of regenerated cotton plants via somatic embryogenesis. Chromosome number counting and flow cytometry analysis revealed that the number of chromosomes and ploidy levels were nearly stable in all regenerated plants except two regenerated plantlets (lost 4 and 5 chromosomes, respectively) which meant that cytological changes were not correlated with the frequency of RAPD and SSR polymorphisms. This result also might mean that the cell lines with variation of chromosome numbers were difficult to regenerate plants.
The invention relates to a method for determining mastitis resistance in bovine subjects, wherein mastitis resistance comprise resistance to both sub-clinical and clinical mastitis. In particular, the method of the invention involves identification of genetic markers and/or Quantitative Trait Locus...... (QTL) for the determination of mastitis resistance in a bovine subject. The determination of mastitis resistance involves resolution of the specific microsatellite status. Furthermore, the invention relates to a diagnostic kit for detection of genetic marker(s) associated with mastitis resistance....... The method and kit of the present invention can be applied for selection of bovine subjects for breeding purposes. Thus, the invention provides a method of genetically selecting bovine subjects with mastitis resistance, thereby yielding cows less prone to mastitis...
The three South African crane species — the Blue Crane (Anthropoides paradisea), the Wattled Crane (Bugeranus carunculatus) and the Grey Crowned Crane (Balearica regulorum regulorum) — are listed as threatened by the IUCN. This study investigated the suitability of Randomly Amplified Polymorphic DNA markers in ...
Dec 15, 2009 ... Appl. Genet. 98: 411-421. Bandelj D, Jakse J, Javornik B (2004). Assessment of genetic variability of olive varieties by microsatellite and AFLP markers. Euphytica, 136: 93-102. Barranco D, Cimato A, Fiorino P, Rallo L, Touzani A, Castañeda C,. Serafín F, Trujillo I (2000). World Catalogue of Olive Varieties,.
Ragy, Merhan Mamdouh; Kamal, Nashwa Nabil
Diabetes is considered an independent risk factor for cognitive impairments. The aim of this study was to evaluate the cognitive disorder of elderly outpatients with and without type 2 diabetes (T2DM) in releationto oxidative stress markers and some inflammatory markers Methodology: Two hundred and twelve participants were classified into four groups according to their fasting blood glucose level, glycosylated hemoglobin (HbA1c) and mini-mental state examination (MMSE) score. Control subjects were 118 subjects, diabetic group without dementia was 54 subjects, diabetic group with dementia was 26 subjects and 14 subjects of dementia without diabetes. Body mass index and waist/hip ratio were measured. Blood glucose, HbA1c, plasma malondialdehyde (MDA), total antioxidant activity (TAC), and some inflammatory markers: C-reactive protein (CRP) and tumor necrosis factor-α (TNF-α) were measured. Diabetic patients have significant increases in FBG, HbA1c, MDA with a significant decrease in TAC compared to control group. In all groups of patients, the levels of CRP, and TNF-α were significantly higher as compared to control group. The highest level of inflammatory markers was detected in diabetic group with dementia. MMSE score was negatively correlated with HbA1c levels and TNF-α and HbA1c levels were positively correlated with all inflammatory markers. In multivariate logistic regression analysis, MDA,CRP, Hb1c, TNF-a, and FBG were the most predictive risk factors for dementia Conclusions: These results suggest that a decrease in anti-oxidant levels and an increase in anti-inflammatory and oxidative stress markers might be involved in the pathophysiology of cognitive disorder associated with T2DM.
Hermes Pineda Santis
natural.Characterization of the genetic diversity of the fish Brycon henni (Characiformes: Characidae in central Colombia with RAPD markers. Knowledge on the genetic diversity of wild fish species is essential for conservation and appropriate management of individuals in repopulation programs. In Colombia, Brycon henni has been reported in the Magdalena and Cauca river basins, but the population and range have diminished as a consequence of anthropic activities. In this study, the Random Amplified Polymorphic DNA (RAPD was used to estimate the actual genetic structure in this species. For the purpose, six sample sites located in the department of Antioquia (Central Chain Mountains of Colombia were used. Thirty five primers (87.5 %, out of forty used, yielded 1 466 reliable and consistent fragments; 417 were considered as unique fragments able to discriminate among the Magdalena (Humarada-1 and Humarada-2 and Cauca (Piedras, La Clara y Guaracú river basins samples, suggesting that each is a discrete unit. This diversity suggests that anthropic effects of over fishing, dam building, deforestation and water pollution, have contributed to the isolation of these fish groups on the high mountains. Brycon moorei and Colossoma macropomum, as an interspecific control groups, were placed out of the B. henni general group, confirming their taxonomic classification through morphologic data. The RAPD technique was useful to know the genetic diversity and to discriminate among B. henni populations from different geographic origins, as a basis for an appropriate plan of repopulation, conservation and wildlife management. Rev. Biol. Trop. 55 (3-4: 1025-1035. Epub 2007 December, 28.
Fluorescence in situ hybridization (FISH) has not been readily exploited for physical mapping of molecular markers in plants due to the technical challenge to visualize small single-copy probes. Signal amplification using tyramide (tyr) FISH can increase sensitivity up to 100 fold. We used tyr-FISH ...
Patrícia Cristina Gomes
Full Text Available Recentemente a produção aquícola brasileira tem apresentado grandeprogresso. Dentre as espécies nativas cultivadas no Brasil, a piapara (Leporinus elongatus tem sido amplamente preconizada. Com objetivo de avaliar os programas de repovoamento, foram analisadas a variabilidade e a divergência genética de três estoques de piapara com a técnica de RAPD (Random Amplified Polymorphic. O primeiro estoque pertence à Estação de Aquicultura e Hidrologia da Duke Energy International (A; o segundo, à piscicultura de Rolândia (B e o terceiro, ao Programa de Repovoamento dos Rios do Paraná (C. Os dezprimers para RAPD utilizados produziram 105 fragmentos polimórficos, conferindo um polimorfismo de 98,1% para os três estoques avaliados. A porcentagem de locos polimórficos e índice de Shannon foi superior para o estoque A. Porém, todos valores foram elevados, indicando alta diversidade intrapopulacional. Os valores de Gst indicam que houvebaixa diferenciação genética entre os estoques A x B e moderada diferenciação entre os demais. O Nm foi maior entre os estoques A x B. A distância genética e o dendrograma indicam que os estoques A x B são menos distantes geneticamente.Latelly, aquiculture production in Brazil has made great strides. Among the native species cultivated in Brazil, piapara (Leporinus elogatus has been widely praised. With the objective of evaluating restocking programs, the variability and genetic divergence ofthree piapara stocks were analyzed using the RAPD (Random Amplified Polymorphic DNA technique. The first stock belongs to the Aquiculture and Hydrology Station of Duke Energy International (A; the second one belongs to a fish farm in the city of Rolândia(B; and the third to the River Restocking Program of Paraná (C. The ten primers used for RAPD produced 105 polymorphic loci, conferring a polymorphism of 98.1% for the three evaluated stocks. Polymorphic loci percentage and Shannon index were higher for stock A
Zhang, He-Cai; Shi, Chang-Ying; Yang, Hui-Hui; Chen, Guang-Wen; Liu, De-Zeng
The randomly amplified polymorphic DNA (RAPD) assay has been used to detect DNA alternation and mutation recently. However, the effectiveness of this method in detecting DNA damage in planarians, a model organism for assessing the toxicity of environmental pollutants is unknown. In the present study, RAPD assay was used to detect the DNA damage in planarians treated by the ionic liquid 1-octyl-3-methylimidazolium bromide ([C8mim]Br) for the first time. Among the 20 test RAPD primers, 13 primers with 60-70% GC content produced unique polymorphic band profiles. A total of 60 bands were observed in the untreated control planarians. In comparison with the control group, the [C8mim]Br-treated groups displayed differences in RAPD patterns in the band intensity, disappearance of normal bands and appearance of new bands. The variation of RAPD profiles showed both concentration- and time-effect relationships. Meanwhile, the genomic template stability (GTS) of treated planarians decreased and exhibited negative correlation to the exposure concentration and time of [C8mim]Br. Our results suggested that [C8mim]Br had genotoxic effects on planarians, and this DNA damage analysis would lay the foundation for further elucidating the toxicity mechanisms of ionic liquids on planarians. Furthermore, RAPD analysis was proved to be a highly sensitive method for the detection of DNA damage induced by environmental pollutants like toxic chemicals on planarians. Copyright © 2016 Elsevier Inc. All rights reserved.
Berretta; Lecuona; Zandomeni; Grau
Random amplified polymorphic DNA (RAPD) with incorporation of fluorescent deoxynucleotides was used to examine the genetic diversity among Beauveria bassiana isolates from Argentina and Brazil. High-resolution DNA fingerprints were generated on line, during polyacrylamide gel electrophoresis of amplification products, by automated laser fluorescence analysis. Each isolate displayed a distinct genotype. Cluster analysis showed a high level of variability among these genotypes. No correlation with geographical origin or host was detected. Nevertheless, a phenetic group of 80% similarity represented mainly the isolates exhibiting high virulence against the sugar cane borer, Diatraea saccharalis. Fluorescence-based RAPD fingerprints provide a useful tool for identifying entomopathogenic fungi, and this technique is specially applicable to screening many isolates in population studies. Copyright 1998 Academic Press.
Full Text Available The genetic diversity among Tunisian pomegranate cultivars has been investigated. Using universal primers, the random amplified polymorphic DNA (RAPD method was used to generate banding profiles from a set of twelve cultivars. Data was then computed with appropriate programs to construct a dendrogram illustrating the relationships between the studied cultivars. Our data proved the efficiency of the designed method to examine the DNA polymorphism in this crop since the tested primers are characterized by a collective resolving power of 12.83. In addition, the cluster analysis has exhibited a parsimonious tree branching independent from the geographic origin of the cultivars. In spite of the relatively low number of primers and cultivars, RAPD constitutes an appropriate procedure to assess the genetic diversity and to survey the phylogenetic relationships in this crop.
Shioda, Hiroko; Satoh, Kanako; Nagai, Fumiko; Okubo, Tomoko; Seto, Takako; Hamano, Tomoko; Kamimura, Hisashi; Kano, Itsu
Juice and integument of leaves of 3 Aloe species, Aloe vera, A. ferox and A. africana, are not allowed to be used as food according to the Pharmaceutical Affairs Law in Japan. On the other hand, whole leaves of A. arborescens can be used as food. The present study was designed to distinguish Aloe species by random amplified polymorphic DNA (RAPD) analysis. DNA was isolated from fresh and dried leaves of the 4 Aloe species. Five out of 32 different 10-mer primers examined were useful for analysis. By comparison of the characteristic bands of PCR products on agarose gel, it was possible to distinguish the 4 species. Thus, the botanical species of Aloe in commercial food products can be identified by RAPD analysis.
Nov 13, 2012 ... The four cultivars of sweet common orange and sweet navel orange was linked together in a separate cluster. ... Key words: Abscisic acid, abscission, Citrus, cluster analysis, deoxyribonucleic acid (DNA) random amplified polymorphic ..... are known to endanger the Citrus industry worldwide. (Hofer, 2007).
Nanvazadeh, Fatemeh; Khosravi, Azar Dokht; Zolfaghari, Mohammad Reza; Parhizgari, Najmeh
Pseudomonas aeruginosa is one of the important causes of nosocomial infections that easily gains resistance to many antibiotics. This opportunistic pathogen is a major health hazard particularly in immunodeficient patients, patients in intensive care units (ICU) and burn units with life threatening outcome. The bacterium may be originated from different or common sources, and comprises a high colonization and transmission capacity. The aim of present study was to investigate the genotypic variation of Pseudomonas aeroginosa strains isolated from burn patients by using Random Amplified Polymorphic DNA (RAPD) method. Totally 70 clinical samples were collected from burn patients in Taleghani Burn Hospital of Ahvaz. Fifty out of total samples were positive for P. aeruginosa by application of conventional culture and biochemical identification tests. DNA was extracted from the isolates and the RAPD-PCR method was applied to the DNA extracts according to standard method using a short single primer of 272. The technique created repetitive electrophoresis patterns which was used for genotypic differentiation. RAPD-PCR, created 9 genotypic profiles designated as I-IX with base pair length ranging from 180 to 2700. Each genotype showed between 3 and 6 different weight DNA bands. Genotype I was the most prevalent, identified in 10 bacterial isolates (20%). Genotypes I, II and VI were mostly common in patients with more severe burn, and were mainly isolated from wound and blood samples obtained from the same patients. In present study, we found RAPD-PCR technique as a useful tool for investigation of the genetic variation among P. aeruginosa strains. This is a rapid, low cost, genotypic method with high discriminatory power. The results could assist to screen for the original of infection caused by this organism with subsequent control of colonization and transmission. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.
José Luis Piña-Escutia
Tigridia pavonia (L.f.) DC. is one of the important phytogenetic resources of México. This species is used as ornamental, food and medicinal purposes. Despite its ornamental and economic potential, there is little information about the genetic variability. In this study, randomly amplified polymorphic DNA (RAPD) primers of 10, 15 and 20 bases were used to assess the level of genetic variation among nine botanical varieties of Tigridia pavoniacollected in three localities within State of Méxic...
Full Text Available In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD technique in nine Turkish commercial rapeseed varieties. The RAPD primers (10-mer oligonucleotides produced 51 scorable loci, 31 loci of which were polymorphic (60.78% and 20 loci (39.22% were monomorphic The RAPD bands were scored as binary matrix data and were analysed using POPGENE version 1.32. At locus level, the values of genetic diversity within population (Hs and total (HT were 0.15 and 0.19 respectively. The genetic differentiation (GST and the gene flow (Nm values between the populations were 0.20 and 2.05 respectively. The mean number of alleles (na, the mean number of effective alleles (nae, and the mean value of genetic diversity (He were 2.00, 1.26, and 0.19 respectively. According to Pearson’s correlation, multiple regression and principal component analyses, eco-geographical conditions in combination had significant effect on genetic indices of commercial B. napus L. varieties were discussed.
Full Text Available The aim of this study was to detect genes for enterotoxins (hbla, entFM and bceT and for emetic toxin (cer, to determine antibiotic resistance, and to estimate intraspecies diversity in B. cereus isolates by RAPD analysis. B. cereus was identified in 12 out of 117 indigenous Bacillus spp. using the classical microbiological methods and PCR. All isolates were resistant to penicillin and ampicillin, two to tetracyclin and four to trimethoprim-sulphamethoxazole. Also, all isolates produced inducible penicillinases and β-lactamase. Toxin genes were detected with PCR. EntFM and cer genes were present in all isolates, hbla in all, but two, and bceT in none. RAPD analysis was performed with four different primers, two of them designed for this study. The intraspecies diversity revealed 10 different patterns at the 90% similarity level. Two separate clusters were formed regardless of a soil type or utilization. The detection of genes encoding toxins in all B. cereus isolates indicated these bacteria as potentially pathogenic and seriously for human health. Regardless of a soil type or utilization, the RAPD analysis showed high intraspecies heterogeneity in B. cereus isolates. To the best of our knowledge, this is the first study to analyse the presence of entero- and emetic toxin genes and genetic heterogeneity in B. cereus isolates from different soil types and different soil utilization in Serbia. [Projekat Ministarstva nauke Republike Srbije, br. TR37006
Bogiel, Tomasz; Gospodarek, Eugenia
P. aeruginosa rods are opportunistic pathogens responsible generally for nosocomial infections. Resistance to carbapenems, observed among them, is a serious threat due to ability to be transmitted between bacterial species. The aim of our study was to evaluate the usefulness of PCR-RAPD technique in typing of 16 carbapenem-resistant P. aeruginosa strains isolated in 2007 from different patients of University HospitalNo. 1 of dr A. Jurasz Collegium Medicum of L. Rydygier in Bydgoszcz Nicolaus Copernicus University in Toruń. Study shows increasing frequency of isolation that type of strains when compared to 2006. Percentage of carbapenem-resistant isolates raised from 12,4% in 2006 to 22.9% in 2007. The majority of examined strains were obtained from patients of the Intensive Care Units (25.0%) and were isolated from bronchoalveolar lavage (25.0%), urine (25.0%) and wound swabs (18.8%) samples. Examined P. aeruginosa strains demonstrated resistance to doripenem (81.3%) and piperacillin (75.0%) and susceptibility to colistin (100.0%), amikacin (81.3%), netilmicin and norfloxacin (75.0% each). Using PCR-RAPD amplification with 208 and 272 primers, 14 and 16 DNA patterns were obtained, respectively. Usefulness of PCR-RAPD in carbapenem-resistant P. aeruginosa strains typing was proved in case of strains presenting similar and/or different antimicrobials susceptibility patterns.
Pham, Toan Duc; Geleta, Mulatu; Bui, Tri Minh; Bui, Tuyen Cach; Merker, Arnulf; Carlsson, Anders S
The purpose of this study was to comparatively analyze the genetic diversity of sesame (Sesamum indicum L.) using agro-morphological and molecular markers. Twelve sesame populations collected from three regions in Cambodia and Vietnam were used in this study. A high genetic variation was revealed both by agro-morphological and RAPD markers within and among the 12 sesame populations. The range of agro-morphological trait based average taxonomic distance among populations (0.02 to 0.47) was wider than that of RAPD based genetic distance (0.06 to 0.27). The mean distance revealed by agro-morphological markers (0.23) and RAPD markers (0.22) was similar. RAPD based analysis revealed a relatively higher genetic diversity in populations from South Vietnam as compared to the other two regions. Interestingly, populations from this region also had higher values for yield related traits such as number of capsules per plant, number of seeds per capsule, and seed yield per plant suggesting positive correlation between the extent of genetic variation within population and yield related traits in sesame. A highly significant positive correlation (r = 0.88, P sesame, their combined use would give superior results. © 2011 The Authors.
Maryam; Jaskani, Muhammad Jafar; Awan, Faisal Saeed; Ahmad, Saeed; Khan, Iqrar A
Microsatellite markers containing simple sequence repeats (SSRs) are a valuable tool for genetic analysis. Date palm is a dioecious and slow flowering and is very difficult to identify the gender of the trees until it reaches the reproductive age (5-10 years). A total of 12 microsatellite primers were used with 30 date palm samples, 14 parents (8 male + 6 females) and 16 progeny (developed from parents breeding) which showed that microsatellites were highly polymorphic, having a great number of alleles. A total of 124 alleles were characterized in 12 SSR loci. On average, there are 9.08 alleles per locus, with a range from 5 to 16 alleles, for primers mpdCIR15 and mpdCIR57, respectively. These primers produced 15 polymorphic loci specifically in male date palm samples and the seedlings harboring the unique fragments were further characterized as male plants. Increasingly, 38.46 % of these loci were scored as homozygous alleles while 61.53 % heterozygous allelic loci were determined. Primer mpdCIR48 produced a specific locus (250/250) in all male samples whereas the same locus was absent in female samples. Similarly, a locus of 300/310 bp reoccurred in 5 date palm male samples using marker DP-168 which indicated that these are the promising candidate marker to detect the sex in date palm seedlings at early stage. The data resulted from combination of 12 primers enabled the 16 seedling samples progeny (developed from parents breeding) of date palm cultivars to divide into two groups i.e., male and female regarding their sex expression comparative to the parents (male + female) using the principle coordinate analysis.
Full Text Available Hordeum vulgare ... 2n=14 5,000 Mb 2012 Sanger (Clone-based), Illumina GA IIx ... 4,990 Mb ... MIRA v3.2.0, CLC Asse...mbly Cell v3.2.2 ... 9,265 GenomeThreader, CuffLinks 26,159 IBSC; http://www.public.ia
Rettinger, A; Broeckl, S; Fink, M; Prodinger, W M; Blum, H; Krebs, S; Domogalla, J; Just, F; Gellert, S; Straubinger, R K; Büttner, M
Alpine Mycobacterium caprae isolates found in cattle and red deer display at least three genetic variations in the region of difference four (RD4) that can be used for further differentiation of the isolates into the subtypes 'Allgäu', 'Karwendel' and 'Lechtal'. Each genomic subtype is thereby characterized by a specific nucleotide deletion pattern in the 12.7-kb RD4 region. Even though M. caprae infections are frequently documented in cattle and red deer, little is known about the transmission routes. Hence, robust markers for M. caprae subtyping are needed to gain insight into the molecular epidemiology. For this reason, a rapid and robust multiplex PCR was developed for the simultaneous detection of three M. caprae RD4 subtypes and was used to subtype a total number of 241 M. caprae isolates from animals (145 cattle, 95 red deer and one fox) from Bavaria and Austria. All three subtypes occur spatially distributed and are found in cattle and in red deer suggesting transmission between the two species. As subtypes are genetically stable in both species it is hypothesized that the described genetic variations developed within the host due to 'within-host replication'. The results of this study recommend the genomic RD4 region as a reliable diagnostic marker for M. caprae subtype differentiation. © 2015 Blackwell Verlag GmbH.
Techer, C; Baron, F; Delbrassinne, L; Belaïd, R; Brunet, N; Gillard, A; Gonnet, F; Cochet, M-F; Grosset, N; Gautier, M; Andjelkovic, M; Lechevalier, V; Jan, S
To evaluate the food safety and spoilage risks associated with psychrotrophic Bacillus cereus group bacteria for the egg product industry and to search for relevant risk markers. A collection of 68 psychrotrophic B. cereus group isolates, coming from pasteurized liquid whole egg products, was analysed through a principal component analysis (PCA) regarding their spoilage and food safety risk potentials. The principal component analysis showed a clear differentiation between two groups within the collection, one half of the isolates representing a safety risk and the other half a spoilage risk. Relevant risk markers were highlighted by PCA, that is (i) for the food safety risk, the presence of the specific 16S rDNA-1m genetic signature and the ability to grow at 43°C on solid medium and (ii) for the spoilage risk, the presence of the cspA genetic signature. This work represents a first step in the development of new diagnostic technologies for the assessment of the microbiological quality of foods likely to be contaminated with psychrotrophic B. cereus group bacteria. © 2014 The Society for Applied Microbiology.
Ioana Virginia Berindean
Full Text Available Sweet cherry (Prunus avium L., originated around the Caspian and Black Sea, is an important fruit tree species of economic interest, and hence, breeding and conservation are requested (. Genetic analysis at the molecular level can be used effectively to study molecular polymorphism existing between intraspecific and interspecific tree species and phylogenetic relationships between them and their hybrids. The purpose of this study was to characterize and determine genetic relationships among the sweet cherry native genotypes belonging to Fruit Research & Development Station Bistrita, Romania, using RAPD markers. To eliminate the existence of possible synonyms from national romanian collection, we collect four Van cultivars, from four different national collection. For molecular analysis of the 16 varieties of sweet cherry were considered 13 RAPD primers selected from the literature. They were later used to determine the genetic variability at the molecular level using PAST program, and the dendrogram was generated based on Jaccard’s genetic distance. The dendrogram constructed by PAST software. The quantity and quality of the DNA obtained was suitable to achieve PCR amplification step. Only seven out of the 13 RAPD primers have generate polymorphic bands. The rest of seven were monomorphics. The most polymorphic primer was OPB10 which generated 11 bands from which 100% were polymorphic.Seven RAPD primers generated a high level of polymorphism which allowed to divide these cherry varieties into two groups according to their genetic geographical origin and the pedigree.
Assessment of genetic diversity on a sample of cocoa accessions resistant to witches' broom disease based on RAPD and pedigree data Avaliação da diversidade genética em uma amostra de acessos de cacau resistentes à doença vassoura-de-bruxa, com base em dados de RAPD e pedigree
Ronaldo Carvalho dos Santos
Full Text Available Genetic diversity in cocoa (Theobroma cacao L. has been assessed based on morphological and molecular markers for germplasm management and breeding purposes. Pedigree data is available in cocoa but it has not been used for assessing genetic relatedness. The geneitic diversity of 30 clonal cocoa accessions resistant to witche´ broom disease, from the CEPEC series, were studied on the basis of RAPD data and pedigree information. Twenty of these accessions descend from the TSA-644 clone, originated from a cross between the Upper Amazon germplasm called Scavina-6, the main source of resistance to witches' broom disease, and IMC-67. The ten remaining clones come from different sources including Amazon and Trinitario germplasm. RAPD data was collected using 16 primers and pedigree information was obtained from the International Cocoa Germplasm Database. Genetic similarities, genetic distances and coefficient of parentage were calculated using available software. Relatively low genetic diversity was observed in this germplasm set, probably because of great genetic relatedness amongst accessions studied and the poor representation of the germplasm. The TSA-644 descendants were more diverse than the other accessions used in the study. This might be due to the origin of the TSA clone, which was derived from highly divergent genotypes. Association between genetic similarities based on RAPD data and coefficient of parentage, based on pedigree data, was very low, probably due to the homogeneity of the breeding stocks and poor pedigree information. These findings are useful to cocoa breeders in planning crosses for the development of hybrid and clonal cultivars.A diversidade genética em cacau (Theobroma cacao L., embasada em dados morfológicos e em marcadores moleculares, tem sido avaliada com fins de manejo de germoplasma e uso no melhoramento genético. Dados de genealogia de cacau, embora disponíveis, não têm sido utilizados. Foi analisada a
Cook, Eliza; Portnyagin, Maxim; Ponomareva, Vera; Bazanova, Lilia; Svensson, Anders; Garbe-Schönberg, Dieter
Contiguous sampling of Holocene ice from the NGRIP core, Greenland, has revealed a new rhyolitic cryptotephra that is geochemically identical to the KHG tephra, a widespread marker deposit originating from the Khangar volcano, Kamchatka. This is the first identification of tephra from the Kamchatka Peninsula in Greenland ice and the first finding of the KHG tephra outside Kamchatka. The NGRIP KHG has an age of 7872 ± 50 a BP 1950, and this date will help improve age models for Kamchatka, where existing age estimates of KHG are too young, thus highlighting the importance of locating long-range, low-concentration cryptotephra deposits in well-dated ice cores. In Greenland KHG is located close to the termination of the 8.2 ka BP cooling event that is also a climate feature in palaeo-records of Kamchatka. This tie-point therefore provides a unique opportunity to synchronise records of environmental change in distal locations.
Zarzoso-Lacoste, D; Jan, P-L; Lehnen, L; Girard, T; Besnard, A-L; Puechmaille, S J; Petit, E J
Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex- and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex- and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments. The use of the DDX3X/Y-Mam sexual marker designed in this study, which shows inter- and intra-chromosomal length polymorphism across placental mammals, together with 8 polymorphic microsatellite markers, produced high quality genetic data with limited genotyping errors and allowed us to reliably distinguish different categories of individuals (males, reproductive and non-reproductive females) and to estimate population sizes. We showed that visual counts represent well adult female numbers and that population composition in maternity colonies changes dynamically during the summer. Before parturition, colonies mainly harbour pregnant and non-pregnant females with a few visiting males whereas after parturition, colonies are mainly composed of mothers and their offspring with a few visiting non-mothers and males. Our approach gives deeper insight into sex- and status-specific behaviour, a prerequisite for understanding population dynamics and developing effective monitoring and management strategies. Provided sufficient samples can be obtained, this approach can be readily applied to a wide range of species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Tranbarger, Timothy John; Kluabmongkol, Wanwisa; Sangsrakru, Duangjai; Morcillo, Fabienne; Tregear, James W; Tragoonrung, Somvong; Billotte, Norbert
The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's number one source of edible vegetable oil, and the richest dietary source of provitamin A. While new elite genotypes from traditional breeding programs provide steady yield increases, the long selection cycle (10-12 years) and the large areas required to cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding programs have the potential to make significant impacts on the rate of genetic improvement but the limited molecular resources, in particular the lack of molecular markers for agronomic traits of interest, restrict the application of molecular breeding schemes for oil palm. In the current study, 6,103 non-redundant ESTs derived from cDNA libraries of developing vegetative and reproductive tissues were annotated and searched for simple sequence repeats (SSRs). Primer pairs from sequences flanking 289 EST-SSRs were tested to detect polymorphisms in elite breeding parents and their crosses. 230 of these amplified PCR products, 88 of which were polymorphic within the breeding material tested. A detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms within the transcripts, and that the main functional category was related to transcription and post-transcriptional regulation. Indeed, SSR polymorphisms were found in sequences encoding AP2-like, bZIP, zinc finger, MADS-box, and NAC-like transcription factors in addition to other transcriptional regulatory proteins and several RNA interacting proteins. The identification of new EST-SSRs that detect polymorphisms in elite breeding material provides tools for molecular breeding strategies. The identification of SSRs within transcripts, in particular those that encode proteins involved in transcriptional and post-transcriptional regulation, will allow insight into the functional roles of these proteins by studying the phenotypic traits
Yadav, Kuldeep; Aggarwal, Ashok; Singh, Narender
Malabar glory lily (Gloriosa superba L.) is a medicinally potent plant species used for the production of alkaloid colchicine. With ever increasing demand, there is a pressing need to conserve it through biotechnological approaches. A large number of complete plantlets were obtained by direct regeneration from the non-dormant tuber explants on Murashige and Skoog (MS) medium supplemented with 2.0 mg/l 6-benzylaminopurine (BAP)+0.5 mg/l α-naphthalene acetic acid (NAA). Large number of plants can be produced in vitro under aseptic conditions, but there is always a danger of producing somaclonal variants by tissue culture technology. Thus, the genetic stability of micropropagated clones was evaluated using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analysis. During the study a total of 80 (50 RAPD and 30 ISSR) primers were screened, out of which 10 RAPD and 7 ISSR primers produced a total of 98 (49 RAPD and 49 ISSR) clear, distinct and reproducible amplicons. The amplification products of the regenerated plants showed similar banding patterns to that of the mother plant thus demonstrating the homogeneity of the micropropagated plants. This is the first report that evaluates the use of genetic markers to establish genetic fidelity of micropropagated G. superba using RAPD and ISSR, which can be successfully applied for the mass multiplication, germplasm conservation and further genetic transformation assays for colchicine production to meet the ever increasing demand of this medicinally potent plant for industrial and pharmaceutical uses. © 2013.
Zhang, J; Zhang, L G
Chinese kale is an original Chinese vegetable of the Cruciferae family. To select suitable parents for hybrid breeding, we thoroughly analyzed the genetic diversity of Chinese kale. Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) molecular markers were used to evaluate the genetic diversity across 21 Chinese kale accessions from AVRDC and Guangzhou in China. A total of 104 bands were detected by 11 RAPD primers, of which 66 (63.5%) were polymorphic, and 229 polymorphic bands (68.4%) were observed in 335 bands amplified by 17 SRAP primer combinations. The dendrogram showed the grouping of the 21 accessions into 4 main clusters based on RAPD data, and into 6 clusters based on SRAP and combined data (RAPD + SRAP). The clustering of accessions based on SRAP data was consistent with petal colors. The Mantel test indicated a poor fit for the RAPD and SRAP data (r = 0.16). These results have an important implication for Chinese kale germplasm characterization and improvement.
Full Text Available Amplified Fragment Length Polymorphism molecular markers (AFLPs has been developed combining procedures of RFLPs and RAPDs molekular markers, i.e. the first step is restriction digestion of the genomic DNA that is followed by selective amplification of the restricted fragments. The advantage of the AFLP technique is that it allows rapid generation of a large number of reproducible markers. The reproducibility of AFLPs markers is assured by the use of restriction site-specific adapters and adapter-specific primers for PCR reaction. Only fragments containing the restriction site sequence plus the additional nucleotides will be amplified and the more selected nucleotides added on the primer sequence the fewer the number of fragments amplified by PCR. The amplified products are normally separated on a sequencing gel and visualized after exposure to X-ray film or by using fluorescent labeled primers. AFLP shave proven to be extremely proficient in revealing diversity at below the species level. A disadvantage of AFLP technique is that AFLPs are essentially a dominant marker system and not able to identify heterozygotes.
Ferguson, Naola M; Hepp, Diego; Sun, Shulei; Ikuta, Nilo; Levisohn, Sharon; Kleven, Stanley H; García, Maricarmen
A total of 67 Mycoplasma gallisepticum field isolates from the USA, Israel and Australia, and 10 reference strains, were characterized by gene-targeted sequencing (GTS) analysis of portions of the putative cytadhesin pvpA gene, the cytadhesin gapA gene, the cytadhesin mgc2 gene, and an uncharacterized hypothetical surface lipoprotein-encoding gene designated genome coding DNA sequence (CDS) MGA_0319. The regions of the surface-protein-encoding genes targeted in this analysis were found to be stable within a strain, after sequencing different in vitro passages of M. gallisepticum reference strains. Gene sequences were first analysed on the basis of gene size polymorphism. The pvpA and mgc2 genes are characterized by the presence of different nucleotide insertions/deletions. However, differentiation of isolates based solely on pvpA/mgc2 PCR size polymorphism was not found to be a reliable method to differentiate among M. gallisepticum isolates. On the other hand, GTS analysis based on the nucleotide sequence identities of individual and multiple genes correlated with epidemiologically linked isolates and with random amplified polymorphic DNA (RAPD) analysis. GTS analysis of individual genes, gapA, MGA_0319, mgc2 and pvpA, identified 17, 16, 20 and 22 sequence types, respectively. GTS analysis using multiple gene sequences mgc2/pvpa and gapA/MGA_0319/mgc2/pvpA identified 38 and 40 sequence types, respectively. GTS of multiple surface-protein-encoding genes showed better discriminatory power than RAPD analysis, which identified 36 pattern types from the same panel of M. gallisepticum strains. These results are believed to provide the first evidence that typing of M. gallisepticum isolates by GTS analysis of surface-protein genes is a sensitive and reproducible typing method and will allow rapid global comparisons between laboratories.
Patrícia da Silva Nascente
Full Text Available Several methodologies in molecular biology have been used in theinvestigation of Malassezia pachydermatis and its differentiation into subtypes. Recent molecular research of this species includes the use of samples isolated from canine otitis externa and dermatitis, as well as from healthy animals, having in view an epidemiologicalstudy of the yeast. The aim of this study was to identify molecular differences in M. pachydermatis samples isolated from dogs with otitis externa. The M. pachydermatis strains were analyzed by means of the Random Amplification Primer DNA - Polimerase Chain Reaction (RAPD–PCR for molecular heterogeneity research. DNA extraction was carried out with phenol-chloroform and the RAPD technique using the AGAATCCGCC primer. A variation was observed in the number and arrangement of the bands among the 49 studied isolates, grouped into nine patterns. Isolate groupings were not found to be related to animal breed, age or sex. It was concluded that M. pachydermatis has differences in its molecular profile, as shown by the molecular technique (RAPD – PCR, which allows isolates to be classified into nine subtypes.Várias metodologias em biologia molecular têm sido aplicadas para estudar a M. pachydermatis diferenciando-a em subgrupos. Recentemente utiliza-se a investigação molecular desta espécie isolada de otite externa e dermatite, e também de isolados da mesma de animais hígidos, para um estudo epidemiológico da levedura. O objetivo deste trabalho foi identificar diferenças moleculares entre isolados de M. pachydermatis obtidos de casos de otite externa canina. Para isto, amostras da levedura provenientes de cães com esta enfermidade foram estudadas através da técnica de Polimorfismo de DNA Amplificado aoAcaso - Reação da Polimerase em Cadeia (RAPD–PCR para pesquisa de heterogeneidade molecular. A extração de DNA foi realizada no processo fenol-cloroformio e a técnica de RAPD foi estudada com o primer
mongolism are high-risk candidates for certain types of leukemia. Similarly, hemophiliacs have a correspondingly high incidence of color blindness . (4...genetically determined characteristics such as color blindness and blood type. GENETIC MARKER STUDIES In 1966 Dr. Cruz-Coke and Dr. Varela reported that...their study had linked color blindness , cirrhosis of the liver and alcoholism. They further hypothesized the existence of a sex-linked carrier gene
Rao, Kiran Prabhaker; Belogolovkin, Victoria
Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.
Tulsiani, Suhella; Craig, S B; Graham, G C
could undermine the use of RAPD-HRM or any other molecular technology. Such genetic attenuation may account for a general decrease seen in titres of rabbit hyperimmune antibodies over time. Before RAPD-HRM can be further advanced as a routine diagnostic tool, strains more representative of the wild...
Semagn, K; Stedje, B; Bjornstad, A
The genetic diversity and structure in 17 wild populations (249 individuals) of Phytolacca dodecandra (endod) sampled along altitudinal gradients of 1600-3000 meters above sea level (m.a.s.l.) in Ethiopia was studied using random amplified polymorphic DNA (RAPD). A total of 70 polymorphic loci (P) scored from 12 RAPD primers were used to calculate different diversity indices within and between populations, habitats, geographical regions, climatic zones and altitude groups. The number of polymorphic loci and overall Shannon information measure (H) in the populations varied from 30 to 55 and from 0.228 to 0.418, respectively. In general, differences in population variability were found significantly correlated to effective population size. Both P and H were significantly higher in an undisturbed than in a disturbed habitat, and in the lowland and central-highland than in the highland altitude group. However, for both parameters the differences were not statistically significant between regions and climatic zones. Genetic distance between populations varied from 0.301 to 0.628. Cluster analysis performed using the genetic distance matrix revealed a clear separation of the highland populations (2501-3000 m.a.s.l.) from those of the lowland/central-highlands (1600-2500 m.a.s.l.) irrespective of their geographical regions and climatic zones. Analysis of molecular variance (AMOVA) indicated that differences in habitat, geographical regions and climatic zones explained 4.6%, 2.5% and 4.6%, respectively. But none of these differences were significant. Altitude explained 17.2% of the total variance and was highly significant. The data, therefore, clearly indicated the association of genetic structure in endod with altitude. The proportion of RAPD variation found among populations (21.2-35.0%) was somewhat intermediate between values reported for selfing and outcrossing species. The fixation index (FST) values (0.350 to 0.384) indicated very high genetic differentiation among
Bogani, P; Simoni, A; Lio', P; Scialpi, A; Buiatti, M
An analysis of the effect of changing physiological conditions on genome evolution in tomato cell populations has been carried out on long-term in vitro cultured clones grown on different auxin-cytokinin equilibria or selected for low-high competence for active defense against Fusarium oxysporum f.sp. lycopersici. RAPD analysis, confirmed through pattern rehybridization, was used as a random tool to measure the genetic variability. Through the use of a modified ANOVA, variation was shown to depend on both the initial genotype and the physiological conditions. Pattern correlation analysis through a mutual information algorithm suggested the fixation of RAPD patterns specific to physiological equilibria. The results are discussed in view of the possible relevance for evolution at hierarchical levels higher than cell populations. Key words : tomato clones, somaclonal variation, RAPD, coadaptation.
Caracterización de bacterias aisladas en larvas de P.V. mediante RAPDs La “Vibriosis luminiscente” reportada por varios laboratorios de larvas del Ecuador es asociada principalmente a la bacteria Vibrio harveyi. Los métodos de identificación bacteriana tradicionales se basan en la observación de características morfológicas y pruebas bioquímicas, sin embargo la identificación de especies bacterianas y en especial de Vibrios ambientales ha presentado ciertas dificultades debido al tiempo qu...
Full Text Available Annually many numbers of pationts with Cutaneous Leishmaniasis (CL have been reported in Kermanshah province- IRAN. The study aimed to identify species of Leishmania isolated from patients with CT in Kermanshah. Seven isolates of Leishmania obtained from patients with CL, without any travelling to other provinces, were cultured in NNN medium. After mass production of leptomonads in RPMI 1640 medium DNA was purified and the species were diagnosed using RAPD-PCR technique. The study of electrophoretic fingerprints of the product of RAPD-PCR in seven isolates showed that Leshmania major was the causative agent of CL patients in Kermanshah province. More studies in this field recommended.
Mostafa, M. G.; Ishtiaq Ahmed, A. S.; M. G. Mustafa; M.G. Rabbane; M.G. Islam; Rafiquzzaman, S. M.
Genetic diversity of two wild Kalibaus, Labeo calbasu populations and one hatchery stock was studied using random amplified polymorphic DNA (RAPD) method. The three 10–mer random primers (OPA01, OPB02 and OPC03) yielded a total of 26 reproducible and consistently scorable RAPD bands of which 15 (57.69%) were considered as polymorphic (P95) indicating a high level of genetic variation in all the studied populations. Among the three populations, Padma population shows low level of genetic diver...
Atia, Mohamed A M; Sakr, Mahmoud M; Mokhtar, Morad M; Adawy, Sami S
Molecular markers are used efficiently in the development and identification of gender-specific PCR-based markers in date palm. There is mounting evidence that different marker systems vary in their mechanisms of detecting polymorphism and genome coverage. Therefore, they could complement each other to generate accurate sex-specific markers in date palm. This chapter describes the uses of PCR-based molecular markers to develop and identify the gender in different date palm genotypes; these are amplified fragment length polymorphism (AFLP), start codon targeted polymorphism (SCoT), conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), and random amplified polymorphic DNA (RAPD). Also described is how to characterize the identified markers by Sanger sequencing and to explore their functions through alignment of their sequences with the Genbank databases.
Full Text Available RAPD analysis of nine Thai pineapple cultivars, including 'Phulae', 'Sawee', 'Tradsithong', 'Phuket', 'Pattavia', 'Intrachitdang', 'Intrachitkhow', 'Petburi No.1', and 'Nanglae', showed that, of 40 arbitrary 10- mer primers, 17 primers gave 206 DNA fragments ranging from 510 to 4,700 bp. One hundred and forty-five (70.4% of the amplified fragments were polymorphic. RAPD analysis using NTSYS-pc Version 2.01e also showed that the similarity coefficients among the cultivars were 0.643-0. 963. The dendrogram indicated that the cultivars were clustered into 3 groups, consistent with the morphological data. The first group, consisting of 'Phuket', 'Phulae', 'Tradsithong', 'Sawee', and 'Petburi No.1', had morphological characteristics of the Queen group, while those of the second ('Intrachitdang' and 'Intrachitkow' and the third ('Nanglae' and 'Pattavia' groups could be determined morphologically to be members of the Spanish and Cayenne groups, respectively. 'Intrachitdang' and 'Intrachitkow' have similarity coefficient of 0.963, while that of 'Phulae' and 'Phuket' is 0.950. These pairs of cultivars are probably the same cultivars. The morphological differences between them are probably caused by mutations, differences in environment and agricultural practices, or combinations of these factors.
Hillol, Chakdar; Pabbi, Sunil
Morphological parameters studied for the twenty selected Nostoc strains were mostly found to be consistent with the earlier reports. But the shape of akinetes observed in this study was a little deviation from the existing descriptions and heterocyst frequency was also found to be different in different strains in spite of growing in the same nitrogen free media. Multiplex RAPD produced reproducible and completely polymorphic amplification profiles for all the strains including some strain specific unique bands which are intended to be useful for identification of those strains. At least one to a maximum of two unique bands was produced by different dual primer combinations. For ten strains out of twenty, strain specific bands were found to be generated. Cluster analysis revealed a vast heterogeneity among these Nostoc strains and no specific clustering based on geographical origin was found except a few strains. It was also observed that morphological data may not necessarily correspond to the genetic data in most of the cases. CCC92 (Nostoc muscorum) and CCC48 (Nostoc punctiforme) showed a high degree of similarity which was well supported by high bootstrap value. The level of similarity of the strains ranged from 0.15 to 0.94. Cluster analysis based on multiplex RAPD showed a good fit revealing the discriminatory power of this technique.
El-Batanouny, M. H.; Amin, R. M.; Ibrahium, M. K.; El Gohary, S.; Naga, M. I.; Salama, M. S.
Helicobacter pylori is one of the most common causes of chronic bacterial infections in humans and is important in the pathogenesis of gastrointestinal disease, such as duodenal ulcer, gastric ulcer, Gastric adenocarcinoma, and lymphoma. Gastric adenocarcinoma remains one of the leading causes of cancer death in the world. The objective of this study was to assess the effect of photodynamic treatment and medication treatment of Helicobacter pylori using RAPD-PCR. The lethal photosensitization effect was determined by mixing suspensions of H.pylori with Toluidine blue O (TBO) and plating out on blood agar before irradiation with Helium neon (He-Ne) 632.8 nm. The susceptibility of Helicobacter pylori isolates to metronidazole and azithromycin were examined by E-test. Nine random primers were used to screen genetic polymorphism in DNA of different H.pylori groups. Six of them produced RAPD products while three failed to generate any product. The resulting data showed that, although the overall genetic differences between control groups and laser treated groups was higher than that between control groups and azithromycin treated groups yet it still law genetic variability. The main cause of cell death of PDT using TBO as a photosensitizer was mainly cell wall and cytoplasmic membrane.
Lee, Ki-Eun; Jeoung, Hye-Young; Lee, Ji-Youn; Lee, Myoung-Heon; Choi, Hwan-Won; Chang, Kyung-Soo; Oh, Young-Hee; An, Dong-Jun
Pasteurella multocida causes various respiratory disease symptoms in pigs, including atrophic rhinitis and pneumonia. In the present study, 69 strains of P. multocida were isolated from 443 pigs with respiratory clinical symptoms at 182 farms located throughout South Korea from 2009 to 2010. A multiplex capsular PCR typing assay revealed that 69 strains of P. multocida isolated in this study had the biosynthetic locus of the capsules of either serogroup A (47 strains, 68.1%) or serogroup D (22 strains, 31.9%). The 22 strains positive for serogroup D-specific primers were divided into four clusters and the 47 strains positive for serogroup A-specific primers were divided into 12 clusters according to the results of Random Amplified Polymorphic DNA (RAPD) analysis. P. multocida strains in the present study were susceptible to most of the antimicrobial agents used. An analysis of antimicrobial resistance and virulence gene pattern combined with RAPD indicated that a certain P. multocida strain appeared to be genetically identical, implying the persistence of the strain within a single farm.
Full Text Available Genetic diversity in Chickpea wilt pathogen has been characterized using 14 isolates of Fusarium oxysporum f. sp. ciceri (foc collected from major pulse growing regions of India. Out of 247 bands produced by 24 Random Amplified Polymorphic DNA (RAPD primers in Foc isolates, 210 (85% were polymorphic. A maximum of 14 amplicons were generated by primer OPF 05 whereas minimum 7 amplicons were generated by primer K7. A total of 24 alleles were produced by twelve simple sequence repeat (SSR primers with an average of two alleles per marker in foc isolates. The maximum number of 4 alleles was obtained with primer SSR 12. SSR amplicon size ranged from 100 to 400 bp. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA cluster analysis based on RAPD and SSR profiles grouped the fourteen foc isolates into four major clusters. The universal Inter Transcribed Spacer (ITS primer pair amplified 630 bp bands in all fourteen foc isolates while significant length polymorphism was obtained only when analysed by restriction digestion with EcoRI and MspI enzymes. The cluster analysis of ITS-RFLP grouped all 14 Foc isolates into three major clusters. The cluster analysis using RAPD, SSR and ITS-RFLP markers show the grouping of Fusarium isolates strictly according to their cultural characteristics and degree of pathogenicity and not the geographical origin. This information will be helpful for pathologists and plant breeders to design effective resistance breeding programs in chickpea taking into account the diversity in wilt pathogen.
Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous
Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.
Full Text Available Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation of Chyavanaprash. Tubers of Ipomoea mauritiana Jacq. (Convolvulaceae, Pueraria tuberosa (Roxb. ex Willd. DC (Fabaceae, Adenia hondala (Gaertn. de Wilde (Passifloraceae and pith of Cycas circinalis L. (Cycadaceae are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguish I. mauritiana from the other Vidari candidates. A putative 600-bp polymorphic sequence, specific to I. mauritiana was identified using randomly amplified polymorphic DNA (RAPD technique. Furthermore, sequence characterized amplified region (SCAR primers (IM1F and IM1R were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authentic I. mauritiana and not in the allied species.
Hermosa, M R; Grondona, I; Díaz-Mínguez, J M; Iturriaga, E A; Monte, E
The genus Trichoderma includes biocontrol agents (BCAs) effective against soilborne plant pathogenic fungi. Several potentially useful strains for biological control are difficult to distinguish from other strains of Trichoderma found in the field. So, there is a need to find ways to monitor these strains when applied to natural pathosystems. We have used random amplified polymorphic DNA (RAPD) markers to estimate genetic variation among sixteen strains of the species T. asperellum, T. atroviride, T. harzianum, T. inhamatum and T. longibrachiatum previously selected as BCAs, and to obtain fingerprinting patterns. Analysis of these polymorphisms revealed four distinct groups, in agreement with previous studies. Some of the RAPD products generated were used to design specific primers. Diagnostic PCR performed using these primers specifically identify the strain T. atroviride 11, showing that DNA markers may be successfully used for identification purposes. This SCAR (sequence-characterised amplified region) marker can clearly distinguish strain 11 from other closely related Trichoderma strains.
Wongsawad, Chalobol; Wongsawad, Pheravut
Stellantchasmus falcatus is a minute intestinal fluke in the family Heterophyidae. Metacercariae, the infective stage, were reported in a marine fish, mullet Liza subviridis, and a fresh water fish, Dermogenus pusillus, in Thailand. Adults were found in chicks, rats, cats, and humans. Morphological studies were done for comparing Stellantchasmus sp. worms found in 2 different fish hosts; their shapes and organ arrangements were very similar except for the prepharynx length. Therefore, the pre...
Uzonur, Irem; Akdeniz, Gamze; Katmer, Zeynep; Ersoy, Seyda Karaman
Urtica dioica is an ethnobotanically and medicinally important Complementary and Alternative Medicine (CAM) plant worldwide and in Turkey; 90 % of herbal CAM applications depend on it in Turkey. It has a wide range of habitats in nearly all continents. It is found in all three phytogeographical regions in Turkey (Euro-Siberian, Irano-Turanian, Mediterranean) with high adaptivity to heterogeneous geographies such as climate, soil types and altitudes. This fact in relation to the assessment of chemical constituents of the plant and combining with further genetic and morphological variation data can assist and enhance the works for the utility and reliability of CAM applications in effect and activity of this plant species. In this work we have made some preliminary experiments with novel approaches to reveal the ecotypes and genetic variation of mighty ecotypes of Urtica dioica from different phytogeographical regions of Turkey (Euro-Siberian and Mediterranean). The ecotypes have heterogeneity in both its parts (leaf, stem, root) as revealed by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) using random primers and High-resolution Melt (HRM) analysis using Urtica dioica specific primers and universal chloroplast DNA (cpDNA) primers and morphological traits such as phenolic contents and antioxidant capacities of plants' leaf infusions as used in medicinal applications in Turkey. This work will contribute a lot for the development of molecular markers to detect the genetic variation and heterogeneity of Urtica dioica to further relate with expected phenotypes that are most useful and relevant in CAM applications.
Parthraj R. Kshirsagar
Full Text Available Highly efficient in vitro regeneration system has been developed for Swertia lawii Burkill, an important herb used as substitute for Swertia chirayita. Shoot tips explants were cultured on MS medium with various phytohormones for multiple shoot production. The best shoot production frequency (100% and maximum shoots (10.4 ± 0.8 were obtained on MS media containing TDZ (3.0 mg l−1 in combination with IBA (0.3 mg l−1. Maximum callus induction (95 ± 4.8% and callus growth (1.7 ± 0.4 gm was achieved on MS medium with 2, 4-D (3.0 mg l−1. Cell suspension cultures were established and studied for their growth kinetics. Shoots were rooted best (22.1 ± 2.5 in 1/2 MS medium with IAA (3.0 mg l−1. The genetic uniformity of the micropropagated clones was assessed using RAPD markers. Out of 405 bands, 400 (98.76% were monomorphic and rest 5 (1.24% were polymorphic. High multiplication frequency and low risk of genetic instability ensures the efficacy of this protocol.
Galina-Pantoja, L.; Siggens, K.; Schriek, van M.G.M.; Heuven, H.C.M.
The goal of this study was to identify pig chromosomal regions associated with susceptibility to salmonellosis. Genomic DNA from pig reference populations with differences in susceptibility to Salmonella enterica serovar Choleraesuis as quantified by spleen and liver bacterial colonization at day 7
Full Text Available The randomly amplified polymorphic DNA (RAPD technique was used to distinguish nucellar and zygotic seedlings resulting from crosses between the ?Montenegrina? (Citrus deliciosa Tenore and? King? (C. nobilis Loureiro tangerines. The aim of the present study was to develop tangerine varieties with a reduced number of seeds and organoleptic characteristics similar to the ?Montenegrina? tangerine. Embryos were isolated from seeds, cultivated in vitro, and acclimated in a greenhouse. Four random primers were used to identify 54 plants of sexual origin from a total of 202 individuals. The degree of polymorphism of each primer was reflected in the number of zygotic plants obtained per primer. Cluster analysis of parents and progeny separated the individuals into distinct groups with a maximum genetic dissimilarity of 20%.
Fumagalli, R; Pezzotta, S; Bernini, F; Racagni, G
Biological markers of tumors are compounds or enzymatic activities measurable in body fluids. Their presence or concentration must be linked to tumoral growth. The markers of the central nervous system tumors are detected in CSF. Alpha-feto-protein, carcinoembryonic antigen, human chorionic gonadotropin, adenohypophyseal peptide hormones, enzymes, etc., have found some application in the early diagnosis of leptomeningeal metastasis. Other applications involve the early detection and recurrency of primary brain tumors, as well as the evaluation of efficacy of their therapy. The tests based on the CSF content of desmosterol and polyamines have been studied extensively. Their rationale is discussed and specificity, sensitivity, efficiency and predictive value are considered. Experimental results concerning a new possible biochemical marker, based on CSF concentration of cyclic adenosine monophosphate, are reported.
Variability was observed for six ... rapid increase in climate change, so there is need to develop high yielding ... the past decade including assessment of genetic diversity in maize ... The SSR gel images and marker data were processed using.
Saputro, Triono Bagus; Dianawati, Siti; Sholihah, Nur Fadlillatus; Ermavitalini, Dini
Maize is one of important cultivated plants in the world, in terms of production rates, utilization rates and demands. Unfortunately, the increment of demands were not followed by the increase of production rates since the cultivation area were significantly decrease. Coastal area is the marginal land that have a good potential to extend the cultivation area. The main challenge of this area is the high content of salt. The aims of this research were try to induce a new varian of local maize through in vitro culture and observe its genetic variation using RAPD. Bluto variety from Madura island was used as an explant in callus induction. Induction of callus were conducted using MS basal medium supplemented with 3 mg/L of 2,4 D under dark condition. While the selection stage was conducted using MS basal medium supplemented with 3 mg/L of 2,4 D with the addition of various concentration of NaCl (0 mg/L; 2500 mg/L; 5000 mg/L; and 7500 mg/L). The research were arranged in a completely randomized design with three replications. The exposion of NaCl were significantly decrease the mass of maize callus. The highest addition of callus weight was 210 mgs in control treatment, while the lowest is in 7500 mg/L with 3 mgs. The RAPD technique was utilized to characterize the genotype of maize callus. Out of five primers, only three primers can produce polymorphic bands named OPA10, OPB07 and OPC02. Taken together, the surviving callus of Bluto varians can be further developed as potential somaclone that has high tolerance to salt stress.
Sharma, Sweta K.
Jatropha curcas (Euphorbiaceae), a drought resistant non edible oil yielding plant, has acquired significant importance as an alternative renewable energy source. Low and inconsistent yields found in field plantations prompted for identification of high yielding clones and their large scale multiplication by vegetative propagation to obtain true to type plants. In the current investigation plantlets of J. curcas generated by axillary bud proliferation (micropropagation) using nodal segments obtained from selected high yielding genotypes were assessed for their genetic stability using Randomly Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) analyses. For RAPD analysis, 21 out of 52 arbitrary decamer primers screened gave clear reproducible bands. In the micropropagated plantlets obtained from the 2nd sub-culture, 4 out of a total of 177 bands scored were polymorphic, but in the 8th and 16th sub-cultures (culture cycle) no polymorphisms were detected. AFLP analysis revealed 0.63%, 0% and 0% polymorphism in the 2nd, 8th and 16th generations, respectively. When different genotypes, viz. IC 56557 16, IC 56557 34 and IC 56557 13, were assessed by AFLP, 0%, 0.31% and 0.47% polymorphisms were found, respectively, indicating a difference in genetic stability among the different genotypes. To the best of our knowledge this is the first report on assessment of genetic stability of micropropagated plantlets in J. curcas and suggests that axillary shoot proliferation can safely be used as an efficient micropropagation method for mass propagation of J. curcas. © 2011 Elsevier B.V.
Avaliação por RAPD de plantas de abacaxizeiro cultivar Smooth Cayenne derivadas do seccionamento do talo e cultura de tecidos Evaluation of pineapple plants cultivar Smooth Cayenne from peduncle division and tissue culture by RAPD
MARIA VITÓRIA CECCHETTI GOTTARDI
Full Text Available Foram coletadas, em área comercial da fazenda Córrego dos Bois, município de Canápolis -- MG, plantas de abacaxizeiro cultivar Smooth Cayenne, para serem avaliadas quanto à propagação pelo método do seccionamento do talo e cultura de tecidos, bem como análise por RAPD das mudas decorrentes destes dois processos de propagação. A propagação pelo seccionamento do talo foi eficiente na produção de mudas, tanto em quantidade como em qualidade, em um curto espaço de tempo, além de apresentar a mesma característica genotípica (análise por RAPD das plantas-matrizes de origem. Já no processo de produção de mudas por cultura de tecidos, não foi obtida uma quantidade suficiente de mudas que comprovasse a utilização de uma metodologia mais sofisticada. Além da perda por contaminação em laboratório de 70% do material em estudo, foi necessária a utilização de um longo período, aproximadamente 18 meses, para a obtenção das mudas. Na análise por RAPD das plantas decorrentes deste processo de propagação, foram observados padrões de bandas diferentes em algumas amostras, as quais podem estar relacionadas com uma possível variação somaclonal.Plants of pineapple Smooth Cayenne cultivar were collected from a commercial area, Córrego dos Bois farm, in Canápolis, state of Minas Gerais, to evaluate two different processes of propagation, peduncle division and tissue culture. These same plants were characterized by RAPD analysis. According to the two propagation method, the peduncle division was efficient in seedlings propagation, in quantity as well as in quality, at a short period of time, resulting the same phenotype and genetic characteristics (RAPD analysis from the matrix descent plants. In the tissue culture method, the quantity of seedlings obtained were not good enough that could prove the use of a sophisticated methodology. Besides loosing 70% of the material, it was necessary to expend a long period of time, at
Kumar, Sushil; Sharma, Ramavtar; Kumar, Vinod; Vyas, Govind K; Rathore, Abhishek
The Thar Desert, a very inhospitable place, accommodates only plant species that survive acute drought, unpredictable precipitation, and those can grow in the limited moisture of sandy soils. Capparis decidua is among one of the few plants able to grow well under these conditions. This species is highly exploited and has been naturally taken, as local people use it for various purposes like food, timber and fuel, although, no management or conservation efforts have been established. The present study was conducted in this arid area of Western Rajasthan (India) with the aim to obtain preliminary molecular information about this group of plants. We evaluated diversity among 46 samples of C. decidua using chemical parameters and random amplified polymorphic DNA (RAPD) markers. Fourteen chemical parameters and eight minerals (total 22 variables) of this species fruits were estimated. A total of 14 RAPD primers produced 235 band positions, of which 81.27% were polymorphic. Jaccard's similarity coefficients for RAPD primers ranged from 0.34 to 0.86 with a mean genetic similarity of 0.50. As per observed coefficient of variation, NDF (Neutral Detergent Fiber) content was found to be the most variable trait followed by starch and soluble carbohydrate. The Manhattan dissimilarity coefficient values for chemical parameters ranged between 0.02-0.31 with an average of 0.092. The present study revealed a very low correlation (0.01) between chemical parameters and RAPD-based matrices. The low correlation between chemical- and RAPD-based matrices indicated that the two methods were different and highly variable. The chemical-based diversity will assist in selection of nutritionally rich samples for medicinal purpose, while genetic diversity to face natural challenges and find sustainable ways to promote conservation for future use.
Full Text Available Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM. Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis. They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.
Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel
Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.
Asensio, Luis; González, Isabel; Fernández, Alicia; Rodríguez, Miguel A; Lobo, Esther; Hernández, Pablo E; García, Teresa; Martín, Rosario
A random amplified polymorphic DNA (RAPD) method was developed for the specific identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets. Using two different reaction primers (S1 and L1), RAPD analysis produced clear fingerprints from which the three fish species could be easily identified. This approach is rapid and reliable and offers the potential to detect fraudulent or unintentional mislabeling of these species in routine seafood authentication analysis.
Full Text Available The objectives of this work were to evaluate the frequency of polyembryony, and to identify zygotic and nucellar seedlings of Citrus volkameriana using RAPD. Twenty-five polyembryonic and eight monoembryonic seeds were cultivated in vitrofor six months. DNA from seedlings was extracted and used in combination with five RAPD primers to identify zygotic or nucellar origin of the seedlings. Environmental conditions of the year affected significantly (POs objetivos deste trabalho foram avaliar a freqüência da poliembrionia e indentificar os seedlings zigóticos e nucelares de Citrus volkameriana usando RAPD. Cultivaram-se in vitro 25 sementes poliembriônicas e 8 monoembriônicas, por seis meses. Extraiu-se o DNA dos seedlings e usou-se em combinação com cinco primers RAPD para identificar a origem zigótica e nucelar das plântulas. Os resultados mostraram que as condições ambientais do ano afetaram significativamente (P<0,05 as características morfológicas dos frutos e o número de embriões por semente. Os índices de sementes poliembriônicas variaram nos três anos de avaliação (30,9%, 44,8% e 54,4%. As características morfológicas não se correlacionaram com a poliembrionia. A cultura in vitro possibilita que todos os embriões de cada semente cresçam, favorecendo os seedlings identificados como zigóticos. Nas sementes poliembriônicas e monoembriônicas, 25,9% e 87,5% dos seedlings, respectivamente, originaram-se sexualmente. Nem todos os seedlings zigóticos foram produzidos por embriões localizados no micrófilo das sementes poliembriônicas.
Uso do Random Amplified Polymorphic DNA (RAPD no estudo populacional do Triatoma brasiliensis Neiva, 1911 Use of Random Amplified Polymorphic DNA (RAPD in the populational study of Triatoma brasiliensis Neiva, 1911
Érika C. Borges
Full Text Available Para o estudo de variabilidade genética em Triatoma brasiliensis, o principal vetor da doença de Chagas no Nordeste brasileiro, espécimes de três diferentes populações intradomiciliares foram analisados. Regiões do DNA genômico foram amplificadas utilizando dois iniciadores randômicos através da técnica de RAPD (Random Amplified Polymorphic DNA, visualizados em géis de poliacrilamida corados pela prata. Os perfis originados se mostraram bastante homogêneos quando comparados intrapopulacionalmente. Populações capturadas em duas regiões diferentes do Estado do Ceará também apresentaram homogeneidade entre si, mas, quando comparadas com a população proveniente do Piauí, foi possível diferenciá-las. Esses resultados, preliminares, indicam que o RAPD pode ser usado com sucesso nos estudos de variabilidade em triatomíneos, bem como sugerem a existência de variabilidade entre diferentes populações de T. brasiliensis pertencentes a uma mesma subespécie.We evaluated the genetic variability of Triatoma brasiliensis, the main vector of Chagas disease in Northeast Brazil, using specimens from three populations. Regions of genomic DNA were amplified by RAPD (Random Amplified Polimorphic DNA, using two primers. The products were visualized after polyacrylamide gel electrophoresis followed by silver staining. A dendrogram constructed through the Dice similarity coefficient allowed for separation of the tested specimens into three distinct groups. The populations captured in areas from Ceará State showed similar profiles, but different from that captured in Piauí State. Our results indicate that RAPD can be used successfully in triatomine studies and suggest the presence of genetic variability between different populations of T. brasiliensis.
Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood
Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.
Pramod Kumar Sairkar
Full Text Available Commercially important Commiphora species are drought-tolerant plants and they are leafless for most of the year. Therefore, it is necessary to develop some molecular marker for the identification. Intended for that, in the present study, species-specific, sequence-characterized amplified regions (SCAR markers were developed for proficient and precise identification of closely related species Commiphora wightii and C. myrrha, which may ensure the quality, safety, and efficacy of medicines made from these plants through adulterous mixing of these plants. Two species-specific RAPD amplicons were selected, gel-purified, cloned, and sequenced after screening of 20 RAPD primers. The sequence of 979 and 590 nucleotides (Genebank accession numbers K90051 and K90052 was used for development of 4 SCAR markers, namely, Sc1P, Sc1Pm, Sc2P, and Sc2Pm. Out of them, the Sc1Pm was specific for C. wightii, while Sc2P discriminated both the Commiphora species. These markers are first reported and will be useful for rapid identification of closely related Commiphora wightii and C. myrrha species.
Sairkar, Pramod Kumar; Sharma, Anjana; Shukla, N P
Commercially important Commiphora species are drought-tolerant plants and they are leafless for most of the year. Therefore, it is necessary to develop some molecular marker for the identification. Intended for that, in the present study, species-specific, sequence-characterized amplified regions (SCAR) markers were developed for proficient and precise identification of closely related species Commiphora wightii and C. myrrha, which may ensure the quality, safety, and efficacy of medicines made from these plants through adulterous mixing of these plants. Two species-specific RAPD amplicons were selected, gel-purified, cloned, and sequenced after screening of 20 RAPD primers. The sequence of 979 and 590 nucleotides (Genebank accession numbers K90051 and K90052) was used for development of 4 SCAR markers, namely, Sc1P, Sc1Pm, Sc2P, and Sc2Pm. Out of them, the Sc1Pm was specific for C. wightii, while Sc2P discriminated both the Commiphora species. These markers are first reported and will be useful for rapid identification of closely related Commiphora wightii and C. myrrha species.
Dias, Ana Karina Kerche; Aoki, Sérgio Moraes; Garcia, José Fernando; Nunes, Cáris Maroni
Cysticercosis is one of the most important zoonosis, not only because of the effects on animal health and its economic consequences, but also due to the serious danger it poses to humans. The two main parasites involved in the taeniasis-cysticercosis complex in Brazil are Taenia saginata and Taenia solium. Differentiating between these two parasites is important both for disease control and for epidemiological studies. The purpose of this work was to identify genetic markers that could be used to differentiate these parasites. Out of 120 oligonucleotide decamers tested in random amplified polymorphic DNA (RAPD) assays, 107 were shown to discriminate between the two species of Taenia. Twenty-one DNA fragments that were specific for each species of Taenia were chosen for DNA cloning and sequencing. Seven RAPD markers were converted into sequence characterized amplified region (SCAR) markers with two specific for T. saginata and five specific for T. solium as shown by agarose gel electrophoresis. These markers were developed as potential tools to differentiate T. solium from T. saginata in epidemiological studies.
Munhoz, R E F; Prioli, A J; Amaral, A T; Scapim, C A; Simon, G A
Diallel analysis was used to obtain information on combining ability, heterosis, estimates of genetic distances by random amplified polymorphic DNA (RAPD) and on their correlations with heterosis, for the popcorn varieties RS 20, UNB2, CMS 43, CMS 42, Zélia, UEM J1, UEM M2, Beija-Flor, and Viçosa, which were crossed to obtain all possible combinations, without reciprocals. The genitors and the 36 F(1) hybrids were evaluated in field trials in Maringá during two growing seasons in a randomized complete block design with three replications. Based on the results, strategies for further studies were developed, including the construction of composites by joining varieties with high general combining ability for grain yield (UNB2 and CMS 42) with those with high general combining ability for popping expansion (Zélia, RS 20 and UEM M2). Based on the RAPD markers, UEM J1 and Zélia were the most genetically distant and RS 20 and UNB2 were the most similar. The low correlation between heterosis and genetic distances may be explained by the random dispersion of the RAPD markers, which were insufficient for the exploitation of the popcorn genome. We concluded that an association between genetic dissimilarity and heterosis based only on genetic distance is not expected without considering the effect of dominant loci.
Telleria, J; Barnabé, C; Ayala, F J; Tibayrenc, M
We have tested a new genetic marker, RADES Probing (RADES-P), on a standard sample of 19 laboratory-cloned stocks of Trypanosoma cruzi, the agent of Chagas disease. This set of stocks, fully characterized using multilocus enzyme electrophoresis (MLEE) and random amplified polymorphic DNA (RAPD), is representative of this parasite's main genetic subdivisions. RADES-P consists in hybridizing RAPD profiles with probes composed of the products of random amplified differentially expressed sequences (RADES). The profiles thus obtained uncover only expressed coding sequences that are as well present on RAPD gels. Direct visual examination and the banding record show that these RADES-P profiles are different of, and not redundant with, both RAPD and RADES patterns obtained on the same set of stocks with the same primers. Phylogenetic character mapping (PCM) of the RADES-P polymorphism fairly confirms the known population structure and phylogenetic diversity of T. cruzi. This suggests that the impact of clonal evolution on T. cruzi has been predominant enough over the long term to carve the polymorphism of all types of DNA sequences, including polymorphisms of expressed coding sequences, although these sequences are subject to natural selection. Copyright © 2013 Elsevier B.V. All rights reserved.
Identificação e validação de marcadores microssatélites ligados ao gene Rpp5 de resistência à ferrugem-asiática-da-soja Identification and validation of microsatellite markers linked to the Rpp5 gene conferring resistance to Asian soybean rust
Thaiza Galhardo Silva Morceli
Full Text Available O objetivo deste trabalho foi identificar novos marcadores microssatélites, ligados ao gene Rpp5 de resistência à ferrugem-da-soja, e validar os marcadores previamente mapeados, para que possam ser utilizados em programas de seleção assistida por marcadores moleculares (SAM. Para tanto, uma população F2 com 100 indivíduos, derivada do cruzamento entre a PI 200526 e a cultivar Coodetec 208, suscetível à ferrugem, foi artificialmente infectada e avaliada quanto à sua reação de resistência à ferrugem. Marcadores microssatélites foram testados nos genitores e em dois "bulks" contrastantes, para a identificação de marcadores ligados. Dois novos marcadores, potencialmente associados à resistência, foram testados em plantas individuais, e se constatou que eles estão ligados ao gene Rpp5 e estão presentes no grupo de ligação N da soja. A eficiência de seleção foi determinada em relação a todos os marcadores ligados ao gene Rpp5, e a combinação entre os marcadores Sat_275+Sat_280 foi de 100%.The main objective of this work was to identify new microsatellite markers, linked to the Rpp5 resistance gene to Asian soybean rust, and to validate previously mapped markers for use in marker-assisted selection (MAS programs. To this end, a F2 population with 100 individuals, derived from crossing between PI 200526 and cultivar Coodetec 208, susceptible to rust, was artificially infected and evaluated for its reaction of resistance to rust. Microsatellite markers were tested on parents and in the two contrasting bulks to identifying linked markers. Two new markers, potentially associated with resistance, were tested in individual plants, and they were found to be linked to gene Rpp5 and to be present in the N linkage group of soybean. The selection efficiencies were determined for all markers linked to gene Rpp5, and the combination of the markers Sat_275+Sat_280 was 100%.
Zhang, Jie; Jiang, Yun; Xuan, Pu; Guo, Yuanlin; Deng, Guangbing; Yu, Maoqun; Long, Hai
Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D. villosum accessions. The two SCAR markers and FISH karyotype of D. villosum could be used for efficient and precise identification of D. villosum chromatin in wheat breeding.
Cerqueira-Silva, C B M; Santos, E S L; Conceição, L D H C S; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X
Little is known about the molecular genetic diversity of most Passiflora species. We used RAPD markers to evaluate the genetic diversity of 24 genotypes of the 'sleep' passion fruit (Passiflora setacea). Twelve primers generated 95 markers, 88% of which were polymorphic. The genetic distance estimated by the complement of the Dice index ranged from 0.29 (among accessions Ps-G1 and Ps-G13) to 0.69 (among accessions Ps-G21 and Ps-G23). Genotype grouping based on the UPGMA algorithm showed considerable variability among genotypes. We conclude that P. setacea has a broad genetic base that could be exploited in breeding programs.
Oct 5, 2016 ... Cluster analysis was constructed using DARwin program version 6.0. Forty eight (48) coconut individuals were clustered into three groups. Key words: Coconut palm (Cocos nucifera ... markers, cluster analysis, diversity. INTRODUCTION ... industry in Kenya (Muhammed et al., 2013). Furthermore, the slow ...
Jul 30, 2014 ... and attempt crosses for genetic improvement of the crop. Key words: Capsicum, genetic diversity, molecular characterization, simple sequence repeats (SSR) markers. INTRODUCTION. Chilli pepper (Capsicum annuum L.) (Solanaceae) has a chromosome number 2n=2x=24. It is indigenous to South.
Apr 3, 2012 ... Oilseed rape (Brassica napus L.) is an important oilseed crop worldwide. The objective of this research was to study the genetic diversity and relationships of B. napus accessions using simple sequence repeat (SSR). A set of 217 genotypes was characterized using 37 SSR markers of mapping on the B.
Full Text Available Background: Leishmaniasis, especially cutaneous leishmaniasis, is considered an important health problem in many parts of Iran including Kharve, Khorasan Razavi province. Cutaneous leishmaniasis is caused by various species of Leishmania, each having a different secondary host. Thus, identifying the parasites’ specie is of paramount importance for containment strategy planning. The morphological differentiation of Leishmania species is not possible, rendering the molecular methods as the sole means to this purpose. Therefore, to identify the causative agent of cutaneous leishmaniasis in Kharve, Random Amplified Polymorphic DNA-PCR (RAPD-PCR was used. Methods: The disease was first confirmed by direct smears. Samples were gathered from 22 patients with established cutaneous leishmaniasis. The samples were immediately cultured in NNN medium, followed by sub-culture in RPMI-1640. Afterwards, DNA was extracted and amplified using RAPD-PCR. Electrophoresis patterns from each isolate were compared with reference strains of Leishmania major (L. major and Leishmania tropica (L. tropica. Results: The results of this study indicated that the parasite causing cutaneous leishmaniasis in Kharve is L. tropica. Conclusion: It seems that L. tropica is the only causative agent of cutaneous leishmaniasis in Kharve, and RAPD-PCR is a suitable tool for Leishmania characterization in epidemiological studies.
Sarmast, Mostafa Khoshhal; Salehi, Hassan; Ramezani, Amin; Abolimoghadam, Ali Asghar; Niazi, Ali; Khosh-Khui, Morteza
Randomly amplified polymorphic DNA (RAPD) was used as a tool to assess the genetic fidelity of in vitro propagated Araucaria excelsa R. Br. var. glauca with explants taken from orthotropic stem along with their related mother plants after treatment with kinetin, 2iP, BA (0.02-0.26 mg/l) and TDZ (0.001-1 mg/l) to produce axillary shoots. TDZ and kinetin induced more shoot and higher length per explant. Results showed a total of 1,676 fragments were generated with 12 RAPD primers in micropropagated plants and their donor mother plants. The number of loci ranged from 6 in OPB 12-18 in OPY 07 with a size ranging from 250 bp in OPH 19-3500 bp in OPH 11. Cluster analysis of RAPD data using UPGMA (unweighted pair group method with arithmetic average) revealed more than 92% genetic similarities between tissue cultured plants and their corresponding mother plant measured by the Jaccard's similarity coefficient. Similarity matrix and PCoA (two dimensional principal coordinate analysis) resulted in the same affinity. Primers had shown 36% polymorphism. However, careful monitoring of tissue culture derived plants might be needed to determine that rooted shoots are adventitious in origin.
Full Text Available Genetic diversity of two wild Kalibaus, Labeo calbasu populations and one hatchery stock was studied using random amplified polymorphic DNA (RAPD method. The three 10–mer random primers (OPA01, OPB02 and OPC03 yielded a total of 26 reproducible and consistently scorable RAPD bands of which 15 (57.69% were considered as polymorphic (P95 indicating a high level of genetic variation in all the studied populations. Among the three populations, Padma population shows low level of genetic diversity (0.1238 compared to other two and it might be caused by habitat degradation in many ways which ultimately affects the genetic variation of Kalibaus. The UPGMA dendrogram based on Nei’s (1972 original measures of genetic distance (D indicated the segregation of two wild and hatchery populations of L. calbasu into two distinct clusters: the Hatchery and Padma populations produced one cluster whereas the Jamuna population belonged to another cluster. This indicates that hatchery brood stock is derived from Padma River. Nevertheless, the preliminary study revealed that RAPD technique could be an effective tool in the assessment of population genetic structure of Kalibaus.
Sandt, Christophe L.; Sockalingum, Ganesh D.; Toubas, Dominique; Aubert, Dominique; Lepan, Herve; Lepouse, Claire; Jaussaud, Maryse; Leon, Alain; Pinon, Jean-Michel; Manfait, Michel
Candida albicans is an opportunistic pathogen, generally though to be of endogenous origin, with however reported outbreaks. Epidemilogy of C. albicans has been studied so far by genotypic methods mainly, including the classical RAPD analysis. Albeit powerful, genotypic techniques are expensive, time consuming and complex to implement. FTIR spectroscopy is simple, rapid, inexpensive and an increasingly used technique for the identification of microorganisms. As a phenotypic method, it provides rapid whole cells 'fingerprinting' using few consumables and can detect very subtle differences between strains of the same species. In this study, C. albicans strains isolated from 50 patients from six hospital units were collected and studied by FTIR spectroscopy and RAPD-PCR. Discrimination of strains was computed using classification algorithms on selected features of the spectral data. Results from 10 patients, for whom iterative sampling was possible, are presented and discussed. Emphasis was laid on the reproducibility of dat for strain-level identification. FTIR analysis shows that (a) the C. albicans spectra were different from one patient to another, (b) seven patients exhibit each a homogeneous group while three patients display each two groups of strains. RAPD-PCR and FTIR analyses correlate quite well showing that FTIR spectroscopy could be a potential epidemiological tool in the control of nosocomial fungal infections.
Eder Jorge de Oliveira
Full Text Available O objetivo deste trabalho foi validar marcadores moleculares, previamente identificados como ligados ao sexo do mamoeiro, para utilização na seleção indireta em genótipos comerciais. Foram analisadas duas variedades do grupo Solo e dois híbridos do grupo Formosa, com utilização de 20 plantas por genótipo, quatro marcadores do tipo SCAR (Sequence Characterized Amplified Region e um RAPD (Random Amplified Polymorphic DNA. O RAPD BC210 permitiu a identificação de todas as plantas femininas e hermafroditas, o que revela grande potencial para ser usado na seleção assistida em alguns dos genótipos mais cultivados no Brasil. Os marcadores do tipo SCAR não permitiram a identificação correta do sexo dos genótipos, pois detectou-se a presença de falso-positivos e falso-negativos nas análises.The objective of this work was the validation of previous discovered sex related molecular markers of papaya, aiming at the indirect selection of Brazilian commercial genotypes. Two varieties of the Solo group and two hybrids of the Formosa group (20 plants for genotype, four SCAR (Sequence Characterized Amplified Region and one RAPD (Random Amplified Polymorphic DNA markers were used. All hermaphrodite and female plants were correctly predicted by RAPD BC210, showing its high potential for marker assisted selection in important commercial genotypes used in Brazil. The SCAR markers did not show the true sex identification of these genotypes, revealing the presence of false positives and negatives in the analyses.
Genetic variation between susceptible and non-susceptible snails to Schistosoma infection using random amplified polymorphic DNA analysis (RAPDs Variação genética entre moluscos susceptíveis e não susceptíveis à infecção pelo Schistosoma através da análise do DNA polimórfico amplificado aleatóriamente (RAPDs
Abdel-Hamid Zaki ABDEL-HAMID
Full Text Available Susceptibility of snails to infection by certain trematodes and their suitability as hosts for continued development has been a bewildering problem in host-parasite relationships. The present work emphasizes our interest in snail genetics to determine what genes or gene products are specifically responsible for susceptibility of snails to infection. High molecular weight DNA was extracted from both susceptible and non-susceptible snails within the same species Biomphalaria tenagophila. RAPD was undertaken to distinguish between the two types of snails. Random primers (10 mers were used to amplify the extracted DNA by the polymerase chain reaction (PCR followed by polyacrylamide gel electrophoresis (PAGE and silver staining. The results suggest that RAPD represents an efficient means of genome comparison, since many molecular markers were detected as genetic variations between susceptible and non-susceptible snails.A susceptibilidade de moluscos à infecção por certos trematódeos e a sua capacidade como hospedeiro para o contínuo desenvolvimento é o problema mais deslumbrante nas relações parasita hospedeiro. O presente trabalho, focaliza nosso interesse na genética dos moluscos para determinar quais genes ou produtos gênicos são especificamente responsáveis pela susceptibilidade do molusco à infecção. DNA de alto peso molecular, foi extraído de ambos moluscos susceptíveis e não susceptíveis da espécie Biomphalaria tenagophila. Iniciadores aleatórios com 10 pares de bases foram usados na amplificação aleatória (RAPD de ambos os DNAs e análise por eletroforese em gel de poliacrilamida e coloração com prata. Os resultados mostram que a amplificação aleatória do DNA representa um eficiente caminho para a comparação dos genomas desde que marcadores moleculares foram detectados como variantes genéticos entre os moluscos susceptíveis e não susceptíveis.
Souza, I G B; Valente, S E S; Britto, F B; de Souza, V A B; Lima, P S C
We evaluated genetic variability of mango (Mangifera indica) accessions maintained in the Active Germplasm Bank of Embrapa Meio-Norte in Teresina, Piauí, Brazil, using RAPDs. Among these accessions, 35 originated from plantings in Brazil, six from the USA and one from India. Genomic DNA, extracted from leaf material using a commercial purification kit, was subjected to PCR with the primers A01, A09, G03, G10, N05, and M16. Fifty-five polymorphic loci were identified, with mean of 9.16 ± 3.31 bands per primer and 100% polymorphism. Application of unweighted pair group method using arithmetic average cluster analysis demonstrated five genotypic groups among the accessions examined. The genotypes Rosa 41, Rosa 48 and Rosa 49 were highly similar (94% similarity), whereas genotypes Sensation and Rosa 18 were the most divergent (only 7% similarity). The mango accessions were found to have considerable genetic variability, demonstrating the importance of analyzing each genotype in a collection in order to efficiently maintain the germplasm collection.
Scataglini, M A; Confalonieri, V A; Lanteri, A A
RAPD technique provides useful information on the geographic origin and dispersal of the boll weevil Anthonomus grandis in South America. Nine populations from Argentina, Brazil, Paraguay, Mexico and USA were analyzed. Weevils were captured on native plants (Misiones province, Argentina) and on cotton cultures, except the sample from the United States (USDA laboratory-reared colony). A sample of the 'Peruvian square weevil', A. vestitus, from Ecuador, was included in the analysis in order to compare interspecific variation. The four primers used in the analysis revealed 41 'anonymous loci'. The neighbor-joining tree based on Nei's distances and values of Nm (migrants per generation), indicate that genetic similarity between samples from Tecomán (Mexico) and Puerto Iguazú (Argentina), is higher than among remaining South American populations. This result supports an hypothesis of natural occurrence of the boll weevil in South America, prior to extensive cotton cultivation. Population outbreaks of the species would be associated with increase of agricultural lands.
Jessica Jeyanthi James Antony
Full Text Available This study was conducted to detect the morphological, histological and molecular diff erences in the second generation of the PVS2 cryopreserved Dendrobium Bobby Messina [DBM] (18 months old culture plantlets. Morphological analyses indicated that similarities and diff erences in cryopreserved DBM plantlets comparing to control stock culture based on selected morphological criteria. Morphological criteria, such as root length, number of shoot per explant and shoot length displayed diff erences, while the other three criteria, leaf diameter, leaf length and PLBs size were similar in cryopreserved compared to the control stock culture plant. Higher amount of homogenous cell population and denser cytoplasm were observed in cryopreserved PLBs compared to control stock culture PLBs based on histological analysis. This suggests the existance of somatic embryogenesis development mechanism taking place during the recovery and regeneration of the cryopreserved PLBs. However, RAPD analyses based on 10 primers indicated that cryopreserved DBM regenerated from vitrifi cation method generated a total of 20 to 39.9% polymorphic bands as compared to stock culture indicating potential somaclonal variation. Hence, an increase percentage of polymorphics bands in cryopreserved plantlets 18 months post cryopreservation as compared to previous report of 10% polymorphic bands in cryopreserved DBM 3 months post cryopreservation.
Aguado, V; Vitas, A I; García-Jalón, I
The incidence of Listeria monocytogenes in a vegetable processing plant was investigated over a 23-month period. Frozen ready-to-eat vegetable samples, well as the plant environment, were sampled. The molecular subtyping techniques, Random Amplified Polymorphic DNA (RAPD) and Restriction Endonuclease Analyses (REA), were performed to help investigate the origin and routes of Listeria dissemination. The low and sporadic incidence of L. monocytogenes made it impossible to establish an epidemiological sequence in the processing plant, though a case of cross-contamination between tomato and ratatouille was detected. Listeria innocua subtyping, however, allowed us to determine the prevalence of several strains in vegetables, and their presence on machinery samples suggested the possibility of cross-contamination during processing. The low incidence of L. monocytogenes indicated that the risk of listeriosis transmission by vegetable consumption is low. On the other hand, the isolation of the same strain of L. innocua in several surveys pointed out the risk of colonisation on surfaces and machinery. The persistence of Listeria spp. is a cause for concern as can lead to future contamination of vegetables processed in the plant and to a possible increased risk for health. Therefore, periodic controls for the presence of Listeria spp. and a further review of the cleaning and disinfection procedures used in frozen vegetable plants are recommended.
Laila Hanum; Rina Sri Kasiamdari; Santosa; Rugayah
Genetic relatedness among duku, kokosan, and pisitan from Indonesia were investigated using random amplified polymorphic DNA (RAPD) markers. Eleven primers (OPA-01, OPA-02, OPA-10, OPB-07, OPB-11, OPB-12, OPB-15, OPT-16, OPU-14, OPU-19, and OPU-20) were used for amplification and yielded a total of 174 DNA bands, of which 167 were polymorphic. Primer OPA-10, OPB-11, OPB-12, OPB-15, and OPU-19 produced all of the polymorphic DNA bands. The size of the amplified DNA fragments ranged from 41-154...
Della Vecchia P.T.
Full Text Available Seed market is becoming global and globalization is growing very fast. To compete favourably in this new global seed world, quality and cost are and will be certanly the key issues. High seed quality can only be obtained by a thorough control of the entire seed production process, step by step from planning to final delivery. That requires science, technology, expertise, experience, good management and certanly, the most important, an absolute and unconditional commitment with quality. Seed testing for quality assurance is one important step in the process of production of high quality seed. In the late years a considerable amount of research has been published, particularly on the use of some Polymerase Chain Reaction DNA based new technologies (RAPD, microsatelites, AFLP for genetic purity determinations in seed testing. As far as we know, no Brazilian seed company is using, on regular basis, RAPD or other molecular marker techniques in the determination of genetic purity in seed testing. Most of these are using morphological or physiological traits expressed by seed, seedling or mature plant and/or electrophoresis of seed or seedling proteins/isoenzymes for that purpose. Main reasons for that are: DNA molecular marker techniques are relatively new; lack of specialized personnel to run DNA molecular marker assays on routine basis; higher cost/sample when compared to proteins/isoenzymes electrophoresis.
Daniel W. H. Robarts
Full Text Available In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR, random-amplified polymorphic DNA (RAPD, and amplified fragment length polymorphism (AFLP to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use. highly variable marker with inherent biological significance.
Caldwell, Jane C; Chiale, Pablo A; Gonzalez, Mario D; Baranchuk, Adrian
We present 2 cases of the slow-fast form of AVNRT with initially narrow QRS complexes followed by sudden unexpected transition to persistently wide QRS complexes due to aberrant intraventricular conduction. Introduction of a properly timed extrastimulus in one case and critical oscillations in cycle length due to short-long coupling in the second case set the stage for the initial bundle branch block. However, persistence of the aberrancy pattern once the initial event abated was maintained by the "linking" phenomenon. Delayed, retrograde concealed activation from the contralateral bundle branch perpetuated the initial bundle branch block. PMID:23840106
Sergio Delmar dos Anjos e Silva
Full Text Available O cultivo do mirtilo está em expansão no Brasil, em especial em regiões de clima temperado, onde há grande demanda em relação a cultivares adaptadas às condições edafoclimáticas regionais. O objetivo deste trabalho foi caracterizar genótipos de mirtilo do programa de melhoramento da Embrapa Clima Temperado, utilizando marcadores moleculares do tipo RAPD e SSR. Foram caracterizados 40 genótipos de mirtilo por RAPD e oito cultivares por microssatélites. Os nove primers utilizados na técnica de RAPD geraram 89 marcadores. A similaridade genética entre os genótipos variou de 64 a 89%. Utilizando a similaridade média (66%, foram obtidos quatro grupos. Foram gerados 11 marcadores a partir de três pares de primers de microssatélites. A similaridade genética entre as cultivares variou de 25 a 75%. Com similaridade média (42,4%, foram obtidos três grupos. Com apenas três pares de primers de SSR, foi possível definir o padrão das oito cultivares de mirtilo, revelando a eficiência da técnica de microssatélite na caracterização de genótipos dessa espécie. Esses resultados revelam a eficiência dos marcadores tipo RAPD e SSR na caracterização de genótipos de mirtilo. Entretanto, os marcadores tipo microssatélites geram resultados mais precisos, sendo os mais recomendados para uso em programas de melhoramento e identificação de cultivares.The blueberry crop planting area is increasing in Brazil, especially in Temperate Climate Zones, generating demands relating to suitable cultivars adapted to regional climate and soil conditions. This work aimed to characterize blueberry genotypes from Embrapa Clima Temperado breeding program, using RAPD and SSR molecular markers. There were characterized 40 blueberry genotypes using RAPD and 8 cultivars using SSR molecular markers. The 9 RAPD primers generated 89 markers. The genetic similarity ranged from 64 to 89%. Through the average similarity (66%, it was possible to identify four
Franciele Cristina Kagueyama
Full Text Available Malassezia pachydermatis (M. pachydermatis is a fungus of importance in human and veterinary medicine. Although a part of the normal microbiota, it can sometimes be present in its pathogenic form, particularly causing otitis and dermatitis in animals. Among human beings, it mainly affects immune compromised patients and newborns, causing simple pustulosis, seborrheic dermatitis, tinea versicolor or fungemia. This study aimed to analyze the genomic polymorphism in M. pachydermatis samples isolated from Canis familiaris (domestic dog, Felis catus (domestic cat, and Myrmecophaga tridactyla (giant anteater. Two hundred and fourteen samples were collected and cultured in Sabouraud agar with chloranphenicol (100mg L-1 and incubated at 37 °C for a period of 7 to 10 days. One hundred and sixty six samples that appeared morphologically comparable to yeast cultures were processed for DNA extraction and PCR was performed for a specific region in the Internal Transcribed Spacer (ITS of M. pachydermatis. Among these, seven (4.21% were negative and 159 (95.79% were positive. Of the 159 positive samples, 102 (64.15% were from animals with clinical signs and 57 (35.85% without clinical signs. Fifty-seven samples were selected at random for RAPD-PCR based genotyping and distributed into four genetic groups. Types I and II were more frequent in animals with clinical signs while type III was frequent in healthy animals. Type IV occurred evenly across animals with or without clinical signs. These results indicate differences in pathogenicity of the fungus based on the genotype.
Full Text Available Eight isolates of Sclerotium rolfsii from four strategically geographical sites of Bangladesh were characterized and their cultural properties like average linear mycelial growth, colony colour, colony consistency, growth pattern and sclerotia formation were studied. Isolates varied in mycelial growth and other growth characteristics and were grouped into three. The highest linear growth was displayed by S8. DNA concentration of eight isolates varied from 1150-7200 ng/μl. DNA fingerprinting by RAPD prompted the grouping of isolates. Selected 3 primers generated 20 bands with size ranging from 100-1500 bp. Out of the 20 bands, 9 bands (45% were polymorphic and 11 bands (55% were monomorphic among the eight isolates of Sclerotium rolfsii. The co-efficient of gene differentiation (Gst was 1.000 reflecting the existence of high level of genetic variations among the 8 isolates. The lowest genetic distance and highest inter isolate similarity was found in S1 and S2 which would be homogeneous. The highest genetic distance and lowest inter isolate similarity found in S3, S7 and S3, S8 pair which would be most divergent isolates. The cluster analysis also revealed that S3, S7 and S8 belong to different clusters. All five varieties of eggplant and tomatoes were graded as susceptible when inoculated with eight isolates. Plant mortality 93.33% was recorded in S4, S6 and in S8. Considering the isolate factor the most virulent isolate would be S8 whereas the less virulent isolate would be S2 and S7. Host plant of S8 was tomato collected from Thakurgaon. S2 and S7 were collected from BAU farm and Dinajpur and host plants were lentil and tomato respectively. It is evident that Sclerotium rolfsii from Thakurgaon on host tomato is more virulent.
Full Text Available The yeast microbiota occurring on different varieties of grapes grown in cool-climate is not completely researched. Therefore, its identification is important to research. On the other hand, yeasts occurring in these fruits can be potentially used as starter cultures to obtain particularly demanded features in the production of wine. In addition, rapid methods for yeast identification allow to eliminate the contamination with pathogenic yeasts, which could cause the loss of wine production. The aim of the study was to isolate and identify the yeasts occurring on the surface of the different varieties of white and red grapes, grown in cool-climate of Poland. Also, the aim was to compare the qualitative and quantitative composition of yeasts on the tested grapes. The 84 cultures of yeasts were isolated, that were initially macroscopic and microscopic analyzed and the purity of cultures was rated on the WL medium. Identification of yeasts by PCR-RAPD was carried using the M13 primer. In the PCR-RFLP method ITS1 and ITS4 primers, as well as restriction enzymes HhaI, HinfI, HaeIII, were used. Preliminary identification of yeasts by standard methods produced results very different from the results obtained by molecular methods. Among the isolated microorganisms yeasts were dominating, but bacteria and molds were also present. Using the PCR-RAPD method most strains of yeasts were identified. Yeast microflora of different varieties of white and red grapes was very similar as the same species of yeasts were identified. Yeasts of the genus Saccharomyces were present in all varieties of grapes. The Rhodotorula mucilaginosa, Saccharomyces cerevisiae, Metschnikowia pulcherrima, Rhodotorula minuta, Pichia kluyveri, Hanseniaspora uvarum and Rhodotorula mucilaginosa were identified by PCR-RAPD. 4 of the 33 tested strains of yeasts were identified by PCR-RFLP. By PCR-RAPD only Hanseniaspora uvarum was identified. The quantity and quality of microorganisms living
Chen, William Y. C.; Wu, Susan Y. J.; Yan, Catherine H.
The notion of noncrossing linked partition arose from the study of certain transforms in free probability theory. It is known that the number of noncrossing linked partitions of [n+1] is equal to the n-th large Schroder number $r_n$, which counts the number of Schroder paths. In this paper we give a bijective proof of this result. Then we introduce the structures of linked partitions and linked cycles. We present various combinatorial properties of noncrossing linked partitions, linked partit...
R. de la Puente
Full Text Available A previous Lens genetic map was improved by adding 31 molecular genetic markers, reaching a total of 190 markers with undistorted segregation. Data were obtained from the segregational analysis of 113 F2 plants generated from a single hybrid of Lens culinaris ssp. culinaris × L. c. ssp. orientalis. The added markers are predominantly codominant (15 SSRs, five CAPSs, four presence-absence polymorphisms, three length polymorphisms, two RAPDs, and two SRAPs. At a LOD score of 3.0, the 190 markers were grouped into eight linkage groups (LG covering 2,234.4 cM, with an average distance between markers of 12.28 cM. This linkage map has reduced the numbers of linkage groups from ten in the previous map to eight. Most of the added markers must be functional markers since primers were mostly designed to amplify transcribed sequences. Some of the amplicons were sequenced to test if they were functional markers. One of the sequences showed homology with the Pisum TFL1a gene, involved in the transition from vegetative to flowering stages. This lentil gene was located in the LG 1 thanks to the presence of a polymorphic microsatellite in the first intron of the gene. Since L. culinaris ssp. orientalis is the primary source of additional genetic variability for lentil, this improved map could help in the use of such variability in lentil breeding programs.
Dec 4, 2013 ... Molecular analysis was performed by using nine random markers in random amplified polymorphic DNA ... MATERIALS AND METHODS. Molecular .... Molecular biological studies of plants, such as the PCR techniques ...
Full Text Available Authentication of Strychnos ligustrina Bl. had been performed at molecular level (DNA with Random Amplified Polymorphic DNA (RAPD method, based on the amplification of random DNA fragments by Polymerase Chain Reaction (PCR with a single arbitrar primer. The aim of this research was obtaining similar banding patterns between DNA of plant Strychnos ligustrina Bl. and DNA of it lignum on local market. Strychnos ligustrina Bl. was determined by UPT Balai Konservasi Tumbuhan Kebun Raya Purwodadi and plants sold as Strychnos ligustrina Bl. were collected as lignum from traditional market at Wonokromo, Rungkut, Genteng, Benowo dan Pabean. DNA from these plants were extracted by modified Cetyltrimethylammonium bromide (CTAB method and amplified by RAPD method. Amplification had been performed by primer OPO-4 had shown banding patterns on the gel electrophoresis which banding patterns were shown by Strychnos ligustrina Bl. and plants sold as Strychnos ligustrina Bl. on Benowo. Based on this early result, we assume that plants sold as Strychnos ligustrina Bl. on Benowo has closely genetic relationship with Strychnos ligustrina Bl.
Full Text Available Randomly amplified polymorphic DNA (RAPD-PCR was applied with ten random 10-mer primers to examine the molecular diversity among methicillin resistant Staphylococcus aureus (MRSA strains in the hospitals and to investigate the epidemiological spread of these strains between different hospitals. The main objective of the study was to identify appropriate primers, which successfully established the clonality of MRSA. Three of the primers yielded particularly discriminatory patterns and they were used to perform the RAPD analysis which revealed different bands ranging from 200 to 1500 bp. Dendogram was created by the un-weighted pair group method using arithmetic (UPGMA average clustering and it was constructed based on the combination results of the new primers (S224, S232 and S395 which represented a novel approach for rapid screening of the strains and also provided the opportunity for monitoring the emergence and determining clonal dissemination of MRSA strains between the hospitals. Dendogram generated two main groups (Group I and II with three clusters (A, B and C and indicated that the strains isolated from the same hospital were closely related and they placed together in the same group. This technique could be of attractive use in controlling the sources and routes of transmission, tracking the spread of strains within hospital and between the hospitals, and especially preventing the nosocomial infections caused by the MRSA.
Full Text Available Este trabalho teve como objetivo caracterizar a diversidade genética, através do marcador molecular RAPD, dos porta-enxertos da Coleção de Citros da Estação Experimental Agronômica da Universidade Federal do Rio Grande do Sul (EEA/UFRGS e acessos de porta-enxertos cítricos coletados em viveiristas da Região do Vale do Rio Caí do estado do Rio Grande do Sul. Para tanto, coletaram-se folhas de nove porta-enxertos cítricos da EEA/UFRGS e de dez acessos de trifoliata (Poncirus trifoliata de viveiristas. Com o uso de nove seqüências inicializadoras, foi possível separar os porta-enxertos cítricos em dois grupos principais, um formado pelo limoeiro ?Cravo? e outro pelo trifoliata e seus híbridos, apresentando alta dissimilaridade genética entre os grupos. Marcadores moleculares RAPD foram eficientes para caracterizar variedades de porta-enxertos de citros e para separar o porta-enxerto P. trifoliata de seus híbridos podendo serem utilizados para caracterização de plantas matrizes, análise de variabilidade genética entre genitores em programas de melhoramento genético de porta-enxertos e para identificar a origem sexual ou nucelar de mudas de trifoliata em viveiros comerciais.
Lopes, H M; Bastos, C S; Boiteux, L S; Foresti, J; Suinaga, F A
Helicoverpa armigera is the most significant pest of agriculture in Asia, Europe, Africa, and Australasia, causing damage to crops greater than US$2 billion annually and until 2013 it was not detected in Brazil. Helicoverpa zea is restricted to the American continent and is important to corn and a secondary pest of cotton and tomatoes. The wide range of crops exploited by H. armigera (mainly cotton, soybeans, chickpea, and corn), the possible mating between these species can promote population shifts, that could be assessed by RAPD-PCR technique. Therefore, the aim of this study was to determine the genetic diversity of H. armigera and H. zea populations by RAPD-PCR analysis. The most important result was the clustering of one H. armigera population in a group predominantly formed by H. zea. It could indicate a possible occurrence of an interspecific cross between these species. This is a concern to Brazilian agriculture due to the possibility of selection of hybrids well adapted to the American environment, which would be inherited from H. zea. The other noxious fact is the possible development of new biotypes resistant to insectides or Bt toxins expressed in transgenic crops, came from H. armigera gene pool.
Matthiessen, Christian Wichmann; Knowles, Richard D.
The European Round Table of Industrialists identified in the 1980ies 14 missing links in the transportation network of the continent. Three of them were found around the Danish island of Zealand. One link is within the nation, the other two are between nations. One link connects heavy economic....... They concentrate traffic flows and create strong transport corridors. They are the basis of new regional development regimes. “Ferries connect systems, fixed links unite systems”....
Full Text Available Variasi genetik ikan batak yang dikoleksi dari daerah Asahan, Aek Sarul (Tarutung, Aek Sirambe, Bahorok (Sumatera Utara, dan Sumedang (Jawa Barat telah diteliti menggunakan metode Random Amplified Polymorphism DNA (RAPD. Primer yang digunakan untuk analisis adalah OPC-01 dan OPC-02. Dari 2 primer yang digunakan hanya OPC-01 yang menunjukkan hasil PCR yang memberikan Polimorfisme. Berdasarkan nilai rata-rata heterozigositas (0,08—0,1250 dan persentase lokus polimorfik (22%—33% secara umum menunjukkan bahwa keragaman genetik ikan batak yang dianalisis tergolong rendah. Hasil analisis RAPD juga menunjukkan bahwa secara genetik tidak ada perbedaan yang nyata di antara kelima populasi ikan batak. The genetic variabilities of Tor soro collected from Asahan, Aek Sarula (Tarutung, Aek Sirambe, Bahorok (North Sumatra, and Sumedang (West Java were examined by RAPD. Primers used for analysis were OPC-01 and OPC-02. From both of the primers, only OPC-01 showed polymorphism. Based on the heterozigosity (0.08—0.1250 and percentage of polimorphyc locus value (22%—33%, indicated that genetic variation of Tor soro of North Sumatra was low. The RAPD analisis showed that no significantly difference among five population.
Hamal, Petr; Hanzen, Juraj; Horn, Frantisek; Trtkova, Jitka; Ruskova, Lenka; Vecerova, Renata; Ruzicka, Filip; Vollekova, Anna; Raclavsky, Vladislav
A case report of ventriculoperitoneal shunt infection caused by Candida lusitaniae in a 6-year-old patient with cerebral astrocytoma and obstructive hydrocephalus is presented briefly with emphasis on the course of antifungal treatment. Seven isolates recovered subsequently from the cerebrospinal fluid were studied retrospectively. To confirm identity, isolates were typed using pulsed-field gel electrophoresis and melting curve of random amplified polymorphic DNA (McRAPD). Further, the ability to form biofilm and its susceptibility to systemic antifungals were evaluated. Using McRAPD, identity of C. lusitaniae isolates showing slight microevolutionary changes in karyotypes was undoubtedly confirmed; successful application of numerical interpretation of McRAPD for typing is demonstrated here for the first time. The strain was also recognized as a strong biofilm producer. Moreover, minimum biofilm inhibitory concentrations were very high, in contrast to low antifungal minimum inhibitory concentrations of isolates. It can be concluded that McRAPD seems to be a simple and reliable method not only for identification but also for typing of yeasts. A ventriculoperitoneal shunt colonized by C. lusitaniae was revealed as the source of this nosocomial infection, and the ability of the strain to form biofilm on its surface likely caused treatment failure.
Full Text Available The aim of this study was to assess the genotoxic effects of environmental chemicals on residents living near landfills. The study was based on samples of amniotic fluid from women living in the intensely polluted areas around the Campania region of Italy compared to a nonexposed control group. We evaluated the genetic effects that this amniotic fluids collected in contaminated sites had on Paracentrotus lividus embryos. DNA damage was detected through changes in RAPD (Random Amplified Polymorphism DNA profiles. The absence of the amplified DNA fragments indicated deletions in Paracentrotus lividus DNA exposed to the contaminated amniotic fluids when compared to equal exposure to uncontaminated fluids. These results show the ability of RAPD-PCR to detect and isolate DNA sequences representing genetic alterations induced in P. lividus embryos. Using this method, we identified two candidate target regions for DNA alterations in the genome of P. lividus. Our research indicates that RAPD-PCR in P. lividus embryo DNA can provide a molecular approach for studying DNA damage from pollutants that can impact human health. To our knowledge, this is the first time that assessment of DNA damage in P. lividus embryos has been tested using the RAPD strategy after exposure to amniotic fluid from residents near waste landfill sites.
Fabiana Augusta Santiago Beltrão
Full Text Available With the objective to analyze the genetc variability in natural populations, 14 accesses of Manihot had been studied pseudglaziovii, collected in the state of the Paraíba, in the microregion Curimataú Paraibano, beyond an access of M. esculenta Cranz (cassava and a natural hybrid between these two species. Five plants of each access had been multiplied through statue and after that cultivated in an experimental area in standardized conditions, to have a homogeneous exteriorizacion of each genotype. The otimizaçãocion of the protocol of extraction of the DNA of some accesses of maniçoba and of two similar species of forager interest and to verify the genetic variability through the amplification with molecular markers RAPD saw PCR. Two methods of extraction of the DNA had been tested. The extraction protocol using detergent CTAB made possible to get clean products, less viscous and oxidized. In the analysis of genetic variability they had been used in a total of 10 starters (primers, and only 3 had produced bands, starter OPD2, OPD3 and OPD8 presented greater percentage of polymorphism followed of the OPD2, with values of 30,7% and 42,8%, respectively. These primers can discriminate molecular differences between the accesses of maniçoba and two similar species.
José Maria D. Gaia
Full Text Available A espécie conhecida como pimenta-de-macaco (Piper aduncum L. possui grande potencial para exploração econômica em função da comprovada utilidade do seu óleo essencial na agricultura e saúde humana. O objetivo deste trabalho foi caracterizar a diversidade genética de populações naturais dessa planta. Um total de dezoito acessos da planta, provenientes de quatro procedências da Amazônia Brasileira, foi examinado por meio de locos de DNA, gerados por análise RAPD (polimorfismo de DNA amplificado ao acaso. O estudo evidenciou a existência de real diversidade entre as populações examinadas, sendo provável que dentro das localidades investigadas, os padrões da diversidade genética acompanhem os padrões de distribuição geográfica.The species known as pimenta-de-macaco (Piper aduncum L. has great economic explotation potential based on the proved usefulness of the essential oil in agriculture and human health. The genetic diversity of their natural populations was characterized. A total of eighteen accessions of the plant, obtained from four different origins in the Brazilian Amazon, was examined by means of DNA loci, generated by RAPD analysis. Real genetic diversity was observed between the analyzed populations and it appear that the patterns of the genetic diversity follow the patterns of the geographical distribution.