Polymorphic Simple Sequence Repeat Markers Research Articles

Molecular Marker Based Discrimination Study of Commiphora Species Distributed in India

Commiphora agallocha, C. caudata, C. stocksiana and C. wightii are the four Commiphora species reported from India of which C. wightii has been extensively used in Ayurveda for its excellent medicinal values. Destructive utilization of these species needs to be checked by means of efficient conservation efforts. The present study is an attempt to species discrimination of Commiphora using analysis of molecular markers. Random Amplified Polymorphic DNAs (RAPD) and Inter Simple Sequence Repeats (ISSR) markers were used for the study considering the fact that no or very little genomic information is available in the genus. One hundred and twenty RAPD and 25 ISSR primers were screened initially from which 25 RAPD and 18 ISSR primers were used for final analysis. RAPD primers amplified 264 fragments from which 18 were monomorphic, 109 were polymorphic and 137 were unique, whereas 18 ISSR markers amplified 132 loci out of which 37 loci were polymorphic, 11 were monomorphic and 84 were unique. The cluster analysis indicated that C. agallocha was genetically distant from the other three species i.e., C. wightii, C. stocksiana and C. caudata. Both RAPD and ISSR markers were able to generate 62 and 42 species specific markers, respectively. The specific molecular markers identified can be converted to Sequence Characterised Amplified Regions which would be helpful for molecular taxonomic study. This investigation would also be helpful to develop an insight into the genetic relationship of the limited number of Commiphora species distributed in India.

Dynamic Changes in the Rice Blast Population in the United States Over Six Decades.

Rice blast disease caused by Magnaporthe oryzae is one of the most destructive diseases of rice. Field isolates of M. oryzae rapidly adapt to their hosts and climate. Tracking the genetic and pathogenic variability of field isolates is essential to understand how M. oryzae interacts with hosts and environments. In this study, a total of 1,022 United States field isolates collected from 1959 to 2015 were analyzed for pathogenicity toward eight international rice differentials. A subset of 457 isolates was genotyped with 10 polymorphic simple sequence repeat (SSR) markers. The average polymorphism information content value of markers was 0.55, suggesting that the SSR markers were highly informative to capture the population variances. Six genetic clusters were identified by both STRUCTURE and discriminant analysis of principal components methods. Overall, Nei's diversity of M. oryzae in the United States was 0.53, which is higher than previously reported in a world rice blast collection (0.19). The observed subdivision was associated with collection time periods but not with geographic origin of the isolates. Races such as IC-17, IE-1, and IB-49 have been identified across almost all collection periods and all clusters; races such as IA-1, IB-17, and IH-1 have a much higher frequency in certain periods and clusters. Both genomic and pathogenicity changes of United States blast isolates were associated with collection year, suggesting that hosts are a driving force for the genomic variability of rice blast fungus.

Genetic structure and relationships within and between cultivated and wild korarima [Aframomum corrorima (Braun) P.C.M. Jansen] in Ethiopia as revealed by simple sequence repeat (SSR) markers

BackgroundKorarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a spice crop native to Ethiopia. Understanding the extent and partitioning of diversity within and among crop landraces and their wild relatives is among the first steps in conserving and measuring their genetic potential. The present study is aimed at characterizing the population genetic structure and relationships between cultivated and wild korarima in the southwestern part of Ethiopia.ResultsWe analyzed a total of 195 individuals representing seven wild and fourteen cultivated populations. Eleven polymorphic simple sequence repeat (SSR) markers were used. We observed a total of 53 alleles across the eleven loci and individuals. In total, 32 alleles were detected in the cultivated populations, whereas 49 alleles were detected in the wild populations. We found higher genetic diversity in wild populations than in the cultivated counterpart. This result implies the potential of wild korarima as a possible source for novel alleles contributing to the improvement of cultivated korarima. Analysis of molecular variance (AMOVA) showed significant but low differentiation between cultivated and wild korarima populations. Similarly, neighbour-joining and STRUCTURE analyses did not group cultivated and wild populations into two distinct clusters. The lack of clear differentiation between cultivated and wild populations could be explained by historical and contemporary gene flow between the two gene pools.ConclusionThe 11 SSR loci developed in this study could be employed to examine genetic diversity and population structure of korarima in other countries as well as other Aframomum species. From the five administrative zones considered in this study, the Bench-Magi and Sheka zone showed populations with high genetic diversity, and these populations could be used as a potential starting point for in-situ and ex-situ germplasm conservation and korarima improvement through breeding programs after proper agronomic evaluation.

Construction of a genetic linkage map based on RAPD, AFLP, and SSR markers for tea plant (Camellia sinensis)

Based on double pseudo-testcross theory, a population of 79 F1 clones, which was derived from a crossing of two tea cultivars using a Japanese tea cultivar “Fushun” (Camellia sinensis) as female parent and a Korean tea cultivar “Kemsull” (C. sinensis) as male parent, was applied to construct a genetic linkage map with different molecular markers. Previously, 143 random amplified polymorphism DNA (RAPD) markers and 11 simple sequence repeat (SSR) loci developed from 41 decamer random primers and 60 published SSR primer pairs, respectively, were used into our mapping analysis. In the study of amplified fragment length polymorphism (AFLP), 2439 bands were generated from 27 primer combinations with an average number of 90.3 bands for each, of which 495 (20.3%) were polymorphic. The majority of those polymorphic markers segregated in accordance with Mendelian segregation ratios at p < 0.01 for 400 (80.8%) or at p < 0.05 for 382 (77.2%), of which 136 (34.0%) or 131 (34.3%) were at 3:1 segregation ratios and 264 (66.0%) or 251 (65.7%) were at 1:1 segregation ratios at p < 0.01 and p < 0.05, respectively. For developing more SSR markers, the transcriptome sequences of flowers and leaves of two parents were obtained using high throughput RNA sequencing and compared. Afterwards, 1800 potential polymorphic SSR markers were successfully developed and 296 of them were selected and experimentally validated with a subset of tea plants (including two parents and six F1 offspring), from which 75 (25.3%) were repeatably amplified and polymorphic between two parents. From that, 29 (38.7%) newly mined SSR markers were heterozygous in “Fushun” and/or “Kemsull” and showed segregant genotypes in F1 seedlings and were adoptable by JoinMap 4.0. Totally, 678 markers including 143 RAPDs, 11 public SSRs, 495 AFLPs, and 29 newly mined SSRs were conjointly used to construct a combined linkage map for tea plant. The new genetic map located 79 RAPDs, 5 public SSRs, 214 AFLPs, and 11 new SSRs developed from RNA seq technique and covered 1441.6 cM with an average distance of 4.7 cM between two adjacent markers. This map will lay a foundation for qualitative or quantitative trait loci (QTLs) analysis of important agronomic traits for tea plant in the future study.

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

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

Marker-assisted pyramiding of bacterial blight and gall midge resistance genes into RPHR-1005, the restorer line of the popular rice hybrid DRRH-3

Bacterial blight (BB) of rice caused by the pathogen Xanthomonas oryzae pv. oryzae and the insect gall midge (GM) (Orseolia oryzae) are two major constraints of rice production. The present study was carried out to improve RPHR-1005, a stable restorer line of the fine-grain-type rice hybrid DRRH-3, for BB and GM resistance through marker-assisted backcross breeding (MABB). Two major GM resistance genes, Gm4 and Gm8, and a major BB resistance gene, Xa21, were selected as target genes for transfer to RPHR-1005. Two sets of backcrosses were carried out to combine either Xa21 + Gm4 or Xa21+ Gm8 into RPHR-1005 using breeding lines in the genetic background of ISM possessing either Gm4 or Gm8 along with Xa21. Foreground selection was performed for Xa21, Gm4, Gm8, and the major fertility restorer genes Rf3 and Rf4 using gene-specific markers, while 61 polymorphic simple sequence repeat (SSR) markers were used for background selection and marker-assisted backcrossing was continued until BC2 generation. A promising homozygous backcross-derived plant at the BC2F2 generation possessing Xa21 + Gm4, and another possessing Xa21 + Gm8, were intercrossed to stack the target resistance genes. At ICF 4 (inter-crossed F4) , three promising lines possessing the three target resistance genes in a homozygous condition along with fine-grain type, complete fertility restoration, and better panicle exsertion than RPHR-1005 have been identified. Among these, a single line, # RPIC-16-65-125, showed better yield, was highly resistant to BB and GM, was of medium–slender grain type, and had complete fertility restoration along with better panicle exsertion and taller plant type than RPHR-1005. This is the first report of combining resistance against BB and GM in the genetic background of a hybrid rice parental line.

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

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

The genetic diversity among strawberry breeding resources based on SSRs

Cultivated strawberry (Fragaria × ananassa Duch.) is a high value horticultural crop. In this study, the genetic diversity of 160 strawberry accessions was determined using five highly polymorphic simple sequence repeat (SSR) markers. Sixty different alleles were identified, with allele frequencies in the range of 0.006 to1. Similarity scores were in the range of 0.034 to 0.963 (average: 0.507). The accessions were categorized into five groups. Group 1 contained two diploid Fragaria vesca species and one unknown accession. Group 2 contained one accession (F x ananassa). Group 3 contained 20 F × ananassa accessions and six unknown accessions. Group 4 contained 48 F. × ananassa accessions, one octaploid Fragaria chiloensis species, and six unknown accessions while Group 5 contained 69 F. × ananassa accessions and six unknown accessions. Accessions within a pedigree were frequently grouped together. A total of 30 novel accessions were categorized alongside existing accessions. These results will allow breeders to develop strategies which incorporate more genetic diversity into new cultivars.

English

Simple sequence repeat (SSR) molecular markers were used for genetic diversity analysis and population structure of the cultivated Pearl millet in Benin, West Africa. In order to assess the level of genetic diversity, 14 polymorphic SSR markers were used to screen 114 accessions from different agro-ecological zones in Benin. SSR markers were found to reveal a total of 57 alleles with an average of 4.071 allele per locus. Genetic diversity index varied from 0.099 to 0.633 with an average of 0.405. The average observed heterozygosity was found to reach 0.425. The analysis of molecular variance showed no real differentiation between regions. Only 5% of genetic variation was observed between samples collected from north-eastern and north-western region. A high level of variation (95%) was observed among accessions. Moreover, both principal component analysis (PCA) and the dendrogram obtained from the genetic distance among accessions revealed the absence of any specific structuration of accessions from each region under study. Our results confirmed diversity among cultivated Pearl millet in Benin and such diversity is not clustering according to geographical patterns. Key words: Cereal, simple sequence repeat (SSR) markers, genetic variability.

Development and characterization of 18 polymorphic SSR markers for Barthea barthei (Melastomataceae).

Premise of the study:To examine population differentiation, simple sequence repeat (SSR) markers were developed in Barthea barthei, a shrub with a disjunct distribution in the southern mainland of China and Taiwan.Methods and Results:We used Illumina HiSeq technology to sequence a genomic library for SSR identification. Twenty-seven SSR loci were developed, of which 18 SSR loci were polymorphic in three populations composed of two varieties of B. barthei. At the population level, the number of alleles ranged from one to seven, and the observed and expected heterozygosity varied from 0 to 0.850 and from 0 to 0.809, respectively. Higher genetic differentiation between the two populations of B. barthei var. barthei (FST = 0.474) was observed relative to the two varieties (FST = 0.387 and 0.418, respectively).Conclusions:These polymorphic SSR markers may be useful for understanding phytogeographic history of B. barthei. Lower genetic differentiation between the two varieties than between the two populations of B. barthei var. barthei suggests that the taxonomic treatment may not hold.

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

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

Simple sequence repeat (SSR) markers for New Zealand mānuka (Leptospermum scoparium) and transferability to kānuka (Kunzea spp.)

ABSTRACTA multi-allelic genetic marker resource for future genetics studies in mānuka (Leptospermum scoparium) and its close relatives has been developed by mining simple sequence repeats (SSR) from a preliminary draft genome assembly of L. scoparium ‘Crimson Glory’. In total, 469 and 169 trinucleotide and dinucleotide repeats, respectively, were detected in a set of 89,619 predicted gene models. Polymerase chain reaction primer pairs were designed for 32 loci exhibiting high sequence similarity to Eucalyptus grandis. These 32 primer pairs were screened over a population of mānuka and 3 accessions of sympatric, related kānuka (genus Kunzea). The 15 polymorphic SSR markers that were successfully developed are now available for genetic analysis in Myrtaceae.

The gene diversity pattern of Diplocarpon rosae populations is shaped by the age, diversity and fungicide treatment of their host populations

Black spot disease caused by the hemibiotrophic ascomycete Diplocarpon rosae is the most devastating disease of field‐grown roses. Although resistance to black spot is an important trait for rose breeding, little information on the diversity of the pathogen is currently available. To date, a number of single‐spore isolates have been characterized based on a set of test genotypes of the host. In this study, six polymorphic simple sequence repeat (SSR) markers for D. rosae were developed and their potential application to single‐spore isolates collected from a wide range of geographic locations within and outside Europe discussed. Populations of the fungus were then analysed in different German rose collections/populations. Gene diversity was highest in older rose collections managed without fungicide application, and lowest in the two‐ to three‐year‐old testing sites of German rose breeders. Additional analyses of a global collection of single samples and populations revealed no unique alleles from any of the locations, indicating that global trading of rose varieties has led to an admixture of the pathogen.

Molecular tagging of pod shattering tolerance trait in soybean[Glycine max (L.) Merrill] genotype MACS-450.

Pod shattering (Dehiscence) severely reduces seed yield in soybean. Molecular tagging of pod shattering resistance can help in the process of breeding for shattering tolerance. In this study, an segregating population of cross (susceptible cultivar Monetta x tolerant genotype MACS-450) was used for bulked segregant analysis (BSA) with 26 SSR (simple sequence repeat) primers known to amplify markers linked to 22 qPDH loci. Among them, eight polymorphic SSR markers, viz., Sat_350 (qPDH1-7), Satt185 (qPDH1-3), Satt674 (qPDH1-5 loci), Satt166 (qPDH3-5), SRM1 (qPDH1 loci) Sat_342 (qPDH3-2), Satt685 (qPDH1-2) and Sat_407 (qPDH3-1) were able to distinguish parents differing for pod shattering of them two primers Satt 166 and SRM1 yielded markers polymorphic in between shattering tolerant and susceptible bulks by amplifying only Satt166-200 bp marker and SRM1-234bp marker only in tolerant bulks. Only Satt166-200 bp marker was observed in tolerant parent, bulks and 14 plants; while another 237 bp marker for pod shattering susceptibility got amplified in 46 plants including 8 plants that were heterozygous for both alleles. SRM1-234 bp marker was observed only in tolerant parent, bulks and 15 plants; while another 237 bp marker for pod shattering susceptibility got amplified in 45 plants. In combined marker analysis, the markers Satt 166 (qPDH3-5 loci) and SRM1 (qPDH1 loci) were linked with pod shattering score and were also confirmed in individual 60 F2 segregants. Hence, these markers could be utilized in the marker assisted for pod shattering resistance/tolerance breeding of qPDH3-5 like and qPDH1 genes.

RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources.

Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained. The quality assessment of assembled unigenes revealed 87.50% of complete and 97.18% partial core eukaryotic genes (CEGs). Sequence similarity analyses and annotation of the unigenes against non-redundant protein (Nr) and Gene Ontology (GO) databases identified 175,882 GO annotations. A total of 11,308 guar unigenes were annotated with various enzyme codes (EC) and categorized in six categories with 55 subclasses. The annotation of biochemical pathways resulted in a total of 11,971 unigenes assigned with 145 KEGG maps and 1759 enzyme codes. The species distribution analysis of the unigenes showed highest similarity with Glycine max genes. A total of 5773 potential simple sequence repeats (SSRs) and 3594 high-quality single nucleotide polymorphisms (SNPs) were identified. Out of 20 randomly selected SSRs for wet laboratory validation, 13 showed consistent PCR amplification in both guar varieties. In silico studies identified 145 polymorphic SSR markers in two varieties. To the best of our knowledge, this is the first report on transcriptome analysis and SNPs identification in guar till date.

Mapping and validation of the quantitative trait loci for leaf stay‐green‐associated parameters in maize

AbstractFunctional stay‐green is generally regarded as a desirable trait of varieties in major crops including maize. In this study, we used an F3:4 recombinant inbred line population with 165 lines from a cross between a stay‐green inbred line (Zheng58) and a model inbred line (B73) using 211 polymorphic simple sequence repeat markers to map quantitative trait loci for three stay‐green‐associated parameters, chlorophyll content, photosystem II photochemical efficiency and stay‐green area, at maturity stage, detected a total of 23 quantitative trait loci (QTL) on nine chromosomes. Single QTL explained 3.7–13.5% of the phenotypic variance. Additionally, we validated some important stay‐green QTL using a heterogeneous inbred family approach and found that the stay‐green‐associated parameters were significantly correlated with the plant yield. This study may contribute to a better insight into the regulatory mechanism behind leaf stay‐green in maize and a novel development of elite maize varieties with delayed leaf senescence through molecular marker‐assisted selection.

Identification of the QTL underlying the vitamin E content of soybean seeds

AbstractVitamin E (VE) is an important antioxidant supplement for human health. Soybean seed extracts are the main source of VE supplements. Therefore, increasing the VE content of soybean seeds is important issue in breeding programmes. To detect quantitative trait loci (QTL) associated with VE in soybean seeds, 238 F6:7 recombinant inbred lines (RILs) were created by crossing a high VE cultivar, ‘Beifeng 9’, with a low VE cultivar, ‘Freeborn’. A genetic map was constructed using 218 polymorphic simple sequence repeat (SSR) markers. Composite interval mapping analysis detected 66 QTLs for contents of individual and total VE, 21 for α‐tocopherol, seventeen for γ‐tocopherol, thirteen for δ‐tocopherol and fifteen for total VE. The QTLs were located on chromosomes 9, 10, 15, 18 and 19. Phenotypic variance underlain by each QTL ranged from 2.4% to 32.6%. Two major QTLs (BARCSOYSSR_10_1140–BARCSOYSSR_10_1188 and BARCSOYSSR_15_0855 to BARCSOYSSR_15_0887) associated with α‐Toc, γ‐Toc, δ‐Toc and total VE contents were mapped on chromosomes 10 and 15. They explained 12.0% and 32.6% of phenotypic variance for α‐Toc; 5.5% and 13.0% for γ‐Toc; 6.6% and 23.6% for δ‐Toc; and 19.6% and 21.8% for total VE. QTL intervals BARCSOYSSR_15_0790–BARCSOYSSR_15_0855 (Qα15_1, Qγ15_1), BARCSOYSSR_15_1113–BARCSOYSSR_15_1159 (Qα15_3, Qδ15_2, QTVE15_4) and BARCSOYSSR_15_1159–BARCSOYSSR_15_1190 (Qα15_4, Qγ15_5, QTVE15_5) were associated with α‐Toc and explained 22.2%, 23.8% and 24.4% of the phenotypic variation in multiple environments. BARCSOYSSR_09_1098–BARCSOYSSR_09_1128 (QTVE9_1) and BARCSOYSSR_15_0887–BARCSOYSSR_15_0935 (QTVE15_2, Qγ15_3) associated with total VE content explained 21.8% and 16.4% of the phenotypic variation in two environments. These QTLs allow for marker‐assisted selection for cultivars with high VE contents.

Mapping of brown planthopper [Nilaparvata lugens (Stål)] resistance gene (bph5) in rice (Oryza sativa L.)

Brown planthopper (BPH) has emerged as one of the most devastating pests of rice in several Asian countries. Cultivation of planthopper resistant varieties is an ecologically acceptable strategy. A population of 255 F2:3 families from the cross Taichung Native 1/ARC10550 was used to map BPH resistance with 106 polymorphic simple sequence repeat markers. The inheritance pattern of different traits suggested that the resistance in ARC10550 is controlled by quantitative traits instead of a single recessive gene. The quantitative trait loci (QTLs) for BPH resistance were analysed for nine phenotypic traits. Several of these phenotypic traits recorded high degree of positive or negative correlations between them, suggesting dependence or redundancy of the tests. QTL analysis revealed that five major loci were associated with resistance, one for damage score (qBphDs6) on chromosome 6, two for nymphal preference at 48 and 72 h (qBphNp(48h)-1 and qBphNp(72h)-12) on chromosome 1 and 12 and two for days to wilt (qBphDw(30)-3 and qBphDw(30)-8) on chromosome 3 and 8 explaining the phenotypic variance of 24.23, 8.69, 7.66, 4.55 and 10.48% respectively. These QTLs indicated the negative additive effects suggesting that the resistant alleles identified were from ARC10550 donor parent. These QTLs jointly explained 55.6% of the phenotypic variance for BPH resistance in this population.

Assessment of allelic diversity among drought-resistant cotton genotypes using microsatellite markers.

Drought, in conjunction with high temperature, is an important environmental constraint to cotton production. Development of cotton varieties with increased tolerance against adverse environmental conditions has been proposed as effective strategy for ensuring reliable yields. In the present study, 30 simple sequence repeat (SSR) primers were used to estimate genetic divergence among 22 cotton genotypes for drought stress tolerance. Genetic diversity is a prerequisite for developing drought resistant cotton genotypes. Eleven SSR primers out of 30 were able to discriminate among the cotton genotypes, implying that 37% of the primers were informative. In total, 41 alleles were detected, with an average of 3.72 alleles per primer. The number of alleles per locus ranged from one (JESPR-284) to six (JESSPR-302), and the allelic diversity in the experimental material was 0.40. Genetic similarity coefficients ranged from 0.87-1.00. The result of principal component analysis confirmed the clustering of 21 cotton genotypes in two groups leaving one genotype (CIM-109) ungrouped. Overall, genetic diversity among the 22 cotton genotypes was low. More polymorphic SSR markers are needed to explore the workable genetic variation among the screened cotton genotypes in future studies.

Detection and characterization of polymorphic simple sequence repeats markers for the analysis of genetic diversity in Indian mungbean [Vigna radiata (L.) Wilczek

Mungbean is a widely cultivated grain legume in Asia, Africa and South America. In this study, 52 varieties of mungbean were profiled with 39 polymorphic SSR primers after screening a total 315 SSR primers. A total of 96 alleles were scored from the 39 primers with an average of 2.46 alleles per locus indicating the low diversity among varieties. The Nei's genetic diversity index and the Shannon information index of SSR primers varied from 0 to 0.649 and 0 to 1.169, respectively. The results showed that the potential transferability of adzuki bean primers (83.3%) was greater than the cowpea primers (25%). The varieties profiled were grouped into four major clusters. But the clustering pattern did not reflect on their geographical origin. Further, the AMOVA indicated presence of moderate genetic differentiation among groups compared to higher differentiation among varieties within populations. The SSR markers identified here will add valuable genomic resources for germplasm characterization, cultivar identification and assessment of genetic diversity of mungbean varieties.