Genetic diversity of African maize inbred lines revealed by SSR markers

Knowledge of genetic diversity (GD) and relationships among maize inbred lines is indispensable in a breeding program. Our objectives were to (1) investigate the level of genetic diversity among maize inbred lines and (2) assess their genetic structures by applying simple sequence repeat (SSR) markers. Fifty-six highland and mid-altitude maize inbred lines obtained from CIMMYT programs in Ethiopia and Zimbabwe were genotyped using 27 SSR loci. All of the genotypes studied could unequivocally be distinguished with the combination of the SSRs used. In total, 104 SSR alleles were identified, with a mean of 3.85 alleles per locus. The average polymorphism information content (PIC) was 0.58. GD expressed as Euclidean distance, varied from 0.28 to 0.73 with an average of 0.59. Cluster analysis using unweighted pair group method with arithmetic average (UPGMA) suggested five groups among the inbred lines. Most of the inbred lines adapted to the highlands and the mid-altitudes were positioned in different clusters with a few discrepancies. The pattern of groupings of the inbred lines was mostly consistent with available pedigree information. The variability detected using SSR markers could potentially contribute towards effective utilization of the inbred lines for the exploitation of heterosis and formation of genetically diverse source populations in Ethiopian maize improvement programs.     

Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

A set of morphological traits and SSR markers were used to determine the genetic relationship among 12 elite thermosensitive genic male sterile (TGMS) lines developed at three different research institutions of India. Agro-morphological data recorded on 20 morphological traits revealed a wide base of genetic variation and a set of four morphological traits could distinguish most of the TGMS lines. Analysis with 30 SSR markers (20 EST-SSRs and 10 genomic SSRs) revealed 27 markers to be polymorphic, amplifying a total of 83 alleles. Each SSR marker amplified 2-6 alleles with an average of 2.76 alleles per marker and a PIC value varying from 0.54 to 0.96. Cluster analysis based on SSR and morphological data clearly differentiated the lines according to their source of origin. Correlation analysis between morphological and molecular data revealed a very poor association (r = 0.06), which could be attributed to selection pressure, genetic drift, sampling error and unknown relationship among related lines. The SSR markers discriminated the genotypes distinctly and quantified the genetic diversity precisely among the TGMS lines. Data on the yield per plant indicated that the genotypes grouping under a similar cluster showed same heterotic behaviour as compared to the genotypes from different clusters when crossed to similar pollinators.     

Analysis of genetic diversity and relationships among waxy maize inbred lines in Korea using SSR markers

Information regarding the genetic diversity and genetic relationships among elite inbred lines is necessary to improve new cultivars in maize breeding programs. In this study, genetic diversity and genetic relationships were investigated among 84 waxy maize inbred lines using 50 SSR markers. A total of 269 alleles were identified at all the loci with an average of 5.38 and a range between 2 and 13 alleles per locus. The gene diversity values varied from 0.383 to 0.923 with an average of 0.641. The cluster tree generated using the described SSR markers recognized two major groups at 32% genetic similarity. Group I included 33 inbred lines while group II included 51 inbred lines. The clustering patterns of most of the waxy maize inbred lines did not clearly agree with their source, pedigree or geographic location. The average GS among all inbred lines was 35.7 ± 10.8. Analysis of waxy maize inbred lines collected from Korea and China at 50 SSR loci revealed higher values of average number of alleles (4.9) and gene diversity (0.638) in Korean inbred lines as compared to Chinese inbred lines (3.5 and 0.563, respectively). The information obtained from the present studies would be very useful for maize breeding programs in Korea.     

Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers

Sweet sorghum (Sorghum bicolor L.) is a type of cultivated sorghums and has been recognized widely as potential alternative source of bio-fuel because of its high fermentable sugar content in the stalk. A substantial variation of sugar content and related traits is known to exist in US sweet sorghum. The objectives of the study were to assess the genetic diversity and relationship among the US sweet sorghum cultivars and lines using SSR markers and to examine the genetic variability within sweet sorghum accessions for sugar content. Sixty-eight sweet sorghum and four grain sorghum cultivars and lines were genotyped with 41 SSR markers that generated 132 alleles with an average of 3.22 alleles per locus. Polymorphism information content (PIC) value, a measure of gene diversity, was 0.40 with a range of 0.03–0.87. The genetic similarity co-efficient was estimated based on the segregation of the 132 SSR alleles. Clustering analysis based on the genetic similarity (GS) grouped the 72 sorghum accessions into 10 distinct clusters. Grouping based on clustering analysis was in good agreement with available pedigree and genetic background information. The study has revealed the genetic relationship of cultivars with unknown parentage to those with known parentage. A number of diverse pairs of sweet sorghum accessions were identified which were polymorphic at many SSR loci and significantly different for sugar content as well. Information generated from this study can be used to select parents for hybrid development to maximize the sugar content and total biomass, and development of segregating populations to map genes controlling sugar content in sweet sorghum.     

Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004

Analysis of genetic diversity changes in existing gene pools of cultivated crops is important for understanding the impact of plant breeding on crop genetic diversity and developing effective indicators for genetic diversity of cultivated plants. The objective of this study was to assess genetic diversity changes in 75 Canadian hard red wheat (Triticum aestivum L.) cultivars released from 1845 to 2004 using 31 simple sequence repeats (SSRs) markers. A total of 267 SSR alleles were detected, and their allelic frequencies ranged from 0.01 to 0.97, with an average of 0.14. Significant allelic reduction was observed at only four SSR loci for the cultivars released from 1970 onwards. However, 51 alleles (about 19%) present in pre-1910 cultivars were undetected in cultivars released after 1990 and were spread over 27 SSR loci. The proportion of SSR variation accounted for by six breeding periods was 12.5%, by four ancestral families, 16.5%, and by eight breeding programs, 8.4%. The average genetic diversity measured by three different band-sharing methods did not change significantly among cultivars released from different breeding periods, breeding programs, and ancestral families. However, genetic shift was obvious in the cultivars released over the six breeding periods, reflecting well the various breeding efforts over years. These results clearly show the allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released over time. Consequently, more effort needs to be made to broaden the wheat breeding base and conserve wheat germplasm.     

Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

Thirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15.4 alleles per locus. The mean polymorphic information content (PIC) score was 0.687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10.1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.     

我国陆地棉基础种质遗传多样性的SSR分子标记分析

利用398对BNL、JESPR、TMB等SSR引物,对不同亲本来源、不同选育时期、不同种植生态区的43份陆地棉基础种质进行了遗传多样性的SSR分子标记分析。扩增产物用8％的非变性聚丙烯酰胺凝胶检测,银染观察并照相。遗传多样性带型分析按位点多态信息量（PIC）,Shannon-weaver多样性指数（H^＋）等方法,利用NTSYSpc2．1软件计算品种间的遗传相似系数（Jaccard系数）,并用类平均法（UPGMA）进行聚类。结果表明所选择多态性引物分布在棉花基因组的第3、4、5、8、9、10、16、18、20、23号等染色体上,36对多态性引物在基础种质中扩增等位基因130个,其中多态性等位基因占80％,每个引物扩增等位基因2～8个,平均3．6个,PIC为0．278～0．865,平均0．62,基因型多样性（H^＋）为0．451～2．039,平均1．102,基础种质问SSR遗传相似系数平均为0．610,变幅为0．409～0．865,这说明所选基础种质基因组水平的多样性较丰富,变化范围大、代表性强。按品种不同选育时期来讲,第一、二、三期基础种质的SSR分子标记平均遗传相似系数分别是0．587、0．630、0．630,说明现代基础种质比早期基础种质在基因组水平的差异呈下降的趋势,可能是由于育种者偏重于使用优质高产性状的亲本品种,致使我国棉花的育种基础逐渐变窄。不同棉区基础种质SSR标记性状差异大,北部特早熟棉区基础种质间的SSR标记的多样性大于黄河、长江棉区,主要原因是长江、黄河棉区的育种过分强调高产、优质品种选育,品种间的差异变小;基础种质中的国内品种SSR相似系数（0．624）比引进品种（0.85）高,说明国内品种在遗传多样性上目前还没有超越国外品种。总之,我国棉花现代基础种质比早期基础种质的遗传多样性呈下降的趋势,黄河、长江主产棉区基础种质的遗传多样性还没有超过国外基础种质,品种间的遗传背景较为狭窄,还必须采用多种途径丰富我国棉花种质资源的遗传多样性。     

Genetic diversity,population structure and validation of SSR markers linked to Sw-5 and I-2 genes in tomato germplasm

Tomato is the world’s second largest cultivated vegetable crop. Tomato spotted wilt virus (TSWV) and fusarium wilt (FW) are the two major biotic stresses in India limiting tomato production. Identification and utilization of resistant lines to realize the full genetic potential of varieties for yield gain is an eco-friendly approach. The present research work involved genetic diversity study of 48 genotypes, augmented from different exotic, and indigenous sources belonging to three species using SSR markers. A total of 195 alleles were generated by employing 84 polymorphic markers. The PIC value was ranged from 0.12 to 0.93. Two sub-populations (K = 2) were revealed by model based structure analysis. The cluster analysis using the UPGMA method classified the genotypes into 6 clusters. Pusa Ruby, EC-310310 and EC-620452 were found to be highly diverse. Molecular characterization of 48 genotypes with SSR markers divulged seven genotypes with Sw-5 gene and nine genotypes with I-2 gene showing resistance to TSWV and FW, respectively and further, on artificial screening, they were found to be phenotypically resistant. Out of 195 alleles generated from 84 polymorphic SSR markers, 43 alleles from 26 SSR markers were identified with positive average allele effect distributed across nine chromosomes and positive average allele effect was identified for the average weight of the fruit, the number of fruits formed per plant, and fusarium wilt PDI score. Fruit weight and fruit yield per plant registered a significant and positive correlations. The identified genotypes with varied backgrounds and performances will be very useful as diversified sources in resistant breeding programs of tomato.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01037-8.     

A genetic linkage map of microsatellite,gene-specific and morphological markers in diploid <Emphasis Type="Italic">Fragaria</Emphasis>

Knowledge of the genetic diversity of a species is important for the choice of crossing parents in line and hybrid breeding. Our objective was to investigate European winter triticale using simple sequence repeat (SSR) markers and the coancestry coefficient (f) with regard to genetic diversity and grouping of germplasm. Three to five primer pairs for each of the 42 chromosomes were selected to analyse 128 European winter triticale varieties and breeding lines. SSR analysis resulted in the identification of 657 alleles with an average of 6.8 alleles per primer pair. The average polymorphism information content (PIC) for polymorphic markers was 0.54. Correlation between f and genetic similarity (GS) estimates based on Rogers Distance was low (r_f×GS(ABDR)=0.33). The analysis of molecular variance (AMOVA) revealed that 84.7% of the total variation was found within breeding companies, and 15.3% among them. In conclusion, SSR markers from wheat and rye provide a powerful tool for assessing genetic diversity in triticale. Even though no distinct groups within the European winter triticale pool could be detected by principal co-ordinate analysis, this study provides basic information about the genetic relationships for breeding purposes.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by H.C. Becker     

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

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

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.     

Genetic diversity and geographical differentiation of Iranian landrace,cultivars, and exotic chickpea lines as revealed by morphological and microsatellite markers

Assessment of the extent of genetic variability within chickpea is fundamental for chickpea breeding and conservation of genetic resources and is particularly useful as a general guide in the choice of parents for breeding hybrids. To establish genetic diversity among 60 accessions of chickpea comprising landraces, internationally developed improved lines, and cultivars, genetic distances were evaluated using 14 simple sequence repeat markers. These markers showed a high level of polymorphism; a total of 59 different alleles were detected, with a mean of 4.2 alleles per locus. The polymorphic information content (PIC) value ranged from 0.31 to 0.89. All the markers, with the exception of TAA170, TA110, GA34, and Ts35, were considered to be informative (PIC > 0.5), indicating their potential usefulness for cultivar identification. Based on the UNJ clustering method, all accessions were clustered in five groups, which indicated the probable origin and region similarity of Iranian landraces over the other cultivars. It also represents a wide diversity among available germplasm. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. As further implications of the findings, this study can be useful for selective breeding for specific traits and in enhancing the genetic base of breeding programs.     

基于SSR标记分析大豆疫霉根腐病抗源的遗传多样性

丰富的遗传多样性可为大豆育种提供宽阔的遗传基础,本研究基于35对SSR标记,对60份东北地区大豆疫霉根腐病抗性品种进行了遗传多样性分析,共检测到189个等位基因,平均每个位点等位变异数5.4个,多态性信息含量指数(PIC)为0.1550~0.8195,平均为0.6636;遗传相似系数的变异范围为0.31~0.74。利用5对高多态性SSR引物构建了60份抗性材料的指纹图谱,这5对SSR引物构建的指纹图谱可以将60份疫霉根腐病抗性材料逐一区分开。采用NTSYS2.10基于遗传距离的聚类分析,将60份抗性材料分为7个类群,其中78.33%的抗性品种(系)的遗传相似系数在0.45~0.74间,表明遗传差异相对较窄,品种间遗传多样性水平较低。聚类分析与群体遗传结构分析结果有部分重合,均反映出不同地区的抗性材料间存在一定的渗透和交流。     

Analysis of molecular diversity and fingerprinting of commercially grown Indian rice hybrids

Twenty-five commercially grown Indian rice hybrids developed by both the public and private sectors, were analysed for molecular diversity and identification of simple sequence repeat (SSR) marker(s) that can distinguish them from each other. For diversity analysis, a total of fifty eight SSR markers providing genome wide coverage, were used. Forty out of fifty eight SSR markers were polymorphic amplifying a total of 121 alleles with molecular weight ranging from 70 bp ?C 280 bp. Further, characterisation of these markers was carried out generating parameters of heterozygosity (0.42), polymorphism information content (0.31), probability of identity (4.2?×?10^?8) and probability of exclusion (99.99%). Cluster analysis based on a set of fourty highly polymorphic SSR markers generated three groups with dissimilarity index values ranging from 0.0 to 0.8. The hybrids based on common female parent IR58025A grouped together indicating a narrow genetic base of hybrid breeding programme. By combining the rapid and simple method of utilising these unique SSR markers alone or in combination, as molecular tags, identification of all the hybrids was possible even without having their parental lines. Twenty SSR loci produced hybrid specific unique alleles, which will be useful in establishing hybrid??s identity. The results have wide prospective in diversifying the genetic base of hybrid breeding programme, identification of rice hybrids, authentication of genetic purity of hybrid seed and protection of IPR.     

Population structure and genetic diversity analysis of Indian and exotic rice (Oryza sativa L.) accessions using SSR markers

In order to understand the population structure and genetic diversity among a set of 82 rice genotypes collected from different parts of the Asian countries including India were characterized using 39 microsatellite loci. The Population structure analysis suggested that the optimum number of subpopulations was four (K = 4) among the rice genotypes, whereas phylogenetic analysis grouped them into three populations. The results obtained from phylogenetic and STRUCTURE analysis proved to be very powerful for the differentiation of rice genotypes based on their place of origin. The genetic diversity analysis using 39 SSR loci yielded 183 scorable alleles, out of which 182 alleles were observed to be polymorphic with an average of 4.8 alleles per locus. The Polymorphism Information Content (PIC) values for all the polymorphic primers across 82 rice genotypes varied from 0.02 to 0.77, with an average of 0.50. Gene diversity (He) was found to be in the range of 0.02 (RM484) to 0.80 (OSR13) with an average value of 0.55, while heterozygosity (Ho) was observed with an average of 0.07, ranging from 0.01 (RM334) to 0.31 (RM316). The present study resulted in identification of seven highly polymorphic SSR loci viz., OSR13, RM152, RM144, RM536, RM489, RM259 and RM271 based on the parameters like PIC value (≥0.70), gene diversity (≥0.71), and polymorphic alleles (≥6). These seven polymorphic primers can effectively be used in further molecular breeding programs and QTL mapping studies of rice since they exhibited very high polymorphism over other loci. SSR analysis resulted in a more definitive separation of clustering of genotypes indicating a higher level of efficiency of SSR markers for the accurate determination of relationships between accessions.     

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had ‘Precoz’ gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers’ preference.     

Analyses of genetic diversity among maize inbred lines differing for resistance to pink borer and post-flowering stalk rot

Identification of the diverse sources of resistance is an important issue among the breeders for developing pest and disease free hybrids, to reduce the inoculum load, to prolong the life of inbred lines/hybrids and to reduce the cost of cultivation. Molecular diversity analysis was carried out among 23 maize inbred lines with respect to post flowering stalk rot and pink borer. Forty six SSR markers were employed among eight post flowering stalk rot (PFSR) and seven pink borer resistant lines along with eight other inbred lines to identify diverse resistant sources for developing resistant heterotic combinations to above pests and diseases. Number of alleles per SSR marker ranged from 2 to 9 averaging 4.11. The polymorphism information content (PIC) ranged from 0.272 to 0.839 with an average of 0.568. Discrimination rate (DR) of the markers ranged from 0.095 to 0.861 with a mean of 0.618. Number of alleles was highly correlated with PIC and DR. The pair-wise genetic dissimilarity values ranged from 0.05 to 0.84 with an overall mean of 0.64. Un-weighted neighbour joining clustering put 23 genotypes in two main clusters, which were further subdivided into 5 and 6 sub-clusters, respectively. We obtained 56 rare and 26 unique alleles in specific inbred lines, which can be used for identification of these lines. The present study has revealed considerable diversity among inbred lines differing for resistance against PFSR and pink borer; and provided ample scope for selection of parents for utilization in heterosis breeding     

Genetic Diversity Analysis of Elite Pearl Millet Inbred Lines using RAPD and SSR Markers

Pearl millet [Pennisetum glaucum (L) R Br] is one of the widely grown cereal crops in the arid and semi-arid regions of Africa and India. We undertook a study to ascertain the genetic diversity in 21 elite inbreds (parental lines of 13 pearl millet hybrids in India) using 20 Random Amplified Polymorphic DNA (RAPD) and 21 Simple Sequence Repeat (SSR) markers. Based on Polymorphism Information Content (PIC) and unique banding profiles, 6 RAPD primers OPD12, OPA16, OPB6, OPA19, OPB5 and OPB1, and 3 SSR markers Xpsmp2208, Xpsmp2223 and Xpsmp2220, were found to be highly discriminative. The PIC values ranged from 0.28 to 0.48 for the RAPD and from 0.24 to 0.60 for the SSR markers. Cluster analysis and principal component analysis of the combined dataset of RAPD and SSR markers indicated moderate genetic divergence among the elite pearl millet germplasm, besides unraveling the genetic relationships among the male sterile lines and the restorers.     

SSR analysis of 38 genotypes of soybean (Glycine Max (L.) Merr.) genetic diversity in India

Sixteen polymorphic Simple sequence repeat (SSR) markers were used to determine the genetic diversity and varietal identification among 38 soybean (Glycine max (L.) Merr.) genotypes which are at present under seed multiplication chain in India. A total of 51 alleles with an average of 2.22 alleles per locus were detected. The polymorphic information content (PIC) among genotypes varied from 0.049 (Sat_243 and Satt337) to 0.526 (Satt431) with an average of 0.199. The pair wise genetic similarity between soybean varieties varied from 0.56 to 0.97 with an average of 0.761. These 16 SSR markers successfully distinguished 12 of the 38 soybean genotypes. These results suggest that used SSR markers are efficient for measuring genetic diversity and relatedness as well as identifying varieties of soybeans. Diverse genetic materials may be used for genetic improvements of soybean genotypes.     

Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek)

Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard’s similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.