Identification of genomic SSRs in cluster bean (Cyamopsis tetragonoloba) and demonstration of their utility in genetic diversity analysis

Abstract

Cluster bean (Cyamopsis tetragonoloba), also known as guar, is an important industrial crop owing to its high gum content in the endosperm. Availability of sufficient genomic resources, especially, DNA markers, greatly aids genetic improvement of a crop. In this study, we identified 1859 genomic SSRs, for the first time, from 1091 scaffolds representing 60% of the cluster bean genome. Further we validated 89 of these markers using 54 cultivated guar accessions and two wild relatives, Cyamopsis serrata and Cyamopsis senegalensis. Seven SSRs were monomorphic even with the wild relatives while 11 were polymorphic only between species with 72 being polymorphic within C. tetragonoloba accessions. Polymorphism information content of the markers ranged from 0.017 to 0.62 with an average of 0.19. Cross-transferability rates of 62% observed for the genomic SSRs suggested divergence between the cultivated and the wild species. Genomic SSRs mined in this study though showed a high proportion of dinucleotide repeats (48.5%), while tri- and tetranucleotide repeats were found to be more polymorphic. Genetic diversity analysis of the 56 accessions using the 82 polymorphic markers could differentiate the cultivated accessions of C. tetragonoloba into four major clusters, two of which had two sub-clusters while the wild accessions formed a separate cluster. Since chromosome-wide distribution of the SSRs is unknown and genetic linkage maps in guar is not available, we used the soybean genome as a reference and identified 29 genome-wide and unlinked SSRs markers. Population structure analysis (PSA) using these markers revealed six subpopulations, more or less similar to the major and sub-clusters identified by the neighbor joining analysis. Further PSA identified an entry from subpopulation 6 to have admixture with the wild relatives. Annotation of the validated genomic SSR containing sequences using green plant nr protein database revealed that 16 of them were genic in nature. This is the first report on genomic SSRs and their utilization in unraveling the genetic diversity in cluster bean.