Population structure analysis of emmer wheat (Triticum dicoccum Schrank) germplasm conserved in National Genebank of India using SSR markers

Knowledge of genetic diversity of crop germplasm is essential for their utilization in breeding programme. Emmer wheat germplasm received less attention for exploring its genetic diversity towards enhancing utilization. Agro-morphological characterization was done for 192 emmer wheat accessions during rabi season 2019-20 and subsequently, 96 accessions were selected for morphological and molecular diversity analysis during 2020-21. We estimated genetic diversity and population structure of 96 diverse dicoccum genotypes conserved in national genebank of India using 56 microsatellite (SSR) markers. The number of alleles per locus ranged from 1 to 6 with an average of 1.68 alleles. A total of 93 alleles were detected with the highest PIC value (0.9912) observed for Xcfd20 marker. Based on ‘STRUCTURE’ analysis, 96 dicoccum accession were divided into two sub-populations. The analysis of molecular variance (AMOVA) revealed that genetic differentiation among subpopulations was low and within subpopulations was high. A cluster analysis based on the Jaccard’s dissimilarity index identified two clusters which was in congruence with population structure. Indigenous and exotic collections were categorized into distinct sub-clusters within the same cluster with some overlapping suggesting limited genomic differentiation between these collections from different geographical regions. Based on the allelic information and cluster analysis, cultivated emmer wheat showed low genetic diversity and narrow genetic base. The low genetic diversity in emmer wheat accessions may be due to limited cultivation in small pockets that emphasized a need to broaden the genetic base of emmer wheat genetic resources for enhancing its utilization.