Microsatellite-based diversity analysis and the development of core-set germplasm in Pakistani barley lines

Illustrating the population structure and genetic diversity in selected germplasm resources (after three-year multi locations trials) plays a key role that directly utilizes the selection of lines in a population for accumulative trait breeding in crops. In order to further understand, the structure of population and genetic variability, this study explored 100 selected lines, conducted for three consecutive years (2016-2019) in swat, University of Malakand, Khyber Pakhtunkhwa Pakistan and Provinces of China (Chongqing and Beijing) with 33 mapped SSR markers. Through an integrated population structure analysis, the study examined a core set of one hundred germplasm of Pakistani origin, along with three approved commercial barley cultivars. The analysis revealed a robust stratification within the population, resulting in the classification of the germplasm into four major subpopulations (PI, PII, PIII, and PIV), as well as an admixture subpopulation consisting of 52, 9, 15, and 27 germplasm, respectively. A total of 133 alleles were identified with a mean value of 0.80 Polymorphic information content. The number of alleles detected by the system varied from two alleles amplified to six with an average of 4.03 per SSR marker pair. The gene diversity ranged from 0.56 to 0.98 with an average of 0.82 in selected germplasm resources. Based on the SSR data, the 100 selected germplasm with three cultivars were classified into four main phylogenetic lineages (LI, LII, LIII and LIV) which corresponded to the phylogenic grouping in genotypes. We assembled a core set of 20 barley genotypes (~1/5 of original population size) to sustain sufficient mapping of SSR marker with Phenotype, in which we proposed four SSR markers, Bmac0040, Bmac0134, Bmag0125 and Bmag0211 for malt gene and marker (Bmac0399) for tolerance to salinity gene, which will be applicable for marker-assisted breeding in barley gene resources.