Utilization of genetic diversity and population structure to reveal prospective drought-tolerant donors in rice

Abstract

Fifty SSR markers were used to assess genetic diversity among 40 drought-tolerant, five moderately drought-tolerant, and three susceptible genotypes to identify new donors for drought tolerance in rice. Out of 50 SSR markers, 17 markers are reported to be linked to major grain yield QTLs under reproductive stage drought stress. 163 (97.7%) out of 167 alleles were found to be polymorphic. The PIC value ranged from 0 to 0.963 with an average of 0.795 per locus. The minor allele frequency varied from 0.312 (RM336) to 0.895 (RM530) with an average of 0.60. The genetic diversity ranged from 0.187 (RM530) to 0.739 (RM336) with an average of 0.51. The cluster analysis grouped all the genotypes into three major clusters at 50% level of genetic dissimilarity. Structure analysis identified two subpopulations among 48 rice genotypes. 81% and 19% of molecular variances were revealed within and among the subpopulations, respectively. The first three principal components explained over 88% of total genetic variation. Two genotypes, Kalakeri and RR-2-6 were identified as new drought-tolerant donors. Kalakeri contributes drought tolerance QTL, qDTY1.1, while RR-2-6 contributes QTLs, qDTY2.2, and qDTY2.3.