Genetic diversity analysis of 50 indigenous rice accessions using SSR markers linked to drought yield QTLs (qDTY)

Abstract

    Understanding the genetic basis of drought tolerance is a key factor in improving rice adaptability under climate change. This study assessed the genetic diversity associated with drought tolerance in 50 Vietnamese local rice varieties using 10 functional SSR markers tightly linked to yield-related QTLs under drought stress (DTY), including qDTY1.1, qDTY3.1, and qDTY12.1. A total of 40 allele were identified, with 2–5 alen per locus and an average PIC value of 0.60, indicating a high level of polymorphism. Both UPGMA clustering and Principal Coordinate Analysis (PCoA) clearly separated the collection into two main groups corresponding to drought-tolerant and drought- susceptible phenotypes. AMOVA revealed that 28.6% of the genetic variation was attributed to differences between these two groups, and the Fst value (0.29) indicated a moderate to high level of genetic differentiation. Several allele at RM1261 (qDTY_1.1) and RM2634 (qDTY_12.1) were found to be specific to drought tolerant varieties and corresponded to previously published DTY-linked alleles. These findings emphasize the substantial genetic diversity of Vietnamese local rice germplasm at DTY regions of the genome, providing a valuable scientific foundation for the selection of parental lines in breeding drought tolerant rice varieties for production.