Population Structure Analysis and Marker Trait Association in Traditional Rice (Oryza sativa L.) Landraces of Kerala under High Temperature Condition

Abstract

Abstract Rice productivity is significantly impacted by a significant abiotic stress called heat stress. To adapt to current or future heat stress, it is necessary to understand the physiological basis of heat tolerance. Thus, the purpose of this study was to assess the physiological, morphological, and yield parameters of fifty traditional rice landraces when subjected to high temperature stress, as well as to identify SSR (Simple Sequence Repeat) markers associated with these traits. The experiment was designed in a completely randomised manner, with two treatment levels, control and high temperature stress (36 ± 2oC), each with three replications. Thirty SSR primers were used to analyze genetic diversity and population structure among 50 traditional rice landraces collected from Regional Agricultural Research Station, Pattambi, Kerala. The fifty traditional rice landraces were clustered using the average linkage method to determine their relationship to one another. The accessions were all grouped primarily into three clusters. According to principal component analysis, under high temperature conditions, the first principal component accounted for 24.602 percent of the variation, while the second component accounted for 20.587 percent of the variation. The accessions were clearly divided into three subpopulations based on population structure analysis. Under high temperature and control conditions, GLM (Generalized Linear Model) analysis revealed highly significant marker trait associations.RM5715, RM10793, and RM471 were among those that showed associations with multiple traits. Molecular markers and identified tolerant accessions can be used in breeding programmes to create high-yielding, temperature-tolerant rice landraces.