Identification of markers for yield and yield-related traits using association mapping analysis in rice (Oryza sativa L.) under rainfed conditions

Abstract

Rice (Oryza sativa L.) grain yield is determined by multiple factors, including ideal plant architecture, appropriate flowering time and adaptability to diverse agro-climatic conditions. However, inadequate water availability in major rice-growing regions has led to increased incidence of drought and other abiotic stresses.  The present investigation was undertaken to identify marker-trait associations for yield and yield-related traits, as well as to assess genetic diversity and population structure under rainfed conditions. A set of 100 genetically diverse rice genotypes, classified into wild, cultivated and germplasm groups, were evaluated under rainfed conditions using 151 Simple Sequence Repeat (SSR) markers and marker-trait associations were analysed through general linear model (GLM) and mixed linear model (MLM)  models using TASSEL and STRUCTURE software during 2020–2021 in the Agriculture Research cum Instructional farm and Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India. A total of 414 alleles were amplified across 151 SSR markers (alleles/locus: 3 to 11 with mean 2.77). The polymorphism information content (PIC) values ranged from 0.019 to 0.498 (mean 0.263) the most informative markers were CS-62, RM28160, RGS-1 and RM-408 (PIC > 0.49). STRUCTURE Harvester (ΔK, K = 3) classified 100 genotypes into three sub-populations (POP1: 85; POP2: 13; POP3: 2). The GLM and MLM identified 90 and 42 significant marker-trait associations respectively (False discovery rate (FDR): 50.1 %), with 10 SSR markers associated with multiple yield-related traits under both models. Eight SSR markers (RM-242, RM-178, RM-154, RM-21, 18646, IND-1, CS-62 and PPC-1SET1) were tightly linked with grain yield across all linkage groups, confirming their suitability for marker-assisted selection. Sarmatia (250.05 g/plot) and IBD-1 (234.55 g/plot) are recommended as donor parents for breeding drought-tolerant rainfed rice varieties.