Association mapping validates previously identified quantitative trait loci for salt tolerance in rice (Oryza sativa L.)

Salinity is the main abiotic stress that limits rice (Oryza sativa L.) production worldwide. An association mapping project was designed to validate quantitative trait loci (QTLs) in rice associated with Na+, K+ and Ca++ accumulation traits identified in our previous study of linkage mapping. Twenty four varieties/lines of rice were phenotyped for biochemical and yield traits. Among these varieties/lines, two mapping parents, Pokkali and IR-36, of our previous linkage mapping study were also included. For marker-trait assessments, both general linear model (GLM) and mixed linear model (MLM) analyses were performed. Thirteen significant marker-trait associations at P <= 0.001 were identified. Associated markers for these marker-trait associations were RM503, RM225, RM152, and RM254 located on chromosomes 3, 6, 8, and 11, respectively. Previously identified QTLs in linkage mapping study for Na+ uptake, Ca++ uptake, total cations uptake, Ca++ uptake ratio, K+ uptake ratio, and Na+/K+ uptake were validated in this study. Heritability values for these traits ranged from 1.00e-05 to 1. Linked markers for these validated QTLs were RM140, RM243, RM203, RM480, RM137, and RM254 located on chromosomes 1, 1, 3, 5, 8, and 11, respectively. These markers will be a valuable resource for marker-assisted breeding (MAB) approach to develop elite salt tolerant rice cultivars. This study demonstrates the potential of association mapping approach to validate previously identified QTLs.