Association Analysis of Germination Ability at Cold Stress in Rice (Oryza sativa L.)

Cold stress is one of the major environmental factors that limit the agricultural productivity of plants. Good performance during germination is important to guarantee fast establishment and uniform crop stand. Improvement of germination ability at cold stress in rice is an important objective in current breeding programs. In this study, 133 rice accessions of diverse origin were genotyped using 247 SSR markers to identify marker– trait associations with traits related with germination ability at cold stress in rice. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r² value for all intrachromosomal loci pairs was 0.0955. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 71 marker–trait associations including 10 MTAs associated with 5 unmapped markers (p<0.01) were identified using 45 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping, and detection of new marker–trait associations associated with traits related with cold tolerance germination in rice will also provide important information for marker assisted breeding.