Genetic structure and association mapping of cold tolerance in improved japonica rice germplasm at the booting stage

Cold tolerance at booting stage is one of the major determinants for a stable yield of rice (Oryza sativa L.) in many high elevation or high latitude regions. Understanding the genetic basis of cold tolerance is crucial for the improvement of cold tolerance through breeding. In this study, association mapping was performed in 347 rice accessions worldwide with different statistical models in order to identify the genetic marker loci/QTL associated with cold tolerance traits at the booting stage. The evaluation of cold tolerance for all the traits was conducted under natural low temperature in Yunnan and cold water irrigation in Jilin. The 148 SSRs were used for the genotyping. Population structure analysis identified three main subpopulations for the accessions that corresponded to major geographic origins. The relative kinship analysis revealed a weak or no relationship for most of the individual pairs. Model comparisons indicated that the Q+K model controlling both population structure (Q) and the relative kinship (K) was performed better than other models in association mapping. In total, 24 markers were identified that were significantly associated with cold tolerance, including five markers in Yunnan and 19 markers in Jilin. Moreover, RM282, RM252, RM335 and RM6824 were identified in multiple environments or years. Many of these identified markers were located either in or nearby the regions where the QTLs have been reported for cold tolerance at booting stage. These results highlighted the targeted regions for future studies and might be subsequently used in breeding programs to trace and select the useful alleles by MAS.