Association mapping of salinity and alkalinity tolerance in improved japonica rice (Oryza sativa L. subsp japonica Kato) germplasm

Salinity and alkalinity seriously threaten global rice production. As a consequence, elucidation of the genetic basis of salinity and alkalinity tolerance is crucial for rice breeding. To identify genetic marker loci/QTLs associated with salinity and alkalinity tolerance, we performed association mapping based on different statistical models using 347 rice accessions from all over the world. Salinity tolerance for all traits was evaluated on saline land along the seashore of Hebei, while alkalinity tolerance at the seedling stage was assessed in the alkaline soil of paddy fields in Jilin. A total of 148 SSRs were used for genotyping. Within the entire population, 64.1 % of SSR locus pairs were in significant linkage disequilibrium (LD) (P < 0.05). Most of this LD was due to the overall population structure, as the percentage of locus pairs in LD was much lower within each subpopulation, ranging from 21.2 to 32.4 %. LD decayed with genetic distance, indicating that linkage was a main cause of LD. Model comparisons indicated that the Q + K model, which controls for both population structure (Q) and relative kinship (K), performed better than other models. A total of 40 markers were identified: 25 related to salinity tolerance and 15 related to alkalinity tolerance. Of the identified markers, 17 were located either in or near regions in which QTLs for salinity and alkalinity tolerance have been previously reported. Furthermore, we identified three of these markers-RM475, RM567, and RM505-in rice under both salinity and alkalinity stress conditions. These results highlight target regions for fine mapping, cloning and molecular breeding by design for rice salinity and alkalinity tolerance.