Title : Genome wide association study on salt tolerance in rice at seedling stage under moderate salinity
Salt threatens rice cultivation in many countries. Hence, breeding new varieties with high salt tolerance is important. Methods: 1,332 rice accessions, including 767 indica accessions, 375 japonica accessions, 104 aus accessions, and 38 aromatic accessions from 3K Rice Genome Project were selected to evaluate salt tolerance via the standard evaluation score (SES) in hydroponics under 60 mM NaCl at the seedling stage. The GWAS in the different panels, viz. whole population and each subspecies group, were analyzed by using a Factored Spectrally Transformed Linear Mixed Model (FaST-LMM) by FaST-LLM software. The analysis was carried out with 235,210 SNPs, of which 58,800 SNPs were used to measure similarities between the accessions, and top three principal components analysis of 588,792 SNPs as covariate. The significant threshold was set at p < 0.0001 (-log10 P-value > 4). Multiple SNPs significant in a range of LD decay in the same chromosome were considered as a single QTL. Results: A total of 12 QTLs associated with SES trait in different panels were identified by GWAS. Among them, only one QTL was detected in two different panels, and each of the 11 others in one panel only. Four QTLs previously reported as related to salt tolerance were found: one QTL in chromosome 4 (peak position at 23.2 Mb), one QTL in chromosome 5 (peak position at 28.4 Mb), and 2 QTLs in chromosome 12 (peak position at 23.6 Mb and 24.2 Mb). Among them, two QTLs were mapped in intervals containing OsBADH1 gene and previously reported regulating salt tolerance, whereas the others were novel QTLs. Conclusions: The identified QTLs, including well-known genes and novel QTLs, would provide useful genetic information for future genetic improvement of salt tolerance in rice.