The Application of Multi-Locus GWAS for the Detection of Salt-Tolerance Loci in Rice

Improving the salt-tolerance of direct-seeding rice at the seed germination stage is a major goal of breeders. Efficiently identifying salt tolerance loci will help researchers develop effective rice breeding strategies. In this study, six multi-locus genome-wide association studies (GWAS) methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, and ISIS EM-BLASSO) were applied to identify quantitative trait nucleotides (QTNs) for the salt tolerance traits of 478 rice accessions with 162, 529 SNPs at the seed germination stage. Among the 371 QTNs detected by the six methods, 56 were identified by at least three methods. Among these 56 QTNs, 12, 6, 7, 4, 13, 12, and 12 were found to be associated with SSI-GI, SSI-VI, SSI-MGT, SSI-IR-24h, SSI-IR-48h, SSI-GR-5d, and SSI-GR-10d, respectively. Additionally, 66 candidate genes were identified in the vicinity of the 56 QTNs, and two of these genes (LOCOs01g45760 and LOCOs10g04860) are involved in auxin biosynthesis according to the enriched GO terms and KEGG pathways. This information will be useful for identifying the genes responsible for rice salt tolerance. A comparison of the six methods revealed that ISIS EM-BLASSO identified the most co-detected QTNs and performed best, with the smallest residual errors and highest computing speed, followed by FASTmrMLM, pLARmEB, mrMLM, pKWmEB, and FASTmrEMMA. Although multi-locus GWAS methods are superior to single-locus GWAS methods, their utility for identifying QTNs may be enhanced by adding a bin analysis to the models or by developing a hybrid method that merges the results from different methods.