A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance of Rice (Oryza sativa) at the Germination Stage

Salt is the major factor limiting crop productivity in saline soils. Development of salt-tolerant rice through molecular breeding methods is necessary to meet the needs of rice breeding. We used 295 accessions, including a heuristic core set (137 accessions) and 158 bred varieties, to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice at the germination stage. All rice collections were re-sequenced and ~1.65 million SNPs/Indels were identified and included in the GWAS. We detected a total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model. After determining linkage disequilibrium blocks associated with significant SNPs/indels, we finally obtained a total of 79 candidate genes for the salt-tolerance phenotypes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD analysis, we identified 17 genes that may contribute to salt tolerance. We conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Principle component analysis suggested that salt tolerance levels in rice (O. sativa) are not strongly correlated with the indica or japonica subgroups. Our study revealed substantial natural variations in candidate salt-tolerance genes in rice at the germination stage, and demonstrated the feasibility of using GWAS to elucidate the genetic factors underlying salt tolerance. This will provide important resources for molecular breeding and functional analysis of the salt tolerance of rice at the germination stage.