Genome-Wide Association Studies of Salt-Tolerance-Related Traits in Rice at the Seedling Stage Using InDel Markers Developed by the Genome Re-Sequencing of IJaponica/I Rice Accessions

Japonica-specific markers are crucial for the analysis of genetic diversity, population structure, evolutionary traits, and genome-wide association study (GWAS) of japonica germplasm accessions. This study developed 402 insertion–deletion (InDel) polymorphic markers based on the re-sequencing of four japonica rice landraces and three japonica rice cultivars. These InDel markers were uniformly distributed across 12 rice chromosomes with high polymorphism and good amplification specificity. The average density of InDel markers on each chromosome was 0.95 Mb per locus. On the basis of these InDel markers, genetic diversity analyses and GWASs for 12 salt-tolerance-related traits were performed using 182 japonica rice accessions. In total, 1204 allelic variants were detected, with an average of 3.00 alleles and 2.10 effective alleles per locus. Based on population structure analysis, 182 japonica rice accessions were divided into four subgroups. The GWAS analyses revealed a total of 14 salt-tolerance-related InDels, which were located on chromosomes 1–5, 9, 10, and 12. Twenty-eight allelic loci were identified, explaining 6.83% to 11.22% of the phenotypic variance. Haplotype analysis detected six InDel markers associated with salt-tolerance-related traits that were significantly different (p < 0.05) or highly significantly different (p < 0.01) among different haplotypes. These markers can be utilized for the molecular identification of salt-tolerant rice germplasm accessions.