Genetic variation and assessment of seven salt tolerance genes in an Indica/Xian rice population

Soil salinity is a major abiotic stressor that influences rice during the entire growth period. Breeding and planting salt-tolerant (ST) rice is an efficient strategy for sustainable agriculture. However, only a few elite natural variations conferring rice salt tolerance have been identified, and the distribution and genetic effects of those ST genes remain poorly understood. Here, we investigated the distribution of seven genes with nine ST-associated single nucleotide polymorphisms (SNPs) in a sequenced Indica/Xian rice population comprising 550 accessions. On the basis of the genotyping of nine SNPs, all the rice accessions were categorized into 21 haplotypes, each of which contained at least four ST genes. Among the nine SNPs, only SKC1 ^184H and OsHKT1;1 ^94K were relatively rarely distributed in this population. Comparative analysis of ST for grouped haplotypes with different target genotypes was performed, and we validated the effects of ST on SKC1 , OsHKT2;3 , OsHKT1;1 , RST1 and OsWRKY53 in multiple rice accessions. Interestingly, we found that SKC1 ^184H plays synergistic roles in ST with SKC1 ^140A and that SKC1 ^184H may originate from rice carrying SKC1 ^140A . RST1 ^530A was previously reported to be associated with salt sensitivity, but it should be corrected to be associated with ST and concurrently with RST1 ^611G in this study. Moreover, we found that OsHKT1;1 ^94K may participate in ST after extended salt treatment, and the expression of OsWRKY53 ^173G was positively correlated with that of SKC1 and conditionally participated in ST dependent on either SKC1 ^140A or SKC1 ^184H . Overall, our results provide further insight into the mechanism and marker-assisted selection improvement of ST in Indica/Xian rice.