Genome-wide association study of salt tolerance at the seed germination stage in rice

TLDR: Seven seed germination-related traits under control and salt-stress conditions and a genome-wide association study based on the re-sequencing of 478 diverse rice accessions are investigated to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection.

Abstract: Improving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions The analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT) From the SSI of VI, six major loci were identified, explaining 202% of the phenotypic variation From the SSI of MGT, five major loci were detected, explaining 264% of the phenotypic variation Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses The strongest association region for the SSI of MGT was identified in a ~ 133 kb interval (15450039–15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na+: K+ ratio, total Na+ uptake, and total K+ concentration The strongest association region for the SSI of VI was detected in a ~ 1642 kb interval (526662–690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT21 and OsNRT22), which affect gene expression under salt stress The haplotype analysis indicated that OsNRT22 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected These results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection