QTL-Seq identified a genomic region on chromosome 1 for soil-salinity tolerance in F 2 progeny of Thai salt-tolerant rice donor line "Jao Khao"

Owing to advances in high-throughput genome sequencing, QTL-Seq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and "Jao Khao" (JK), a Thai salt-tolerant variety. A total of 462 F progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G') analysis, which is based on calculating the allele frequency differences or Δ(SNP index). Both methods detected the overlapping interval region, wherein CMS-bulk was mapped at two loci in the 38.41-38.85 Mb region with 336 SNPs on chromosome 1 ( ) and the 26.13-26.80 Mb region with 1,011 SNPs on chromosome 3 ( ); the Δ(SNP index) peaks were -0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26-38.95 Mb region on chromosome 1 with 575 SNPs ( ) and a Δ(SNP index) peak of -0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the and traits on chromosome 1. Based on the CMS trait, stably expressed 6%-18% of the phenotypic variance in the two validation populations, while accounted for 16%-20% of the phenotypic variance in one validation population based on the TN trait. The findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage.