Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativaL.) Using QTL-Seq and RNA-Seq

Background Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited. Results Here, an F(2:3)population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL,qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using Delta SNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed nearqRSL7, and regional QTL mapping was performed using 199 individuals from the F(2:3)population. We then confirmed and narrowed downqRSL7to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference inOs07g0569700(OsSAP16) between IR36 and Weiguo.OsSAP16encodes a stress-associated protein whose expression is increased under drought stress. Conclusion These results indicate thatOsSAP16was the candidate gene ofqRSL7. The results is useful for gene cloning ofqRSL7and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).