Combined QTL-seq and QTL mapping strategies identify genes related to alkalinity tolerance in rice seedlings

Soil alkalinity can expose plants to deleterious stress that can limit plant growth and development, reducing crop productivity. While many studies have explored the damage that high salt levels can cause to rice crops, there has been only limited research focused on rice adaptation to alkaline stress conditions. In the present study, the duration of seedling survival and associated physiological traits when exposed to alkaline conditions were assessed in 920 F 2:3 populations crossed from Ken-jing8 and Dong-nong425 rice varieties. Three relevant quantitative trait locus (QTL) were identified through a combination of a QTL-seq-based SNP index and an ED algorithm, with the highest identified peak at qATS9 . Further genotype scanning was performed for these 920 lines, and a linkage map was constructed with KASP markers that were anchored at qATS9 within a physical interval of 57.01 Kb. The relationships between the qATS9 locus and the survival days of seedlings, shoot Na + concentration, root Na + concentration, and shoot K + concentration under alkaline stress were assessed, revealing that this locus explained 13.9–18.0% of total phenotypic variance. Whole genome sequence information from both parents and analyses of differential expression patterns under alkaline stress conditions were used to identify candidate genes associated with this locus, including a C 2 H 2 zinc finger protein (LOC_Os09g27650), an F-box domain-containing protein (LOC_Os09g27660), and a microtubule-associated protein (LOC_Os09g27700). Overall, these results highlight the value of combining QTL-seq and KASP marker-based linkage mapping as means of identifying candidate genes associated with particular phenotypes of interest. In future work, allelic variants of these candidate genes in the Ken-jing8 parental variety, which exhibits superior tolerance for alkaline conditions, will be analyzed to better understand the molecular basis of alkaline tolerance in rice crops in an effort to breed more resilient cultivars.