Identification of QTL for seedling stage salinity tolerance in rice (Oryza sativa L.) using selective genotyping

The main objective of this study was to use a selective genotyping strategy to map seedling stage salt tolerance quantitative trait loci (QTL) in rice and compare them to previously found QTL for this characteristic. Under hydroponics condition, 1156 F2 populations produced from a hybrid between a salt-sensitive variety (ADT 45) and a salt-tolerant landrace (Nona Bokra) were assessed for seedling stage tolerance. Based on salinity screening, the F2 population had 131 resistant and 48 sensitive extremes, and their selfed progeny (F3) were evaluated for physiological parameters associated to salt tolerance and yield components. Salinity screening resulted in the selection of 36 most tolerant and 24 most susceptible individuals from the F2 and F3 population. In this population, the realized heritability for salt tolerance was determined to be 0.26. Genotyping was carried out on 60 chosen F2 plants using 70 polymorphic markers, yielding a genetic linkage map extending 1795 cM with an average marker interval of 25.64 cM. Trait-based analysis (TBA) or selective genotyping was used for discovering a total of 16 QTL for QTL mapping, with the majority of QTL influencing the shoot Na+:K+ ratio. One Saltol locus, which was closely related to marker RM3412, had a LOD score of 5.43 and accounted for 34% of the phenotypic variance in shoot Na+:K+ ratio. The Saltol area co-localized QTL for shoot Na+:K+ ratio, shoot Na+ content, and leaf chlorophyll content. The discovered QTL on chromosomes 1, 3, 5, 6, and 12 correlate to previously identified salt tolerance areas, making them prospective marker-assisted selection (MAS) candidate QTL for MAS. Overall, this study adds to our understanding of the genetic basis of salt tolerance in rice and identifies prospective QTL for future breeding efforts utilizing MAS.