New QTL for Salt Tolerance at the Seedling Stage in Rice var. Hasawi Using Recombinant Inbred Lines

Novel quantitative trait loci (QTL) for seedlingstage salt tolerance were determined in Hasawi variety of rice (Oryza sadva L.) using 384-plex single nucleotide polymorphism (SNP) markers. The F6 recombinant inbred lines (RILs) population, which was produced from the cross IR29 x Hasawi, generated phenotypic data for seedling length and weight, biomass, shoot sodium (Na+) and potassium (K+) concentration, and Na-K ratio. Genotyping analysis resulted in a linkage map length of 1379.80 cM with an average of 8 cM interval, thereby producing a total of 17 significant QTLs. Most of the QTLs detected were for seedling vigor, specifically: two for visual salt injury (qSES1, qSES4); three for shoot length (qSL1, qSL9, qSL12); two for root fresh weight (qRFW4.1, qRFW4.2); three for root dry weight (qRDW12, qRDW4.1, qRDW4.2); one for reduction in root length (qRLRED1); two for shoot fresh weight (qSFW4 and qSFW12); three for shoot dry weight (qSDW4.1, qSDW4.2, and qSDVV7); and one for shoot sodium concentration (qSNC1). Two largeeffect QTLs from chromosome 1 were found to be responsible for 37.6% of the phenotypic variation in visual saltinjury score and 41.1% of the variation in shoot length. Four QTL clusters were found in this study: one in chromosome 1 for visual salt injury and shoot sodium concentration, two in chromosome 4 responsible for seedling vigor, and one in chromosome 12, contributing to vigor as well. The results suggest that Hasawi employs a different salttolerance mechanism since very few studies reported QTLs in chromosomes 2, 9, and 12. The single nucleotide polymorphism (SNP) markers which co-segregrated with identified QTLs could be potential candidates for markeraided breeding.