New QTL for salt tolerance at the seedling stage in rice var. Hasawi using recombinant inbred lines
2017
Pascual, E.D. | Dela Viña, C.B. | Mendioro, M.S., | Hernandez, J.E., | Amas, J.C., | Sajise, A.G.C., | Gregorio, G.B
Novel quantitative trait loci (QTL) for seedling-stage salt tolerance were determined in Hasawi variety of rice (Oryza sativa L.) using 384-plex single nucleotide polymorphism (SNP) markers. The F sub 6 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 sup +) and potassium (K sup +) 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 qSDW7); and one for shoot sodium concentration (qSNC1). Two large-effect QTLs from chromosome 1 were found to be responsible for 37.6 of the phenotypic variation in visual salt-injury 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 chromosome 12, contributing to vigor as well. The results suggest that Hasawi employs a different salt-tolerance mechanism since very few studies reported QTLs in chromosomes 2, 9, and 12. The single nucleotide polymorphism (SNP) markers which co-segregated with identified QTLs could be potential candidates for marker-aided breeding.
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