Mapping of Quantitative Trait Locus QTL for drought tolerance in rice

Abstract

newline Drought is a major abiotic constraint for rice production worldwide. The newlinereproductive stage drought stress (RSDS) leads to a huge loss in grain yield. The newlineprospecting of new donor cultivars with identification and introgression of large effect newlinedrought tolerance related QTLs is essential to develop drought-tolerant rice varieties. The newlinepresent study was conducted with the aim of mapping quantitative trait locus (QTLs) newlineassociated with drought tolerance in rice. newlineWith a total of 3417 GBS (Genotyping by sequencing) based polymorphic SNP newline(Single nucleotide polymorphism) markers distributed over the rice chromosomes a newlinesaturated linkage map spanning 1924.136 cM was constructed with an average marker newlinedensity of 0.56 cM using an F3 mapping population developed by crossing traditional Ahu newlinerice cultivar Koniahu (drought tolerant) with Disang (drought susceptible). Using inclusive newlinecomposite interval mapping (ICIM) approach 172 genomic regions associated with grain newlineyield and related traits were detected in 198 F3 and F4 segregating lines evaluated for two newlineconsecutive seasons under both RSDS and irrigated control conditions. Of which, 102 newlineQTLs were identified under RSDS with LOD (Logarithm of odds) score value ranging newlinebetween 2.53 to 7.51 and phenotypic variance explained (PVE) value of 1.97 to 12.42 per newlinecent. While 70 QTLs with LOD score value ranging between 2.50 to 10.07 and PVE value newlineof 2.35 to 11.46 per cent were detected under control condition. In total, nine QTLs were newlinemajor QTLs having a PVE value 10. Among the QTLs identified under RSDS, 72 newline(70.59%) QTLs were novel whereas 30 (29.41%) QTLs were observed to be co-localized newlineor overlapped with genomic regions previously mapped for the same trait/ QTLs. Five newlineputative QTLs namely, qGY2.00, qGY5.05, qGY6.16, qGY9.19, qGY10.20 were found to newlinebe associated with grain yield under drought. Further, fourteen CAPS (Cleaved Amplified newlinePolymorphic Sequences) were developed from selected eight novel QTLs linked SNP newlineregions and validated in parental cultivars along with ten F5 generation RILs. Putative gene newlineidentification within eight QTL regions detected a total of 3341 genes in which 1516 newline(45.63%) genes were annotated to at least one gene ontology (GO) term. newlineThe putative QTLs and candidate genes identified in the present study need to be newlinefurther validated, which will be helpful for the improvement of drought tolerance in rice.