Mapping and Validation of Quantitative Trait Loci for Root Architectural Traits in Rice (<i>Oryza sativa</i>) under Non-Stress and Salinity Stress Conditions

Abstract

Root architectural traits are governed by many genes exhibiting polygenic inheritance. The dissection of the genetic basis of root traits could be achieved by mapping of quantitative trait loci (QTLs) using molecular markers. The present study was conducted aiming at identifying root QTLs in rice using a recombinant inbred line (RIL) population derived from At354 and Bg352. At354 has less extensive, thin root structure and Bg352 has apparently large extensive, dense root structure. Ninety one RILs were phenotypically assessed for root traits namely, root volume (RV), top root girth (TRG), root dry weight (RDW) and root length (RL) under hydroponics. Frequency distributions of these traits indicated broad spectrum of genetic variability in the RIL population. Quantitative Trait Loci (QTLs) were mapped using Single Nucleotide Polymorphism (SNP) markers investigated from a previous study corresponding to same RILs. Results revealed eight QTLs associated with TRG and RDW explaining phenotypic variation ranging from 8.3% to 14.8% under non-stress hydroponics. Identified root QTLs were located within the narrow flanking SNP marker intervals of chromosome 2, 4, 5, 7, 8 and 10. Of them, six root QTLs were co-localized exactly within the same flanking regions of previously identified root QTLs under salinity stress, indicating their contribution under both stress and non-stress conditions. The same donor alleles have contributed in both set of QTLs and these results validated and confirmed the fidelity of the QTLs detected on TRG and RDW. Moreover, this study found a closely associated, user friendly, simple sequence repeat marker, RM24894 to the QTL qNTRG10 and qNRDW10 which could facilitate marker assisted breeding.