Novel quantitative trait loci for yield and yield related traits identified in Basmati rice (Oryza sativa)

Increasing crop productivity is one of the prime goals of crop breeding research. Rice grain yield is a complex quantitative trait governed by polygenes. Although several QTLs governing grain yield traits have been reported and limited attempts have been made to map QTLs for grain yield parameters in Basmati rice. A population from the cross Sonasal and Pusa Basmati 1121 comprising 352 RILs was generated through the single seed descent method. A total of 12 QTLs governing yield and yield-related traits were mapped on six chromosomes, namely, 1, 2, 3, 7, 8 and 9, of which five QTLs were novel. We identified a novel and robust epistatic QTL (qPH1.1 and qPL1.1) governing plant height and panicle length, flanked by the markers RM5336-RM1 on chromosome 1. The gene encoding brassinosteroid insensitive 1-associated receptor kinase 1 precursor is the putative candidate gene underlying this epistatic QTL. Another novel QTL, qNT3.1, governing tiller number was bracketed to a region of .77 Mb between the markers RM15247 and RM15281 on chromosome 3. Of the 57 annotated gene models, Os03g0437600 encoding alpha/beta-fold hydrolase, a homologous to AtKai2 is a putative candidate gene underlying the novel QTL qNT3.1. The other QTLs such as qDFF1.1 governing days to 50% flowering co-localizes with the gene Ghd7, QTL for plant height qPH1.2 co-localizes with the gene sd1, the QTLs for panicle length co-localizes with FUWA and DEP2, the QTL for tiller number co-localizes with OsRLCK57 and QTLs for thousand-grain weight co-localize with the major gene GS3. The QTLs identified in the current study can be effectively used in marker-assisted selection for developing Basmati rice varieties with a higher yield.