Molecular mapping of quantitative trait loci for flag leaf length and other agronomic traits in rice (Oryza sativa)

Flag leaf architecture is a very important trait which ensures the yield bearing capacity of plants by providing excellent source for photosynthesis. In this study, quantitative trait loci (QTLs) for flag leaf length and other traits were identified using rice recombinant inbred lines (RILs) derived from HP2216 × Tetep. A total of 12 QTLs were identified for the four traits located on seven different chromosomes of rice and analysis of interaction among the QTLs revealed additive effect for the leaf length and epistatic main effect for panicle length. More interestingly a QTL qLL12.1 responsible for the flag leaf length was identified on chromosome 12 within the marker interval RM247-RM6296 consistently at three climatic zones in India. Furthermore to saturate the qLL12.1 interval, additional 58 simple sequence repeat (SSR) markers were used for polymorphism survey which showed that qLL12.1 region was more conserved among parental lines. Finally, two polymorphic SSR markers were used for saturation of qLL12.1 region. Consequently, candidate gene approach was used to compliment QTL mapping. Co-localization of linkage map with physical map revealed 75 genes with evidence for expression. Functional annotation of these genes using in silico approaches and detailed literature search revealed nine candidate genes for flag leaf length. The stable QTL qLL12.1 identified in this study will provide starting point for map based cloning of leaf length related genes and tightly linked flanking markers can be used in marker assisted breeding programmes