Oryza nivara allele of a major effect QTL qFLA1.1 increases flag leaf area in rice

A stable back cross introgression line IL65 (IET22161) (Swarna/O. nivara-BC2F6) of rice was used to map flag leaf related traits in F2 and F3. A total of 12 QTLs were mapped for flag leaf related traits on two chromosomes with each QTL explaining 3 to 21% phenotypic variance (PV). Interestingly, a novel 12Mb QTL cluster (RM8094 - RM9) that controls 7 traits was identified on long arm of chromosome 1 where QTLs qSPAD1.2, qSPAD1.3 for SPAD, qFLL1.1, qFLL1.2 for flag leaf length, qFLW1.1, qFLW1.2 for flag leaf width, qFLA1.1, qFLA1.2 for flag leaf area, qPH1.1, qPH1.2 for plant height, qDTF1.2, qDTF1.3 for days to flowering and qHI1.2, qHI1.3 for harvest index were co-located. Among these, one major effect QTL qFLA1.1 for flag leaf area was identified in a 9Mb region between RM8094 and RM5638. There was an adjacent minor effect QTL qFLA1.2 in a 3Mb region between RM5638 and RM9. Together these two QTLs and with leaf area increasing QTL allele from O. nivara explained 19.7% PV. The QTL for flag leaf related traits can be fine mapped and considered for breeding rice varieties with higher flag leaf area, photosynthetic rate and grain yield.