Mapping Novel QTLs Associated with Grain Number and Primary Branching in Rice using New plant type derived RILs

Background Grain number per panicle, thousand-grain weight, panicle branching and productive tiller number per unit area are the major yield-attributing traits in rice. The yield plateau for more than two decades, demands for the identification of novel genes or QTLs (genome) from diverse germplasm. The current study aims to identify the genes/QTLs for grain number and primary branch number using yield-attributing traits. Results RIL population consisting of 175 lines derived from PR126 and Pusa NPT34. Total of 25 QTLs were identified for different traits, among which 18 were found distributed in five hotspots. Seven QTLs were having major effects and the remaining showed minor effects on the respective target traits. QTLs, qFGN9.1 for grain number lying at the marker interval, RM444-RM6920 and qPBN11.1 for primary branches lying at the marker interval of RM144-RM6965 on chromosome 9 and 11, were found novel respectively. A largest QTL hotspot on chromosome 6, harboured QTLs for GN, PH, PL, PBN, and YLD. 17 putative candidate gene models were identified through in silico analysis which involves in inflorescence development. The major gene models include APETALA genes, MADS box family proteins and WD40 which directly controls panicle branching, spikelet development. Therefore, further fine mapping of marker intervals can help in narrowing the genomic region and trait specific marker development. It enables more precise introgression of QTLs, for primary branches, grain number and other panicle architecture related traits into elite cultivars. Conclusion The scope of future study may involve the fine mapping of the major QTLs to identify the more closely linked marker, development of gene based or functional markers and cloning to understand the molecular mechanism of the gene/QTLs. It also helps us to use these genes in breeding program for more precise marker assisted selection and transfer.