Mapping novel QTLs associated with grain number and primary branching in rice using new plant type derived RILs

The increase in the productivity of rice has become very limited due to limited major genes for key yield-attributing traits, namely, grain number per panicle, thousand-grain weight, panicle primary branching, and productive tiller number. To break this barrier, there’s an immediate demand to identify novel genes or quantitative trait loci (QTLs) from diverse germplasm. This study aims to address this challenge by specifically identifying genes and QTLs controlling grain number and primary branch number in order to facilitate future molecular breeding efforts. QTL mapping was done using a custom microsatellite linkage map constructed for the Recombinant inbred lines (RILs). RIL population consisting of 175 lines derived from PR126 and Pusa NPT34 were used for QTL mapping, and mapping population was evaluated at three locations namely Delhi, Karnal and Aduthurai. Total of 25 QTLs were identified for nine traits, among which 13 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. Seventeen 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 primary 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. In the present study, QTLs were mapped for grain number, panicle primary branching and yield attributed traits and identified two novel genomic regions for grain number and panicle primary branching. We have identified four QTL hotspots comprising 13 QTLS and the remaining QTLs present outside the hotspots. Further fine mapping of marker intervals can help in narrowing the genomic region and in identifying candidate genes to enable more precise marker-assisted selection for primary branches and grain number.