SNP-based QTL mapping and identification of panicle structure-related genes in rice

Rice is a staple crop providing a significant portion of the global food supply. It is then crucial to develop strategies for breeding high-yield cultivars to meet global food security challenges, including the UN's zero-hunger goal. In this study, QTL mapping was employed to pinpoint key genomic regions linked to traits influencing rice yield, with a focus on panicle structure-a critical determinant of grain number. Over two consecutive years, QTLs were identified using 88 JJ625LG/Namchan Recombinant Inbred Lines (JNRILs), revealing several candidate genes. Notably, Gn1a, a known regulator of grain number, was mapped within qNS1 and qNSSr1-1, while the sd1 gene, linked to plant height, was detected across multiple QTLs. Furthermore, a novel gene, OsNSMq3 (Os03g0843800), encoding a methyltransferase, was identified in various QTLs, with haplotype and sequence homology analysis suggesting its role in enhancing yield by influencing panicle structure development. The increase in primary and secondary branches, driven by these genes, leads to a higher number of spikelets per panicle, thereby boosting yield. These findings underscore the potential of candidate genes from stable QTLs as valuable tools in molecular breeding to develop high-yield rice cultivars, addressing global hunger and aiding food supply in refugee crises.