Grain shape in rice: a Genome-wide association study of the effector genes

Rice is an important grain crop widely cultivated across the world. Its yield and quality have always been the focus of breeders’ attention, significantly impacting world food security. Rice grain shape, primarily characterized by grain length and width, is an important quantitative trait controlled by multiple genes, which not only directly affects rice yield but is also closely related to rice quality. Therefore, mining and utilizing the main QTLs and genes responsible for grain shape regulation is significant for breeding high-yielding rice varieties. In this study, 265 natural population materials were used to characterize the related phenotypes of grain length (GL), grain width (GW), and the grain length-width ratio (GLWR) over 2 years, revealing abundant phenotypic variations. Genome-wide association studies (GWAS) combined with 4,451,085 single-nucleotide polymorphism (SNP) markers distributed on 12 chromosomes, identified 61 significantly related QTLs, 14 of which are similar to previously reported rice grain type-related loci. Among these 61, three GL related QTLs (qGL3.1, qGL3.2 and qGL10.2), 1 GW related QTL (qGW5.1) and 11 GLWR related QTLs (qGLWR2.1, qGLWR2.3, qGLWR3.3, qGLWR3.4, qGLWR3.5, qGLWR4.2, qGLWR5.2, qGLWR5.3, qGLWR6.1, qGLWR9.2 and qGLWR10.2) were detected in two consecutive years. Three candidate genes, LOC_Os03g39710, LOC_Os05g09480, and LOC_Os09g36350, were identified through functional annotation and haplotype analysis of these co-existing QTLs. In brief, we detected 14, 12, and 35 QTLs associated with GL, GW, and GLWR, respectively. We further screened the grain shape-related candidate genes by functional annotation and haplotype analysis of all genes in the QTL regions. This study lays the foundation for further cloning and genetic regulation of rice grain-shape genes, providing innovative insights for rice molecular breeding designs.