Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study

Abstract Background Grain weight and grain shape are important agronomic traits that affect the yield potential quality of rice. Both controlled by multiple genes. The 3,000 Rice Genomes Project (3 K RGP) greatly facilitates discovery agriculturally genetic variants germplasm resources for shape. Results Abundant natural variations distinct phenotic differentiation among subgroups in were observed a large population 2,453 accessions from 3 RGP. A total 21 stable quantitative trait nucleotides (QTNs) four consistently identified at least two 3-year trials genome-wide association study (GWAS), including six new QTNs ( qTGW3.1 , qTGW9, qTGW11 qGL4/qRLW4 qGL10 qRLW1 ) We further predicted seven candidate genes Os03g0186600 Os09g0544400 Os11g0163600 Os04g0580700 Os10g0399700 Os10g0400100 Os01g0171000 high-density gene-based haplotype analyses. favorable haplotypes five previously cloned elite with high TGW RLW also provided. Conclusions Our results deepen understanding basis rice provide valuable information improving through molecular breeding.