Grain Yield Gene Sequence Analysis across 3K RGP Panel Provides Elite Haplotypes and Haplotype Combinations for Rice Yield Improvement

Grain size is a quantitative trait controlled by multiple genes. Though many genes regulating grain size have been reported in rice, their superior haplotypes or haplotype combinations for developing elite varieties remain elusive. In this study, we found that haplotypes of 35 previously functionally characterized genes governing grain yield significantly varied in the 3000 rice genome project (3K RGP) panel. Twenty-four of these genes had 2–6 haplotypes based on non-synonymous single nucleotide polymorphisms (SNPs), while the remaining 11 genes had only one haplotype. A total of 75 haplotypes in the 24 genes were identified. Also, we conducted an association analysis between the 75 haplotypes and 100-grain weight, and found that haplotype SG1c had the highest grain weight, followed by GW8e and DEP1e, while GW8f and GLW7d had the lowest. Furthermore, OsBAK1, D2, TGW6, BG1, SRS3, GL7, GW8 and GW6a haplotypes could distinguish japonica and indica, and thus were associated with rice domestication. Haplotype combination analysis showed that four haplotypes including MAPK6b, BAK1b, GL7d and SRS3b were the superior haplotype combination, and explained a possible genetic basis for accession superiority with the highest grain weight. Haplotype identification of genes controlling grain size variation will provide the theoretical basis for developing elite rice varieties with superior haplotypes or haplotype combinations of target genes and provide valuable molecular breeding targets.