Haplotypes Differences in Growth Regulating Factor 4 (GRF4) for Yield and Biomass Traits in Rice (Oryza sativa L.)

Haplotype breeding assists in improvement of traits through introgression of superior haplotypes. Growth Regulating Factor 4 (GRF4) regulates yield and nitrogen use efficiency in rice. Further, through regulation of MYB61, GRF4 also regulates the plant biomass in rice. However, the trait effects of different GRF4 haplotypes on yield and biomass relationship is not understood properly. This study hypothesised that GRF4 haplotypes affects the yield and biomass relationship and studied the haplotype differences of GRF4 in 335 rice accessions for yield and biomass relationship. Fixation index (Fst) of GRF4 haplotypes were found to be higher (0.31) between indica and japonica as compared to indica and aus (0.18), japonica and aus ecotypes (0.18). Further, marker trait association identified five significant associations one for flag leaf length (Chr02:28862688), two each for biomass (Chr02:28862385, Chr02:28868744) and grain number (Chr02:28861294, Chr02:28863481), and one for seed yield per plant (Chr02:28868744). Among the traits associated with haplotypes, Hap4 showed higher yield and biomass relationship (r2 = 0.82), whereas the superior haplotype for yield (Hap1) showed relatively lesser biomass and yield relationship (r2 = 0.60). Besides, two favourable SNPs regulating grain number and non-favourable SNP for flag leaf width was fixed in the IRRI elite lines and popular rice varieties. This indicates yield and biomass relationship between the GRF4 haplotypes varies in the rice genotypes. Further, balancing the breeding or genome editing strategies for yield and biomass has potential for genetic improvement in rice.