Cloning and functional analysis of the main QTL gene qBGW1 that controls rice grain width

Rice yield is determined by three factors, namely single grain weight, the number of grains per panicle and the number of panicles per unit area. Although many rice yield- related gene loci have been characterised, how grain size development is genetically controlled remains unclear. We have isolated a large-grain mutant in the background of the japonica rice variety Azucena (AZU). Using a large population for genetic crossing, quantitative trait loci (QTL) localisation and bulked segregant analysis, we have successfully cloned the main QTL gene responsible for the grain width and named it qBGW1. This gene, unlike the previously reported ‘big-grain’ genes, encodes a transcription factor that may function in the light signalling pathway during grain development. Furthermore, the 5′-flanking sequences, namely the promoter regions, of this gene in japonica and indica rice varieties are highly variable, suggesting potential differential regulation at this locus by upstream regulators on grain width. In the proposed study, we will first construct the knockout mutants and overexpression lines of this gene in japonica and indica rice varieties, respectively, for phenotyping. Subsequently, physiological, biochemical and molecular approaches will be used to analyse how the light signal regulates the expression of qBGW1 and the development of grain width in these transgenic lines. To determine the downstream target genes and upstream regulators of qBGW1, traditional RNA sequencing experiments will be performed in parallel with chromatin immunoprecipitation sequencing and molecular methods for further validation. The outcome of this study would be: (a) the understanding of the function and molecular mechanism of qBGW1 in rice, (b) the development of molecular markers of this gene for marker-assisted selection and breeding, and (c) the construction of some useful germplasm resources for rice high- yield breeding.