[Map-based cloning and functional analysis of the golden panicle and brown rice gene gpr1]

The colors of panicle hull and brown rice are crucial agronomic traits in rice, which are widely used in breeding and genetic research. Here, a rice variety named 'LAL SAR' characterized by golden panicle and brown rice was identified from Nepal. Genetic analysis revealed that these phenotypes were controlled by a single recessive nuclear gene, which was designated as gpr1 (golden panicle and brown rice 1). Using the strategy of map-based cloning, we mapped gpr1 into a 47 kb interval on the rice chromosome 3 and identified its candidate gene as LOC_Os03g60509. This gene encodes a chalcone isomerase, a key enzyme in the flavonoid biosynthetic pathway. Through PCR sequencing and RT-PCR analysis, a long-fragment insertion was found in the promoter of gpr1 in 'LAL SAR', which completely suppressed the expression of this gene. Using CRISPR/Cas9 technology, we successfully knocked out GPR1 (the dominant allele of gpr1) from a Oryza sativa subsp. japonica variety 'Zhonghua 11'. The knockout mutant plants exhibited golden panicles and brown rice, with significantly increased naringenin chalcone content in the hull. Our results indicate that GPR1 participates in the flavonoid biosynthesis, providing a critical theoretical foundation and a gene resource for rice quality improvement and genetic enhancement.