The Chaling wild rice(CL), four cultivated rice accessions, and a segregating F2 population derived from CL and a three-way cross of CL/Lun5S//R996 were used to select against the domestication genes Rc and Rd for pericarp color using marker-assisted selection(MAS). Significant sequence divergence was identified between the CL Rc allele and those of cultivated cultivars. Notably, a 14-bp InDel insertion in exon 6 of the CL Rc gene introduced an additional exon, thereby extending the coding sequence, whereas this insertion is absent in cultivated cultivars, leading to premature termination of translation. In contrast, the Rd alleles showed no functional variation between CL and cultivated rice, suggesting that Rc is the critical gene responsible for the brown-red pericarp of CL. Four functional markers(Rc-1, Rc-2, Rc-3 and Rc-4) were developed, of which Rc-2, Rc-3, and Rc-4 showed polymorphism between CL and cultivated rice and were effective for MAS. These markers were further converted into high-resolution melting(HRM) markers, enabling high-throughput genotyping without electrophoresis.