Haplo-pheno analysis of the Rc gene reveals association with yield parameters in pigmented rice

Traditional rice genotypes often have pigmented pericarps such as green, red, brown and black, while widely cultivated varieties typically exhibit white pericarps. Although white polished rice is generally preferred for consumption, pigmented rice offers notable health benefits due to its antioxidant properties. However, pigmented rice varieties typically have lower yield potential compared to white rice varieties. To address this limitation, we employed haplotype analysis to explore associations between pericarp pigmentation and yield traits. Since the Rc gene is a major regulator of pericarp colour in rice, the haplotypes of the Rc gene were characterized using 231 accessions from the 3K rice panel, categorizing them by three distinct pericarp colour scores (scores 0, 1 and 9). The score 0 consists of accessions with green, brown, red, light red, dark red and black pericarp colours. Score 1 includes non-pigmented rice accessions having white and off-white pericarp colours. Score 9 is a subset of score 0 and it includes accessions depicting various shades of red in the pericarp colour. The major haplotype H2, associated with score 0, was significantly enhanced (p value <0.05) in the number of panicles and tillers per plant. For pericarp colour score 1, the haplotype H2 was identified as superior, exhibiting significantly (p value <0.05) earlier flowering, reduced chaffy grains and increased tillers per plant. These findings suggest that haplotype-based breeding of pigmented rice varieties targeting superior haplotypes associated with increased yield traits offers a promising strategy to enhance the yield potential of coloured rice.