Genetic analysis of purple pigmentation in rice seed and vegetative parts - implications on developing high-yielding purple rice (Oryza sativa L.).

Pigmentation in rice grains is an important quality parameter. Purple-coloured rice (Oryza sativa L.) indicates the presence of high anthocyanin with benefits of antioxidant properties. However, the genetic mechanism of grain colour is not fully understood. Therefore, the study focused on understanding pigmentation in grain pericarp and vegetative parts, and its relationship with blast resistance and enhanced grain yield. Three local cultivars from the northeastern region (NER) of India - Chakhao Poireiton (purple), Mang Meikri (light brown), and Kala Joha (white) - along with high-yielding varieties (HYVs) Shasharang (light brown) and Sahbhagi dhan (white) were used to develop biparental populations. The findings suggested that pigmentation in vegetative tissue was governed by the inter-allelic interaction of several genes. Haplotype analysis revealed that Kala3 complemented Kala4 in enhancing purple pigmentation and that Kala4 is not the only gene responsible for purple colour as evident by the presence of a desired allele for markers RID3 and RID4 (Kala4 locus) in Chakhao Poireiton and Kala Joha irrespective of their pericarp colour, implying the involvement of some other additional, unidentified genes/loci. RID3 and RID4 together with RM15191 (Kala3 locus) could be employed as a reliable marker set for marker-assisted selection (MAS). Pericarp colour was strongly correlated with colour in different vegetative parts, but showed a negative correlation with grain yield. Pb1, reported to be associated with panicle blast resistance, contributed to leaf blast resistance. Transgressive segregants for improved pigmentation and high yield were identified. The selection of lines exhibiting coloured pericarp, high anthocyanin content, aroma, blast resistance, and increased yield compared to their respective HYV parents will be valuable resources in the rice breeding programme.