Deciphering the inheritance and QTL-seq aided mapping of the candidate locus governing pericarp pigmentation in Manipur black rice

Manipur black rice is a speciality rice characterised by black pigmented pericarp due to anthocyanin accumulation. We have investigated the inheritance of black pericarp pigmentation through classical genetic analysis in a Manipur black rice cultivar, Chakhao Poireiton. Total anthocyanin content was quantified using cyanidin-3-glucoside and peonidin-3-glucoside as standards in an F2: 3 population generated from the cross, Pusa 1652/Chakhao Poireiton. Also, mapping of the putative candidate loci was attempted using QTL-seq approach. The trait genetics indicated supplementary gene action with a segregation ratio of 9 (black): 3 (brown): 4 (white). QTL-seq analysis identified a genomic region between 26.82 to 27.97Mb on chromosome 4 as associated with pericarp colour. The identified region was found to carry three putative genes, LOC_Os04g47040, LOC_Os04g47059 and LOC_Os04g47080 with functions associated with pericarp colouration. Besides, 10 SNPs with modifier effect were identified in the intergenic region between LOC_Os04g47040 and LOC_Os04g47059, indicating possible regulation of trait in the upstream of LOC_Os04g47059, which needs further validation. Segregation pattern and the putative candidate loci identified in this study implicate future advancements toward breeding black rice.