Allelic variation at capsanthin capsorubin synthase gene for ripening fruit color in chilli (Capsicum annuum L.)

Twenty six accessions of Capsicum annum with varied ripening color were screened for total carotenoids (0.0040.47%), red carotenoids (0–0.27%) and yellow carotenoids (0.004–0.2%) and also to obtain some new or useful alleles associated with ripening color in chilli, using gene-specific marker. Considerable genetic variability for carotenoids was observed along with the allelic variations of candidate gene Capsanthin capsorubin synthase (Ccs). The results revealed that Ccs gene coding region was present in yellow pepper line LCA 1068 (Aparna) suggesting Ccs gene deletion is not a prerequisite for change in color from red to yellow. Ccs coding region contained no introns but did exhibit polymorphism among chilli lines studied resulting in amino acid changes. Novel allelic variants were found in Byadagi Dabbi (dark red) and LCA1068 (yellow) in the study, which could provide candidate/allele specific molecular markers for selection of lines that may be used in chilli quality breeding for varied colors.