Mapping immature fruit colour‐related genes via bulked segregant analysis combined with whole‐genome re‐sequencing in pepper (Capsicum annuum)

Abstract

AbstractFruit colour is one of the most intuitive economic traits attracting consumers' attention for horticultural crops. Many genes associated with mature fruit colour have been identified in pepper, but genes influencing immature fruit colour are mainly unknown. In the present study, pepper inbred lines with light‐yellow (CSJ009) and green (CSJ010) immature fruit colour were used as female and male parents, respectively, to generate an F2 segregation population. Genetic analysis indicated that the light‐yellow immature fruit colour in CSJ009 is controlled by a single recessive gene, tentatively named as ly. The single‐nucleotide polymorphism (SNP)‐index analysis and genetic linkage analysis delimited the ly locus into a 6.51 Mbp region on chromosome 9, and four candidate genes Capana09g000680, Capana09g000671, Capana09g000715 and Capana09g000692 were identified in the linkage region. Nonsense mutation of APRR2 may be responsible for the low carotenoid content in immature CSJ009 fruits. These results lay a foundation for future immature fruit colour improvement via molecular genetics approaches and further identification of new immature fruit colour‐related genes in pepper.