SLAF-based construction of a high-density genetic map and its application in QTL mapping of carotenoids content in citrus fruit.

Carotenoids are important antioxidant components in the human diet. To develop carotenoid-rich agricultural products by genetic intervention, understanding the genetic basis of carotenoids variation is essential. In this study, we constructed a high-density integrated genetic map with 3,817 molecular markers using specific-locus amplified fragment (SLAF) sequencing from a C. reticulata x P. trifoliata F1 pseudo-testcross population. A total of 17 significant quantitative trait loci (QTLs) distributed on Chromosomes (Chr) 2, 3, 5, 6 and 9 were detected to determine the carotenoid variation in the population. In particular, three QTL co-localizations for multiple carotenoid constituents were observed on Chr 2, 3 and 9, one of which was located on Chr2: 34,654,608~ 35430715 accounted for 20.1%~ 25.4% of the variation of luteoxanthin, auroxanthin, lutein, violaxanthin and the total carotenoid content. Overall, this study provides a genetic foundation for marker-assisted selection (MAS) breeding of nutritionally enhanced citrus fruit.