Genetic diversity of lycopene epsilon cylase, a carotenoid synthetic gene, among Thai local and commercial papaya cultivars

Carotenoids are groups of tetraterprenoids found naturally contributing to peel and pulp colour in fruits. Carotenoids play important roles in human health including being provitamin A and antioxidants. Papaya (Carica papaya L.) is among fruits with high carotenoid contents with yellow, orange and red flesh colour containing variation of carotenoid molecules. Within carotenoid biosynthetic pathway, conversion of lycopene to alpha carotene by lycopene epsilon cyclase (Lye) is one of the crucial steps for regulating carotenoid content. In this study, genetic diversity of Lye was investigated in fifteen papaya samples. Sequence analysis indicated the presence of a single copy of this gene locating in supercontig 28 of papaya genome. Twenty-four pairs of gene specific primers were designed and used to amplify DNA fragment with approximate size of 520-600 base pairs. The results revealed a total of 22 single nucleotide polymorphisms (SNPs) and 3 insertion/deletion. SNPs type C/T had the highest frequency. Almost all of DNA variation was located in intron. One C/A transversion resulted in the conversion of amino acid serine to arginine in exon 1. Phylogenetic analysis indicated that Lye genes from these papaya samples could be divided into two clusters; solo type and Mexico type.