Objective To identify the polymorphisms of functional markers for the key carotenoids biosynthetic genes PSY1, LCYE and CrtRB1 in sweet corn and their effects on the contents of carotenoid for a better understanding of the functions of these genes so as to provide a reference and basis for bio-fortification breeding of pro-vitamin A.

Method  The contents of carotenoid components were measured by HPLC in 47 sweet corn elite inbred lines.Six functional markers for PSY1, LCYE and CrtRB1 genes were synthesized and amplified to detect the genotypes of these lines.The effects of single gene haplotype and joint haplotype were analyzed using the functional polymorphic sites of PSY1, LCYE, and CrtRB1 genes together with the carotenoid content variation.

Result and conclusion  The polymorphism was detected in 5 functional markers except for indel4 for CrtRB1.The haplotype with Indel1and Indel4 for PSY1 could explain 14.81% of the zeaxanthin content variation and 13.00% of the total carotenoid content variation.The haplotype with 5′Indel and 3′Indel for LCYE could explain 15.77% of β-carotene content variation, 20.75% of pro-vitamin A content variation and 15.92% of the total carotenoids content variation.No significant effect was detected in the haplotype of CrtRB1.The joint haplotype of PSY1, LCYE and CrtRB1 could explain 37.20% of β-carotene content variation, 40.71% of pro-vitamin A content variation and 41.11% of the total carotenoids content variation.The joint effect of PSY1, LCYE and CrtRB1 was higher than that of single gene.PSY1 and LCYE genes are important in the biosynthesis of carotenoid.Their functional markers can be used in the molecular-assisted selection and provide a theoretical basis for biofortification of pro-vitamin A in sweet corn by breeding.