Identification of polymorphism and function of LCYE allele in sweet corns

【Objective】The purpose of this investigation was to identify the polymorphisms of LCYE gene and the variation of β-carotene and carotenoids for understanding LCYE allele function in sweet corns and providing the reference and basis for biofortification breeding of pro-vitamin A.【Method】 The contents of β-carotene and total carotenoid were measured by HPLC in 47 sweet corn inbred lines. The whole length of LCYE was amplified, cloned and sequenced. Association analysis was performed by combining the sequences of LCYE gene with the content of β-carotene and total carotenoid.【Result and conclusion】 The total of 75 polymorphism sites were detected in this study, which included 49 polymorphism sites located on the non-coding chromosome region and 26 polymorphism sites located on the exons of the LCYE gene. All these sites on the exons were SNPs and most of them were located on the fifth exon except for the forth and the ninth exon with a conserved sequence. All 13 detected INDELs located on the non-coding region. The fragment of these INDELs ranged from 1 to 40 bp and most of them were from 4 bp to 8 bp. Three polymorphic sites were detected to be associated with β-carotenoid and 6 polymorphic sites were detected to be associated with total carotenoid. Exon 1-2 and exon 5-6 were found to be significantly associated with these two phonotypes. The result identifies that LCYE gene is related to the biosynthetic pathway of the carotenoids and provides the theoretical basis for biofortificated breeding of pro-vitamin A in sweet corns.