The New 5'-UTR LcyE Allele Correlates with Increased Expression of the Lycopene-ε-Cyclase Gene Determining the Flow of the β-ε Branch of the Carotenoid Biosynthesis Pathway in Maize

Abstract The color of the maize (Zea mays L.) grain is determined by the content and composition of carotenoids, including provitamin A, which is a product of the β-β (β-carotene, β-cryptoxanthin) and β-ɛ (α-carotene) branches of carotenogenesis. The ratio of the fluxes of the branches depends on the activity of the lycopene-ɛ-cyclase LcyE, which determines the β-ɛ branch. In this work, we analyzed allelic variants of the LcyE gene, which are potentially effective for increasing the biosynthesis of β-carotene, in 20 maize inbred lines of domestic selection, which differ in grain color. The 5'-UTR regions of the LcyE gene were amplified and sequenced. Fragment analysis showed the presence of allele 2 in four lines and the new allele 5 in 16 lines. The polymorphism of the new allele 5 was characterized—four single nucleotide polymorphisms and two deletions. The comparison of cis-regulatory elements in the analyzed 5'-UTR region in alleles 2 and 5 revealed a difference in binding sites with transcription factors. Expression of the LcyE gene was determined in the leaves of two lines with allele 2 and three lines with allele 5. A direct relationship was shown between the presence of allele 5 and a decrease in gene expression: the level of gene transcription in the case of allele 2 was 10–15 times higher than in the case of the allele 5. It has been suggested that the presence of allele 5 of the LcyE gene in the maize genome correlates with a decrease or suppression of the LcyE expression and, with stable activity of other carotenogenesis enzymes, with grain color. The use of allele 5 donors in combination with a known dark yellow or orange color of the grain can be used in the breeding of maize with increased synthesis of provitamin A in the grain.