Sequence variation in 3'UTR region of crtRB1 gene and its effect on β-carotene accumulation in maize kernel

beta-carotene fortification of maize has emerged as a potential, long-term and sustainable approach to alleviate vitamin A deficiency in humans. Among the several genes involved in the carotenoid biosynthetic pathway, the 543 bp allele at crtRB1 3'TE (Transposable Element) gene (allele 1, without insertion) is associated with higher beta-carotene accumulation. Estimation of beta-carotene through high performance liquid chromatography showed that the CIMMYT genotypes with allele 1 had high kernel beta-carotene content whereas the Indian inbreds with the same allele had low beta-carotene content. To know the reason for this variation, allele 1 of crtRB1 3'TE gene was sequenced from a set of 11 diverse maize inbreds collected from CIMMYT and Indian germplasm. The sequence data of the allele 1 revealed the presence of 13 single nucleotide polymorphisms (SNPs) and 7 insertions and deletions (InDels). Exonic region had two SNPs, intronic region had one SNP and one InDel, whereas 3'-untranslated region (UTR) region of the gene showed 10 SNPs and 6 InDels. Among the several SNPs and InDels, SNP4, SNP13, InDel6 and InDel7 identified in the 3'-UTR region clearly differentiated the high and the low beta-carotene genotypes. These 3'-UTR polymorphisms in allele 1 of the crtRB1 3'TE gene could be associated with the variation in kernel beta-carotene accumulation by regulating the translation and stability of the mRNA. The SNPs and the InDels associated with higher level of beta-carotene will be used as a gene-based marker(s) in selection of genotypes and to develop biofortified maize hybrids to alleviate vitamin A deficiency in humans.