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Identification of SNP and InDel variations in the promoter and 5′ untranslated regions of γ-tocopherol methyl transferase (ZmVTE4) affecting higher accumulation of α-tocopherol in maize kernel

Das, Abhijit Kumar, Chhabra, Rashmi, Muthusamy, Vignesh, Chauhan, Hema Singh, Zunjare, Rajkumar Uttamrao, Hossain, Firoz
The crop journal 2019 v.7 no.4 pp. 469-479
5' untranslated regions, alleles, alpha-tocopherol, corn, gamma-tocopherol, haplotypes, mutants, promoter regions, seeds, sequence analysis, single nucleotide polymorphism, transferases
Deficiency of vitamin-E or tocopherol causes neurological and cardiovascular disorders in humans. Though maize kernel is rich in total tocopherol, the level of α-tocopherol possessing the highest vitamin-E activity is low. Mutant allele of ZmVTE4 with deletion of 7 bp and 118 bp (0/0: most favorable haplotype) in 5′UTR and promoter region, respectively significantly enhances α-tocopherol in maize kernel than wild type haplotype (7/118). α-tocopherol estimation in 15 diverse inbreds revealed that mean α-/γ-tocopherol and α-/total-tocopherol was much higher in genotypes with favorable haplotype (1.51 and 0.41) than unfavorable class (0.19 and 0.13), respectively. However even within favorable class, α-tocopherol ranged from 4.76 to 30.07 μg g−1. Sequence analysis of part of 5′UTR and promoter of ZmVTE4 among the genotypes with favorable haplotype revealed 14 SNPs (SNP1 to SNP14) and eight InDels (InDel1 to InDel8). SNP7 at 606 bp (G to A), and InDels viz., InDel1 (27 bp), InDel4 (27 bp) and InDel8 (14 bp) differentiated low and high α-tocopherol accumulating inbreds with favorable haplotype. Hence the newly identified SNP and InDels in addition to the already reported InDels can be useful in selection of favorable genotypes with higher α-tocopherol in maize.