Molecular characterization of 5' UTR of the lycopene epsilon cyclase (lcyE) gene among exotic and indigenous inbreds for its utilization in maize biofortification.

Maize grains are the important source of food and energy, but possess very low proA (< 2.5 µg/g) compared to target level of 15 µg/g set by HarvestPlus to alleviate VAD. Favorable allele having variation in 5' untranslated region (UTR) of lycopene epsilon cyclase (lcyE) gene enhances concentration of proA in maize. To identify the sequence variation in 5' UTR of lcyE, a set of diverse 13 inbreds of indigenous and exotic origin was characterized for allelic constitution of lcyE. Inbreds possessed wide variation in proA (1.62-23.12 µg/g) with a mean of 9.64 µg/g. The proA in CIMMYT-HarvestPlus genotypes having favorable allele of lcyE was very high (22.28 µg/g), whereas the Indian inbreds with the same allele possessed very low proA (2.48 µg/g). Eight genotypes viz., HKI161, HKI163, HKI161-PV, HKI163-PV, HKI193-1-PV, HKI193-2-PV, HP704-22 and HP704-23 revealed the presence of favorable allele, while VQL1, DMRIL47, MGU-PV-123/C6, HKI193-1 and HKI193-2 showed the presence of unfavorable allele of lcyE gene. Sequence comparison of favorable allele of Indian (HKI161 and HKI163) and exotic genotypes (HP704-22 and HP704-23) revealed seven SNPs having three transitions (SNP1 and SNP3: G to A, SNP2: C to T) and four transversions (SNP4: C to G, SNP5: T to G, SNP6: G to C and SNP7: G to T). Four SNPs (SNP1: position 446, SNP2: position 458, SNP3: position 459 and SNP4: position 483) discriminated the low- and high- proA lines having favorable allele of lcyE 5'TE. These SNPs hold significance in enrichment of proA in maize for marker development and their use in marker-assisted selection.