Objective 3: Designing and validation of gene-based marker(s) for lpa-1 and lpa-2 in maize:

Selected maize inbreds contrasting for phytate content were subjected to molecular analysis with the primers designed from lpa-1 gene sequence obtained from NCBI. The Gene specific primers were designed from the primer blast and the following are the details of the lpa-1 gene specific primers.

Lpa-2 gene (GRMZM2G456626) sequence was retrieved from MaizeGDB. Primers were designed from the reference sequence. Complete gene was amplified from available lpa-2, VQL1, V407 and VQL373. Overlapping primers were used to sequence complete gene from all these four genotypes. Only one (G/A) SNP was found in the coding region. As non-low phytate genotype VQL1 and low phytate genotype lpa-2 carry same allele of that SNP (G), it does not appear to be a functional polymorphism.