Development of a single nucleotide polymorphism (SNP) marker for detection of the low phytic acid (lpa1-1) gene used during maize breeding

Breeding for low phytic acid (LPA) in maize is hampered by a tedious and destructive colorimetric assay in mature dry grain. There are no molecular markers available for the single recessive gene of lpa1-1, restricting breeding programmes. The aim of this study is to develop a molecular marker to identify the lpa1-1 gene at the early vegetative plant stage. The parental lines are temperate LPA line (CM 32) and tropical line (P 16). The lpa1-1 allele is due to a single amino acid change from alanine to valine. The nature of the single nucleotide polymorphism (SNP) marker was validated by DNA sequencing of the parental PCR products. Using high resolution melt (HRM) profiles and normalised difference plots, we successfully differentiated the homozygous dominant (wild type), homozygous recessive (LPA) and heterozygous genotypes. The reduced phytate content of the LPA parental line was confirmed. The profiles from low cost crude and high quality DNA extraction were comparable when distinguishing between the parental lines. The cost of HRM analysis was 8% of the cost of PCR amplification and DNA sequencing. The development of the marker will make maize breeding for LPA efficient and fast, and it will enable the earlier release of lpa1-1 varieties.Keywords: High resolution melt (HRM) analysis, low phytic acid, maize, single nucleotide polymorphism (SNP) markerAfrican Journal of Biotechnology Vol. 12(9), pp. 892-90