Unraveling molecular architecture, development and validation of Anthocyanin1 gene-based novel breeder-friendly markers for utilization in genomics-assisted breeding of blue maize

Abstract

Anthocyanin-rich ‘blue maize’ is emerging as a superfood worldwide. Traditionally maize grains lack anthocyanin, thus warrant attention from the breeders. Here, full-length 4467 bp Anthocyanin1 (A1) gene was sequenced among five wild-type (A1) and five mutant (a1) maize inbreds. A set of 21 InDel-based markers was developed and used for studying allelic diversity among 28 wild-type and 20 mutant-type inbreds. The major allele frequency ranging 0.417–0.938 had polymorphism information content ranging 0.110–0.574. Phylogenetic analysis categorized 48 inbreds into two clusters and 47 haplotypes. The epimerase domain of the Nicotinamide adenine dinucleotide (NAD)-dependent epimerase family was identified as a major functional domain of 357 amino acid long dihydroflavonol-4-reductase protein. Two polymorphisms viz., (i) G (wild-type) to T (mutant-type) single nucleotide polymorphism (SNP) in the promoter, and (ii) 712 bp or 7 bp InDel (insertion in mutant) in exon-4 differentiated the wild-type and mutant allele. Two breeder-friendly PCR-based codominant markers viz., a gene-based allele-specific Cleaved amplified polymorphic sequence (CAPS) marker (MGU-A1–1053) and a functional InDel-based marker (MGU-A1–2840), were developed and validated among 48 inbreds and four F2 populations. These markers can be effectively utilized in genomics-assisted breeding for blue maize that holds great potential to address malnutrition through a sustainable and cost-effective approach.