Mapping genes associated with anthocyanin in maize kernels using BSA-seq technology

Anthocyanin is a phenotypic trait in fresh corn that enhances both its nutritional and economic value. To identify genes regulating anthocyanin accumulation in maize kernels, we developed an F₂ segregating population by crossing black and white waxy maize lines, followed by self-pollination. Statistical analysis of kernel coloration in the F2:3 population revealed a highly significant segregation between black and white phenotypes, prompting bulked segregant analysis sequencing (BSA-seq) of phenotype-based pools. Integrating phenotypic data with genome sequencing, we mapped the anthocyanin-associated locus to a 107.9-113.2 Mb region on chromosome 6. Within this interval, 116 annotated genes were identified, including 53 genes with nonsynonymous mutations and 17 with frameshift mutations. Gene annotation highlighted three key candidates potentially involved in anthocyanin biosynthesis: Zm00001eb276450 (ANR), Zm00001eb276870 (WD40), and Zm00001eb276640 (MYB). These findings provide a valuable foundation for elucidating the genetic mechanisms underlying anthocyanin accumulation in maize kernels and offer promising candidate genes for the rapid development of fresh-eating maize varieties with enhanced anthocyanin content.