pl‐bol3, a complex allele of the anthocyanin regulatory pl1 locus that arose in a naturally occurring maize population

SummaryThe pl1 gene encodes a MYB‐related transcriptional activator committed to the regulation of anthocyanin biosynthesis in maize. Here, we report the genetic and molecular characterisation of pl‐bol3, an Andean allele displaying features that make it different from all the known pl1 alleles. pl‐bol3 has partial, light‐independent expression, and it is active mainly in the juvenile phase of growth. It has a complex molecular structure, containing multiple pl1 gene copies, thus being the first complex locus discovered in the c1/pl1 family. Although the composite genes of the complex locus encode proteins identical to other functional PL1 proteins, the putative promoters of the pl‐bol3 gene are different from the promoters of Pl‐Rhoades (Pl‐Rh) and pl1 sun‐red alleles. The intensity and the tissue specificity of anthocyanin production directed by pl‐bol3 differ significantly from that of Pl‐Rh and the original pl‐W22, and are specified by the interaction of pl‐bol3 with the different r1/b1 gene family members and the competence of pl‐bol3 to different pigment tissues. This allele represents a natural example of gene duplication and diversification of expression, giving rise to a significant change in phenotype and, in this way, is analogous to the complex r1 locus in maize. Analysis of the pl‐bol3 allele contributes to understanding the generation of diversity associated with multiple‐copy genes and the molecular basis of allele‐specific gene expression.