The basic color factor, the C locus, encodes a regulatory gene controlling transcription of chalcone synthase genes in onions (Allium cepa)

Abstract

In onions (Allium cepa), a variety of bulb colors exist ranging from white, yellow, to red, with different intermediate shades. In order to identify the function of the basic color factor, the C locus, which is required for any color production, a candidate gene approach was attempted utilizing anthocyanin synthesis pathway genes. RT-PCR was carried out to examine differential expression of the genes involved in the anthocyanin synthesis pathway among four different bulb colors: recessive white, dominant white, yellow, and red. The transcription of two homologous chalcone synthase (CHS) genes (CHS-A and CHS-B) was significantly reduced in both dominant and recessive white onions. The reduced transcription of CHS genes was also observed in white, but not yellow, F₂ plants originating from the cross between white and yellow onions. Single nucleotide polymorphism (SNP) markers tagging parental alleles of CHS genes were utilized to determine whether the reduced transcription of CHS genes was caused by mutations in CHS genes or other regulatory genes. In the F₂ populations originating from the cross between recessive white and yellow or red parents, the SNP markers tagging two parental alleles of the CHS-A and CHS-B genes did not co-segregate with the genotype of the C locus. These results suggest that the basic color factor is likely to be a regulatory gene controlling CHS gene transcription.