A novel allele of the goldfish chdB gene: Functional evaluation and evolutionary considerations

The twin tail of ornamental goldfish is known to be caused by a nonsense mutation in one chordin paralogue gene. Our previous molecular studies in goldfish revealed that the ancestral chordin gene was duplicated, creating the chdA and chdB genes, and the subsequent introduction of a stop codon allele in the chdA gene (chdA(E127X)) caused the twin-tail morphology. The chdA(E127X) allele was positively selected by breeders, and the allele was genetically fixed in the ornamental twin-tail goldfish population. However, little is known about the evolutionary history of the chdB paralogue, begging the question: are there the functionally distinct alleles at the chdB locus, and if so, how did they evolve? To address these questions, we conducted molecular sequencing of the chdB gene from five different goldfish strains and discovered two alleles at the chdB gene locus; the two alleles are designated chdB(1) and chdB(2). The chdB(1) allele is the major allele and was found in all investigated goldfish strains, whereas the chdB(2) allele is minor, having only been found in one twin-tail strain. Genetic analyses further suggested that these two alleles are functionally different with regard to survivability (chdB(1) > chdB(2)). These results led us to presume that in contrast to the chdA locus, the chdB locus has tended to be eliminated from the population. We also discuss how the chdB(2) allele was retained in the goldfish population, despite its disadvantageous function. This study provides empirical evidence of the long-term retention of a disadvantageous allele under domesticated conditions.