Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (Z St Z + sex chromosomes) and hemizygous Almond females (Z St W) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (Z St Z St) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons.
18Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. 19One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are 20 distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait 21 controlled by the classical Stipper (St) locus. Heterozygous males (Z St Z + sex chromosomes) and 22hemizygous Almond females (Z St W) are favored by breeders for their attractive plumage. In 23 contrast, homozygous Almond males (Z St Z St ) develop severe eye defects and lack all plumage 24 pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the 25 molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons 26 and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) 27within the differentiated region that captures complete or partial coding sequences of four genes, 28including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes 29 within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond 30 birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and 31 all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage 32 pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic 33 evolution in pigeons. 34 35 AUTHOR SUMMARY 36The genetic changes responsible for different animal color patterns are poorly understood, 37 due in part to a paucity of research organisms that are both genetically tractable and phenotypically 38 diverse. Domestic pigeons (Columba livia) have been artificially selected for many traits, 39including an enormous variety of color patterns that are variable both within and among different 40 breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in 41 pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. 42Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons 43 with two copies of the Almond mutation have severely depleted pigmentation and congenital eye 44 defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that 45Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for 46 the formation of pigment granules. We also found that different numbers of copies of this region 47 are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears 48 a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons 49 suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights 50 the role of gene copy number variation as a potential driver of rapid phenotypic evolution. 51 52 INTRODUCTION 53In natural populations of animals, pigment colors and patterns impact ma...
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