A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)

Bruders, Rebecca; Hollebeke, Hannah Van; Osborne, Edward J.; Kronenberg, Zev; Maclary, Emily; Yandell, Mark; Shapiro, Michael D.

doi:10.1371/journal.pgen.1008274

Cited by 42 publications

(37 citation statements)

References 112 publications

(141 reference statements)

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“…In the posterior RPE, we saw a significant but relatively modest pigmentation reduction in homozygous Almond eyes relative to all other genotypes. This situation is analogous to what is observed in the plumage: hemizygous and heterozygous Almond pigeons have reduced (but still plentiful) feather pigmentation, but homozygotes lose almost all plumage pigmentation [36]. In developing homozygous feathers, but not in other genotypes, we saw a collapse of the pigment synthesis gene expression pathway.…”

Section: Discussionsupporting

confidence: 78%

“…Another potential route to eye structural defects is the “leaking” of toxic pigment cell components. In humans, pigmentary glaucoma (PG) and pigment dispersal syndrome (PDS) affect anterior eye structures and are sometimes associated with mutations in PMEL [60], PMEL is critical for melanosome maturation and physically interacts with MLANA [38], a protein that is encoded in the Almond genomic candidate region of pigeons [36]. In cases of PDS, pigment disperses from the iris to surrounding tissues and induces other defects, such as increased ocular pressure and corneal endothelial pigment deposition [61].…”

Section: Discussionmentioning

confidence: 99%

“…Previously, we identified a 359-kb candidate region for Almond on the Z-chromosome [36]. This region contains eight annotated protein-coding genes, none of which have fixed coding changes in Almond birds.…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, Slc16a13 does not have a known role in pigmentation, and the function of this gene is poorly understood beyond its genomic association with type 2 diabetes [50–55]. We therefore proposed Mlana as a strong candidate gene for Almond [36].…”

Section: Introductionmentioning

confidence: 99%

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The Almond plumage color pattern is associated with eye pigmentation defects in the domestic pigeon (Columba livia)

Bruders

Sidesinger

Shapiro

2020

Preprint

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Changes in epidermal pigmentation are associated with eye defects in humans and other vertebrates. In the rock pigeon (Columba livia), the sex-linked Almond color pattern is characterized by hypopigmentation of epidermal structures. The trait is controlled by the classical Stipper (St) locus, and homozygous (ZStZSt) Almond males often have severe eye defects. Heterozygous (ZStZ+) and hemizygous (ZStW) pigeons do not typically have obvious eye defects, suggesting that higher dosage of the mutant allele is deleterious. Because Almond pigeons have pronounced hypopigmentation in epidermal structures, we hypothesized that they might also have reduced eye pigmentation. Here, we examined pigmentation in the iris, ciliary body, anterior retinal pigmented epithelium (RPE), and posterior RPE in pigeons with and without Almond alleles. We found that pigmentation of anterior segment structures was reduced in birds with at least one Almond allele. However, posterior eye pigmentation was substantially reduced only in homozygous Almond birds. We postulate that the gradient of effects on eye pigmentation is due to the different embryological origins of anterior and posterior eye pigment-producing cells.

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Section: Discussionsupporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Almond plumage color pattern is associated with eye pigmentation defects in the domestic pigeon (Columba livia)

Bruders

Sidesinger

Shapiro

2020

Preprint

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“…Domestic animal genetic resources provide an excellent opportunity to study the causative mutations and regulatory mechanisms responsible for coat color diversity ( Henkel et al. 2019 ; Bruders et al. 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis)

Liu

Zhao

et al. 2020

Molecular Biology and Evolution

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Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied GWAS, comparative population genomics and biological experiments to show that the 2,809 bp long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3’ truncated and containing only 5’ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5’ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.

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Duck pan‐genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution

Wang,

Hua,

et al. 2023

iMeta

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Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan‐genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan‐genome together with high‐depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE‐derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan‐genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.

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A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)

Cited by 42 publications

References 112 publications

The Almond plumage color pattern is associated with eye pigmentation defects in the domestic pigeon (Columba livia)

The Almond plumage color pattern is associated with eye pigmentation defects in the domestic pigeon (Columba livia)

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis)

Duck pan‐genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution

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