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

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          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.

          Author summary

          The genetic changes responsible for different animal color patterns are poorly understood, due in part to a paucity of research organisms that are both genetically tractable and phenotypically diverse. Domestic pigeons ( Columba livia) have been artificially selected for many traits, including an enormous variety of color patterns that are variable both within and among different breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons with two copies of the Almond mutation have severely depleted pigmentation and congenital eye defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for the formation of pigment granules. We also found that different numbers of copies of this region are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights the role of gene copy number variation as a potential driver of rapid phenotypic evolution.

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          A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

          Heng Li (2011)
          Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. http://samtools.sourceforge.net. hengli@broadinstitute.org.
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            The genomic signature of dog domestication reveals adaptation to a starch-rich diet.

            The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.
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              Vitiligo

              Vitiligo, an acquired pigmentary disorder of unknown origin, is the most frequent cause of depigmentation worldwide, with an estimated prevalence of 1%. The disorder can be psychologically devastating and stigmatising, especially in dark skinned individuals. Vitiligo is clinically characterised by the development of white macules due to the loss of functioning melanocytes in the skin or hair, or both. Two forms of the disease are well recognised: segmental and non-segmental vitiligo (the commonest form). To distinguish between these two forms is of prime importance because therapeutic options and prognosis are quite different. The importance of early treatment and understanding of the profound psychosocial effect of vitiligo will be emphasised throughout this Seminar.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: MethodologyRole: SoftwareRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: ResourcesRole: SoftwareRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, CA USA )
                1553-7390
                1553-7404
                20 May 2020
                May 2020
                : 16
                : 5
                : e1008274
                Affiliations
                [1 ] School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
                [2 ] Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
                HudsonAlpha Institute for Biotechnology, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-9694-0598
                http://orcid.org/0000-0001-6652-8017
                http://orcid.org/0000-0002-7627-9808
                http://orcid.org/0000-0003-2900-4331
                Article
                PGENETICS-D-19-01008
                10.1371/journal.pgen.1008274
                7239393
                32433666
                0cb6d146-2965-4a4c-8989-b55d7ce08fe3
                © 2020 Bruders et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 20 June 2019
                : 9 April 2020
                Page count
                Figures: 5, Tables: 0, Pages: 25
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01GM115996
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R35GM131787
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: DEB-1149160
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: GRF 1256065
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01GM104390
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: T32GM007464
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100001033, Jane Coffin Childs Memorial Fund for Medical Research;
                Award Recipient :
                This work was supported by the National Science Foundation (CAREER DEB-1149160 to M.D.S.; GRF 1256065 to R.B.) and the National Institutes of Health (R01GM115996 and R35GM131787 to M.D.S., R01GM104390 to M.Y., fellowship T32GM007464 to Z.K.). This investigation has been aided by a grant to E.M. from The Jane Coffin Childs Memorial Fund for Medical Research. We acknowledge a computer time allocation from the Center for High Performance Computing at the University of Utah. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Anatomy
                Animal Anatomy
                Feathers
                Medicine and Health Sciences
                Anatomy
                Animal Anatomy
                Feathers
                Biology and Life Sciences
                Zoology
                Animal Anatomy
                Feathers
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Birds
                Pigeons
                Biology and Life Sciences
                Genetics
                Genomics
                Animal Genomics
                Bird Genomics
                Biology and Life Sciences
                Genetics
                Animal Genetics
                Bird Genetics
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Alleles
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Epithelial Cells
                Chromatophores
                Melanocytes
                Biology and Life Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Epithelial Cells
                Chromatophores
                Melanocytes
                Medicine and Health Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Epithelial Cells
                Chromatophores
                Melanocytes
                Biology and Life Sciences
                Computational Biology
                Genome Complexity
                Copy Number Variation
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Complexity
                Copy Number Variation
                Custom metadata
                New whole-genome resequencing data generated for this study are available from the NCBI Short Read Archive in SRA SRP176668, accessions SRR8420387-SRR8420407 and SRR9003406-SRR9003411. Results from Sanger sequencing are deposited in Genbank with the accession numbers MN862483-MN862494. All other relevant data are within the manuscript and its Supporting Information files.

                Genetics
                Genetics

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