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Cited by 134Genetic and phenotypic traits in livestockGenetic Mapping and Diversity in Plants and AnimalsGenomics and Phylogenetic Studies

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Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

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Dong, Yang, Zhang, Xiaolei, Xie, Min, Arefnezhad, Babak, Wang, Zongji, Wang, Wenliang, Feng, Shaohong, Huang, Guodong, Guan, Rui, Shen, Wenjing, Bunch, Rowan, McCulloch, Russell, Li, Qiye, Li, Bo, Zhang, Guojie, Xu, Xun, Kijas, James W., Salekdeh, Ghasem Hosseini, Wang, Wen, Jiang, Yu·2015·BMC Genomics
DOI 10.1186/s12864-015-1606-1PMC PMC4455334
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Abstract

BACKGROUND: Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics. RESULTS: We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits. CONCLUSION: Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.

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Crossref · 10.1186/s12864-015-1606-1

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Figures

Fig. 1 Genomic synteny of assembled chromosomes between wild goat (right half) and domestic goat (left half). In the right half, (a) distribution of gene counts in 1-Mb non-overlapping windows; (b) Distribution of CNV gain region (>800 bp in domestic goats using wild goat as reference) counts in 1-Mb non-overlapping windows; (c) Distribution of CNV loss region counts in 1-Mb non-overlapping windows. (d) In the left half, candidate domestication loci in domestic goat genome
Fig. 1 Genomic synteny of assembled chromosomes between wild goat (right half) and domestic goat (left half). In the right half, (a) distribution of gene counts in 1-Mb non-overlapping windows; (b) Distribution of CNV gain region (>800 bp in domestic goats using wild goat as reference) counts in 1-Mb non-overlapping windows; (c) Distribution of CNV loss region counts in 1-Mb non-overlapping windows. (d) In the left half, candidate domestication loci in domestic goat genomeCC BY · PubMed Central
Fig. 2 Photos of wild goat and re-sequenced domestic goat breeds with CNV ratio curve around the ASIP gene region. The CNV ratios (CNV ratio = Read Depth/One average fold depth in whole genome, e.g. CNV ratios fluctuating around two means the read depth of the region is two-fold of the mean in whole genome) calculated within 200-bp sliding windows with 100-bp slide steps were shown as scatter plot and fitted with moving average trend line. Around ASIP (wild goat scaffold1142:1,447,546-1,449,086 bp) region, Bamu wild goat, Khonj wild goat, Yunnan black goat and two Rangeland goats were detected as having one copy while two Boer goats and a Cashmere goat were detected as having at least two copies. Panel 1: wild goat (tan) (Photo is provided by Ghasem Hosseini Salekdeh.); (a) Bamu wild goat; (b) Khonj wild goat. Panel 2: Yunnan Black goat (black); Panel 3–4: Rangeland goats (dark brown and black); Panel 5–6: Boer goats (banded and Schwartzal); Panel 7: Cashmere goat (white) (Photos of Panel 3–7 are provided by James Kijas)
Fig. 2 Photos of wild goat and re-sequenced domestic goat breeds with CNV ratio curve around the ASIP gene region. The CNV ratios (CNV ratio = Read Depth/One average fold depth in whole genome, e.g. CNV ratios fluctuating around two means the read depth of the region is two-fold of the mean in whole genome) calculated within 200-bp sliding windows with 100-bp slide steps were shown as scatter plot and fitted with moving average trend line. Around ASIP (wild goat scaffold1142:1,447,546-1,449,086 bp) region, Bamu wild goat, Khonj wild goat, Yunnan black goat and two Rangeland goats were detected as having one copy while two Boer goats and a Cashmere goat were detected as having at least two copies. Panel 1: wild goat (tan) (Photo is provided by Ghasem Hosseini Salekdeh.); (a) Bamu wild goat; (b) Khonj wild goat. Panel 2: Yunnan Black goat (black); Panel 3–4: Rangeland goats (dark brown and black); Panel 5–6: Boer goats (banded and Schwartzal); Panel 7: Cashmere goat (white) (Photos of Panel 3–7 are provided by James Kijas)CC BY · PubMed Central
Fig. 3 Molecular phylogenetic analysis of MYADM family by maximum likelihood method. (CAAE: gene in wild goat; CAHI: gene in domestic goat) Three copies in wild goat MYADM family highlighted with red, Cae022711, Cae022915 and Cae022887, were detected as losses in all domestic goat breeds
Fig. 3 Molecular phylogenetic analysis of MYADM family by maximum likelihood method. (CAAE: gene in wild goat; CAHI: gene in domestic goat) Three copies in wild goat MYADM family highlighted with red, Cae022711, Cae022915 and Cae022887, were detected as losses in all domestic goat breedsCC BY · PubMed Central
Fig. 4 Unique amino acid changes in CCKA receptor (CCKAR) sequences and their roles in satiety regulation in domestic goats. (a) Alignment of CCKA receptor sequences among human (H. sapiens), cattle (B. taurus), wild goat (C. aegagrus) and dometic goat (C. hircus). Amino acids unique to domestic goats are shown. Completely identical residues in all receptor homologues are shown in white letters with black background, similar residues are shown in black letters with gray background, and distinct residues are shown in black letters with white background. (b) Transmembrane topology of CCKAR. The binding region (the third extracellular loop) affected in the domestic goat is highlighted with yellow. (c) Structural model of the third extracellular loop of CCKAR. Locations of the ligand binding loop with altered sequences in the domestic goat are shown
Fig. 4 Unique amino acid changes in CCKA receptor (CCKAR) sequences and their roles in satiety regulation in domestic goats. (a) Alignment of CCKA receptor sequences among human (H. sapiens), cattle (B. taurus), wild goat (C. aegagrus) and dometic goat (C. hircus). Amino acids unique to domestic goats are shown. Completely identical residues in all receptor homologues are shown in white letters with black background, similar residues are shown in black letters with gray background, and distinct residues are shown in black letters with white background. (b) Transmembrane topology of CCKAR. The binding region (the third extracellular loop) affected in the domestic goat is highlighted with yellow. (c) Structural model of the third extracellular loop of CCKAR. Locations of the ligand binding loop with altered sequences in the domestic goat are shownCC BY · PubMed Central

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Research works printed but not linked: 1

  1. Nowak RM. Walker's Mammals of the World, 6th edn, vol. II: The Johns Hopkins University Press, Baltimore, MD. 1991:1135-1238.

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Metadata

Authors
Dong, Y., Zhang, X., Xie, M., Arefnezhad, B., Wang, Z., Wang, W., Feng, S., Huang, G., Guan, R., Shen, W., Bunch, R., McCulloch, R., Li, Q., Li, B., Zhang, G., Xu, X., Kijas, J. W., Salekdeh, G. H., Wang, W., & Jiang, Y.
Affiliations
  • Kunming University of Science and Technology (CN)
  • Kunming Institute of Zoology (CN)
  • BGI Group (China) (CN)
  • Agricultural Biotechnology Research Institute of Iran (IR)
  • Commonwealth Scientific and Industrial Research Organisation (AU)
  • Royan Institute (IR)
Corresponding author
  • Wang, Wenliang
  • Kijas, James W.
  • Salekdeh, Ghasem Hosseini
  • Wang, Wen
  • Jiang, Yu
ORCID
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2015-06-05
Volume
16
Issue
1
Pages
431-431
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/s12864-015-1606-1
PMC
PMC4455334
OpenAlex
W1561398821
Cited by
116
References
77
Citations by year
2026: 5 · 2025: 11 · 2024: 17 · 2023: 12 · 2022: 4 · 2021: 18 · 2020: 16 · 2019: 11 · 2018: 9 · 2017: 8 · 2016: 5
FWCI
5.04
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
Funders
  • Government of Jiangxi Province
  • Environmental Protection Administration, Executive Yuan, R.O.C. Taiwan
  • National Key Research and Development Program of China (2013CB835200)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
goat domestication, Capra aegagrus, bezoar, goats, reference genome, copy number variation, coat color genes, rapidly evolving genes, immune response, production traits, goat breeds
MeSH terms
Amino Acid Sequence, Animals, Animals, Domestic, Animals, Wild, Breeding, DNA, Biological Evolution, Goats, Immune System, Male, Molecular Sequence Data, Nervous System, Phylogeny, Genetic Variation, Sequence Alignment, Genome, Protein Structure, Tertiary, Receptor, Cholecystokinin A, DNA Copy Number Variations, Myelin and Lymphocyte-Associated Proteolipid Proteins

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