Signature of Balancing Selection at the MC1R Gene in Kunming Dog Populations
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{"title"=>"Signature of Balancing Selection at the MC1R Gene in Kunming Dog Populations", "type"=>"journal", "authors"=>[{"first_name"=>"Guo dong", "last_name"=>"Wang", "scopus_author_id"=>"56331494000"}, {"first_name"=>"Lu guang", "last_name"=>"Cheng", "scopus_author_id"=>"55589537900"}, {"first_name"=>"Ruo xi", "last_name"=>"Fan", "scopus_author_id"=>"55588859900"}, {"first_name"=>"David M.", "last_name"=>"Irwin", "scopus_author_id"=>"35237354400"}, {"first_name"=>"Shu sheng", "last_name"=>"Tang", "scopus_author_id"=>"55588922300"}, {"first_name"=>"Jian guo", "last_name"=>"Peng", "scopus_author_id"=>"55588983600"}, {"first_name"=>"Ya ping", "last_name"=>"Zhang", "scopus_author_id"=>"55881841300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23424634", "doi"=>"10.1371/journal.pone.0055469", "sgr"=>"84873720796", "scopus"=>"2-s2.0-84873720796", "issn"=>"19326203", "pui"=>"368331924"}, "id"=>"5c333650-7330-32e7-9bf8-ef29def84d09", "abstract"=>"Coat color in dog breeds is an excellent character for revealing the power of artificial selection, as it is extremely diverse and likely the result of recent domestication. Coat color is generated by melanocytes, which synthesize pheomelanin (a red or yellow pigment) or eumelanin (a black or brown pigment) through the pigment type-switching pathway, and is regulated by three genes in dogs: MC1R (melanocortin receptor 1), CBD103 (β-defensin 103), and ASIP (agouti-signaling protein precursor). The genotypes of these three gene loci in dog breeds are associated with coat color pattern. Here, we resequenced these three gene loci in two Kunming dog populations and analyzed these sequences using population genetic approaches to identify evolutionary patterns that have occurred at these loci during the recent domestication and breeding of the Kunming dog. The analysis showed that MC1R undergoes balancing selection in both Kunming dog populations, and that the Fst value for MC1R indicates significant genetic differentiation across the two populations. In contrast, similar results were not observed for CBD103 or ASIP. These results suggest that high heterozygosity and allelic differences at the MC1R locus may explain both the mixed color coat, of yellow and black, and the difference in coat colors in both Kunming dog populations.", "link"=>"http://www.mendeley.com/research/signature-balancing-selection-mc1r-gene-kunming-dog-populations", "reader_count"=>31, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>7}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>7}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>24}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}}, "reader_count_by_country"=>{"Sweden"=>1, "Japan"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/484716", "https://ndownloader.figshare.com/files/484718", "https://ndownloader.figshare.com/files/484725", "https://ndownloader.figshare.com/files/484729", "https://ndownloader.figshare.com/files/484731", "https://ndownloader.figshare.com/files/484733", "https://ndownloader.figshare.com/files/484735"], "description"=>"<div><p>Coat color in dog breeds is an excellent character for revealing the power of artificial selection, as it is extremely diverse and likely the result of recent domestication. Coat color is generated by melanocytes, which synthesize pheomelanin (a red or yellow pigment) or eumelanin (a black or brown pigment) through the pigment type-switching pathway, and is regulated by three genes in dogs: <em>MC1R</em> (melanocortin receptor 1), <em>CBD103</em> (β-defensin 103), and <em>ASIP</em> (agouti-signaling protein precursor). The genotypes of these three gene loci in dog breeds are associated with coat color pattern. Here, we resequenced these three gene loci in two Kunming dog populations and analyzed these sequences using population genetic approaches to identify evolutionary patterns that have occurred at these loci during the recent domestication and breeding of the Kunming dog. The analysis showed that <em>MC1R</em> undergoes balancing selection in both Kunming dog populations, and that the Fst value for <em>MC1R</em> indicates significant genetic differentiation across the two populations. In contrast, similar results were not observed for <em>CBD103</em> or <em>ASIP</em>. These results suggest that high heterozygosity and allelic differences at the <em>MC1R</em> locus may explain both the mixed color coat, of yellow and black, and the difference in coat colors in both Kunming dog populations.</p> </div>", "links"=>[], "tags"=>["balancing", "kunming", "populations"], "article_id"=>156549, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Guo-Dong Wang", "Lu-guang Cheng", "Ruo-xi Fan", "David M. Irwin", "Shu-sheng Tang", "Jian-guo Peng", "Ya-Ping Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0055469.s001", "https://dx.doi.org/10.1371/journal.pone.0055469.s002", "https://dx.doi.org/10.1371/journal.pone.0055469.s003", "https://dx.doi.org/10.1371/journal.pone.0055469.s004", "https://dx.doi.org/10.1371/journal.pone.0055469.s005", "https://dx.doi.org/10.1371/journal.pone.0055469.s006", "https://dx.doi.org/10.1371/journal.pone.0055469.s007"], "stats"=>{"downloads"=>18, "page_views"=>44, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Signature_of_Balancing_Selection_at_the_MC1R_Gene_in_Kunming_Dog_Populations__/156549", "title"=>"Signature of Balancing Selection at the <em>MC1R</em> Gene in Kunming Dog Populations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-02-12 01:49:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/490687"], "description"=>"<p>Each node in the network represents a different haplotype, and the size of each circle is proportional to the haplotype frequency. Circles are color-coded according to population (<i>Black:</i> BB population; <i>Grey:</i> WB population). The number of nucleotide differences between the haplotypes is shown on the branches of the network.</p>", "links"=>[], "tags"=>["networks", "genealogy", "haplotypes", "kunming"], "article_id"=>161206, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Guo-Dong Wang", "Lu-guang Cheng", "Ruo-xi Fan", "David M. Irwin", "Shu-sheng Tang", "Jian-guo Peng", "Ya-Ping Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055469.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_networks_showing_the_genealogy_of_MC1R_A_and_CBD103_B_haplotypes_in_two_Kunming_dog_populations_/161206", "title"=>"Median-joining networks showing the genealogy of <i>MC1R</i> (A) and <i>CBD103</i> (B) haplotypes in two Kunming dog populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-12 00:20:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/490822"], "description"=>"***<p>Statistically significant at the 0.1% level.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>161339, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Guo-Dong Wang", "Lu-guang Cheng", "Ruo-xi Fan", "David M. Irwin", "Shu-sheng Tang", "Jian-guo Peng", "Ya-Ping Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055469.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_of_population_structure_/161339", "title"=>"Summary statistics of population structure.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-12 00:22:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/490570"], "description"=>"<p>A) Wolf Black (WB) population. B) Back Black (BB) population. As shown, WB individuals have black and yellow all over their body, while BB individuals have black on their backs and yellow on their abdomen and limbs.</p>", "links"=>[], "tags"=>["illustrating", "differences", "colors", "kunming"], "article_id"=>161085, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Guo-Dong Wang", "Lu-guang Cheng", "Ruo-xi Fan", "David M. Irwin", "Shu-sheng Tang", "Jian-guo Peng", "Ya-Ping Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055469.g001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Photographs_illustrating_the_differences_in_coat_colors_between_the_two_Kunming_dog_populations_/161085", "title"=>"Photographs illustrating the differences in coat colors between the two Kunming dog populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-12 00:18:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/490851"], "description"=>"**<p>Statistically significant at the 1% level.</p>", "links"=>[], "tags"=>["kunming"], "article_id"=>161373, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Guo-Dong Wang", "Lu-guang Cheng", "Ruo-xi Fan", "David M. Irwin", "Shu-sheng Tang", "Jian-guo Peng", "Ya-Ping Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055469.t001", "stats"=>{"downloads"=>8, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Polymorphism_statistics_and_neutral_tests_in_the_Kunming_dog_populations_/161373", "title"=>"Polymorphism statistics and neutral tests in the Kunming dog populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-12 00:22:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/490750"], "description"=>"<p>The demographic history of the Kunming dog populations can be divided into two stages: domestication and breeding periods. A) The domestication period started ∼15,000 years ago (t<sub>3</sub>). Ne represents the effective population size of the wolf population and N<sub>1</sub> represents the size of the founder population of domesticated dogs. Domesticated dog underwent a period of population expansion, represented by the growth parameter α. B) The breeding period for the Kunming dog breeds started ∼70 years ago. N<sub>2</sub> represents the size of the founder population of the Kunming dogs. Both Kunming dog breeds underwent a population size reduction (N3) followed by a period of population expansion (t<sub>1</sub>, N<sub>4</sub>). C) Standard coalescent simulations under different N<sub>1</sub> (100, 500, and 1000) in the WB population. D) Standard coalescent simulations under different N<sub>1</sub> (100, 500, and 1000) in the BB population. E) Standard coalescent simulations under different growth parameter α (98.24, 122.8, and 147.37) in the WB population. F) Standard coalescent simulations under growth parameter α (98.24, 122.8, and 147.37) in the BB population.</p>", "links"=>[], "tags"=>["coalescent", "simulations", "genealogy", "kunming"], "article_id"=>161269, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Guo-Dong Wang", "Lu-guang Cheng", "Ruo-xi Fan", "David M. Irwin", "Shu-sheng Tang", "Jian-guo Peng", "Ya-Ping Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055469.g003", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Standard_coalescent_simulations_under_the_neutral_model_on_the_genealogy_of_the_Kunming_dogs_/161269", "title"=>"Standard coalescent simulations under the neutral model on the genealogy of the Kunming dogs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-12 00:21:09"}

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  • {"unique-ip"=>"10", "full-text"=>"12", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"4", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"2", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"3", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"8", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Veterinary science", "average_usage"=>[313, 571, 709, 825, 944, 1048, 1145, 1261, 1354, 1434, 1524, 1599, 1684]}]}
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