Genetic Distinctiveness of the Herdwick Sheep Breed and Two Other Locally Adapted Hill Breeds of the UK
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{"title"=>"Genetic distinctiveness of the Herdwick sheep breed and two other locally adapted hill breeds of the UK", "type"=>"journal", "authors"=>[{"first_name"=>"Dianna", "last_name"=>"Bowles", "scopus_author_id"=>"35902363500"}, {"first_name"=>"Amanda", "last_name"=>"Carson", "scopus_author_id"=>"26022902800"}, {"first_name"=>"Peter", "last_name"=>"Isaac", "scopus_author_id"=>"7006686933"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84900439505", "pmid"=>"24489968", "doi"=>"10.1371/journal.pone.0087823", "pui"=>"373070280", "isbn"=>"1932-6203", "issn"=>"19326203", "scopus"=>"2-s2.0-84900439505"}, "id"=>"efcaa37b-55c4-3d57-8022-919f9f98b366", "abstract"=>"There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits) and PRLR (reproductive performance traits) also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the lentivirus.", "link"=>"http://www.mendeley.com/research/genetic-distinctiveness-herdwick-sheep-breed-two-other-locally-adapted-hill-breeds-uk", "reader_count"=>28, "reader_count_by_academic_status"=>{"Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>2, "Student > Master"=>2, "Other"=>5, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>2, "Student > Master"=>2, "Other"=>5, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Agricultural and Biological Sciences"=>14, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Business, Management and Accounting"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Social Sciences"=>2, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United States"=>2, "India"=>1}, "group_count"=>0}

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  • {"files"=>["https://ndownloader.figshare.com/files/1366492"], "description"=>"<p>The proportion of membership of each of the three breeds Rough Fell, Dalesbred and Herdwick in each of the three clusters inferred by Structure shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087823#pone-0087823-g003\" target=\"_blank\">Figure 3</a>.</p>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases", "breeds", "dalesbred", "herdwick", "clusters", "inferred"], "article_id"=>918087, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087823.t005", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_proportion_of_membership_of_each_of_the_three_breeds_Rough_Fell_Dalesbred_and_Herdwick_in_each_of_the_three_clusters_inferred_by_Structure_shown_in_Figure_3_/918087", "title"=>"The proportion of membership of each of the three breeds Rough Fell, Dalesbred and Herdwick in each of the three clusters inferred by Structure shown in Figure 3.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-29 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1366493", "https://ndownloader.figshare.com/files/1366494", "https://ndownloader.figshare.com/files/1366495", "https://ndownloader.figshare.com/files/1366496", "https://ndownloader.figshare.com/files/1366497"], "description"=>"<div><p>There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with <i>RXFP2</i> (horn traits) and <i>PRLR</i> (reproductive performance traits) also distinguished the three breeds. Significantly, an SNP linked to <i>TMEM154</i>, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the lentivirus.</p></div>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases", "distinctiveness", "herdwick", "breed", "locally", "adapted", "breeds"], "article_id"=>918088, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087823.s001", "https://dx.doi.org/10.1371/journal.pone.0087823.s002", "https://dx.doi.org/10.1371/journal.pone.0087823.s003", "https://dx.doi.org/10.1371/journal.pone.0087823.s004", "https://dx.doi.org/10.1371/journal.pone.0087823.s005"], "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_Distinctiveness_of_the_Herdwick_Sheep_Breed_and_Two_Other_Locally_Adapted_Hill_Breeds_of_the_UK_/918088", "title"=>"Genetic Distinctiveness of the Herdwick Sheep Breed and Two Other Locally Adapted Hill Breeds of the UK", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-29 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1366491"], "description"=>"<p>Genotype classes and frequencies of alleles for SNP locus OAR10_29511510 (horn associated).</p>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases", "classes", "frequencies", "alleles", "snp", "locus", "oar10_29511510"], "article_id"=>918086, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087823.t004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotype_classes_and_frequencies_of_alleles_for_SNP_locus_OAR10_29511510_horn_associated_/918086", "title"=>"Genotype classes and frequencies of alleles for SNP locus OAR10_29511510 (horn associated).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-29 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1366488"], "description"=>"<p>The retrotype classification defined in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087823#pone.0087823-Chessa1\" target=\"_blank\">[17]</a> and based on the combination of the four common retroviral insertions in a population is shown in the Table, ‘present’ is highlighted in bold style font.</p>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases", "retrotype", "classification", "defined", "retroviral", "insertions", "highlighted"], "article_id"=>918083, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087823.t001", "stats"=>{"downloads"=>2, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_retrotype_classification_defined_in_17_and_based_on_the_combination_of_the_four_common_retroviral_insertions_in_a_population_is_shown_in_the_Table_present_is_highlighted_in_bold_style_font_/918083", "title"=>"The retrotype classification defined in [17] and based on the combination of the four common retroviral insertions in a population is shown in the Table, ‘present’ is highlighted in bold style font.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-29 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1366487"], "description"=>"<p>The microsatellite data were analysed with Structure; the most likely number of populations to explain the data was for K = 3 (−1525.1). Rough Fell corresponds with cluster 1, Dalesbred with cluster 2 and Herdwick with cluster 3 (all others).</p>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases", "microsatellite"], "article_id"=>918082, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087823.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_microsatellite_data_/918082", "title"=>"Analysis of microsatellite data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-29 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1366490"], "description"=>"<p>Genotype classes and frequencies of alleles for SNP locus OAR16_41943180 (reproductive traits).</p>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases", "classes", "frequencies", "alleles", "snp", "locus", "oar16_41943180"], "article_id"=>918085, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087823.t003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotype_classes_and_frequencies_of_alleles_for_SNP_locus_OAR16_41943180_reproductive_traits_/918085", "title"=>"Genotype classes and frequencies of alleles for SNP locus OAR16_41943180 (reproductive traits).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-29 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1366489"], "description"=>"<p>Allele A, homozygosity for <i>TMEM154</i> 35K; Allele G, homozygosity for <i>TMEM154</i> 35E.</p>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases", "classes", "frequencies", "alleles", "snp", "locus", "lentiviral"], "article_id"=>918084, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087823.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotype_classes_and_frequencies_of_alleles_for_SNP_locus_MV_lentiviral_susceptibility_/918084", "title"=>"Genotype classes and frequencies of alleles for SNP locus (MV lentiviral susceptibility).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-29 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1366486"], "description"=>"<p>The four most common retrovirus events (enJSRV-18, enJSRV-7, enJS5F16, enJSRV-8) were used by Chessa <i>et al </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087823#pone.0087823-Chessa1\" target=\"_blank\">[17]</a> to construct a classification scheme based on retrotypes. The pie charts show the relative proportion of retrotypes in each of the three hill breeds in this study. For ease of comparison, the colouring of each retrotype is the same as used in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087823#pone.0087823-Chessa1\" target=\"_blank\">[17]</a>, and pie charts of example breeds from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087823#pone.0087823-Chessa1\" target=\"_blank\">[17]</a> are also illustrated in the Figure.</p>", "links"=>[], "tags"=>["Agricultural production", "Sustainable agriculture", "Biochemistry", "Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "genetics", "Science education", "Science policy and economics", "Veterinary diseases"], "article_id"=>918081, "categories"=>["Biological Sciences", "Medicine", "Science Policy"], "users"=>["Dianna Bowles", "Amanda Carson", "Peter Isaac"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087823.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_retrotypes_/918081", "title"=>"Analysis of retrotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-29 03:54:05"}

PMC Usage Stats | Further Information

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Relative Metric

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