Identification of Copy Number Variations in Xiang and Kele Pigs
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{"title"=>"Identification of copy number variations in Xiang and Kele pigs", "type"=>"journal", "authors"=>[{"first_name"=>"Jian", "last_name"=>"Xie", "scopus_author_id"=>"57199944599"}, {"first_name"=>"Rongrong", "last_name"=>"Li", "scopus_author_id"=>"57145218700"}, {"first_name"=>"Sheng", "last_name"=>"Li", "scopus_author_id"=>"57192464901"}, {"first_name"=>"Xueqin", "last_name"=>"Ran", "scopus_author_id"=>"35913815900"}, {"first_name"=>"Jiafu", "last_name"=>"Wang", "scopus_author_id"=>"55742561000"}, {"first_name"=>"Jicai", "last_name"=>"Jiang", "scopus_author_id"=>"53877583600"}, {"first_name"=>"Pengju", "last_name"=>"Zhao", "scopus_author_id"=>"56799647300"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"608396166", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0148565", "scopus"=>"2-s2.0-84959423337", "pmid"=>"26840413", "sgr"=>"84959423337"}, "id"=>"80b67897-63e9-3eef-8baa-c8446aebf81f", "abstract"=>"Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated Sus scrofa genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds.", "link"=>"http://www.mendeley.com/research/identification-copy-number-variations-xiang-kele-pigs", "reader_count"=>7, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>5, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4219642"], "description"=>"<div><p>Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated <i>Sus scrofa</i> genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds.</p></div>", "links"=>[], "tags"=>["5 loss events", "litter sizes", "copy number variations", "PorcineSNP 60 genotyping data", "CNVR", "Xiang population", "22 Kele pigs", "genomic variation", "Sus scrofa genes", "Kele Pigs Xiang", "16 gain events", "98 Xiang pigs", "Kele pigs", "Copy Number Variations", "172 candidate CNV regions", "ATP biosynthetic processes", "Chinese pig breeds", "pig genome"], "article_id"=>2576128, "categories"=>["Genetics", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases"], "users"=>["Jian Xie", "Rongrong Li", "Sheng Li", "Xueqin Ran", "Jiafu Wang", "Jicai Jiang", "Pengju Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0148565", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_Copy_Number_Variations_in_Xiang_and_Kele_Pigs/2576128", "title"=>"Identification of Copy Number Variations in Xiang and Kele Pigs", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-02-03 12:33:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/4219675"], "description"=>"<p>Comparison of CNVRs identified in the current study with previously reported porcine CNVRs.</p>", "links"=>[], "tags"=>["5 loss events", "litter sizes", "copy number variations", "PorcineSNP 60 genotyping data", "CNVR", "Xiang population", "22 Kele pigs", "genomic variation", "Sus scrofa genes", "Kele Pigs Xiang", "16 gain events", "98 Xiang pigs", "Kele pigs", "Copy Number Variations", "172 candidate CNV regions", "ATP biosynthetic processes", "Chinese pig breeds", "pig genome"], "article_id"=>2576158, "categories"=>["Genetics", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases"], "users"=>["Jian Xie", "Rongrong Li", "Sheng Li", "Xueqin Ran", "Jiafu Wang", "Jicai Jiang", "Pengju Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0148565.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparison_of_CNVRs_identified_in_the_current_study_with_previously_reported_porcine_CNVRs_/2576158", "title"=>"Comparison of CNVRs identified in the current study with previously reported porcine CNVRs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-02-03 12:33:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/4219669"], "description"=>"<p>Enriched Gene Ontology (GO) terms identified in this study.</p>", "links"=>[], "tags"=>["5 loss events", "litter sizes", "copy number variations", "PorcineSNP 60 genotyping data", "CNVR", "Xiang population", "22 Kele pigs", "genomic variation", "Sus scrofa genes", "Kele Pigs Xiang", "16 gain events", "98 Xiang pigs", "Kele pigs", "Copy Number Variations", "172 candidate CNV regions", "ATP biosynthetic processes", "Chinese pig breeds", "pig genome"], "article_id"=>2576155, "categories"=>["Genetics", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases"], "users"=>["Jian Xie", "Rongrong Li", "Sheng Li", "Xueqin Ran", "Jiafu Wang", "Jicai Jiang", "Pengju Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0148565.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Enriched_Gene_Ontology_GO_terms_identified_in_this_study_/2576155", "title"=>"Enriched Gene Ontology (GO) terms identified in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-02-03 12:33:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/4219660"], "description"=>"<p>Individuals were plotted according to their coordinates on the biplot of x versus y. Blue: Xiang breed, Red: Kele breed.</p>", "links"=>[], "tags"=>["5 loss events", "litter sizes", "copy number variations", "PorcineSNP 60 genotyping data", "CNVR", "Xiang population", "22 Kele pigs", "genomic variation", "Sus scrofa genes", "Kele Pigs Xiang", "16 gain events", "98 Xiang pigs", "Kele pigs", "Copy Number Variations", "172 candidate CNV regions", "ATP biosynthetic processes", "Chinese pig breeds", "pig genome"], "article_id"=>2576149, "categories"=>["Genetics", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases"], "users"=>["Jian Xie", "Rongrong Li", "Sheng Li", "Xueqin Ran", "Jiafu Wang", "Jicai Jiang", "Pengju Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0148565.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Hierarchical_clustering_analysis_based_on_all_available_CNVR_information_/2576149", "title"=>"Hierarchical clustering analysis based on all available CNVR information.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-03 12:33:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/4219648"], "description"=>"<p>The X-axis values represent the chromosome position in Mb, based on the <i>Sus scrofa</i> 10.2 reference genome assembly. The Y-axis values show the chromosome number.</p>", "links"=>[], "tags"=>["5 loss events", "litter sizes", "copy number variations", "PorcineSNP 60 genotyping data", "CNVR", "Xiang population", "22 Kele pigs", "genomic variation", "Sus scrofa genes", "Kele Pigs Xiang", "16 gain events", "98 Xiang pigs", "Kele pigs", "Copy Number Variations", "172 candidate CNV regions", "ATP biosynthetic processes", "Chinese pig breeds", "pig genome"], "article_id"=>2576134, "categories"=>["Genetics", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases"], "users"=>["Jian Xie", "Rongrong Li", "Sheng Li", "Xueqin Ran", "Jiafu Wang", "Jicai Jiang", "Pengju Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0148565.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Distribution_of_detected_CNVRs_in_Xiang_and_Kele_pigs_/2576134", "title"=>"Distribution of detected CNVRs in Xiang and Kele pigs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-03 12:33:15"}

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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