Genome-Wide Association Mapping for Identification of Quantitative Trait Loci for Rectal Temperature during Heat Stress in Holstein Cattle
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{"title"=>"Genome-Wide Association Mapping for Identification of Quantitative Trait Loci for Rectal Temperature during Heat Stress in Holstein Cattle", "type"=>"journal", "authors"=>[{"first_name"=>"Serdal", "last_name"=>"Dikmen", "scopus_author_id"=>"8280302600"}, {"first_name"=>"John B.", "last_name"=>"Cole", "scopus_author_id"=>"7403376306"}, {"first_name"=>"Daniel J.", "last_name"=>"Null", "scopus_author_id"=>"26531450800"}, {"first_name"=>"Peter J.", "last_name"=>"Hansen", "scopus_author_id"=>"7403235771"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"369424087", "sgr"=>"84880724183", "issn"=>"19326203", "pmid"=>"23935954", "scopus"=>"2-s2.0-84880724183", "doi"=>"10.1371/journal.pone.0069202"}, "id"=>"73ee5968-f8ee-3207-8d32-129f132578db", "abstract"=>"Heat stress compromises production, fertility, and health of dairy cattle. One mitigation strategy is to select individuals that are genetically resistant to heat stress. Most of the negative effects of heat stress on animal performance are a consequence of either physiological adaptations to regulate body temperature or adverse consequences of failure to regulate body temperature. Thus, selection for regulation of body temperature during heat stress could increase thermotolerance. The objective was to perform a genome-wide association study (GWAS) for rectal temperature (RT) during heat stress in lactating Holstein cows and identify SNPs associated with genes that have large effects on RT. Records on afternoon RT where the temperature-humidity index was ≥78.2 were obtained from 4,447 cows sired by 220 bulls, resulting in 1,440 useable genotypes from the Illumina BovineSNP50 BeadChip with 39,759 SNP. For GWAS, 2, 3, 4, 5, and 10 adjacent SNP were averaged to identify consensus genomic regions associated with RT. The largest proportion of SNP variance (0.07 to 0.44%) was explained by markers flanking the region between 28,877,547 and 28,907,154 bp on Bos taurus autosome (BTA) 24. That region is flanked by U1 (28,822,883 to 28,823,043) and NCAD (28,992,666 to 29,241,119). In addition, the SNP at 58,500,249 bp on BTA 16 explained 0.08% and 0.11% of the SNP variance for 2- and 3-SNP analyses, respectively. That contig includes SNORA19, RFWD2 and SCARNA3. Other SNPs associated with RT were located on BTA 16 (close to CEP170 and PLD5), BTA 5 (near SLCO1C1 and PDE3A), BTA 4 (near KBTBD2 and LSM5), and BTA 26 (located in GOT1, a gene implicated in protection from cellular stress). In conclusion, there are QTL for RT in heat-stressed dairy cattle. These SNPs could prove useful in genetic selection and for identification of genes involved in physiological responses to heat stress.", "link"=>"http://www.mendeley.com/research/genomewide-association-mapping-identification-quantitative-trait-loci-rectal-temperature-during-heat-2", "reader_count"=>55, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>6, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Student > Master"=>13, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>6, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Student > Master"=>13, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>41, "Veterinary Science and Veterinary Medicine"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>41}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Colombia"=>2, "Sweden"=>1, "Austria"=>1, "United States"=>1, "Brazil"=>1, "France"=>1, "Spain"=>1}, "group_count"=>4}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1128288"], "description"=>"<p>The 20 loci with the largest proportion of SNP variance explained for rectal temperature using 5-SNP sliding windows.</p>", "links"=>[], "tags"=>["Animal management", "Animal genetics", "Animal performance", "Animal production", "genetics", "population genetics", "Genetic polymorphism", "genomics", "Functional genomics", "Population biology", "Animal types", "Large animals", "20", "loci", "largest", "snp", "variance", "explained", "rectal", "5-snp", "sliding"], "article_id"=>752990, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Serdal Dikmen", "John B. Cole", "Daniel J. Null", "Peter J. Hansen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069202.t003", "stats"=>{"downloads"=>12, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_20_loci_with_the_largest_proportion_of_SNP_variance_explained_for_rectal_temperature_using_5_SNP_sliding_windows_/752990", "title"=>"The 20 loci with the largest proportion of SNP variance explained for rectal temperature using 5-SNP sliding windows.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-23 09:36:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1128284"], "description"=>"<p>Proportion of SNP variance explained by 3-SNP moving windows for rectal temperature from a single-step GBLUP analysis.</p>", "links"=>[], "tags"=>["Animal management", "Animal genetics", "Animal performance", "Animal production", "genetics", "population genetics", "Genetic polymorphism", "genomics", "Functional genomics", "Population biology", "Animal types", "Large animals", "snp", "variance", "explained", "3-snp", "moving", "windows", "rectal", "single-step", "gblup"], "article_id"=>752986, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Serdal Dikmen", "John B. Cole", "Daniel J. Null", "Peter J. Hansen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069202.g001", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportion_of_SNP_variance_explained_by_3_SNP_moving_windows_for_rectal_temperature_from_a_single_step_GBLUP_analysis_/752986", "title"=>"Proportion of SNP variance explained by 3-SNP moving windows for rectal temperature from a single-step GBLUP analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 09:36:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1128293", "https://ndownloader.figshare.com/files/1128294", "https://ndownloader.figshare.com/files/1128296", "https://ndownloader.figshare.com/files/1128302", "https://ndownloader.figshare.com/files/1128303", "https://ndownloader.figshare.com/files/1128304", "https://ndownloader.figshare.com/files/1128305", "https://ndownloader.figshare.com/files/1128307", "https://ndownloader.figshare.com/files/1128310"], "description"=>"<div><p>Heat stress compromises production, fertility, and health of dairy cattle. One mitigation strategy is to select individuals that are genetically resistant to heat stress. Most of the negative effects of heat stress on animal performance are a consequence of either physiological adaptations to regulate body temperature or adverse consequences of failure to regulate body temperature. Thus, selection for regulation of body temperature during heat stress could increase thermotolerance. The objective was to perform a genome-wide association study (GWAS) for rectal temperature (RT) during heat stress in lactating Holstein cows and identify SNPs associated with genes that have large effects on RT. Records on afternoon RT where the temperature-humidity index was ≥78.2 were obtained from 4,447 cows sired by 220 bulls, resulting in 1,440 useable genotypes from the Illumina BovineSNP50 BeadChip with 39,759 SNP. For GWAS, 2, 3, 4, 5, and 10 adjacent SNP were averaged to identify consensus genomic regions associated with RT. The largest proportion of SNP variance (0.07 to 0.44%) was explained by markers flanking the region between 28,877,547 and 28,907,154 bp on <i>Bos taurus</i> autosome (BTA) 24. That region is flanked by <i>U1</i> (28,822,883 to 28,823,043) and <i>NCAD</i> (28,992,666 to 29,241,119). In addition, the SNP at 58,500,249 bp on BTA 16 explained 0.08% and 0.11% of the SNP variance for 2- and 3-SNP analyses, respectively. That contig includes <i>SNORA19</i>, <i>RFWD2</i> and <i>SCARNA3</i>. Other SNPs associated with RT were located on BTA 16 (close to <i>CEP170</i> and <i>PLD5),</i> BTA 5 (near <i>SLCO1C1</i> and <i>PDE3A</i>), BTA 4 (near <i>KBTBD2</i> and <i>LSM5</i>), and BTA 26 (located in <i>GOT1</i>, a gene implicated in protection from cellular stress). In conclusion, there are QTL for RT in heat-stressed dairy cattle. These SNPs could prove useful in genetic selection and for identification of genes involved in physiological responses to heat stress.</p></div>", "links"=>[], "tags"=>["Animal management", "Animal genetics", "Animal performance", "Animal production", "genetics", "population genetics", "Genetic polymorphism", "genomics", "Functional genomics", "Population biology", "Animal types", "Large animals", "quantitative", "loci", "rectal", "holstein"], "article_id"=>752995, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Serdal Dikmen", "John B. Cole", "Daniel J. Null", "Peter J. Hansen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0069202.s001", "https://dx.doi.org/10.1371/journal.pone.0069202.s002", "https://dx.doi.org/10.1371/journal.pone.0069202.s003", "https://dx.doi.org/10.1371/journal.pone.0069202.s004", "https://dx.doi.org/10.1371/journal.pone.0069202.s005", "https://dx.doi.org/10.1371/journal.pone.0069202.s006", "https://dx.doi.org/10.1371/journal.pone.0069202.s007", "https://dx.doi.org/10.1371/journal.pone.0069202.s008", "https://dx.doi.org/10.1371/journal.pone.0069202.s009"], "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_Wide_Association_Mapping_for_Identification_of_Quantitative_Trait_Loci_for_Rectal_Temperature_during_Heat_Stress_in_Holstein_Cattle_/752995", "title"=>"Genome-Wide Association Mapping for Identification of Quantitative Trait Loci for Rectal Temperature during Heat Stress in Holstein Cattle", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-23 09:36:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1128286"], "description"=>"<p>Proportion of SNP variance explained by 5-SNP moving windows for rectal temperature from a single-step GBLUP analysis.</p>", "links"=>[], "tags"=>["Animal management", "Animal genetics", "Animal performance", "Animal production", "genetics", "population genetics", "Genetic polymorphism", "genomics", "Functional genomics", "Population biology", "Animal types", "Large animals", "snp", "variance", "explained", "5-snp", "moving", "windows", "rectal", "single-step", "gblup"], "article_id"=>752988, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Serdal Dikmen", "John B. Cole", "Daniel J. Null", "Peter J. Hansen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069202.g002", "stats"=>{"downloads"=>2, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportion_of_SNP_variance_explained_by_5_SNP_moving_windows_for_rectal_temperature_from_a_single_step_GBLUP_analysis_/752988", "title"=>"Proportion of SNP variance explained by 5-SNP moving windows for rectal temperature from a single-step GBLUP analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 09:36:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1128289"], "description"=>"<p>The 20 loci with the largest proportion of SNP variance explained for rectal temperature using 3-SNP sliding windows.</p>", "links"=>[], "tags"=>["Animal management", "Animal genetics", "Animal performance", "Animal production", "genetics", "population genetics", "Genetic polymorphism", "genomics", "Functional genomics", "Population biology", "Animal types", "Large animals", "20", "loci", "largest", "snp", "variance", "explained", "rectal", "3-snp", "sliding"], "article_id"=>752991, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Serdal Dikmen", "John B. Cole", "Daniel J. Null", "Peter J. Hansen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069202.t002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_20_loci_with_the_largest_proportion_of_SNP_variance_explained_for_rectal_temperature_using_3_SNP_sliding_windows_/752991", "title"=>"The 20 loci with the largest proportion of SNP variance explained for rectal temperature using 3-SNP sliding windows.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-23 09:36:44"}

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Relative Metric

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