Genome-Wide Association Studies Using Haplotypes and Individual SNPs in Simmental Cattle
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{"title"=>"Genome-wide association studies using haplotypes and individual SNPs in simmental cattle", "type"=>"journal", "authors"=>[{"first_name"=>"Yang", "last_name"=>"Wu", "scopus_author_id"=>"55796194800"}, {"first_name"=>"Huizhong", "last_name"=>"Fan", "scopus_author_id"=>"55655241100"}, {"first_name"=>"Yanhui", "last_name"=>"Wang", "scopus_author_id"=>"55954404700"}, {"first_name"=>"Lupei", "last_name"=>"Zhang", "scopus_author_id"=>"24482712100"}, {"first_name"=>"Xue", "last_name"=>"Gao", "scopus_author_id"=>"24466407700"}, {"first_name"=>"Yan", "last_name"=>"Chen", "scopus_author_id"=>"56394275300"}, {"first_name"=>"Junya", "last_name"=>"Li", "scopus_author_id"=>"7410071953"}, {"first_name"=>"Hong Yan", "last_name"=>"Ren", "scopus_author_id"=>"23971022000"}, {"first_name"=>"Huijiang", "last_name"=>"Gao", "scopus_author_id"=>"7402971218"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84908203087", "pui"=>"600198820", "doi"=>"10.1371/journal.pone.0109330", "isbn"=>"1460-2083 (Electronic)\\r0964-6906 (Linking)", "sgr"=>"84908203087", "pmid"=>"25330174"}, "id"=>"31600ea9-371b-3f3a-b5e3-47c4acd16e45", "abstract"=>"Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mechanisms of quantitative traits. Prompted by the achievements of studies examining economic traits in cattle and to verify the consistency of these two methods using real data, the current study was conducted to construct the haplotype structure in the bovine genome and to detect relevant genes genuinely affecting a carcass trait and a meat quality trait. Using the Illumina BovineHD BeadChip, 942 young bulls with genotyping data were introduced as a reference population to identify the genes in the beef cattle genome significantly associated with foreshank weight and triglyceride levels. In total, 92,553 haplotype blocks were detected in the genome. The regions of high linkage disequilibrium extended up to approximately 200 kb, and the size of haplotype blocks ranged from 22 bp to 199,266 bp. Additionally, the individual SNP analysis and the haplotype-based analysis detected similar regions and common SNPs for these two representative traits. A total of 12 and 7 SNPs in the bovine genome were significantly associated with foreshank weight and triglyceride levels, respectively. By comparison, 4 and 5 haplotype blocks containing the majority of significant SNPs were strongly associated with foreshank weight and triglyceride levels, respectively. In addition, 36 SNPs with high linkage disequilibrium were detected in the GNAQ gene, a potential hotspot that may play a crucial role for regulating carcass trait components.", "link"=>"http://www.mendeley.com/research/genomewide-association-studies-using-haplotypes-individual-snps-simmental-cattle", "reader_count"=>45, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Student > Doctoral Student"=>2, "Researcher"=>5, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>11, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Student > Doctoral Student"=>2, "Researcher"=>5, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>11, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Nursing and Health Professions"=>1, "Materials Science"=>1, "Agricultural and Biological Sciences"=>30, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>30}, "Computer Science"=>{"Computer Science"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>5}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Canada"=>1, "Belgium"=>1, "Philippines"=>1, "United Kingdom"=>1, "Italy"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1724933"], "description"=>"<p>A and B are the plots for foreshank weight and triglyceride levels in the single marker analysis, respectively. C and D are the plots for foreshank weight and triglyceride levels in the haplotype analysis, respectively. Chromosome 1–30 is shown separated by colors, and marker positions are indicated by the ticks on the horizontal axis. In each plot, the genome-wide significance level is shown as a horizontal reference line. The single marker results for both traits show several overlapping SNPs in each map, and this apparent overlap may easily lead to misunderstandings. These SNPs are actually located within close physical proximity, and the P values are nearly the same or even identical.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210464, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.g004", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Manhattan_plots_of_genome_wide_association_studies_for_two_target_traits_/1210464", "title"=>"Manhattan plots of genome-wide association studies for two target traits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-20 02:58:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1725008"], "description"=>"<p>Associated haplotype blocks and nearby candidate genes for triglyceride levels.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210523, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.t004", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Associated_haplotype_blocks_and_nearby_candidate_genes_for_triglyceride_levels_/1210523", "title"=>"Associated haplotype blocks and nearby candidate genes for triglyceride levels.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-20 02:58:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1725006"], "description"=>"<p>Associated haplotype blocks and nearby candidate genes for foreshank weight.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210522, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.t003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Associated_haplotype_blocks_and_nearby_candidate_genes_for_foreshank_weight_/1210522", "title"=>"Associated haplotype blocks and nearby candidate genes for foreshank weight.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-20 02:58:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1725002"], "description"=>"<p>A total of 36 SNPs constitute this strong linkage disequilibrium region in chromosome 8. Solid lines mark the identified block.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210517, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.g007", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_haplotype_structure_of_the_hotspot_area_for_influencing_the_carcass_weight_component_/1210517", "title"=>"Potential haplotype structure of the hotspot area for influencing the carcass weight component.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-20 02:58:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1724883"], "description"=>"<p>Number of haplotype blocks per chromosome.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210414, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_haplotype_blocks_per_chromosome_/1210414", "title"=>"Number of haplotype blocks per chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-20 02:58:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1724912"], "description"=>"<p>Kinship among individuals in the reference population.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210443, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.g003", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kinship_among_individuals_in_the_reference_population_/1210443", "title"=>"Kinship among individuals in the reference population.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-20 02:58:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1724897"], "description"=>"<p>Using the R package, three principal components of markers for each individual are used to show the population stratification of the reference population.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210428, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.g002", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_structure_map_drawn_from_the_first_three_principal_components_/1210428", "title"=>"Population structure map drawn from the first three principal components.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-20 02:58:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1725004"], "description"=>"<p>Associated SNPs and nearby candidate genes for foreshank weight.</p>", "links"=>[], "tags"=>["Illumina BovineHD BeadChip", "5 haplotype blocks", "snp", "GWAS", "gnaq", "gene", "carcass trait components", "beef cattle genome", "meat quality trait", "triglyceride levels", "foreshank weight", "Linkage disequilibrium"], "article_id"=>1210519, "categories"=>["Biological Sciences"], "users"=>["Yang Wu", "Huizhong Fan", "Yanhui Wang", "Lupei Zhang", "Xue Gao", "Yan Chen", "Junya Li", "Hongyan Ren", "Huijiang Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109330.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Associated_SNPs_and_nearby_candidate_genes_for_foreshank_weight_/1210519", "title"=>"Associated SNPs and nearby candidate genes for foreshank weight.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-20 02:58:28"}
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PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}, {"subject_area"=>"/Biology and life sciences/Population biology", "average_usage"=>[312, 475]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[285]}, {"subject_area"=>"/Medicine and health sciences/Nutrition", "average_usage"=>[285]}]}
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