Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig
Publication Date
June 26, 2013
Journal
PLOS ONE
Authors
Suneel K. Onteru, Danielle M. Gorbach, Jennifer M. Young, Dorian J. Garrick, et al
Volume
8
Issue
6
Pages
e61756
DOI
https://dx.plos.org/10.1371/journal.pone.0061756
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0061756
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23840294
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694077
Europe PMC
http://europepmc.org/abstract/MED/23840294
Web of Science
000321424400001
Scopus
84879470635
Mendeley
http://www.mendeley.com/research/whole-genome-association-studies-residual-feed-intake-related-traits-pig
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Mendeley | Further Information

{"title"=>"Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig", "type"=>"journal", "authors"=>[{"first_name"=>"Suneel K.", "last_name"=>"Onteru", "scopus_author_id"=>"24724912200"}, {"first_name"=>"Danielle M.", "last_name"=>"Gorbach", "scopus_author_id"=>"26021226400"}, {"first_name"=>"Jennifer M.", "last_name"=>"Young", "scopus_author_id"=>"36731866300"}, {"first_name"=>"Dorian J.", "last_name"=>"Garrick", "scopus_author_id"=>"7004472921"}, {"first_name"=>"Jack C.M.", "last_name"=>"Dekkers", "scopus_author_id"=>"7007008087"}, {"first_name"=>"Max F.", "last_name"=>"Rothschild", "scopus_author_id"=>"7201381912"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"369200416", "sgr"=>"84879470635", "pmid"=>"23840294", "scopus"=>"2-s2.0-84879470635", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0061756", "issn"=>"19326203"}, "id"=>"f149379a-0894-3207-959c-c6298f9d71e1", "abstract"=>"BACKGROUND Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency. METHODOLOGY/PRINCIPAL FINDINGS Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping. CONCLUSIONS/SIGNIFICANCE Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.", "link"=>"http://www.mendeley.com/research/whole-genome-association-studies-residual-feed-intake-related-traits-pig", "reader_count"=>38, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>31, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>1, "Poland"=>1, "India"=>1}, "group_count"=>0}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1101344"], "description"=>"<p><b>Part A</b> depicts association analyses performed by the PLINK software for each SNP. The X axis shows SNPs across chromosomes SSC1 to X, unassigned cintigs, Y and completely unmapped SNP. The Y axis contains the negative logarithm of the P values adjusted for genomic control. Each spot is a SNP. The green color SNPs are those located in 1 Mb window regions that explain more than 0.2% of genetic variance in part B. <b>Part B</b> illustrates results from the Bayes B model averaging approach used in the Gensel software. Different colors on the X axis indicate genome wide 1 Mb SNP windows from chromosome 1 to X, unassigned contigs and completely unmapped SNP. The markers from completely unmapped and unassigned contigs were not included in the cumulative genetic variance. The Y axis represents percent genetic variance explained by each 1 Mb window. <b>Part C</b> shows association analyses with the PLINK software based on haplotypes, which were derived for 1 Mb windows that explained a higher than 0.2% of genetic variance in part B. The X axis has haplotypes on specific chromosomes. The Y axis shows the negative logarithm of the P values corrected by genomic control. The arrows in parts A, B and C show the similarities in significant locations of the associated SNPs, SNP windows and their haplotypes. The 1 Mb windows that explained higher than 0.2% percent genetic variance in Gensel analyses and/or were significant in the PLINK analyses were considered to be important putative QTL for BF. <i>ACOXL</i>: acyl-coenzyme A oxidase-like; <i>AEBP1</i>: adipocyte enhancer binding protein 1; <i>Env</i>: envelope protein.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "genome", "studies"], "article_id"=>731712, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g008", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_genome_association_studies_for_back_fat_BF_/731712", "title"=>"Whole genome association studies for back fat (BF).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101341"], "description"=>"<p><b>Part A</b> depicts association analyses performed by the PLINK software for each SNPs. The X axis shows SNPs across chromosomes 1 to X, unassigned contigs, Y and completely unmapped SNP. The Y axis represents the negative logarithm of the P values corrected for genomic control. Each spot is a SNP. The green color SNPs are those located in 1 Mb window regions that explain more than 0.2% of genetic variance in part B. <b>Part B</b> illustrates results from the Bayes B model averaging approach used in the GenSel software. Different colors on the X axis indicate genome wide 1 Mb SNP windows from chromosome 1 to X, unassigned contigs, Y and completely unmapped SNP. The markers from completely unmapped and unassigned contigs were not included in the cumulative genetic variance. The Y axis represents percent genetic variance explained by each 1 Mb window. <b>Part C</b> shows association analyses with the PLINK software based on haplotypes, which were derived for 1 Mb windows that explained a higher than 0.2% of genetic variance in part B. The X axis depicts chromosomal positions of haplotypes. The Y axis shows the negative logarithm of the P values corrected by genomic control. The arrows in parts A, B and C show the similarities in significant locations of the associated SNPs, SNP windows and their haplotypes. The 1 Mb windows that explained higher than 0.2% percent genetic variance in GenSel analyses and/or were significant in the PLINK analyses were considered to be important putative QTL for ADFI. <i>SGMS1</i>: spingomyelin synthase 1; <i>CBLN4</i>: cerebellin 4; <i>KCNK1</i>: potassium channel, subfamily K, member 1; <i>MC4R</i>: melanocortin 4 receptor; <i>PAQR5</i>: progestin and adipoQ receptor family member V; <i>GNG4</i>: guanine nucleotide binding protein 4; <i>SORCS3</i>: sortilin-related vps10 domain containing receptor 3.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "genome", "studies", "intake"], "article_id"=>731710, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_genome_association_studies_for_average_daily_feed_intake_ADFI_/731710", "title"=>"Whole genome association studies for average daily feed intake (ADFI).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101336"], "description"=>"<p>The X axis indicates in different colors from left to right, SNP locations from chromosomes 1 to X, unassigned contigs, Y, and completely unmapped SNPs, using <i>Sus scrofa</i> genome build10.2. The Y axis represents the minus log of the P-value for the allele frequency difference between the two lines for each SNP,. The dashed line shows the P-value threshold. SSC: Pig chromosome; FDR: False discovery rate; <i>KCNJ15:</i> Potassium inwardly rectifying channel, subfamily J, member 15; <i>ELOVL2</i>: Elongation of very long chain fatty acids 2; <i>TFAP2A</i>: Transcription factor AP-2 (Activating enhancer binding protein 2)—alpha; <i>GPX2</i>: Glutathione peroxidase 2.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "differences", "residual", "intake", "lines"], "article_id"=>731707, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_frequency_differences_between_the_Low_and_High_residual_feed_intake_lines_at_generation_8_/731707", "title"=>"Allele frequency differences between the Low and High residual feed intake lines at generation 8.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101334"], "description"=>"<p><b>Figure A indicates identical-by-state (IBS) clustering. The X and Y axes represent IBS mean and IBS variance. Figure B shows multi-dimensional clustering.</b> The X and Y-axes indicate dimensions 1 and 2, respectively. The black color cluster includes animals from generations 3–8 of the Low RFI line, the green cluster includes animals from generations 4–8 of the High RFI line, and the red cluster includes animals from generations 1 and 2 of the Low RFI line and generation 0, which is the founder population from which RFI selection lines originated.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "residual", "intake", "plink"], "article_id"=>731706, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g002", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_the_residual_feed_intake_RFI_population_by_the_PLINK_software_/731706", "title"=>"Clustering of the residual feed intake (RFI) population by the PLINK software.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101347"], "description"=>"@<p> The 1 Mb windows are presented in descending order based on the percent genetic variance explained greater than 0.4%.</p>*<p>Posterior probability that the SNPs in 1 Mb window could explain the genetic variance greater than zero (PPA: Posterior probability of association).</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "qtl", "regions", "residual", "intake", "mb", "snp"], "article_id"=>731715, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Important_candidate_QTL_regions_associated_with_the_residual_feed_intake_RFI_by_1_Mb_SNP_windows_/731715", "title"=>"Important candidate QTL regions associated with the residual feed intake (RFI) by 1 Mb SNP windows.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101346"], "description"=>"<p>SNPs with significant (P value<0.0001 and FDR P value<0.05) allele frequency differences in generation 8 between Low and High RFI selection lines.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "fdr", "allele", "differences", "rfi"], "article_id"=>731714, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNPs_with_significant_P_value_lt_0_0001_and_FDR_P_value_lt_0_05_allele_frequency_differences_in_generation_8_between_Low_and_High_RFI_selection_lines_/731714", "title"=>"SNPs with significant (P value<0.0001 and FDR P value<0.05) allele frequency differences in generation 8 between Low and High RFI selection lines.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101339"], "description"=>"<p><b>Part A</b> depicts association analyses performed by the PLINK software for each SNP. The X axis shows SNPs across chromosomes 1 to X, unassigned contigs, Y and completely unmapped SNP. The Y axis represents the negative logarithm of the P-values corrected for genomic control. Each spot is a SNP. The green color SNPs are those located in 1 Mb window regions that explain more than 0.2% of genetic variance in part B. <b>Part B</b> illustrates results from the Bayes B model averaging approach used in the GenSel software. Different colors on the X axis indicate genome wide 1 Mb SNP windows from chromosome 1 to X, unassigned contigs, Y and completely unmapped SNP. The markers from completely unmapped and unassigned contigs were not included in the cumulative genetic variance. The Y axis represents percent genetic variance explained by each 1 Mb window. <b>Part C</b> shows association analyses with the PLINK software based on haplotypes, which were derived for 1 Mb windows that explained a higher than 0.2% of genetic variance in part B. The X axis shows chromosomal positions of the haplotypes. The Y axis shows the negative logarithm of the P-values corrected by genomic control. The arrows in parts A, B and C show the similarities in the significant locations. The 1 Mb windows that explained a higher than 0.2% percent of genetic variance in the Bayesian analyses and/or were significant in the PLINK analyses were considered to be important putative QTL for RFI. <i>GNG4</i>: guanine nucleotide binding protein 4; <i>GLP1R</i>: glucagon-like peptide 1 receptor; <i>CDKAL1:</i> cyclin-dependent kinase 5 regulatory subunit associated protein 1-like 1.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "genome", "studies", "residual", "intake"], "article_id"=>731709, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_genome_association_studies_for_residual_feed_intake_RFI_/731709", "title"=>"Whole genome association studies for residual feed intake (RFI).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101337"], "description"=>"<p>Parts A, B and C show the allele frequency differences for the SNPs near to the <i>KCNJ15</i> gene on SSC13 (ASGA0060074), near the <i>ELOVL2</i> and <i>TFAP2A</i> gene on SSC7 (ASGA0030976), and near the GPX2 gene on SSC7 (ALGA0043495), respectively. <i>KCNJ15:</i> potassium inwardly rectifying channel, subfamily J, member 15; <i>ELOVL2</i>: elongation of very long chain fatty acids 2; <i>TFAP2A</i>: transcription factor AP-2 (activating enhancer binding protein 2)—alpha; <i>GPX2</i>: glutathione peroxidase 2. The X axes represent generations and Y-axes show allele frequencies.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "differences", "residual", "intake", "lines", "snps"], "article_id"=>731708, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_frequency_differences_between_the_residual_feed_intake_selection_lines_for_the_significant_SNPs_in_each_generation_/731708", "title"=>"Allele frequency differences between the residual feed intake selection lines for the significant SNPs in each generation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101333"], "description"=>"<p>The animals in blue boxes were phenotyped and genotyped and included in the analyses. G: Generation; P: Parity. Please refer to references <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061756#pone.0061756-Cai1\" target=\"_blank\">[2]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061756#pone.0061756-Young1\" target=\"_blank\">[10]</a> for the population structure, which defines generation and parity.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis"], "article_id"=>731705, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_sampled_/731705", "title"=>"Population sampled.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101348", "https://ndownloader.figshare.com/files/1101349", "https://ndownloader.figshare.com/files/1101350", "https://ndownloader.figshare.com/files/1101351", "https://ndownloader.figshare.com/files/1101352", "https://ndownloader.figshare.com/files/1101353", "https://ndownloader.figshare.com/files/1101354", "https://ndownloader.figshare.com/files/1101355"], "description"=>"<div><p>Background</p><p>Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency.</p><p>Methodology/Principal findings</p><p>Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., <i>GLP1R, CDKAL, SGMS1</i>) with RFI and ADFI, of regions with energy homeostasis (e.g., <i>MC4R</i>, <i>PGM1</i>, <i>GPR81</i>) and muscle growth related genes (e.g., <i>TGFB1</i>) with ADG, and of fat metabolism genes (e.g., <i>ACOXL</i>, <i>AEBP1</i>) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., <i>KLHL31</i>) was identified for subsequent fine mapping.</p><p>Conclusions/significance</p><p>Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.</p></div>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "genome", "studies", "residual", "intake"], "article_id"=>731716, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061756.s001", "https://dx.doi.org/10.1371/journal.pone.0061756.s002", "https://dx.doi.org/10.1371/journal.pone.0061756.s003", "https://dx.doi.org/10.1371/journal.pone.0061756.s004", "https://dx.doi.org/10.1371/journal.pone.0061756.s005", "https://dx.doi.org/10.1371/journal.pone.0061756.s006", "https://dx.doi.org/10.1371/journal.pone.0061756.s007", "https://dx.doi.org/10.1371/journal.pone.0061756.s008"], "stats"=>{"downloads"=>21, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_Genome_Association_Studies_of_Residual_Feed_Intake_and_Related_Traits_in_the_Pig_/731716", "title"=>"Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101345"], "description"=>"<p><b>Part A</b> depicts association analyses performed by the PLINK software for each SNP. The X axis shows SNPs across chromosomes SSC1 to X, unassigned contigs, Y and unmapped SNP. The Y axis contains the negative logarithm of the P values adjusted for genomic control. Each spot is a SNP. The green color SNPs are those located in 1 Mb window regions that explain more than 0.2% of genetic variance in part B. <b>Part B</b> illustrates results from the Bayes B model averaging approach used in the Gensel software. Different colors on the X axis indicate genome wide 1 Mb SNP windows from chromosome 1 to X, unassigned contigs, Y and completely unmapped SNP. The markers from completely unmapped and unassigned contigs were not included in the cumulative genetic variance. The Y axis represents percent genetic variance explained by each 1 Mb window. <b>Part C</b> shows association analyses with the PLINK software based on haplotypes, which were selected from the 1 Mb windows that explained a higher than 0.2% of genetic variance in part B. The X axis has haplotypes on specific chromosomes. The Y axis shows the negative logarithm of the P values corrected by genomic control. The arrows in parts A, B and C show the similarities in significant locations of the associated SNPs, SNP windows and their haplotypes. The 1 Mb windows that explained higher than 0.2% percent genetic variance in Gensel analyses and/or were very highly significant even after genomic control followed by FDR (P value<0.05) in the PLINK analyses were considered to be important QTL for LMA. <i>KLHL31</i>: kelch like 31.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "genome", "studies", "loin"], "article_id"=>731713, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g009", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_genome_association_studies_for_loin_muscle_area_LMA_/731713", "title"=>"Whole genome association studies for loin muscle area (LMA).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1101343"], "description"=>"<p><b>Part A</b> depicts association analyses performed by the PLINK software for each SNP. The X axis shows SNPs across chromosomes SSC1 to X, unassigned contigs, Y and completely unmapped SNP. The Y axis contains the negative logarithm of the P values adjusted for genomic control. Each spot is a SNP. The green color SNPs are those located in 1 Mb window regions that explain more than 0.2% of genetic variance in part B. <b>Part B</b> illustrates results from the Bayes B model averaging approach used in the Gensel software. Different colors on the X axis indicate genome wide 1MB SNP windows from chromosome 1 to X, unassigned contigs and completely unmapped SNP. The markers from completely unmapped and unassigned contigs were not included in the cumulative genetic variance. The Y axis represents percent genetic variance explained by each 1 Mb window. <b>Part C</b> shows association analyses with the PLINK software based on haplotypes, which were derived for 1 Mb windows that explained a higher than 0.2% of genetic variance in part B. The X axis has haplotypes on specific chromosomes. The Y axis shows the negative logarithm of the P values corrected by genomic control. The arrows in parts A, B and C show the similarities in significant locations of the associated SNPs, SNP windows and their haplotypes. The 1 Mb windows that explained higher than 0.2% percent genetic variance in Gensel analyses and/or were significant in the PLINK analyses were considered to be important putative QTL for ADG. <i>MC4R</i>: melanocortin 4 receptor; <i>TGFBI</i>: transforming growth factor beta induced protein ig-h3; <i>PGM1</i>: phosphoglucomutase 1; <i>GPR81</i>: G-protein coupled receptor 81; U6: spliceosomal RNA.</p>", "links"=>[], "tags"=>["Animal management", "Animal breeding", "Animal genetics", "Animal performance", "genetics", "population genetics", "Genetic polymorphism", "Genome-wide association studies", "genomics", "Genome analysis tools", "Linkage maps", "Trait locus analysis", "genome"], "article_id"=>731711, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Suneel K. Onteru", "Danielle M. Gorbach", "Jennifer M. Young", "Dorian J. Garrick", "Jack C. M. Dekkers", "Max F. Rothschild"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061756.g007", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_genome_association_analyses_for_average_daily_gain_ADG_/731711", "title"=>"Whole genome association analyses for average daily gain (ADG).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-26 06:44:15"}

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Relative Metric

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