Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data
Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of...
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| Veröffentlicht in: | PloS one 2021-08, Vol.16 (8), p.e0256091-e0256091 |
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| creator | Canive, Maria González-Recio, Oscar Fernández, Almudena Vázquez, Patricia Badia-Bringué, Gerard Lavín, José Luis Garrido, Joseba M Juste, Ramón A Alonso-Hearn, Marta |
| description | Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain. |
| doi_str_mv | 10.1371/journal.pone.0256091 |
| format | Article |
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Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0256091</identifier><identifier>PMID: 34449805</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Antibodies ; Biology and Life Sciences ; Bos taurus ; Case-Control Studies ; Cattle ; Cattle - genetics ; Cattle Diseases - microbiology ; Colorectal cancer ; Dairy industry ; Diagnosis ; Diagnostic systems ; Diagnostic tests ; Diagnostic Tests, Routine ; Disease susceptibility ; Enzyme-Linked Immunosorbent Assay - veterinary ; Estimates ; Female ; Gene mapping ; Genes ; Genetic Predisposition to Disease - genetics ; Genome-Wide Association Study - veterinary ; Genomes ; Genotype ; Genotypes ; Graduate studies ; Health aspects ; Heritability ; Immunomodulation ; Infections ; Inflammatory bowel disease ; Inflammatory diseases ; Linear Models ; Male ; Mastitis ; Medical diagnosis ; Methods ; Milk production ; Molecular modelling ; Mycobacterium avium ; Mycobacterium avium - genetics ; Mycobacterium avium - pathogenicity ; Mycobacterium avium complex ; Mycobacterium avium subsp. paratuberculosis - genetics ; Nucleotide sequence ; Nucleotides ; Oligonucleotide Array Sequence Analysis ; Paratuberculosis ; Paratuberculosis - microbiology ; Phenotype ; Phenotypes ; Polymorphism, Single Nucleotide - genetics ; Quantitative Trait Loci ; Research and Analysis Methods ; Single-nucleotide polymorphism ; Spain ; Susceptibility ; Tissue culture ; Tissues ; Tuberculosis ; Tuberculosis - diagnosis ; Tuberculosis - genetics ; Tuberculosis - veterinary ; Vaccines ; Whole Genome Sequencing</subject><ispartof>PloS one, 2021-08, Vol.16 (8), p.e0256091-e0256091</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Canive et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Canive et al 2021 Canive et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-69d1c725e60ecd9406f02f68c443b06a71843db2f02dd03a833b28725e644db13</citedby><cites>FETCH-LOGICAL-c692t-69d1c725e60ecd9406f02f68c443b06a71843db2f02dd03a833b28725e644db13</cites><orcidid>0000-0001-5979-347X ; 0000-0002-9106-4063</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8396740/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8396740/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34449805$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Smith, Rebecca Lee</contributor><creatorcontrib>Canive, Maria</creatorcontrib><creatorcontrib>González-Recio, Oscar</creatorcontrib><creatorcontrib>Fernández, Almudena</creatorcontrib><creatorcontrib>Vázquez, Patricia</creatorcontrib><creatorcontrib>Badia-Bringué, Gerard</creatorcontrib><creatorcontrib>Lavín, José Luis</creatorcontrib><creatorcontrib>Garrido, Joseba M</creatorcontrib><creatorcontrib>Juste, Ramón A</creatorcontrib><creatorcontrib>Alonso-Hearn, Marta</creatorcontrib><title>Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain.</description><subject>Analysis</subject><subject>Animals</subject><subject>Antibodies</subject><subject>Biology and Life Sciences</subject><subject>Bos taurus</subject><subject>Case-Control Studies</subject><subject>Cattle</subject><subject>Cattle - genetics</subject><subject>Cattle Diseases - microbiology</subject><subject>Colorectal cancer</subject><subject>Dairy industry</subject><subject>Diagnosis</subject><subject>Diagnostic systems</subject><subject>Diagnostic tests</subject><subject>Diagnostic Tests, Routine</subject><subject>Disease susceptibility</subject><subject>Enzyme-Linked Immunosorbent Assay - veterinary</subject><subject>Estimates</subject><subject>Female</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic Predisposition to Disease - genetics</subject><subject>Genome-Wide Association Study - veterinary</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Graduate studies</subject><subject>Health aspects</subject><subject>Heritability</subject><subject>Immunomodulation</subject><subject>Infections</subject><subject>Inflammatory bowel disease</subject><subject>Inflammatory diseases</subject><subject>Linear Models</subject><subject>Male</subject><subject>Mastitis</subject><subject>Medical diagnosis</subject><subject>Methods</subject><subject>Milk production</subject><subject>Molecular modelling</subject><subject>Mycobacterium avium</subject><subject>Mycobacterium avium - genetics</subject><subject>Mycobacterium avium - pathogenicity</subject><subject>Mycobacterium avium complex</subject><subject>Mycobacterium avium subsp. paratuberculosis - genetics</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Paratuberculosis</subject><subject>Paratuberculosis - microbiology</subject><subject>Phenotype</subject><subject>Phenotypes</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Quantitative Trait Loci</subject><subject>Research and Analysis Methods</subject><subject>Single-nucleotide polymorphism</subject><subject>Spain</subject><subject>Susceptibility</subject><subject>Tissue culture</subject><subject>Tissues</subject><subject>Tuberculosis</subject><subject>Tuberculosis - diagnosis</subject><subject>Tuberculosis - genetics</subject><subject>Tuberculosis - veterinary</subject><subject>Vaccines</subject><subject>Whole Genome Sequencing</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk91qFDEUxwdRbK2-gWhAEL3YNZlkMpMboRS1C5WCX7chk5zZTckk4yRT7VP6Sman29KVXshAEjK_8z9fOUXxnOAloTV5dxGm0Su3HIKHJS4rjgV5UBwSQcsFLzF9eOd8UDyJ8QLjijacPy4OKGNMNLg6LP6sDPhkO6tVssGj0CEXtEUqxrypBAb9smmD4hQ1DMm21tl0hVJAn690aJVOMNqpR-pyu8apjcMSDWpUaWph1JML0UZkfQd61rcenQYXE-RDdpkcoClav0Y69K31cxBxG4Wxau1DTFajBDFFpLxBth-mOaRNcLBYgw89oAg_J_AakFFJPS0edcpFeLbbj4rvHz98OzldnJ1_Wp0cny00F2VacGGIrssKOAZtBMO8w2XHG80YbTFXNWkYNW2Zb43BVDWUtmUzGzBmWkKPipfXukPOUO56EWVuQ5VLW4kyE6trwgR1IYfR9mq8kkFZOV-EcS3VmNNzIAkoQimpDGtrRhkRnakNGKFIXTPDddZ6v_M2tT0YnVs2Krcnuv_H241ch0vZUMFrhrPAm53AGHK1YpK9zQ11TnkI0xw3x1Tgpsroq3_Q-7PbUWuVE8j9Ddmv3orKY17n91ULITK1vIfKn4He6vxwO5vv9wze7hlkJsHvtFZTjHL19cv_s-c_9tnXd9gNKJc2Mbhpfm77ILsG9RhiHKG7LTLBcjt3N9WQ27mTu7nLZi_uNujW6GbQ6F8khS5u</recordid><startdate>20210827</startdate><enddate>20210827</enddate><creator>Canive, Maria</creator><creator>González-Recio, Oscar</creator><creator>Fernández, Almudena</creator><creator>Vázquez, Patricia</creator><creator>Badia-Bringué, Gerard</creator><creator>Lavín, José Luis</creator><creator>Garrido, Joseba M</creator><creator>Juste, Ramón A</creator><creator>Alonso-Hearn, Marta</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-5979-347X</orcidid><orcidid>https://orcid.org/0000-0002-9106-4063</orcidid></search><sort><creationdate>20210827</creationdate><title>Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data</title><author>Canive, Maria ; González-Recio, Oscar ; Fernández, Almudena ; Vázquez, Patricia ; Badia-Bringué, Gerard ; Lavín, José Luis ; Garrido, Joseba M ; Juste, Ramón A ; Alonso-Hearn, Marta</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-69d1c725e60ecd9406f02f68c443b06a71843db2f02dd03a833b28725e644db13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Antibodies</topic><topic>Biology and Life Sciences</topic><topic>Bos taurus</topic><topic>Case-Control Studies</topic><topic>Cattle</topic><topic>Cattle - genetics</topic><topic>Cattle Diseases - microbiology</topic><topic>Colorectal cancer</topic><topic>Dairy industry</topic><topic>Diagnosis</topic><topic>Diagnostic systems</topic><topic>Diagnostic tests</topic><topic>Diagnostic Tests, Routine</topic><topic>Disease susceptibility</topic><topic>Enzyme-Linked Immunosorbent Assay - veterinary</topic><topic>Estimates</topic><topic>Female</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genetic Predisposition to Disease - genetics</topic><topic>Genome-Wide Association Study - veterinary</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Graduate studies</topic><topic>Health aspects</topic><topic>Heritability</topic><topic>Immunomodulation</topic><topic>Infections</topic><topic>Inflammatory bowel disease</topic><topic>Inflammatory diseases</topic><topic>Linear Models</topic><topic>Male</topic><topic>Mastitis</topic><topic>Medical diagnosis</topic><topic>Methods</topic><topic>Milk production</topic><topic>Molecular modelling</topic><topic>Mycobacterium avium</topic><topic>Mycobacterium avium - genetics</topic><topic>Mycobacterium avium - pathogenicity</topic><topic>Mycobacterium avium complex</topic><topic>Mycobacterium avium subsp. paratuberculosis - genetics</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Paratuberculosis</topic><topic>Paratuberculosis - microbiology</topic><topic>Phenotype</topic><topic>Phenotypes</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Quantitative Trait Loci</topic><topic>Research and Analysis Methods</topic><topic>Single-nucleotide polymorphism</topic><topic>Spain</topic><topic>Susceptibility</topic><topic>Tissue culture</topic><topic>Tissues</topic><topic>Tuberculosis</topic><topic>Tuberculosis - diagnosis</topic><topic>Tuberculosis - genetics</topic><topic>Tuberculosis - veterinary</topic><topic>Vaccines</topic><topic>Whole Genome Sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Canive, Maria</creatorcontrib><creatorcontrib>González-Recio, Oscar</creatorcontrib><creatorcontrib>Fernández, Almudena</creatorcontrib><creatorcontrib>Vázquez, Patricia</creatorcontrib><creatorcontrib>Badia-Bringué, Gerard</creatorcontrib><creatorcontrib>Lavín, José Luis</creatorcontrib><creatorcontrib>Garrido, Joseba M</creatorcontrib><creatorcontrib>Juste, Ramón A</creatorcontrib><creatorcontrib>Alonso-Hearn, Marta</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Canive, Maria</au><au>González-Recio, Oscar</au><au>Fernández, Almudena</au><au>Vázquez, Patricia</au><au>Badia-Bringué, Gerard</au><au>Lavín, José Luis</au><au>Garrido, Joseba M</au><au>Juste, Ramón A</au><au>Alonso-Hearn, Marta</au><au>Smith, Rebecca Lee</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-08-27</date><risdate>2021</risdate><volume>16</volume><issue>8</issue><spage>e0256091</spage><epage>e0256091</epage><pages>e0256091-e0256091</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>34449805</pmid><doi>10.1371/journal.pone.0256091</doi><tpages>e0256091</tpages><orcidid>https://orcid.org/0000-0001-5979-347X</orcidid><orcidid>https://orcid.org/0000-0002-9106-4063</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2021-08, Vol.16 (8), p.e0256091-e0256091 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2565449592 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Antibodies Biology and Life Sciences Bos taurus Case-Control Studies Cattle Cattle - genetics Cattle Diseases - microbiology Colorectal cancer Dairy industry Diagnosis Diagnostic systems Diagnostic tests Diagnostic Tests, Routine Disease susceptibility Enzyme-Linked Immunosorbent Assay - veterinary Estimates Female Gene mapping Genes Genetic Predisposition to Disease - genetics Genome-Wide Association Study - veterinary Genomes Genotype Genotypes Graduate studies Health aspects Heritability Immunomodulation Infections Inflammatory bowel disease Inflammatory diseases Linear Models Male Mastitis Medical diagnosis Methods Milk production Molecular modelling Mycobacterium avium Mycobacterium avium - genetics Mycobacterium avium - pathogenicity Mycobacterium avium complex Mycobacterium avium subsp. paratuberculosis - genetics Nucleotide sequence Nucleotides Oligonucleotide Array Sequence Analysis Paratuberculosis Paratuberculosis - microbiology Phenotype Phenotypes Polymorphism, Single Nucleotide - genetics Quantitative Trait Loci Research and Analysis Methods Single-nucleotide polymorphism Spain Susceptibility Tissue culture Tissues Tuberculosis Tuberculosis - diagnosis Tuberculosis - genetics Tuberculosis - veterinary Vaccines Whole Genome Sequencing |
| title | Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data |
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