Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks.
Identifieur interne : 000B77 ( PubMed/Corpus ); précédent : 000B76; suivant : 000B78Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks.
Auteurs : F. Bertolini ; J C S. Harding ; B. Mote ; A. Ladinig ; G S Plastow ; M F RothschildSource :
- Animal genetics [ 1365-2052 ] ; 2017.
English descriptors
- KwdEn :
- Animals, Coronavirus Infections (epidemiology), Coronavirus Infections (genetics), Coronavirus Infections (immunology), Coronavirus Infections (veterinary), Disease Outbreaks, Porcine epidemic diarrhea virus (physiology), Sus scrofa, Swine, Swine Diseases (epidemiology), Swine Diseases (genetics), Swine Diseases (immunology).
- MESH :
- epidemiology : Coronavirus Infections, Swine Diseases.
- genetics : Coronavirus Infections, Swine Diseases.
- immunology : Coronavirus Infections, Swine Diseases.
- physiology : Porcine epidemic diarrhea virus.
- veterinary : Coronavirus Infections.
- Animals, Disease Outbreaks, Sus scrofa, Swine.
Abstract
Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome-wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks. Samples from 262 animals (156 dead and 106 recovered) belonging to several commercial lines were collected from five different farms in three different countries (USA, Canada and Germany) and genotyped with the porcine 80K SNP chip. Mean Fst value was calculated in 1-Mb non-overlapping windows between dead and recovered individuals, and the results were normalized to find differences within the comparison. Seven windows with high divergence between dead and recovered were detected-five on chromosome 2, one on chromosome 4 and one on chromosome 15-in total encompassing 152 genes. Several of these genes are either under- or overexpressed in many virus infections, including Coronaviridae (such as SARS-CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to PED development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, ATPase activity). Taken together this information provides a first genomic picture of PEDV resilience in suckling piglets.
DOI: 10.1111/age.12522
PubMed: 27943331
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pubmed:27943331Le document en format XML
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Mote</name><affiliation><nlm:affiliation>Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ladinig, A" sort="Ladinig, A" uniqKey="Ladinig A" first="A" last="Ladinig">A. Ladinig</name><affiliation><nlm:affiliation>University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Wien, 1210, Austria.</nlm:affiliation></affiliation></author><author><name sortKey="Plastow, G S" sort="Plastow, G S" uniqKey="Plastow G" first="G S" last="Plastow">G S Plastow</name><affiliation><nlm:affiliation>Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Rothschild, M F" sort="Rothschild, M F" uniqKey="Rothschild M" first="M F" last="Rothschild">M F Rothschild</name><affiliation><nlm:affiliation>Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:27943331</idno><idno type="pmid">27943331</idno><idno type="doi">10.1111/age.12522</idno><idno type="wicri:Area/PubMed/Corpus">000B77</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000B77</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks.</title><author><name sortKey="Bertolini, F" sort="Bertolini, F" uniqKey="Bertolini F" first="F" last="Bertolini">F. Bertolini</name><affiliation><nlm:affiliation>Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Harding, J C S" sort="Harding, J C S" uniqKey="Harding J" first="J C S" last="Harding">J C S. Harding</name><affiliation><nlm:affiliation>Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Mote, B" sort="Mote, B" uniqKey="Mote B" first="B" last="Mote">B. Mote</name><affiliation><nlm:affiliation>Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ladinig, A" sort="Ladinig, A" uniqKey="Ladinig A" first="A" last="Ladinig">A. Ladinig</name><affiliation><nlm:affiliation>University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Wien, 1210, Austria.</nlm:affiliation></affiliation></author><author><name sortKey="Plastow, G S" sort="Plastow, G S" uniqKey="Plastow G" first="G S" last="Plastow">G S Plastow</name><affiliation><nlm:affiliation>Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Rothschild, M F" sort="Rothschild, M F" uniqKey="Rothschild M" first="M F" last="Rothschild">M F Rothschild</name><affiliation><nlm:affiliation>Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Animal genetics</title><idno type="eISSN">1365-2052</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Coronavirus Infections (epidemiology)</term><term>Coronavirus Infections (genetics)</term><term>Coronavirus Infections (immunology)</term><term>Coronavirus Infections (veterinary)</term><term>Disease Outbreaks</term><term>Porcine epidemic diarrhea virus (physiology)</term><term>Sus scrofa</term><term>Swine</term><term>Swine Diseases (epidemiology)</term><term>Swine Diseases (genetics)</term><term>Swine Diseases (immunology)</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term><term>Swine Diseases</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus Infections</term><term>Swine Diseases</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Coronavirus Infections</term><term>Swine Diseases</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Porcine epidemic diarrhea virus</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Disease Outbreaks</term><term>Sus scrofa</term><term>Swine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome-wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks. Samples from 262 animals (156 dead and 106 recovered) belonging to several commercial lines were collected from five different farms in three different countries (USA, Canada and Germany) and genotyped with the porcine 80K SNP chip. Mean F<sub>st</sub> value was calculated in 1-Mb non-overlapping windows between dead and recovered individuals, and the results were normalized to find differences within the comparison. Seven windows with high divergence between dead and recovered were detected-five on chromosome 2, one on chromosome 4 and one on chromosome 15-in total encompassing 152 genes. Several of these genes are either under- or overexpressed in many virus infections, including Coronaviridae (such as SARS-CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to PED development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, ATPase activity). Taken together this information provides a first genomic picture of PEDV resilience in suckling piglets.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27943331</PMID><DateCompleted><Year>2017</Year><Month>03</Month><Day>09</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>18</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-2052</ISSN><JournalIssue CitedMedium="Internet"><Volume>48</Volume><Issue>2</Issue><PubDate><Year>2017</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Animal genetics</Title><ISOAbbreviation>Anim. Genet.</ISOAbbreviation></Journal><ArticleTitle>Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks.</ArticleTitle><Pagination><MedlinePgn>228-232</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/age.12522</ELocationID><Abstract><AbstractText>Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome-wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks. Samples from 262 animals (156 dead and 106 recovered) belonging to several commercial lines were collected from five different farms in three different countries (USA, Canada and Germany) and genotyped with the porcine 80K SNP chip. Mean F<sub>st</sub> value was calculated in 1-Mb non-overlapping windows between dead and recovered individuals, and the results were normalized to find differences within the comparison. Seven windows with high divergence between dead and recovered were detected-five on chromosome 2, one on chromosome 4 and one on chromosome 15-in total encompassing 152 genes. Several of these genes are either under- or overexpressed in many virus infections, including Coronaviridae (such as SARS-CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to PED development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, ATPase activity). Taken together this information provides a first genomic picture of PEDV resilience in suckling piglets.</AbstractText><CopyrightInformation>© 2016 Stichting International Foundation for Animal Genetics.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bertolini</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Harding</LastName><ForeName>J C S</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mote</LastName><ForeName>B</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ladinig</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Wien, 1210, Austria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Plastow</LastName><ForeName>G S</ForeName><Initials>GS</Initials><AffiliationInfo><Affiliation>Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rothschild</LastName><ForeName>M F</ForeName><Initials>MF</Initials><AffiliationInfo><Affiliation>Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>12</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Anim Genet</MedlineTA><NlmUniqueID>8605704</NlmUniqueID><ISSNLinking>0268-9146</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName><QualifierName UI="Q000662" MajorTopicYN="Y">veterinary</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004196" MajorTopicYN="N">Disease Outbreaks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053485" MajorTopicYN="N">Porcine epidemic diarrhea virus</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D034421" MajorTopicYN="N">Sus scrofa</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013552" MajorTopicYN="N">Swine</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013553" MajorTopicYN="N">Swine Diseases</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000276" MajorTopicYN="Y">immunology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">F
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