Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks
Identifieur interne : 000707 ( Pmc/Checkpoint ); précédent : 000706; suivant : 000708Genomic 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 [ 0268-9146 ] ; 2016.
Abstract
Porcine epidemic diarrhea virus (
Url:
DOI: 10.1111/age.12522
PubMed: 27943331
PubMed Central: 7159462
Affiliations:
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PMC:7159462Le document en format XML
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<front><div type="abstract" xml:lang="en"><title>Summary</title>
<p>Porcine epidemic diarrhea virus (<styled-content style="fixed-case" toggle="no">PEDV</styled-content>
) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, <styled-content style="fixed-case" toggle="no">PED</styled-content>
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 <styled-content style="fixed-case" toggle="no">PED</styled-content>
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 (<styled-content style="fixed-case" toggle="no">USA</styled-content>
, Canada and Germany) and genotyped with the porcine 80K <styled-content style="fixed-case" toggle="no">SNP</styled-content>
chip. Mean <italic>F</italic>
<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 <styled-content style="fixed-case" toggle="no">SARS</styled-content>
‐CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to <styled-content style="fixed-case" toggle="no">PED</styled-content>
development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, <styled-content style="fixed-case" toggle="no">ATP</styled-content>
ase activity). Taken together this information provides a first genomic picture of <styled-content style="fixed-case" toggle="no">PEDV</styled-content>
resilience in suckling piglets.</p>
</div>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Anim Genet</journal-id>
<journal-id journal-id-type="iso-abbrev">Anim. Genet</journal-id>
<journal-id journal-id-type="doi">10.1111/(ISSN)1365-2052</journal-id>
<journal-id journal-id-type="publisher-id">AGE</journal-id>
<journal-title-group><journal-title>Animal Genetics</journal-title>
</journal-title-group>
<issn pub-type="ppub">0268-9146</issn>
<issn pub-type="epub">1365-2052</issn>
<publisher><publisher-name>John Wiley and Sons Inc.</publisher-name>
<publisher-loc>Hoboken</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27943331</article-id>
<article-id pub-id-type="pmc">7159462</article-id>
<article-id pub-id-type="doi">10.1111/age.12522</article-id>
<article-id pub-id-type="publisher-id">AGE12522</article-id>
<article-categories><subj-group subj-group-type="overline"><subject>Short Communication</subject>
</subj-group>
<subj-group subj-group-type="heading"><subject>Short Communications</subject>
</subj-group>
</article-categories>
<title-group><article-title>Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks</article-title>
<alt-title alt-title-type="left-running-head">Bertolini <italic>et al</italic>
.</alt-title>
</title-group>
<contrib-group><contrib id="age12522-cr-0001" contrib-type="author" corresp="yes"><name><surname>Bertolini</surname>
<given-names>F.</given-names>
</name>
<xref ref-type="aff" rid="age12522-aff-0001"><sup>1</sup>
</xref>
<address><email>fbert@iastate.edu</email>
</address>
</contrib>
<contrib id="age12522-cr-0002" contrib-type="author"><name><surname>Harding</surname>
<given-names>J. C. S.</given-names>
</name>
<xref ref-type="aff" rid="age12522-aff-0002"><sup>2</sup>
</xref>
</contrib>
<contrib id="age12522-cr-0003" contrib-type="author"><name><surname>Mote</surname>
<given-names>B.</given-names>
</name>
<xref ref-type="aff" rid="age12522-aff-0003"><sup>3</sup>
</xref>
</contrib>
<contrib id="age12522-cr-0004" contrib-type="author"><name><surname>Ladinig</surname>
<given-names>A.</given-names>
</name>
<xref ref-type="aff" rid="age12522-aff-0004"><sup>4</sup>
</xref>
</contrib>
<contrib id="age12522-cr-0005" contrib-type="author"><name><surname>Plastow</surname>
<given-names>G. S.</given-names>
</name>
<xref ref-type="aff" rid="age12522-aff-0005"><sup>5</sup>
</xref>
</contrib>
<contrib id="age12522-cr-0006" contrib-type="author"><name><surname>Rothschild</surname>
<given-names>M. F.</given-names>
</name>
<xref ref-type="aff" rid="age12522-aff-0001"><sup>1</sup>
</xref>
</contrib>
</contrib-group>
<aff id="age12522-aff-0001"><label><sup>1</sup>
</label>
<named-content content-type="organisation-division">Department of Animal Science</named-content>
<institution>Iowa State University</institution>
<city>Ames</city>
<named-content content-type="country-part">IA</named-content>
<postal-code>50011‐3150</postal-code>
<country country="US">USA</country>
</aff>
<aff id="age12522-aff-0002"><label><sup>2</sup>
</label>
<named-content content-type="organisation-division">Department of Large Animal Clinical Sciences</named-content>
<named-content content-type="organisation-division">Western College of Veterinary Medicine</named-content>
<institution>University of Saskatchewan</institution>
<city>Saskatoon</city>
<named-content content-type="country-part">SK</named-content>
<postal-code>S7N 5B4</postal-code>
<country country="CA">Canada</country>
</aff>
<aff id="age12522-aff-0003"><label><sup>3</sup>
</label>
<named-content content-type="organisation-division">Department of Animal Science</named-content>
<institution>University of Nebraska</institution>
<city>Lincoln</city>
<named-content content-type="country-part">NE</named-content>
<postal-code>68583‐0908</postal-code>
<country country="US">USA</country>
</aff>
<aff id="age12522-aff-0004"><label><sup>4</sup>
</label>
<named-content content-type="organisation-division">University Clinic for Swine</named-content>
<named-content content-type="organisation-division">Department for Farm Animals and Veterinary Public Health</named-content>
<institution>University of Veterinary Medicine Vienna</institution>
<city>Wien</city>
<postal-code>1210</postal-code>
<country country="AT">Austria</country>
</aff>
<aff id="age12522-aff-0005"><label><sup>5</sup>
</label>
<named-content content-type="organisation-division">Livestock Gentec</named-content>
<named-content content-type="organisation-division">Department of Agricultural, Food and Nutritional Science</named-content>
<institution>University of Alberta</institution>
<city>Edmonton</city>
<named-content content-type="country-part">AB, T6G 2R3</named-content>
<country country="CA">Canada</country>
</aff>
<author-notes><corresp id="correspondenceTo"><label>*</label>
Address for correspondence<break></break>
F. Bertolini, Department of Animal Science, Iowa State University, Ames, IA 50011‐3150, USA.<break></break>
E‐mail: <email>fbert@iastate.edu</email>
<break></break>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>12</day>
<month>12</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="ppub"><month>4</month>
<year>2017</year>
</pub-date>
<volume>48</volume>
<issue>2</issue>
<issue-id pub-id-type="doi">10.1111/age.2017.48.issue-2</issue-id>
<fpage>228</fpage>
<lpage>232</lpage>
<history><date date-type="accepted"><day>29</day>
<month>9</month>
<year>2016</year>
</date>
</history>
<permissions><pmc-comment> Copyright © 2017 Stichting International Foundation for Animal Genetics </pmc-comment>
<copyright-statement content-type="article-copyright">© 2016 Stichting International Foundation for Animal Genetics</copyright-statement>
<license><license-p>This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.</license-p>
</license>
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<self-uri content-type="pdf" xlink:href="file:AGE-48-228.pdf"></self-uri>
<abstract id="age12522-abs-0001"><title>Summary</title>
<p>Porcine epidemic diarrhea virus (<styled-content style="fixed-case" toggle="no">PEDV</styled-content>
) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, <styled-content style="fixed-case" toggle="no">PED</styled-content>
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 <styled-content style="fixed-case" toggle="no">PED</styled-content>
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 (<styled-content style="fixed-case" toggle="no">USA</styled-content>
, Canada and Germany) and genotyped with the porcine 80K <styled-content style="fixed-case" toggle="no">SNP</styled-content>
chip. Mean <italic>F</italic>
<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 <styled-content style="fixed-case" toggle="no">SARS</styled-content>
‐CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to <styled-content style="fixed-case" toggle="no">PED</styled-content>
development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, <styled-content style="fixed-case" toggle="no">ATP</styled-content>
ase activity). Taken together this information provides a first genomic picture of <styled-content style="fixed-case" toggle="no">PEDV</styled-content>
resilience in suckling piglets.</p>
</abstract>
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<award-group id="funding-0002"><funding-source>Genome Alberta's 2014 Program</funding-source>
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<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>
<name sortKey="Ladinig, A" sort="Ladinig, A" uniqKey="Ladinig A" first="A." last="Ladinig">A. Ladinig</name>
<name sortKey="Mote, B" sort="Mote, B" uniqKey="Mote B" first="B." last="Mote">B. Mote</name>
<name sortKey="Plastow, G S" sort="Plastow, G S" uniqKey="Plastow G" first="G. S." last="Plastow">G. S. Plastow</name>
<name sortKey="Rothschild, M F" sort="Rothschild, M F" uniqKey="Rothschild M" first="M. F." last="Rothschild">M. F. Rothschild</name>
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