Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations.
Identifieur interne : 000946 ( Main/Exploration ); précédent : 000945; suivant : 000947Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations.
Auteurs : Julien Prunier [Canada] ; Isabelle Giguère [Canada] ; Natalie Ryan [Canada] ; Robert Guy [Canada] ; Raju Soolanayakanahally [Canada] ; Nathalie Isabel [Canada] ; John Mackay [Royaume-Uni] ; Ilga Porth [Canada]Source :
- Molecular ecology [ 1365-294X ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Adaptation, Physiological, DNA Copy Number Variations, Genome, Polymorphism, Single Nucleotide, Populus.
- physiology : Populus.
- Comparative Genomic Hybridization, Genomics, Phenotype.
Abstract
Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intraprovenance cross (north-north cross, 58th parallel) and an interprovenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water-use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast-evolving pathogens.
DOI: 10.1111/mec.14836
PubMed: 30270494
Affiliations:
- Canada, Royaume-Uni
- Angleterre, Colombie-Britannique , Oxfordshire, Québec
- Oxford, Québec (ville), Vancouver
- Université Laval, Université d'Oxford, Université de la Colombie-Britannique
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type="state">Québec</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Centre for Forest Research, Université Laval, Québec, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Forest Research, Université Laval, Québec, Quebec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Giguere, Isabelle" sort="Giguere, Isabelle" uniqKey="Giguere I" first="Isabelle" last="Giguère">Isabelle Giguère</name><affiliation wicri:level="4"><nlm:affiliation>Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Centre for Forest Research, Université Laval, Québec, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Forest Research, Université Laval, Québec, Quebec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Ryan, Natalie" sort="Ryan, Natalie" uniqKey="Ryan N" first="Natalie" last="Ryan">Natalie Ryan</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of 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</region></placeName></affiliation></author><author><name sortKey="Soolanayakanahally, Raju" sort="Soolanayakanahally, Raju" uniqKey="Soolanayakanahally R" first="Raju" last="Soolanayakanahally">Raju Soolanayakanahally</name><affiliation wicri:level="1"><nlm:affiliation>Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, Saskatchewan, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, Saskatchewan</wicri:regionArea><wicri:noRegion>Saskatchewan</wicri:noRegion></affiliation></author><author><name sortKey="Isabel, Nathalie" sort="Isabel, Nathalie" uniqKey="Isabel N" first="Nathalie" last="Isabel">Nathalie Isabel</name><affiliation wicri:level="1"><nlm:affiliation>Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Québec, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Québec, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation></author><author><name sortKey="Mackay, John" sort="Mackay, John" uniqKey="Mackay J" first="John" last="Mackay">John Mackay</name><affiliation wicri:level="4"><nlm:affiliation>Department of Plant Sciences, University of Oxford, Oxford, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Plant Sciences, University of Oxford, Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="country">Angleterre</region><region type="comté" nuts="2">Oxfordshire</region></placeName><orgName type="university">Université d'Oxford</orgName></affiliation></author><author><name sortKey="Porth, Ilga" sort="Porth, Ilga" uniqKey="Porth I" first="Ilga" last="Porth">Ilga Porth</name><affiliation wicri:level="4"><nlm:affiliation>Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Centre for Forest Research, Université Laval, Québec, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Forest Research, Université Laval, Québec, Quebec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author></analytic><series><title level="j">Molecular ecology</title><idno type="eISSN">1365-294X</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Physiological (genetics)</term><term>Comparative Genomic Hybridization (MeSH)</term><term>DNA Copy Number Variations (genetics)</term><term>Genome (genetics)</term><term>Genomics (MeSH)</term><term>Phenotype (MeSH)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Populus (genetics)</term><term>Populus (physiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adaptation physiologique (génétique)</term><term>Génome (génétique)</term><term>Génomique (MeSH)</term><term>Hybridation génomique comparative (MeSH)</term><term>Phénotype (MeSH)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Variations de nombre de copies de segment d'ADN (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Adaptation, Physiological</term><term>DNA Copy Number Variations</term><term>Genome</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Adaptation physiologique</term><term>Génome</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term><term>Variations de nombre de copies de segment d'ADN</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Comparative Genomic Hybridization</term><term>Genomics</term><term>Phenotype</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génomique</term><term>Hybridation génomique comparative</term><term>Phénotype</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F<sub>1</sub> progenies of an intraprovenance cross (north-north cross, 58th parallel) and an interprovenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water-use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast-evolving pathogens.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30270494</PMID><DateCompleted><Year>2019</Year><Month>11</Month><Day>27</Day></DateCompleted><DateRevised><Year>2019</Year><Month>11</Month><Day>27</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><Volume>28</Volume><Issue>6</Issue><PubDate><Year>2019</Year><Month>03</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations.</ArticleTitle><Pagination><MedlinePgn>1476-1490</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.14836</ELocationID><Abstract><AbstractText>Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F<sub>1</sub> progenies of an intraprovenance cross (north-north cross, 58th parallel) and an interprovenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water-use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast-evolving pathogens.</AbstractText><CopyrightInformation>© 2018 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Prunier</LastName><ForeName>Julien</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0002-4839-3857</Identifier><AffiliationInfo><Affiliation>Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centre for Forest Research, Université Laval, Québec, Quebec, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giguère</LastName><ForeName>Isabelle</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centre for Forest Research, Université Laval, Québec, Quebec, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ryan</LastName><ForeName>Natalie</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guy</LastName><ForeName>Robert</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Soolanayakanahally</LastName><ForeName>Raju</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, Saskatchewan, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Isabel</LastName><ForeName>Nathalie</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Québec, Quebec, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>MacKay</LastName><ForeName>John</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Plant Sciences, University of Oxford, Oxford, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Porth</LastName><ForeName>Ilga</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centre for Forest Research, Université Laval, Québec, Quebec, Canada.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Agency>National Sciences and Engineering Research Council of Canada</Agency><Country>International</Country></Grant><Grant><Agency>Le Ministère de l'Économie, de la Science et de l'Innovation</Agency><Country>International</Country></Grant><Grant><Agency>Natural Resources Canada</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>10</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000222" MajorTopicYN="N">Adaptation, Physiological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055028" MajorTopicYN="N">Comparative Genomic Hybridization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056915" MajorTopicYN="N">DNA Copy Number Variations</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="N">Genome</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus
</Keyword><Keyword MajorTopicYN="Y">CNVs</Keyword><Keyword MajorTopicYN="Y">aCGH technology</Keyword><Keyword MajorTopicYN="Y">adaptation</Keyword><Keyword MajorTopicYN="Y">climate</Keyword><Keyword MajorTopicYN="Y">genome hotspots</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>05</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>07</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>07</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>10</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>10</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30270494</ArticleId><ArticleId IdType="doi">10.1111/mec.14836</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li><li>Royaume-Uni</li></country><region><li>Angleterre</li><li>Colombie-Britannique </li><li>Oxfordshire</li><li>Québec</li></region><settlement><li>Oxford</li><li>Québec (ville)</li><li>Vancouver</li></settlement><orgName><li>Université Laval</li><li>Université d'Oxford</li><li>Université de la Colombie-Britannique</li></orgName></list><tree><country name="Canada"><region name="Québec"><name sortKey="Prunier, Julien" sort="Prunier, Julien" uniqKey="Prunier J" first="Julien" last="Prunier">Julien Prunier</name></region><name sortKey="Giguere, Isabelle" sort="Giguere, Isabelle" uniqKey="Giguere I" first="Isabelle" last="Giguère">Isabelle Giguère</name><name sortKey="Giguere, Isabelle" sort="Giguere, Isabelle" uniqKey="Giguere I" first="Isabelle" last="Giguère">Isabelle Giguère</name><name sortKey="Guy, Robert" sort="Guy, Robert" uniqKey="Guy R" first="Robert" last="Guy">Robert Guy</name><name sortKey="Isabel, Nathalie" sort="Isabel, Nathalie" uniqKey="Isabel N" first="Nathalie" last="Isabel">Nathalie Isabel</name><name sortKey="Porth, Ilga" sort="Porth, Ilga" uniqKey="Porth I" first="Ilga" last="Porth">Ilga Porth</name><name sortKey="Porth, Ilga" sort="Porth, Ilga" uniqKey="Porth I" first="Ilga" last="Porth">Ilga Porth</name><name sortKey="Prunier, Julien" sort="Prunier, Julien" uniqKey="Prunier J" first="Julien" last="Prunier">Julien Prunier</name><name sortKey="Ryan, Natalie" sort="Ryan, Natalie" uniqKey="Ryan N" first="Natalie" last="Ryan">Natalie Ryan</name><name sortKey="Soolanayakanahally, Raju" sort="Soolanayakanahally, Raju" uniqKey="Soolanayakanahally R" first="Raju" last="Soolanayakanahally">Raju Soolanayakanahally</name></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Mackay, John" sort="Mackay, John" uniqKey="Mackay J" first="John" last="Mackay">John Mackay</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
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Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:30270494
|texte= Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:30270494" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
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