Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina.
Identifieur interne : 002202 ( Main/Exploration ); précédent : 002201; suivant : 002203Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina.
Auteurs : Michaël Pernaci [France] ; Stéphane De Mita [France] ; Axelle Andrieux [France] ; Jérémy Pétrowski [France] ; Fabien Halkett [France] ; Sébastien Duplessis [France] ; Pascal Frey [France]Source :
- Frontiers in plant science [ 1664-462X ] ; 2014.
Abstract
The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring.
DOI: 10.3389/fpls.2014.00454
PubMed: 25309554
PubMed Central: PMC4159982
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Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy</wicri:regionArea><wicri:noRegion>UMR1136 Vandoeuvre-lès-Nancy</wicri:noRegion><orgName type="university">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName></affiliation></author><author><name sortKey="De Mita, Stephane" sort="De Mita, Stephane" uniqKey="De Mita S" first="Stéphane" last="De Mita">Stéphane De Mita</name><affiliation wicri:level="4"><nlm:affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy</wicri:regionArea><wicri:noRegion>UMR1136 Vandoeuvre-lès-Nancy</wicri:noRegion><orgName type="university">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName></affiliation></author><author><name sortKey="Andrieux, Axelle" sort="Andrieux, Axelle" uniqKey="Andrieux A" first="Axelle" last="Andrieux">Axelle Andrieux</name><affiliation wicri:level="4"><nlm:affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy</wicri:regionArea><wicri:noRegion>UMR1136 Vandoeuvre-lès-Nancy</wicri:noRegion><orgName type="university">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName></affiliation></author><author><name sortKey="Petrowski, Jeremy" sort="Petrowski, Jeremy" uniqKey="Petrowski J" first="Jérémy" last="Pétrowski">Jérémy Pétrowski</name><affiliation wicri:level="4"><nlm:affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy</wicri:regionArea><wicri:noRegion>UMR1136 Vandoeuvre-lès-Nancy</wicri:noRegion><orgName type="university">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName></affiliation></author><author><name sortKey="Halkett, Fabien" sort="Halkett, Fabien" uniqKey="Halkett F" first="Fabien" last="Halkett">Fabien Halkett</name><affiliation wicri:level="4"><nlm:affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy</wicri:regionArea><wicri:noRegion>UMR1136 Vandoeuvre-lès-Nancy</wicri:noRegion><orgName type="university">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName></affiliation></author><author><name sortKey="Duplessis, Sebastien" sort="Duplessis, Sebastien" uniqKey="Duplessis S" first="Sébastien" last="Duplessis">Sébastien Duplessis</name><affiliation wicri:level="4"><nlm:affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy</wicri:regionArea><wicri:noRegion>UMR1136 Vandoeuvre-lès-Nancy</wicri:noRegion><orgName type="university">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName></affiliation></author><author><name sortKey="Frey, Pascal" sort="Frey, Pascal" uniqKey="Frey P" first="Pascal" last="Frey">Pascal Frey</name><affiliation wicri:level="4"><nlm:affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy</wicri:regionArea><wicri:noRegion>UMR1136 Vandoeuvre-lès-Nancy</wicri:noRegion><orgName type="university">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25309554</PMID><DateCompleted><Year>2014</Year><Month>10</Month><Day>13</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina.</ArticleTitle><Pagination><MedlinePgn>454</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2014.00454</ELocationID><Abstract><AbstractText>The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pernaci</LastName><ForeName>Michaël</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>De Mita</LastName><ForeName>Stéphane</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Andrieux</LastName><ForeName>Axelle</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pétrowski</LastName><ForeName>Jérémy</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Halkett</LastName><ForeName>Fabien</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Duplessis</LastName><ForeName>Sébastien</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Frey</LastName><ForeName>Pascal</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136 Champenoux, France ; Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>09</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Mendelian segregation</Keyword><Keyword MajorTopicYN="N">fungal pathogen</Keyword><Keyword MajorTopicYN="N">genome mapping</Keyword><Keyword MajorTopicYN="N">genome sequencing</Keyword><Keyword MajorTopicYN="N">linkage mapping</Keyword><Keyword MajorTopicYN="N">progeny</Keyword><Keyword MajorTopicYN="N">selfing</Keyword><Keyword MajorTopicYN="N">single-nucleotide polymorphism</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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IdType="pubmed">21627704</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Metz</li><li>Nancy</li></settlement><orgName><li>Université de Lorraine</li></orgName></list><tree><country name="France"><region name="Grand Est"><name sortKey="Pernaci, Michael" sort="Pernaci, Michael" uniqKey="Pernaci M" first="Michaël" last="Pernaci">Michaël Pernaci</name></region><name sortKey="Andrieux, Axelle" sort="Andrieux, Axelle" uniqKey="Andrieux A" first="Axelle" last="Andrieux">Axelle Andrieux</name><name sortKey="De Mita, Stephane" sort="De Mita, Stephane" uniqKey="De Mita S" first="Stéphane" last="De Mita">Stéphane De Mita</name><name sortKey="Duplessis, Sebastien" sort="Duplessis, Sebastien" uniqKey="Duplessis S" first="Sébastien" last="Duplessis">Sébastien Duplessis</name><name sortKey="Frey, Pascal" sort="Frey, Pascal" uniqKey="Frey P" first="Pascal" last="Frey">Pascal Frey</name><name sortKey="Halkett, Fabien" sort="Halkett, Fabien" uniqKey="Halkett F" first="Fabien" last="Halkett">Fabien Halkett</name><name sortKey="Petrowski, Jeremy" sort="Petrowski, Jeremy" uniqKey="Petrowski J" first="Jérémy" last="Pétrowski">Jérémy Pétrowski</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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