Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology.
Identifieur interne : 001447 ( Main/Exploration ); précédent : 001446; suivant : 001448Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology.
Auteurs : Anatoly V. Zhigunov [Russie] ; Pavel S. Ulianich [Russie] ; Marina V. Lebedeva [Russie] ; Peter L. Chang [États-Unis] ; Sergey V. Nuzhdin [États-Unis] ; Elena K. Potokina [Russie]Source :
- BMC plant biology [ 1471-2229 ] ; 2017.
Descripteurs français
- KwdFr :
- Amélioration des plantes (MeSH), Banque de gènes (MeSH), Cartographie de restriction (MeSH), Chromosomes de plante (MeSH), Hybridation génétique (MeSH), Liaison génétique (MeSH), Locus de caractère quantitatif (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (génétique), Techniques de génotypage (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
BACKGROUND
Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe.
RESULTS
We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation.
CONCLUSIONS
The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.
DOI: 10.1186/s12870-017-1127-y
PubMed: 29143610
PubMed Central: PMC5688504
Affiliations:
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Ulianich</name><affiliation wicri:level="1"><nlm:affiliation>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg</wicri:regionArea><wicri:noRegion>St. Petersburg</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg</wicri:regionArea><wicri:noRegion>St. Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Lebedeva, Marina V" sort="Lebedeva, Marina V" uniqKey="Lebedeva M" first="Marina V" last="Lebedeva">Marina V. 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Chang</name><affiliation wicri:level="4"><nlm:affiliation>University of Southern California, Los Angeles, CA, 90089, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Southern California, Los Angeles, CA, 90089</wicri:regionArea><orgName type="university">Université de Californie du Sud</orgName><placeName><settlement type="city">Los Angeles</settlement><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Nuzhdin, Sergey V" sort="Nuzhdin, Sergey V" uniqKey="Nuzhdin S" first="Sergey V" last="Nuzhdin">Sergey V. Nuzhdin</name><affiliation wicri:level="4"><nlm:affiliation>University of Southern California, Los Angeles, CA, 90089, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Southern California, Los Angeles, CA, 90089</wicri:regionArea><orgName type="university">Université de Californie du Sud</orgName><placeName><settlement type="city">Los Angeles</settlement><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Potokina, Elena K" sort="Potokina, Elena K" uniqKey="Potokina E" first="Elena K" last="Potokina">Elena K. Potokina</name><affiliation wicri:level="1"><nlm:affiliation>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia. e.potokina@vir.nw.ru.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg</wicri:regionArea><wicri:noRegion>St. Petersburg</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia. e.potokina@vir.nw.ru.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg</wicri:regionArea><wicri:noRegion>St. Petersburg</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Saint Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russia. e.potokina@vir.nw.ru.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Saint Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034</wicri:regionArea><wicri:noRegion>199034</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (MeSH)</term><term>Gene Library (MeSH)</term><term>Genetic Linkage (MeSH)</term><term>Genotyping Techniques (MeSH)</term><term>Hybridization, Genetic (MeSH)</term><term>Plant Breeding (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (genetics)</term><term>Quantitative Trait Loci (MeSH)</term><term>Restriction Mapping (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amélioration des plantes (MeSH)</term><term>Banque de gènes (MeSH)</term><term>Cartographie de restriction (MeSH)</term><term>Chromosomes de plante (MeSH)</term><term>Hybridation génétique (MeSH)</term><term>Liaison génétique (MeSH)</term><term>Locus de caractère quantitatif (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (génétique)</term><term>Techniques de génotypage (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Plant</term><term>Gene Library</term><term>Genetic Linkage</term><term>Genotyping Techniques</term><term>Hybridization, Genetic</term><term>Plant Breeding</term><term>Polymorphism, Single Nucleotide</term><term>Quantitative Trait Loci</term><term>Restriction Mapping</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Amélioration des plantes</term><term>Banque de gènes</term><term>Cartographie de restriction</term><term>Chromosomes de plante</term><term>Hybridation génétique</term><term>Liaison génétique</term><term>Locus de caractère quantitatif</term><term>Polymorphisme de nucléotide simple</term><term>Techniques de génotypage</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29143610</PMID><DateCompleted><Year>2018</Year><Month>03</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>Suppl 1</Issue><PubDate><Year>2017</Year><Month>Nov</Month><Day>14</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology.</ArticleTitle><Pagination><MedlinePgn>180</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12870-017-1127-y</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhigunov</LastName><ForeName>Anatoly V</ForeName><Initials>AV</Initials><AffiliationInfo><Affiliation>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ulianich</LastName><ForeName>Pavel S</ForeName><Initials>PS</Initials><AffiliationInfo><Affiliation>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lebedeva</LastName><ForeName>Marina V</ForeName><Initials>MV</Initials><AffiliationInfo><Affiliation>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Peter L</ForeName><Initials>PL</Initials><AffiliationInfo><Affiliation>University of Southern California, Los Angeles, CA, 90089, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nuzhdin</LastName><ForeName>Sergey V</ForeName><Initials>SV</Initials><AffiliationInfo><Affiliation>University of Southern California, Los Angeles, CA, 90089, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Potokina</LastName><ForeName>Elena K</ForeName><Initials>EK</Initials><AffiliationInfo><Affiliation>Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia. e.potokina@vir.nw.ru.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia. e.potokina@vir.nw.ru.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Saint Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russia. e.potokina@vir.nw.ru.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>11</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant Biol</MedlineTA><NlmUniqueID>100967807</NlmUniqueID><ISSNLinking>1471-2229</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="Y">Chromosomes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008040" MajorTopicYN="N">Genetic Linkage</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060005" MajorTopicYN="N">Genotyping Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006824" MajorTopicYN="N">Hybridization, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000069600" MajorTopicYN="N">Plant Breeding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D040641" MajorTopicYN="N">Quantitative Trait Loci</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015183" MajorTopicYN="Y">Restriction Mapping</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">European aspen</Keyword><Keyword MajorTopicYN="N">Full-sibling population</Keyword><Keyword MajorTopicYN="N">Growth-related traits</Keyword><Keyword MajorTopicYN="N">High resolution linkage map</Keyword><Keyword MajorTopicYN="N">Intra-specific cross</Keyword><Keyword MajorTopicYN="N">QTL mapping</Keyword><Keyword MajorTopicYN="N">RADseq</Keyword><Keyword MajorTopicYN="N">SNP</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>3</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29143610</ArticleId><ArticleId IdType="doi">10.1186/s12870-017-1127-y</ArticleId><ArticleId IdType="pii">10.1186/s12870-017-1127-y</ArticleId><ArticleId IdType="pmc">PMC5688504</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Plant Biol (Stuttg). 2015 Jan;17(1):256-61</Citation><ArticleIdList><ArticleId IdType="pubmed">24943351</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2000 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Ulianich</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Chang, Peter L" sort="Chang, Peter L" uniqKey="Chang P" first="Peter L" last="Chang">Peter L. Chang</name></region><name sortKey="Nuzhdin, Sergey V" sort="Nuzhdin, Sergey V" uniqKey="Nuzhdin S" first="Sergey V" last="Nuzhdin">Sergey V. Nuzhdin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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