Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.
Identifieur interne : 001947 ( Main/Exploration ); précédent : 001946; suivant : 001948Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.
Auteurs : Chunfa Tong [République populaire de Chine] ; Huogen Li [République populaire de Chine] ; Ying Wang [République populaire de Chine] ; Xuran Li [République populaire de Chine] ; Jiajia Ou [République populaire de Chine] ; Deyuan Wang [République populaire de Chine] ; Houxi Xu [République populaire de Chine] ; Chao Ma [République populaire de Chine] ; Xianye Lang [République populaire de Chine] ; Guangxin Liu [République populaire de Chine] ; Bo Zhang [République populaire de Chine] ; Jisen Shi [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Plant.
- genetics : Chimera, Populus.
- Chromosome Mapping, Genetic Linkage, Genome, Plant, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide.
Abstract
Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides 'I-69' and male Populus simonii 'L3'. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.
DOI: 10.1371/journal.pone.0150692
PubMed: 26964097
PubMed Central: PMC4786213
Affiliations:
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Le document en format XML
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China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Bo" sort="Zhang, Bo" uniqKey="Zhang B" first="Bo" last="Zhang">Bo Zhang</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Shi, Jisen" sort="Shi, Jisen" uniqKey="Shi J" first="Jisen" 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uniqKey="Li H" first="Huogen" last="Li">Huogen Li</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Ying" sort="Wang, Ying" uniqKey="Wang Y" first="Ying" last="Wang">Ying Wang</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Li, Xuran" sort="Li, Xuran" uniqKey="Li X" first="Xuran" last="Li">Xuran Li</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Ou, Jiajia" sort="Ou, Jiajia" uniqKey="Ou J" first="Jiajia" last="Ou">Jiajia Ou</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Deyuan" sort="Wang, Deyuan" uniqKey="Wang D" first="Deyuan" last="Wang">Deyuan Wang</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Houxi" sort="Xu, Houxi" uniqKey="Xu H" first="Houxi" last="Xu">Houxi Xu</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Chao" sort="Ma, Chao" uniqKey="Ma C" first="Chao" last="Ma">Chao Ma</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Lang, Xianye" sort="Lang, Xianye" uniqKey="Lang X" first="Xianye" last="Lang">Xianye Lang</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Guangxin" sort="Liu, Guangxin" uniqKey="Liu G" first="Guangxin" last="Liu">Guangxin Liu</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Bo" sort="Zhang, Bo" uniqKey="Zhang B" first="Bo" last="Zhang">Bo Zhang</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Shi, Jisen" sort="Shi, Jisen" uniqKey="Shi J" first="Jisen" last="Shi">Jisen Shi</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chimera (genetics)</term><term>Chromosome Mapping (MeSH)</term><term>DNA, Plant (genetics)</term><term>Genetic Linkage (MeSH)</term><term>Genome, Plant (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Cartographie chromosomique (MeSH)</term><term>Chimère (génétique)</term><term>Génome végétal (MeSH)</term><term>Liaison génétique (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (génétique)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chimera</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Chimère</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Genetic Linkage</term><term>Genome, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term><term>Génome végétal</term><term>Liaison génétique</term><term>Polymorphisme de nucléotide simple</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides 'I-69' and male Populus simonii 'L3'. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26964097</PMID><DateCompleted><Year>2016</Year><Month>08</Month><Day>01</Day></DateCompleted><DateRevised><Year>2019</Year><Month>02</Month><Day>19</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>3</Issue><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.</ArticleTitle><Pagination><MedlinePgn>e0150692</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0150692</ELocationID><Abstract><AbstractText>Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides 'I-69' and male Populus simonii 'L3'. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Chunfa</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Huogen</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Ying</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Xuran</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ou</LastName><ForeName>Jiajia</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Deyuan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Houxi</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Chao</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lang</LastName><ForeName>Xianye</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Guangxin</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Bo</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Jisen</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal 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IdType="pubmed">24256998</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Tong, Chunfa" sort="Tong, Chunfa" uniqKey="Tong C" first="Chunfa" last="Tong">Chunfa Tong</name></noRegion><name sortKey="Lang, Xianye" sort="Lang, Xianye" uniqKey="Lang X" first="Xianye" last="Lang">Xianye Lang</name><name sortKey="Li, Huogen" sort="Li, Huogen" uniqKey="Li H" first="Huogen" last="Li">Huogen Li</name><name sortKey="Li, Xuran" sort="Li, Xuran" uniqKey="Li X" first="Xuran" last="Li">Xuran Li</name><name sortKey="Liu, Guangxin" sort="Liu, Guangxin" uniqKey="Liu G" first="Guangxin" last="Liu">Guangxin Liu</name><name sortKey="Ma, Chao" sort="Ma, Chao" uniqKey="Ma C" first="Chao" last="Ma">Chao Ma</name><name sortKey="Ou, Jiajia" sort="Ou, Jiajia" uniqKey="Ou J" first="Jiajia" last="Ou">Jiajia Ou</name><name sortKey="Shi, Jisen" sort="Shi, Jisen" uniqKey="Shi J" first="Jisen" last="Shi">Jisen Shi</name><name sortKey="Wang, Deyuan" sort="Wang, Deyuan" uniqKey="Wang D" first="Deyuan" last="Wang">Deyuan Wang</name><name sortKey="Wang, Ying" sort="Wang, Ying" uniqKey="Wang Y" first="Ying" last="Wang">Ying Wang</name><name sortKey="Xu, Houxi" sort="Xu, Houxi" uniqKey="Xu H" first="Houxi" last="Xu">Houxi Xu</name><name sortKey="Zhang, Bo" sort="Zhang, Bo" uniqKey="Zhang B" first="Bo" last="Zhang">Bo Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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