Two-stage identification of SNP effects on dynamic poplar growth.
Identifieur interne : 000C12 ( Main/Exploration ); précédent : 000C11; suivant : 000C13Two-stage identification of SNP effects on dynamic poplar growth.
Auteurs : Jingyuan Liu [République populaire de Chine] ; Meixia Ye [République populaire de Chine] ; Sheng Zhu [République populaire de Chine] ; Libo Jiang [République populaire de Chine] ; Mengmeng Sang [République populaire de Chine] ; Jingwen Gan [République populaire de Chine] ; Qian Wang [République populaire de Chine] ; Minren Huang [République populaire de Chine] ; Rongling Wu [République populaire de Chine, États-Unis]Source :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- croissance et développement : Populus.
- génétique : Polymorphisme de nucléotide simple, Populus.
- Modèles génétiques, Modèles statistiques, Phénotype, Étude d'association pangénomique.
English descriptors
- KwdEn :
- MESH :
- genetics : Polymorphism, Single Nucleotide, Populus.
- growth & development : Populus.
- Genome-Wide Association Study, Models, Genetic, Models, Statistical, Phenotype.
Abstract
This project proposes an approach to identify significant single nucleotide polymorphism (SNP) effects, both additive and dominant, on the dynamic growth of poplar in diameter and height. The annual changes in yearly phenotypes based on regular observation periods are considered to represent multiple responses. In total 156,362 candidate SNPs are studied, and the phenotypes of 64 poplar trees are recorded. To address this ultrahigh dimensionality issue, this paper adopts a two-stage approach. First, the conventional genome-wide association studies (GWAS) and the distance correlation sure independence screening (DC-SIS) methods (Li et al., 2012) were combined to reduce the model dimensions at the sample size; second, a grouped penalized regression was applied to further refine the model and choose the final sparse SNPs. The multiple response issue was also carefully addressed. The SNP effects on the dynamic diameter and height growth patterns of poplar were systematically analyzed. In addition, a series of intensive simulation studies was performed to validate the proposed approach.
DOI: 10.1111/tpj.13777
PubMed: 29168265
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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last="Wang">Qian Wang</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name><affiliation wicri:level="1"><nlm:affiliation>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing 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wicri:level="1"><nlm:affiliation>Department of Statistics in School of Economics, Wang Yanan Institute for Studies in Economics, Fujian Key Laboratory of Statistical Science, Xiamen University, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Statistics in School of Economics, Wang Yanan Institute for Studies in Economics, Fujian Key Laboratory of Statistical Science, Xiamen University</wicri:regionArea><wicri:noRegion>Xiamen University</wicri:noRegion></affiliation></author><author><name sortKey="Ye, Meixia" sort="Ye, Meixia" uniqKey="Ye M" first="Meixia" last="Ye">Meixia Ye</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Zhu, Sheng" sort="Zhu, Sheng" uniqKey="Zhu S" first="Sheng" last="Zhu">Sheng Zhu</name><affiliation wicri:level="1"><nlm:affiliation>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Libo" sort="Jiang, Libo" uniqKey="Jiang L" first="Libo" last="Jiang">Libo Jiang</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Sang, Mengmeng" sort="Sang, Mengmeng" uniqKey="Sang M" first="Mengmeng" last="Sang">Mengmeng Sang</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Gan, Jingwen" sort="Gan, Jingwen" uniqKey="Gan J" first="Jingwen" last="Gan">Jingwen Gan</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Qian" sort="Wang, Qian" uniqKey="Wang Q" first="Qian" last="Wang">Qian Wang</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name><affiliation wicri:level="1"><nlm:affiliation>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Public Health Sciences, Penn State Hershey College of Medicine, Hershey, PA17033, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Public Health Sciences, Penn State Hershey College of Medicine, Hershey, PA17033</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome-Wide Association Study (MeSH)</term><term>Models, Genetic (MeSH)</term><term>Models, Statistical (MeSH)</term><term>Phenotype (MeSH)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Modèles génétiques (MeSH)</term><term>Modèles statistiques (MeSH)</term><term>Phénotype (MeSH)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Populus (croissance et développement)</term><term>Populus (génétique)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Polymorphism, Single Nucleotide</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Polymorphisme de nucléotide simple</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome-Wide Association Study</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Phenotype</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Phénotype</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">This project proposes an approach to identify significant single nucleotide polymorphism (SNP) effects, both additive and dominant, on the dynamic growth of poplar in diameter and height. The annual changes in yearly phenotypes based on regular observation periods are considered to represent multiple responses. In total 156,362 candidate SNPs are studied, and the phenotypes of 64 poplar trees are recorded. To address this ultrahigh dimensionality issue, this paper adopts a two-stage approach. First, the conventional genome-wide association studies (GWAS) and the distance correlation sure independence screening (DC-SIS) methods (Li et al., 2012) were combined to reduce the model dimensions at the sample size; second, a grouped penalized regression was applied to further refine the model and choose the final sparse SNPs. The multiple response issue was also carefully addressed. The SNP effects on the dynamic diameter and height growth patterns of poplar were systematically analyzed. In addition, a series of intensive simulation studies was performed to validate the proposed approach.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29168265</PMID><DateCompleted><Year>2018</Year><Month>08</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>08</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>93</Volume><Issue>2</Issue><PubDate><Year>2018</Year><Month>01</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>Two-stage identification of SNP effects on dynamic poplar growth.</ArticleTitle><Pagination><MedlinePgn>286-296</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/tpj.13777</ELocationID><Abstract><AbstractText>This project proposes an approach to identify significant single nucleotide polymorphism (SNP) effects, both additive and dominant, on the dynamic growth of poplar in diameter and height. The annual changes in yearly phenotypes based on regular observation periods are considered to represent multiple responses. In total 156,362 candidate SNPs are studied, and the phenotypes of 64 poplar trees are recorded. To address this ultrahigh dimensionality issue, this paper adopts a two-stage approach. First, the conventional genome-wide association studies (GWAS) and the distance correlation sure independence screening (DC-SIS) methods (Li et al., 2012) were combined to reduce the model dimensions at the sample size; second, a grouped penalized regression was applied to further refine the model and choose the final sparse SNPs. The multiple response issue was also carefully addressed. The SNP effects on the dynamic diameter and height growth patterns of poplar were systematically analyzed. In addition, a series of intensive simulation studies was performed to validate the proposed approach.</AbstractText><CopyrightInformation>© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jingyuan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Statistics in School of Economics, Wang Yanan Institute for Studies in Economics, Fujian Key Laboratory of Statistical Science, Xiamen University, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Meixia</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Sheng</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Libo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sang</LastName><ForeName>Mengmeng</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gan</LastName><ForeName>Jingwen</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Qian</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Minren</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Rongling</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Public Health Sciences, Penn State Hershey College of Medicine, Hershey, PA17033, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>12</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="Y">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015233" MajorTopicYN="N">Models, Statistical</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="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">dynamic growth pattern</Keyword><Keyword MajorTopicYN="Y">feature screening</Keyword><Keyword MajorTopicYN="Y">gene selection</Keyword><Keyword MajorTopicYN="Y">multiple response</Keyword><Keyword MajorTopicYN="Y">two-stage approach</Keyword><Keyword MajorTopicYN="Y">ultrahigh dimensional data</Keyword><Keyword MajorTopicYN="Y">variable selection</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>07</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>10</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>10</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>8</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29168265</ArticleId><ArticleId IdType="doi">10.1111/tpj.13777</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Pennsylvanie</li></region></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Liu, Jingyuan" sort="Liu, Jingyuan" uniqKey="Liu J" first="Jingyuan" last="Liu">Jingyuan Liu</name></noRegion><name sortKey="Gan, Jingwen" sort="Gan, Jingwen" uniqKey="Gan J" first="Jingwen" last="Gan">Jingwen Gan</name><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name><name sortKey="Jiang, Libo" sort="Jiang, Libo" uniqKey="Jiang L" first="Libo" last="Jiang">Libo Jiang</name><name sortKey="Sang, Mengmeng" sort="Sang, Mengmeng" uniqKey="Sang M" first="Mengmeng" last="Sang">Mengmeng Sang</name><name sortKey="Wang, Qian" sort="Wang, Qian" uniqKey="Wang Q" first="Qian" last="Wang">Qian Wang</name><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><name sortKey="Ye, Meixia" sort="Ye, Meixia" uniqKey="Ye M" first="Meixia" last="Ye">Meixia Ye</name><name sortKey="Zhu, Sheng" sort="Zhu, Sheng" uniqKey="Zhu S" first="Sheng" last="Zhu">Sheng Zhu</name></country><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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