Two-stage identification of SNP effects on dynamic poplar growth.
Identifieur interne : 001068 ( Main/Curation ); précédent : 001067; suivant : 001069Two-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
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<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>
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<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>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Polymorphisme de nucléotide simple</term>
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</keywords>
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<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>
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<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>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName>
<ForeName>Jingyuan</ForeName>
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<AffiliationInfo><Affiliation>Department of Public Health Sciences, Penn State Hershey College of Medicine, Hershey, PA17033, USA.</Affiliation>
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<Keyword MajorTopicYN="Y">two-stage approach</Keyword>
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<Keyword MajorTopicYN="Y">variable selection</Keyword>
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<Month>10</Month>
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