Genome-wide association studies of callus differentiation for the desert tree, Populus euphratica.
Identifieur interne : 000371 ( Main/Exploration ); précédent : 000370; suivant : 000372Genome-wide association studies of callus differentiation for the desert tree, Populus euphratica.
Auteurs : Qianru Zhang [République populaire de Chine] ; Zhifang Su [République populaire de Chine] ; Yunqian Guo [République populaire de Chine] ; Shilong Zhang [République populaire de Chine] ; Libo Jiang [République populaire de Chine] ; Rongling Wu [République populaire de Chine, États-Unis]Source :
- Tree physiology [ 1758-4469 ] ; 2020.
Abstract
Callus differentiation is a key developmental process in plant regeneration from cells. A better understanding of the genetic architecture of callus differentiation timing can help improve tissue transformation and the efficiency of artificial propagation. In this study, we investigated genotypic variation in callus differentiation capacity among 297 diverse P. euphratica trees sampled from a natural population. We employed a genome-wide association study (GWAS) of binary and growth-based parameters to identify loci and characterize the genetic architecture and genetic network underlying regulation of callus differentiation in P. euphratica. The results of this GWAS experiment suggested potential associations controlling whether the callus could differentiate and the process of callus differentiation. We identified multiple significant quantitative trait loci (QTLs), including the genes LOG1 and LOG7 and a locus containing WOX1. We reconstructed a genetic network that visualizes how each QTL interacts uniquely with other variants, and several core QTLs were detected that are involved in the degree of callus differentiation, providing potential targets for selection. This study represents one of the first to identify genetic variants affecting callus differentiation in a forest tree. Our results suggest that callus differentiation may be a typical qualitative-quantitative trait controlled by a major gene as well as polygenes across the genome of P. euphratica. This GWAS will help to design more complex and specific molecular tools for systematically manipulating organ regeneration.
DOI: 10.1093/treephys/tpaa098
PubMed: 32761189
Affiliations:
- République populaire de Chine, États-Unis
- Pennsylvanie
- Pékin, University Park (Pennsylvanie)
- Université d'État de Pennsylvanie
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China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, 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 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></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>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, 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 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author></analytic><series><title level="j">Tree physiology</title><idno type="eISSN">1758-4469</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Callus differentiation is a key developmental process in plant regeneration from cells. A better understanding of the genetic architecture of callus differentiation timing can help improve tissue transformation and the efficiency of artificial propagation. In this study, we investigated genotypic variation in callus differentiation capacity among 297 diverse P. euphratica trees sampled from a natural population. We employed a genome-wide association study (GWAS) of binary and growth-based parameters to identify loci and characterize the genetic architecture and genetic network underlying regulation of callus differentiation in P. euphratica. The results of this GWAS experiment suggested potential associations controlling whether the callus could differentiate and the process of callus differentiation. We identified multiple significant quantitative trait loci (QTLs), including the genes LOG1 and LOG7 and a locus containing WOX1. We reconstructed a genetic network that visualizes how each QTL interacts uniquely with other variants, and several core QTLs were detected that are involved in the degree of callus differentiation, providing potential targets for selection. This study represents one of the first to identify genetic variants affecting callus differentiation in a forest tree. Our results suggest that callus differentiation may be a typical qualitative-quantitative trait controlled by a major gene as well as polygenes across the genome of P. euphratica. This GWAS will help to design more complex and specific molecular tools for systematically manipulating organ regeneration.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32761189</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1758-4469</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Aug</Month><Day>06</Day></PubDate></JournalIssue><Title>Tree physiology</Title><ISOAbbreviation>Tree Physiol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide association studies of callus differentiation for the desert tree, Populus euphratica.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">tpaa098</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1093/treephys/tpaa098</ELocationID><Abstract><AbstractText>Callus differentiation is a key developmental process in plant regeneration from cells. A better understanding of the genetic architecture of callus differentiation timing can help improve tissue transformation and the efficiency of artificial propagation. In this study, we investigated genotypic variation in callus differentiation capacity among 297 diverse P. euphratica trees sampled from a natural population. We employed a genome-wide association study (GWAS) of binary and growth-based parameters to identify loci and characterize the genetic architecture and genetic network underlying regulation of callus differentiation in P. euphratica. The results of this GWAS experiment suggested potential associations controlling whether the callus could differentiate and the process of callus differentiation. We identified multiple significant quantitative trait loci (QTLs), including the genes LOG1 and LOG7 and a locus containing WOX1. We reconstructed a genetic network that visualizes how each QTL interacts uniquely with other variants, and several core QTLs were detected that are involved in the degree of callus differentiation, providing potential targets for selection. This study represents one of the first to identify genetic variants affecting callus differentiation in a forest tree. Our results suggest that callus differentiation may be a typical qualitative-quantitative trait controlled by a major gene as well as polygenes across the genome of P. euphratica. This GWAS will help to design more complex and specific molecular tools for systematically manipulating organ regeneration.</AbstractText><CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Qianru</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Zhifang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Yunqian</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Shilong</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Libo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Rongling</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>08</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Tree Physiol</MedlineTA><NlmUniqueID>100955338</NlmUniqueID><ISSNLinking>0829-318X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Euphrates poplar</Keyword><Keyword MajorTopicYN="N">callus differentiation</Keyword><Keyword MajorTopicYN="N">genetic network</Keyword><Keyword MajorTopicYN="N">growth equation</Keyword><Keyword MajorTopicYN="N">quantitative trait loci</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>06</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>8</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>8</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>8</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32761189</ArticleId><ArticleId IdType="pii">5881855</ArticleId><ArticleId IdType="doi">10.1093/treephys/tpaa098</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>Pékin</li><li>University Park (Pennsylvanie)</li></settlement><orgName><li>Université d'État de Pennsylvanie</li></orgName></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Zhang, Qianru" sort="Zhang, Qianru" uniqKey="Zhang Q" first="Qianru" last="Zhang">Qianru Zhang</name></noRegion><name sortKey="Guo, Yunqian" sort="Guo, Yunqian" uniqKey="Guo Y" first="Yunqian" last="Guo">Yunqian Guo</name><name sortKey="Jiang, Libo" sort="Jiang, Libo" uniqKey="Jiang L" first="Libo" last="Jiang">Libo Jiang</name><name sortKey="Jiang, Libo" sort="Jiang, Libo" uniqKey="Jiang L" first="Libo" last="Jiang">Libo Jiang</name><name sortKey="Su, Zhifang" sort="Su, Zhifang" uniqKey="Su Z" first="Zhifang" last="Su">Zhifang Su</name><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><name sortKey="Zhang, Qianru" sort="Zhang, Qianru" uniqKey="Zhang Q" first="Qianru" last="Zhang">Qianru Zhang</name><name sortKey="Zhang, Shilong" sort="Zhang, Shilong" uniqKey="Zhang S" first="Shilong" last="Zhang">Shilong Zhang</name><name sortKey="Zhang, Shilong" sort="Zhang, Shilong" uniqKey="Zhang S" first="Shilong" last="Zhang">Shilong Zhang</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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