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Genetic variation in transcription factors and photosynthesis light-reaction genes regulates photosynthetic traits.

Identifieur interne : 000E75 ( Main/Exploration ); précédent : 000E74; suivant : 000E76

Genetic variation in transcription factors and photosynthesis light-reaction genes regulates photosynthetic traits.

Auteurs : Longxin Wang [République populaire de Chine] ; Qingzhang Du [République populaire de Chine] ; Jianbo Xie [République populaire de Chine] ; Daling Zhou [République populaire de Chine] ; Beibei Chen [République populaire de Chine] ; Haijiao Yang [République populaire de Chine] ; Deqiang Zhang [République populaire de Chine]

Source :

RBID : pubmed:30032300

Descripteurs français

English descriptors

Abstract

Transcription factors (TFs) play crucial roles in regulating the production of the components required for photosynthesis; elucidating the mechanisms by which underlying genetic variation in TFs affects complex photosynthesis-related traits may improve our understanding of photosynthesis and identify ways to improve photosynthetic efficiency. Promoter analysis of 96 nuclear-encoded Populus tomentosa Carr. genes within this pathway revealed 47 motifs responsive to light, stress, hormones and organ-specific regulation, as well as 86 TFs that might bind these motifs. Using phenotype-genotype associations, we identified 244 single-nucleotide polymorphisms (SNPs) within 105 genes associated with 12 photosynthesis-related traits. Most (30.33%) of these SNPs were located in intronic regions and these SNPs explained 18.66% of the mean phenotypic variation in the photosynthesis-related traits. Additionally, expression quantitative trait loci (eQTL) mapping identified 216 eQTLs associated with 110 eGenes (genes regulated by eQTLs), explaining 14.12% of the variability of gene expression. The lead SNPs of 12.04% of the eQTLs also contributed to phenotypic variation. Among these, a SNP in zf-Dof 5.6 (G120_9287) affected photosynthesis by modulating the expression of a sub-regulatory network of eight other TFs, which in turn regulate 55 photosynthesis-related genes. Furthermore, epistasis analysis identified a large interacting network representing 732 SNP-SNP pairs, of which 354 were photosynthesis gene-TF pairs, emphasizing the important roles of TFs in affecting photosynthesis-related traits. We combined eQTL and epistasis analysis and found 32 TFs harboring eQTLs being epistatic to their targets (identified by eQTL analysis), of which 15 TFs were also associated with photosynthesis traits. We therefore constructed a schematic model of TFs involved in regulating the photosynthetic light reaction pathway. Taken together, our results provide insight into the genetic regulation of photosynthesis, and may drive progress in the marker-assisted selection of desirable P. tomentosa genotypes with more efficient photosynthesis.

DOI: 10.1093/treephys/tpy079
PubMed: 30032300


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<keywords scheme="KwdEn" xml:lang="en">
<term>Epistasis, Genetic (MeSH)</term>
<term>Gene Expression Regulation, Plant (radiation effects)</term>
<term>Light (MeSH)</term>
<term>Linkage Disequilibrium (MeSH)</term>
<term>Photosynthesis (genetics)</term>
<term>Plant Growth Regulators (physiology)</term>
<term>Polymorphism, Single Nucleotide (MeSH)</term>
<term>Populus (genetics)</term>
<term>Populus (radiation effects)</term>
<term>Promoter Regions, Genetic (MeSH)</term>
<term>Quantitative Trait Loci (MeSH)</term>
<term>Stress, Physiological (MeSH)</term>
<term>Transcription Factors (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Déséquilibre de liaison (MeSH)</term>
<term>Facteur de croissance végétal (physiologie)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Locus de caractère quantitatif (MeSH)</term>
<term>Lumière (MeSH)</term>
<term>Photosynthèse (génétique)</term>
<term>Polymorphisme de nucléotide simple (MeSH)</term>
<term>Populus (effets des radiations)</term>
<term>Populus (génétique)</term>
<term>Régions promotrices (génétique) (MeSH)</term>
<term>Régulation de l'expression des gènes végétaux (effets des radiations)</term>
<term>Stress physiologique (MeSH)</term>
<term>Épistasie (MeSH)</term>
</keywords>
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<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="physiology" xml:lang="en">
<term>Plant Growth Regulators</term>
</keywords>
<keywords scheme="MESH" qualifier="effets des radiations" xml:lang="fr">
<term>Populus</term>
<term>Régulation de l'expression des gènes végétaux</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Photosynthesis</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Facteurs de transcription</term>
<term>Photosynthèse</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="physiologie" xml:lang="fr">
<term>Facteur de croissance végétal</term>
</keywords>
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<term>Gene Expression Regulation, Plant</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Epistasis, Genetic</term>
<term>Light</term>
<term>Linkage Disequilibrium</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Promoter Regions, Genetic</term>
<term>Quantitative Trait Loci</term>
<term>Stress, Physiological</term>
</keywords>
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<term>Déséquilibre de liaison</term>
<term>Locus de caractère quantitatif</term>
<term>Lumière</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Régions promotrices (génétique)</term>
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<div type="abstract" xml:lang="en">Transcription factors (TFs) play crucial roles in regulating the production of the components required for photosynthesis; elucidating the mechanisms by which underlying genetic variation in TFs affects complex photosynthesis-related traits may improve our understanding of photosynthesis and identify ways to improve photosynthetic efficiency. Promoter analysis of 96 nuclear-encoded Populus tomentosa Carr. genes within this pathway revealed 47 motifs responsive to light, stress, hormones and organ-specific regulation, as well as 86 TFs that might bind these motifs. Using phenotype-genotype associations, we identified 244 single-nucleotide polymorphisms (SNPs) within 105 genes associated with 12 photosynthesis-related traits. Most (30.33%) of these SNPs were located in intronic regions and these SNPs explained 18.66% of the mean phenotypic variation in the photosynthesis-related traits. Additionally, expression quantitative trait loci (eQTL) mapping identified 216 eQTLs associated with 110 eGenes (genes regulated by eQTLs), explaining 14.12% of the variability of gene expression. The lead SNPs of 12.04% of the eQTLs also contributed to phenotypic variation. Among these, a SNP in zf-Dof 5.6 (G120_9287) affected photosynthesis by modulating the expression of a sub-regulatory network of eight other TFs, which in turn regulate 55 photosynthesis-related genes. Furthermore, epistasis analysis identified a large interacting network representing 732 SNP-SNP pairs, of which 354 were photosynthesis gene-TF pairs, emphasizing the important roles of TFs in affecting photosynthesis-related traits. We combined eQTL and epistasis analysis and found 32 TFs harboring eQTLs being epistatic to their targets (identified by eQTL analysis), of which 15 TFs were also associated with photosynthesis traits. We therefore constructed a schematic model of TFs involved in regulating the photosynthetic light reaction pathway. Taken together, our results provide insight into the genetic regulation of photosynthesis, and may drive progress in the marker-assisted selection of desirable P. tomentosa genotypes with more efficient photosynthesis.</div>
</front>
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<Journal>
<ISSN IssnType="Electronic">1758-4469</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>38</Volume>
<Issue>12</Issue>
<PubDate>
<Year>2018</Year>
<Month>12</Month>
<Day>01</Day>
</PubDate>
</JournalIssue>
<Title>Tree physiology</Title>
<ISOAbbreviation>Tree Physiol</ISOAbbreviation>
</Journal>
<ArticleTitle>Genetic variation in transcription factors and photosynthesis light-reaction genes regulates photosynthetic traits.</ArticleTitle>
<Pagination>
<MedlinePgn>1871-1885</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/treephys/tpy079</ELocationID>
<Abstract>
<AbstractText>Transcription factors (TFs) play crucial roles in regulating the production of the components required for photosynthesis; elucidating the mechanisms by which underlying genetic variation in TFs affects complex photosynthesis-related traits may improve our understanding of photosynthesis and identify ways to improve photosynthetic efficiency. Promoter analysis of 96 nuclear-encoded Populus tomentosa Carr. genes within this pathway revealed 47 motifs responsive to light, stress, hormones and organ-specific regulation, as well as 86 TFs that might bind these motifs. Using phenotype-genotype associations, we identified 244 single-nucleotide polymorphisms (SNPs) within 105 genes associated with 12 photosynthesis-related traits. Most (30.33%) of these SNPs were located in intronic regions and these SNPs explained 18.66% of the mean phenotypic variation in the photosynthesis-related traits. Additionally, expression quantitative trait loci (eQTL) mapping identified 216 eQTLs associated with 110 eGenes (genes regulated by eQTLs), explaining 14.12% of the variability of gene expression. The lead SNPs of 12.04% of the eQTLs also contributed to phenotypic variation. Among these, a SNP in zf-Dof 5.6 (G120_9287) affected photosynthesis by modulating the expression of a sub-regulatory network of eight other TFs, which in turn regulate 55 photosynthesis-related genes. Furthermore, epistasis analysis identified a large interacting network representing 732 SNP-SNP pairs, of which 354 were photosynthesis gene-TF pairs, emphasizing the important roles of TFs in affecting photosynthesis-related traits. We combined eQTL and epistasis analysis and found 32 TFs harboring eQTLs being epistatic to their targets (identified by eQTL analysis), of which 15 TFs were also associated with photosynthesis traits. We therefore constructed a schematic model of TFs involved in regulating the photosynthetic light reaction pathway. Taken together, our results provide insight into the genetic regulation of photosynthesis, and may drive progress in the marker-assisted selection of desirable P. tomentosa genotypes with more efficient photosynthesis.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Wang</LastName>
<ForeName>Longxin</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Du</LastName>
<ForeName>Qingzhang</ForeName>
<Initials>Q</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Xie</LastName>
<ForeName>Jianbo</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhou</LastName>
<ForeName>Daling</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Chen</LastName>
<ForeName>Beibei</ForeName>
<Initials>B</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Yang</LastName>
<ForeName>Haijiao</ForeName>
<Initials>H</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhang</LastName>
<ForeName>Deqiang</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</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>
</Article>
<MedlineJournalInfo>
<Country>Canada</Country>
<MedlineTA>Tree Physiol</MedlineTA>
<NlmUniqueID>100955338</NlmUniqueID>
<ISSNLinking>0829-318X</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010937">Plant Growth Regulators</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D004843" MajorTopicYN="N">Epistasis, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName>
<QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008027" MajorTopicYN="N">Light</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010788" MajorTopicYN="N">Photosynthesis</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010937" MajorTopicYN="N">Plant Growth Regulators</DescriptorName>
<QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D040641" MajorTopicYN="N">Quantitative Trait Loci</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013312" MajorTopicYN="N">Stress, Physiological</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="received">
<Year>2018</Year>
<Month>02</Month>
<Day>20</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2018</Year>
<Month>06</Month>
<Day>19</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2018</Year>
<Month>7</Month>
<Day>23</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2019</Year>
<Month>3</Month>
<Day>19</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2018</Year>
<Month>7</Month>
<Day>23</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">30032300</ArticleId>
<ArticleId IdType="pii">5055868</ArticleId>
<ArticleId IdType="doi">10.1093/treephys/tpy079</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations>
<list>
<country>
<li>République populaire de Chine</li>
</country>
<settlement>
<li>Pékin</li>
</settlement>
</list>
<tree>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Wang, Longxin" sort="Wang, Longxin" uniqKey="Wang L" first="Longxin" last="Wang">Longxin Wang</name>
</noRegion>
<name sortKey="Chen, Beibei" sort="Chen, Beibei" uniqKey="Chen B" first="Beibei" last="Chen">Beibei Chen</name>
<name sortKey="Chen, Beibei" sort="Chen, Beibei" uniqKey="Chen B" first="Beibei" last="Chen">Beibei Chen</name>
<name sortKey="Du, Qingzhang" sort="Du, Qingzhang" uniqKey="Du Q" first="Qingzhang" last="Du">Qingzhang Du</name>
<name sortKey="Du, Qingzhang" sort="Du, Qingzhang" uniqKey="Du Q" first="Qingzhang" last="Du">Qingzhang Du</name>
<name sortKey="Wang, Longxin" sort="Wang, Longxin" uniqKey="Wang L" first="Longxin" last="Wang">Longxin Wang</name>
<name sortKey="Xie, Jianbo" sort="Xie, Jianbo" uniqKey="Xie J" first="Jianbo" last="Xie">Jianbo Xie</name>
<name sortKey="Xie, Jianbo" sort="Xie, Jianbo" uniqKey="Xie J" first="Jianbo" last="Xie">Jianbo Xie</name>
<name sortKey="Yang, Haijiao" sort="Yang, Haijiao" uniqKey="Yang H" first="Haijiao" last="Yang">Haijiao Yang</name>
<name sortKey="Yang, Haijiao" sort="Yang, Haijiao" uniqKey="Yang H" first="Haijiao" last="Yang">Haijiao Yang</name>
<name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
<name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
<name sortKey="Zhou, Daling" sort="Zhou, Daling" uniqKey="Zhou D" first="Daling" last="Zhou">Daling Zhou</name>
<name sortKey="Zhou, Daling" sort="Zhou, Daling" uniqKey="Zhou D" first="Daling" last="Zhou">Daling Zhou</name>
</country>
</tree>
</affiliations>
</record>

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