Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis.
Identifieur interne : 000E35 ( Main/Exploration ); précédent : 000E34; suivant : 000E36Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis.
Auteurs : Weibing Zhuang [République populaire de Chine] ; Tianyu Liu [République populaire de Chine] ; Shenchun Qu [République populaire de Chine] ; Binhua Cai [République populaire de Chine] ; Yalong Qin [République populaire de Chine] ; Fengjiao Zhang [République populaire de Chine] ; Zhong Wang [République populaire de Chine]Source :
- Scientific reports [ 2045-2322 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- anatomie et histologie : Feuilles de plante, Populus.
- génétique : Populus.
- Gene Ontology, Mutation de type INDEL, Polymorphisme de nucléotide simple, Séquençage du génome entier.
English descriptors
- KwdEn :
- MESH :
- anatomy & histology : Plant Leaves, Populus.
- genetics : Populus.
- Gene Ontology, INDEL Mutation, Polymorphism, Single Nucleotide, Whole Genome Sequencing.
Abstract
Leaf scorch exists as a common phenomenon in the development of plant, especially when plants encounter various adversities, which leads to great losses in agricultural production. Both Jinhong poplar (JHP) and Caihong poplar (CHP) (Populus deltoids) are obtained from a bud sport on Zhonghong poplar. Compared with CHP, JHP always exhibits leaf scorch, poor growth, premature leaf discoloration, and even death. In this study, the candidate genes associated with leaf scorch between JHP and CHP were identified by the whole genome resequencing using Illumina HiSeqTM. There were 218,880 polymorphic SNPs and 46,933 indels between JHP and CHP, respectively. Among these, the candidate genes carrying non-synonymous SNPs in coding regions were classified into 6 groups. The expression pattern of these candidate genes was also explored in JHP and CHP among different sampling stages. Combined with the qRT-PCR analysis, the results showed that genes associated with transport of various nutritional elements, senescence and MYB transcription factor might play important roles during the process of leaf scorch in Populus deltoids. Four genes belonging to these three groups carried more than three SNPs in their coding sequence, which might play important roles in leaf scorch. The above results provided candidate genes involved in leaf scorch in Populus deltoids, and made us better understand the molecular regulation mechanism of leaf scorch in Populus deltoids.
DOI: 10.1038/s41598-018-33739-7
PubMed: 30401919
PubMed Central: PMC6219557
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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210014</wicri:regionArea><wicri:noRegion>210014</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Tianyu" sort="Liu, Tianyu" uniqKey="Liu T" first="Tianyu" last="Liu">Tianyu Liu</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095</wicri:regionArea><wicri:noRegion>210095</wicri:noRegion></affiliation></author><author><name sortKey="Qu, Shenchun" sort="Qu, Shenchun" uniqKey="Qu S" first="Shenchun" last="Qu">Shenchun Qu</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095</wicri:regionArea><wicri:noRegion>210095</wicri:noRegion></affiliation></author><author><name sortKey="Cai, Binhua" sort="Cai, Binhua" uniqKey="Cai B" first="Binhua" last="Cai">Binhua Cai</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095</wicri:regionArea><wicri:noRegion>210095</wicri:noRegion></affiliation></author><author><name sortKey="Qin, Yalong" sort="Qin, Yalong" uniqKey="Qin Y" first="Yalong" last="Qin">Yalong Qin</name><affiliation wicri:level="1"><nlm:affiliation>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014</wicri:regionArea><wicri:noRegion>210014</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Fengjiao" sort="Zhang, Fengjiao" uniqKey="Zhang F" first="Fengjiao" last="Zhang">Fengjiao Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014</wicri:regionArea><wicri:noRegion>210014</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Zhong" sort="Wang, Zhong" uniqKey="Wang Z" first="Zhong" last="Wang">Zhong Wang</name><affiliation wicri:level="1"><nlm:affiliation>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. wangzhong19@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014</wicri:regionArea><wicri:noRegion>210014</wicri:noRegion></affiliation></author></analytic><series><title level="j">Scientific reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Ontology (MeSH)</term><term>INDEL Mutation (MeSH)</term><term>Plant Leaves (anatomy & histology)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (anatomy & histology)</term><term>Populus (genetics)</term><term>Whole Genome Sequencing (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Feuilles de plante (anatomie et histologie)</term><term>Gene Ontology (MeSH)</term><term>Mutation de type INDEL (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (anatomie et histologie)</term><term>Populus (génétique)</term><term>Séquençage du génome entier (MeSH)</term></keywords><keywords scheme="MESH" qualifier="anatomie et histologie" xml:lang="fr"><term>Feuilles de plante</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="anatomy & histology" xml:lang="en"><term>Plant Leaves</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Ontology</term><term>INDEL Mutation</term><term>Polymorphism, Single Nucleotide</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Gene Ontology</term><term>Mutation de type INDEL</term><term>Polymorphisme de nucléotide simple</term><term>Séquençage du génome entier</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Leaf scorch exists as a common phenomenon in the development of plant, especially when plants encounter various adversities, which leads to great losses in agricultural production. Both Jinhong poplar (JHP) and Caihong poplar (CHP) (Populus deltoids) are obtained from a bud sport on Zhonghong poplar. Compared with CHP, JHP always exhibits leaf scorch, poor growth, premature leaf discoloration, and even death. In this study, the candidate genes associated with leaf scorch between JHP and CHP were identified by the whole genome resequencing using Illumina HiSeqTM. There were 218,880 polymorphic SNPs and 46,933 indels between JHP and CHP, respectively. Among these, the candidate genes carrying non-synonymous SNPs in coding regions were classified into 6 groups. The expression pattern of these candidate genes was also explored in JHP and CHP among different sampling stages. Combined with the qRT-PCR analysis, the results showed that genes associated with transport of various nutritional elements, senescence and MYB transcription factor might play important roles during the process of leaf scorch in Populus deltoids. Four genes belonging to these three groups carried more than three SNPs in their coding sequence, which might play important roles in leaf scorch. The above results provided candidate genes involved in leaf scorch in Populus deltoids, and made us better understand the molecular regulation mechanism of leaf scorch in Populus deltoids.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30401919</PMID><DateCompleted><Year>2019</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2019</Year><Month>10</Month><Day>24</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>11</Month><Day>06</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis.</ArticleTitle><Pagination><MedlinePgn>16416</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-018-33739-7</ELocationID><Abstract><AbstractText>Leaf scorch exists as a common phenomenon in the development of plant, especially when plants encounter various adversities, which leads to great losses in agricultural production. Both Jinhong poplar (JHP) and Caihong poplar (CHP) (Populus deltoids) are obtained from a bud sport on Zhonghong poplar. Compared with CHP, JHP always exhibits leaf scorch, poor growth, premature leaf discoloration, and even death. In this study, the candidate genes associated with leaf scorch between JHP and CHP were identified by the whole genome resequencing using Illumina HiSeqTM. There were 218,880 polymorphic SNPs and 46,933 indels between JHP and CHP, respectively. Among these, the candidate genes carrying non-synonymous SNPs in coding regions were classified into 6 groups. The expression pattern of these candidate genes was also explored in JHP and CHP among different sampling stages. Combined with the qRT-PCR analysis, the results showed that genes associated with transport of various nutritional elements, senescence and MYB transcription factor might play important roles during the process of leaf scorch in Populus deltoids. Four genes belonging to these three groups carried more than three SNPs in their coding sequence, which might play important roles in leaf scorch. The above results provided candidate genes involved in leaf scorch in Populus deltoids, and made us better understand the molecular regulation mechanism of leaf scorch in Populus deltoids.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhuang</LastName><ForeName>Weibing</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. wanmeiabc@hotmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Tianyu</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qu</LastName><ForeName>Shenchun</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cai</LastName><ForeName>Binhua</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qin</LastName><ForeName>Yalong</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Fengjiao</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zhong</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. wangzhong19@163.com.</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>2018</Year><Month>11</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Sci Rep</MedlineTA><NlmUniqueID>101563288</NlmUniqueID><ISSNLinking>2045-2322</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054643" MajorTopicYN="N">INDEL Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName><QualifierName UI="Q000033" MajorTopicYN="Y">anatomy & histology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000033" MajorTopicYN="Y">anatomy & histology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000073336" MajorTopicYN="Y">Whole Genome Sequencing</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>01</Month><Day>23</Day></PubMedPubDate><PubMedPubDate 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sort="Liu, Tianyu" uniqKey="Liu T" first="Tianyu" last="Liu">Tianyu Liu</name><name sortKey="Qin, Yalong" sort="Qin, Yalong" uniqKey="Qin Y" first="Yalong" last="Qin">Yalong Qin</name><name sortKey="Qu, Shenchun" sort="Qu, Shenchun" uniqKey="Qu S" first="Shenchun" last="Qu">Shenchun Qu</name><name sortKey="Wang, Zhong" sort="Wang, Zhong" uniqKey="Wang Z" first="Zhong" last="Wang">Zhong Wang</name><name sortKey="Zhang, Fengjiao" sort="Zhang, Fengjiao" uniqKey="Zhang F" first="Fengjiao" last="Zhang">Fengjiao Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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