Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar.
Identifieur interne : 000511 ( Main/Exploration ); précédent : 000510; suivant : 000512Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar.
Auteurs : Tashbek Nvsvrot [République populaire de Chine] ; Wenxiu Xia [République populaire de Chine] ; Zheng'Ang Xiao [République populaire de Chine] ; Chang Zhan [République populaire de Chine] ; Meifeng Liu [République populaire de Chine] ; Xiaoqing Yang [République populaire de Chine] ; Yan Zhang [République populaire de Chine] ; Nian Wang [République populaire de Chine]Source :
- Phytopathology [ 0031-949X ] ; 2020.
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English descriptors
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- MESH :
Abstract
Poplar trees (Populus spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by Melampsora spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (R) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an R gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the R gene could be used as a diagnostic marker for future poplar molecular breeding.
DOI: 10.1094/PHYTO-10-19-0402-R
PubMed: 31958037
Affiliations:
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last="Nvsvrot">Tashbek Nvsvrot</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Xia, Wenxiu" sort="Xia, Wenxiu" uniqKey="Xia W" first="Wenxiu" last="Xia">Wenxiu Xia</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Logistics Service Group, Wuhan University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Logistics Service Group, Wuhan University, Wuhan, 430070</wicri:regionArea><orgName type="university">Université de Wuhan</orgName><placeName><settlement type="city">Wuhan</settlement><region type="province">Hubei</region></placeName></affiliation></author><author><name sortKey="Xiao, Zheng Ang" sort="Xiao, Zheng Ang" uniqKey="Xiao Z" first="Zheng'Ang" last="Xiao">Zheng'Ang Xiao</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Zhan, Chang" sort="Zhan, Chang" uniqKey="Zhan C" first="Chang" last="Zhan">Chang Zhan</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Meifeng" sort="Liu, Meifeng" uniqKey="Liu M" first="Meifeng" last="Liu">Meifeng Liu</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Xiaoqing" sort="Yang, Xiaoqing" uniqKey="Yang X" first="Xiaoqing" last="Yang">Xiaoqing Yang</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Yan" sort="Zhang, Yan" uniqKey="Zhang Y" first="Yan" last="Zhang">Yan Zhang</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Nian" sort="Wang, Nian" uniqKey="Wang N" first="Nian" last="Wang">Nian Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author></analytic><series><title level="j">Phytopathology</title><idno type="ISSN">0031-949X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Basidiomycota (MeSH)</term><term>Chromosome Mapping (MeSH)</term><term>Disease Resistance (MeSH)</term><term>Genes, vpr (MeSH)</term><term>Humans (MeSH)</term><term>Plant Diseases (MeSH)</term><term>Populus (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Basidiomycota (MeSH)</term><term>Cartographie chromosomique (MeSH)</term><term>Gènes vpr (MeSH)</term><term>Humains (MeSH)</term><term>Maladies des plantes (MeSH)</term><term>Populus (MeSH)</term><term>Résistance à la maladie (MeSH)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Basidiomycota</term><term>Chromosome Mapping</term><term>Disease Resistance</term><term>Genes, vpr</term><term>Humans</term><term>Plant Diseases</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Basidiomycota</term><term>Cartographie chromosomique</term><term>Gènes vpr</term><term>Humains</term><term>Maladies des plantes</term><term>Populus</term><term>Résistance à la maladie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Poplar trees (<i>Populus</i> spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by <i>Melampsora</i> spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (<i>R</i>) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an <i>R</i> gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the <i>R</i> gene could be used as a diagnostic marker for future poplar molecular breeding.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">31958037</PMID><DateCompleted><Year>2020</Year><Month>04</Month><Day>07</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><Volume>110</Volume><Issue>4</Issue><PubDate><Year>2020</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Combining QTL Mapping with Genome Resequencing Identifies an Indel in an <i>R</i> Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar.</ArticleTitle><Pagination><MedlinePgn>900-906</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-10-19-0402-R</ELocationID><Abstract><AbstractText>Poplar trees (<i>Populus</i> spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by <i>Melampsora</i> spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (<i>R</i>) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an <i>R</i> gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the <i>R</i> gene could be used as a diagnostic marker for future poplar molecular breeding.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nvsvrot</LastName><ForeName>Tashbek</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xia</LastName><ForeName>Wenxiu</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Logistics Service Group, Wuhan University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiao</LastName><ForeName>Zheng'ang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhan</LastName><ForeName>Chang</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Meifeng</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiaoqing</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Nian</ForeName><Initials>N</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9185-4199</Identifier><AffiliationInfo><Affiliation>College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phytopathology</MedlineTA><NlmUniqueID>9427222</NlmUniqueID><ISSNLinking>0031-949X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="Y">Basidiomycota</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060467" MajorTopicYN="N">Disease Resistance</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016334" MajorTopicYN="N">Genes, vpr</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="Y">Populus</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">QTL mapping</Keyword><Keyword MajorTopicYN="N">R gene indel</Keyword><Keyword MajorTopicYN="N">genetics and resistance</Keyword><Keyword MajorTopicYN="N">genome resequencing</Keyword><Keyword MajorTopicYN="N">leaf rust disease resistance</Keyword><Keyword MajorTopicYN="N">poplar</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31958037</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-10-19-0402-R</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Hubei</li></region><settlement><li>Wuhan</li></settlement><orgName><li>Université de Wuhan</li></orgName></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Nvsvrot, Tashbek" sort="Nvsvrot, Tashbek" uniqKey="Nvsvrot T" first="Tashbek" last="Nvsvrot">Tashbek Nvsvrot</name></noRegion><name sortKey="Liu, Meifeng" sort="Liu, Meifeng" uniqKey="Liu M" first="Meifeng" last="Liu">Meifeng Liu</name><name sortKey="Nvsvrot, Tashbek" sort="Nvsvrot, Tashbek" uniqKey="Nvsvrot T" first="Tashbek" last="Nvsvrot">Tashbek Nvsvrot</name><name sortKey="Wang, Nian" sort="Wang, Nian" uniqKey="Wang N" first="Nian" last="Wang">Nian Wang</name><name sortKey="Wang, Nian" sort="Wang, Nian" uniqKey="Wang N" first="Nian" last="Wang">Nian Wang</name><name sortKey="Xia, Wenxiu" sort="Xia, Wenxiu" uniqKey="Xia W" first="Wenxiu" last="Xia">Wenxiu Xia</name><name sortKey="Xia, Wenxiu" sort="Xia, Wenxiu" uniqKey="Xia W" first="Wenxiu" last="Xia">Wenxiu Xia</name><name sortKey="Xiao, Zheng Ang" sort="Xiao, Zheng Ang" uniqKey="Xiao Z" first="Zheng'Ang" last="Xiao">Zheng'Ang Xiao</name><name sortKey="Yang, Xiaoqing" sort="Yang, Xiaoqing" uniqKey="Yang X" first="Xiaoqing" last="Yang">Xiaoqing Yang</name><name sortKey="Zhan, Chang" sort="Zhan, Chang" uniqKey="Zhan C" first="Chang" last="Zhan">Chang Zhan</name><name sortKey="Zhang, Yan" sort="Zhang, Yan" uniqKey="Zhang Y" first="Yan" last="Zhang">Yan Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:31958037
|texte= Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:31958037" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |