Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.
Identifieur interne : 000F78 ( Main/Exploration ); précédent : 000F77; suivant : 000F79Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.
Auteurs : Tristan E. Coram [États-Unis] ; Matthew L. Settles ; Meinan Wang ; Xianming ChenSource :
- TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik [ 0040-5752 ] ; 2008.
Descripteurs français
- KwdFr :
- Cartographie physique de chromosome (MeSH), Gènes de plante (MeSH), Hybridation d'acides nucléiques (MeSH), Immunité innée (génétique), Maladies des plantes (génétique), Maladies des plantes (immunologie), Maladies des plantes (microbiologie), Polymorphisme génétique (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Triticum (génétique).
- MESH :
- génétique : Immunité innée, Maladies des plantes, Triticum.
- immunologie : Maladies des plantes.
- microbiologie : Maladies des plantes.
- Cartographie physique de chromosome, Gènes de plante, Hybridation d'acides nucléiques, Polymorphisme génétique, Régulation de l'expression des gènes végétaux.
English descriptors
- KwdEn :
- Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Immunity, Innate (genetics), Nucleic Acid Hybridization (MeSH), Physical Chromosome Mapping (MeSH), Plant Diseases (genetics), Plant Diseases (immunology), Plant Diseases (microbiology), Polymorphism, Genetic (MeSH), Triticum (genetics).
- MESH :
- genetics : Immunity, Innate, Plant Diseases, Triticum.
- immunology : Plant Diseases.
- microbiology : Plant Diseases.
- Gene Expression Regulation, Plant, Genes, Plant, Nucleic Acid Hybridization, Physical Chromosome Mapping, Polymorphism, Genetic.
Abstract
DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The 55 K Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC(7):F(4)) that differ for the Yr5 stripe rust resistance locus, with the objective of developing genetic markers linked to Yr5. Ninety-one probe sets showing ELPs and 118 SFP-containing probe sets were identified between isolines, of which just nine ELP probe sets also contained SFPs. The proportion of the transcriptome estimated to be variable between isolines from this analysis was 0.30% for the ELPs and 0.39% for the SFPs, which was highly similar to the theoretical genome difference between isolines of ~0.39%. Using wheat-rice synteny, both ELPs and SFPs mainly clustered on long arms of rice chromosomes four and seven, which are syntenous to wheat chromosomes 2L (Yr5 locus) and 2S, respectively. The strong physical correlation between the two types of polymorphism indicated that the ELPs may be regulated by cis-acting DNA polymorphisms. Twenty SFPs homologous to rice 4L were used to develop additional genetic markers for Yr5. Physical mapping of the probe sets containing SFPs to wheat chromosomes identified nine on the target chromosome 2BL, thus wheat-rice synteny greatly enhanced the selection of SFPs that were located on the desired wheat chromosome. Of these nine, four were converted into polymorphic cleaved amplified polymorphic sequence (CAPS) markers between Yr5 and yr5 isolines, and one was mapped within 5.3 cM of the Yr5 locus. This study represents the first array-based polymorphism survey in near-isogenic genotypes, and the results are applied to an agriculturally important trait.
DOI: 10.1007/s00122-008-0784-5
PubMed: 18470504
Affiliations:
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Coram</name><affiliation wicri:level="2"><nlm:affiliation>Wheat Genetics, Quality, Physiology and Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99163, USA. tristan.coram@ars.usda.gov</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Wheat Genetics, Quality, Physiology and Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99163</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Settles, Matthew L" sort="Settles, Matthew L" uniqKey="Settles M" first="Matthew L" last="Settles">Matthew L. Settles</name></author><author><name sortKey="Wang, Meinan" sort="Wang, Meinan" uniqKey="Wang M" first="Meinan" last="Wang">Meinan Wang</name></author><author><name sortKey="Chen, Xianming" sort="Chen, Xianming" uniqKey="Chen X" first="Xianming" last="Chen">Xianming Chen</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18470504</idno><idno type="pmid">18470504</idno><idno type="doi">10.1007/s00122-008-0784-5</idno><idno type="wicri:Area/Main/Corpus">001029</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001029</idno><idno type="wicri:Area/Main/Curation">001029</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001029</idno><idno type="wicri:Area/Main/Exploration">001029</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.</title><author><name sortKey="Coram, Tristan E" sort="Coram, Tristan E" uniqKey="Coram T" first="Tristan E" last="Coram">Tristan E. Coram</name><affiliation wicri:level="2"><nlm:affiliation>Wheat Genetics, Quality, Physiology and Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99163, USA. tristan.coram@ars.usda.gov</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Wheat Genetics, Quality, Physiology and Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99163</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Settles, Matthew L" sort="Settles, Matthew L" uniqKey="Settles M" first="Matthew L" last="Settles">Matthew L. Settles</name></author><author><name sortKey="Wang, Meinan" sort="Wang, Meinan" uniqKey="Wang M" first="Meinan" last="Wang">Meinan Wang</name></author><author><name sortKey="Chen, Xianming" sort="Chen, Xianming" uniqKey="Chen X" first="Xianming" last="Chen">Xianming Chen</name></author></analytic><series><title level="j">TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik</title><idno type="ISSN">0040-5752</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Immunity, Innate (genetics)</term><term>Nucleic Acid Hybridization (MeSH)</term><term>Physical Chromosome Mapping (MeSH)</term><term>Plant Diseases (genetics)</term><term>Plant Diseases (immunology)</term><term>Plant Diseases (microbiology)</term><term>Polymorphism, Genetic (MeSH)</term><term>Triticum (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cartographie physique de chromosome (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Hybridation d'acides nucléiques (MeSH)</term><term>Immunité innée (génétique)</term><term>Maladies des plantes (génétique)</term><term>Maladies des plantes (immunologie)</term><term>Maladies des plantes (microbiologie)</term><term>Polymorphisme génétique (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Triticum (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Immunity, Innate</term><term>Plant Diseases</term><term>Triticum</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Immunité innée</term><term>Maladies des plantes</term><term>Triticum</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Nucleic Acid Hybridization</term><term>Physical Chromosome Mapping</term><term>Polymorphism, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie physique de chromosome</term><term>Gènes de plante</term><term>Hybridation d'acides nucléiques</term><term>Polymorphisme génétique</term><term>Régulation de l'expression des gènes végétaux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The 55 K Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC(7):F(4)) that differ for the Yr5 stripe rust resistance locus, with the objective of developing genetic markers linked to Yr5. Ninety-one probe sets showing ELPs and 118 SFP-containing probe sets were identified between isolines, of which just nine ELP probe sets also contained SFPs. The proportion of the transcriptome estimated to be variable between isolines from this analysis was 0.30% for the ELPs and 0.39% for the SFPs, which was highly similar to the theoretical genome difference between isolines of ~0.39%. Using wheat-rice synteny, both ELPs and SFPs mainly clustered on long arms of rice chromosomes four and seven, which are syntenous to wheat chromosomes 2L (Yr5 locus) and 2S, respectively. The strong physical correlation between the two types of polymorphism indicated that the ELPs may be regulated by cis-acting DNA polymorphisms. Twenty SFPs homologous to rice 4L were used to develop additional genetic markers for Yr5. Physical mapping of the probe sets containing SFPs to wheat chromosomes identified nine on the target chromosome 2BL, thus wheat-rice synteny greatly enhanced the selection of SFPs that were located on the desired wheat chromosome. Of these nine, four were converted into polymorphic cleaved amplified polymorphic sequence (CAPS) markers between Yr5 and yr5 isolines, and one was mapped within 5.3 cM of the Yr5 locus. This study represents the first array-based polymorphism survey in near-isogenic genotypes, and the results are applied to an agriculturally important trait.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18470504</PMID><DateCompleted><Year>2008</Year><Month>10</Month><Day>09</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0040-5752</ISSN><JournalIssue CitedMedium="Print"><Volume>117</Volume><Issue>3</Issue><PubDate><Year>2008</Year><Month>Aug</Month></PubDate></JournalIssue><Title>TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik</Title><ISOAbbreviation>Theor Appl Genet</ISOAbbreviation></Journal><ArticleTitle>Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.</ArticleTitle><Pagination><MedlinePgn>401-11</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00122-008-0784-5</ELocationID><Abstract><AbstractText>DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The 55 K Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC(7):F(4)) that differ for the Yr5 stripe rust resistance locus, with the objective of developing genetic markers linked to Yr5. Ninety-one probe sets showing ELPs and 118 SFP-containing probe sets were identified between isolines, of which just nine ELP probe sets also contained SFPs. The proportion of the transcriptome estimated to be variable between isolines from this analysis was 0.30% for the ELPs and 0.39% for the SFPs, which was highly similar to the theoretical genome difference between isolines of ~0.39%. Using wheat-rice synteny, both ELPs and SFPs mainly clustered on long arms of rice chromosomes four and seven, which are syntenous to wheat chromosomes 2L (Yr5 locus) and 2S, respectively. The strong physical correlation between the two types of polymorphism indicated that the ELPs may be regulated by cis-acting DNA polymorphisms. Twenty SFPs homologous to rice 4L were used to develop additional genetic markers for Yr5. Physical mapping of the probe sets containing SFPs to wheat chromosomes identified nine on the target chromosome 2BL, thus wheat-rice synteny greatly enhanced the selection of SFPs that were located on the desired wheat chromosome. Of these nine, four were converted into polymorphic cleaved amplified polymorphic sequence (CAPS) markers between Yr5 and yr5 isolines, and one was mapped within 5.3 cM of the Yr5 locus. This study represents the first array-based polymorphism survey in near-isogenic genotypes, and the results are applied to an agriculturally important trait.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Coram</LastName><ForeName>Tristan E</ForeName><Initials>TE</Initials><AffiliationInfo><Affiliation>Wheat Genetics, Quality, Physiology and Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99163, USA. tristan.coram@ars.usda.gov</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Settles</LastName><ForeName>Matthew L</ForeName><Initials>ML</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Meinan</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Xianming</ForeName><Initials>X</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>05</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Theor Appl Genet</MedlineTA><NlmUniqueID>0145600</NlmUniqueID><ISSNLinking>0040-5752</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007113" MajorTopicYN="N">Immunity, Innate</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009693" 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sortKey="Settles, Matthew L" sort="Settles, Matthew L" uniqKey="Settles M" first="Matthew L" last="Settles">Matthew L. Settles</name><name sortKey="Wang, Meinan" sort="Wang, Meinan" uniqKey="Wang M" first="Meinan" last="Wang">Meinan Wang</name></noCountry><country name="États-Unis"><region name="Washington (État)"><name sortKey="Coram, Tristan E" sort="Coram, Tristan E" uniqKey="Coram T" first="Tristan E" last="Coram">Tristan E. Coram</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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