RustFungiGenomicsV1, Main, Exploration, bibRecord, 000606

A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

Identifieur interne : 000606 ( Main/Exploration ); précédent : 000605; suivant : 000607

A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

Auteurs : Zahirul I. Talukder [États-Unis] ; Li Gong [États-Unis] ; Brent S. Hulke [États-Unis] ; Venkatramana Pegadaraju [États-Unis] ; Qijian Song [États-Unis] ; Quentin Schultz [États-Unis] ; Lili Qi [États-Unis]

Source :

PloS one [ 1932-6203 ] ; 2014.

RBID : pubmed:25014030

Descripteurs français

KwdFr :
- Basidiomycota (pathogénicité), Basidiomycota (physiologie), Cartographie chromosomique (MeSH), Génome végétal (MeSH), Génotype (MeSH), Helianthus (génétique), Helianthus (immunologie), Helianthus (microbiologie), Immunité des plantes (génétique), Liaison génétique (MeSH), Locus de caractère quantitatif (MeSH), Maladies des plantes (génétique), Maladies des plantes (immunologie), Marqueurs génétiques (MeSH), Phénotype (MeSH), Polymorphisme de nucléotide simple (MeSH), Sélection (MeSH).
MESH :
- génétique : Helianthus, Immunité des plantes, Maladies des plantes.
- immunologie : Helianthus, Maladies des plantes.
- microbiologie : Helianthus.
- pathogénicité : Basidiomycota.
- physiologie : Basidiomycota.
- Cartographie chromosomique, Génome végétal, Génotype, Liaison génétique, Locus de caractère quantitatif, Marqueurs génétiques, Phénotype, Polymorphisme de nucléotide simple, Sélection.

English descriptors

KwdEn :
- Basidiomycota (pathogenicity), Basidiomycota (physiology), Breeding (MeSH), Chromosome Mapping (MeSH), Genetic Linkage (MeSH), Genetic Markers (MeSH), Genome, Plant (MeSH), Genotype (MeSH), Helianthus (genetics), Helianthus (immunology), Helianthus (microbiology), Phenotype (MeSH), Plant Diseases (genetics), Plant Diseases (immunology), Plant Immunity (genetics), Polymorphism, Single Nucleotide (MeSH), Quantitative Trait Loci (MeSH).
MESH :
- chemical : Genetic Markers.
- genetics : Helianthus, Plant Diseases, Plant Immunity.
- immunology : Helianthus, Plant Diseases.
- microbiology : Helianthus.
- pathogenicity : Basidiomycota.
- physiology : Basidiomycota.
- Breeding, Chromosome Mapping, Genetic Linkage, Genome, Plant, Genotype, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci.

Abstract

A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.

DOI: 10.1371/journal.pone.0098628
PubMed: 25014030
PubMed Central: PMC4094432

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<term>Basidiomycota (physiology)</term>
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<term>Chromosome Mapping (MeSH)</term>
<term>Genetic Linkage (MeSH)</term>
<term>Genetic Markers (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Genotype (MeSH)</term>
<term>Helianthus (genetics)</term>
<term>Helianthus (immunology)</term>
<term>Helianthus (microbiology)</term>
<term>Phenotype (MeSH)</term>
<term>Plant Diseases (genetics)</term>
<term>Plant Diseases (immunology)</term>
<term>Plant Immunity (genetics)</term>
<term>Polymorphism, Single Nucleotide (MeSH)</term>
<term>Quantitative Trait Loci (MeSH)</term>
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<term>Basidiomycota (physiologie)</term>
<term>Cartographie chromosomique (MeSH)</term>
<term>Génome végétal (MeSH)</term>
<term>Génotype (MeSH)</term>
<term>Helianthus (génétique)</term>
<term>Helianthus (immunologie)</term>
<term>Helianthus (microbiologie)</term>
<term>Immunité des plantes (génétique)</term>
<term>Liaison génétique (MeSH)</term>
<term>Locus de caractère quantitatif (MeSH)</term>
<term>Maladies des plantes (génétique)</term>
<term>Maladies des plantes (immunologie)</term>
<term>Marqueurs génétiques (MeSH)</term>
<term>Phénotype (MeSH)</term>
<term>Polymorphisme de nucléotide simple (MeSH)</term>
<term>Sélection (MeSH)</term>
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<term>Maladies des plantes</term>
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<term>Maladies des plantes</term>
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<term>Chromosome Mapping</term>
<term>Genetic Linkage</term>
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<term>Genotype</term>
<term>Phenotype</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Quantitative Trait Loci</term>
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<term>Génotype</term>
<term>Liaison génétique</term>
<term>Locus de caractère quantitatif</term>
<term>Marqueurs génétiques</term>
<term>Phénotype</term>
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<front><div type="abstract" xml:lang="en">A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping. </div>
</front>
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<Month>03</Month>
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<Month>11</Month>
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<Title>PloS one</Title>
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<ArticleTitle>A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.</ArticleTitle>
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<Abstract><AbstractText>A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping. </AbstractText>
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<AffiliationInfo><Affiliation>Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America.</Affiliation>
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<ForeName>Li</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America.</Affiliation>
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<ForeName>Brent S</ForeName>
<Initials>BS</Initials>
<AffiliationInfo><Affiliation>Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America.</Affiliation>
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<Author ValidYN="Y"><LastName>Pegadaraju</LastName>
<ForeName>Venkatramana</ForeName>
<Initials>V</Initials>
<AffiliationInfo><Affiliation>BioDiagnostics Inc., River Falls, Wisconsin, United States of America.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Song</LastName>
<ForeName>Qijian</ForeName>
<Initials>Q</Initials>
<AffiliationInfo><Affiliation>Soybean Genomics and Improvement Lab, USDA- Agricultural Research Service, Beltsville, Maryland, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Schultz</LastName>
<ForeName>Quentin</ForeName>
<Initials>Q</Initials>
<AffiliationInfo><Affiliation>BioDiagnostics Inc., River Falls, Wisconsin, United States of America.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Qi</LastName>
<ForeName>Lili</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America.</Affiliation>
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<QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName>
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<MeshHeading><DescriptorName UI="D001947" MajorTopicYN="N">Breeding</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008040" MajorTopicYN="N">Genetic Linkage</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006368" MajorTopicYN="N">Helianthus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName>
<QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName>
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<MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName>
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<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName>
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<MeshHeading><DescriptorName UI="D057865" MajorTopicYN="N">Plant Immunity</DescriptorName>
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<MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName>
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<MeshHeading><DescriptorName UI="D040641" MajorTopicYN="Y">Quantitative Trait Loci</DescriptorName>
</MeshHeading>
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<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year>
<Month>10</Month>
<Day>18</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2014</Year>
<Month>05</Month>
<Day>06</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2014</Year>
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A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

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