Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers.
Identifieur interne : 003666 ( Main/Exploration ); précédent : 003665; suivant : 003667Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers.
Auteurs : Antonio Cabrera [États-Unis] ; Alex Kozik ; Werner Howad ; Pere Arus ; Amy F. Iezzoni ; Esther Van Der KnaapSource :
- BMC genomics [ 1471-2164 ] ; 2009.
Descripteurs français
- KwdFr :
- Arabidopsis (génétique), Cartographie chromosomique (méthodes), Locus de caractère quantitatif (MeSH), Marqueurs génétiques (MeSH), Populus (génétique), Prunus (génétique), Rosaceae (génétique), Similitude de séquences d'acides nucléiques (MeSH), Synténie (MeSH), Séquence conservée (génétique), Techniques d'amplification d'acides nucléiques (MeSH), Étiquettes de séquences exprimées (MeSH).
- MESH :
- génétique : Arabidopsis, Populus, Prunus, Rosaceae, Séquence conservée.
- méthodes : Cartographie chromosomique.
- Locus de caractère quantitatif, Marqueurs génétiques, Similitude de séquences d'acides nucléiques, Synténie, Techniques d'amplification d'acides nucléiques, Étiquettes de séquences exprimées.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Chromosome Mapping (methods), Conserved Sequence (genetics), Expressed Sequence Tags (MeSH), Genetic Markers (MeSH), Nucleic Acid Amplification Techniques (MeSH), Populus (genetics), Prunus (genetics), Quantitative Trait Loci (MeSH), Rosaceae (genetics), Sequence Homology, Nucleic Acid (MeSH), Synteny (MeSH).
- MESH :
- chemical : Genetic Markers.
- genetics : Arabidopsis, Conserved Sequence, Populus, Prunus, Rosaceae.
- methods : Chromosome Mapping.
- Expressed Sequence Tags, Nucleic Acid Amplification Techniques, Quantitative Trait Loci, Sequence Homology, Nucleic Acid, Synteny.
Abstract
BACKGROUND
Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies.
RESULTS
We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae.
CONCLUSION
Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.
DOI: 10.1186/1471-2164-10-562
PubMed: 19943965
PubMed Central: PMC2789105
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Iezzoni</name></author><author><name sortKey="Van Der Knaap, Esther" sort="Van Der Knaap, Esther" uniqKey="Van Der Knaap E" first="Esther" last="Van Der Knaap">Esther Van Der Knaap</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19943965</idno><idno type="pmid">19943965</idno><idno type="doi">10.1186/1471-2164-10-562</idno><idno type="pmc">PMC2789105</idno><idno type="wicri:Area/Main/Corpus">003381</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003381</idno><idno type="wicri:Area/Main/Curation">003381</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003381</idno><idno type="wicri:Area/Main/Exploration">003381</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers.</title><author><name sortKey="Cabrera, Antonio" sort="Cabrera, Antonio" uniqKey="Cabrera A" first="Antonio" last="Cabrera">Antonio Cabrera</name><affiliation wicri:level="2"><nlm:affiliation>Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA. cabrera.16@buckeyemail.osu.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH 44691</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Kozik, Alex" sort="Kozik, Alex" uniqKey="Kozik A" first="Alex" last="Kozik">Alex Kozik</name></author><author><name sortKey="Howad, Werner" sort="Howad, Werner" uniqKey="Howad W" first="Werner" last="Howad">Werner Howad</name></author><author><name sortKey="Arus, Pere" sort="Arus, Pere" uniqKey="Arus P" first="Pere" last="Arus">Pere Arus</name></author><author><name sortKey="Iezzoni, Amy F" sort="Iezzoni, Amy F" uniqKey="Iezzoni A" first="Amy F" last="Iezzoni">Amy F. Iezzoni</name></author><author><name sortKey="Van Der Knaap, Esther" sort="Van Der Knaap, Esther" uniqKey="Van Der Knaap E" first="Esther" last="Van Der Knaap">Esther Van Der Knaap</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Chromosome Mapping (methods)</term><term>Conserved Sequence (genetics)</term><term>Expressed Sequence Tags (MeSH)</term><term>Genetic Markers (MeSH)</term><term>Nucleic Acid Amplification Techniques (MeSH)</term><term>Populus (genetics)</term><term>Prunus (genetics)</term><term>Quantitative Trait Loci (MeSH)</term><term>Rosaceae (genetics)</term><term>Sequence Homology, Nucleic Acid (MeSH)</term><term>Synteny (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (génétique)</term><term>Cartographie chromosomique (méthodes)</term><term>Locus de caractère quantitatif (MeSH)</term><term>Marqueurs génétiques (MeSH)</term><term>Populus (génétique)</term><term>Prunus (génétique)</term><term>Rosaceae (génétique)</term><term>Similitude de séquences d'acides nucléiques (MeSH)</term><term>Synténie (MeSH)</term><term>Séquence conservée (génétique)</term><term>Techniques d'amplification d'acides nucléiques (MeSH)</term><term>Étiquettes de séquences exprimées (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Conserved Sequence</term><term>Populus</term><term>Prunus</term><term>Rosaceae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Populus</term><term>Prunus</term><term>Rosaceae</term><term>Séquence conservée</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cartographie chromosomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Expressed Sequence Tags</term><term>Nucleic Acid Amplification Techniques</term><term>Quantitative Trait Loci</term><term>Sequence Homology, Nucleic Acid</term><term>Synteny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Locus de caractère quantitatif</term><term>Marqueurs génétiques</term><term>Similitude de séquences d'acides nucléiques</term><term>Synténie</term><term>Techniques d'amplification d'acides nucléiques</term><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19943965</PMID><DateCompleted><Year>2010</Year><Month>01</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><PubDate><Year>2009</Year><Month>Nov</Month><Day>29</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers.</ArticleTitle><Pagination><MedlinePgn>562</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-10-562</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. 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IdType="pubmed">15241595</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Ohio</li></region></list><tree><noCountry><name sortKey="Arus, Pere" sort="Arus, Pere" uniqKey="Arus P" first="Pere" last="Arus">Pere Arus</name><name sortKey="Howad, Werner" sort="Howad, Werner" uniqKey="Howad W" first="Werner" last="Howad">Werner Howad</name><name sortKey="Iezzoni, Amy F" sort="Iezzoni, Amy F" uniqKey="Iezzoni A" first="Amy F" last="Iezzoni">Amy F. Iezzoni</name><name sortKey="Kozik, Alex" sort="Kozik, Alex" uniqKey="Kozik A" first="Alex" last="Kozik">Alex Kozik</name><name sortKey="Van Der Knaap, Esther" sort="Van Der Knaap, Esther" uniqKey="Van Der Knaap E" first="Esther" last="Van Der Knaap">Esther Van Der Knaap</name></noCountry><country name="États-Unis"><region name="Ohio"><name sortKey="Cabrera, Antonio" sort="Cabrera, Antonio" uniqKey="Cabrera A" first="Antonio" last="Cabrera">Antonio Cabrera</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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