A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Autor: Antoine Kremer, Florian Alberto, Emilie Chancerel, A. Buonamici, Claudia Mattioni, Catherine Bodénès, H.P. Koelewijn, Fiorella Villani, Giovanni G. Vendramin, Jean-Marc Frigerio, Erwan Guichoux, Ziortza Ikaran, Ana Herrán, Oliver Gailing, Pablo G. Goicoechea, Saneyoshi Ueno, Pierre-Yves Dumoulin, Antoine de Daruvar, Federico Sebastiani, M. Cherubini, Cyril Cabane, Christophe Plomion, Jerome Durand
Přispěvatelé: Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Dipartimento di Biotecnologie Agrarie, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Università degli Studi di Firenze [Firenze], Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2
Jazyk: angličtina
Rok vydání: 2010
Předmět:
0106 biological sciences
MESH: Genome
Plant
Cost-Benefit Analysis
polymorphisme
Minisatellite Repeats
MESH: Genetic Markers
CHENE ROUVRE
01 natural sciences
Quercus
CHENE PEDONCULE
QUERCUS ROBUR
QUERCUS PETRAEA
CHENE
QUERCUS SESSILIFLORA
CARTOGRAPHIE GENETIQUE
Genetic map
CE - Molecular Ecology Ecotoxicology and Wildlife Management
Data Mining
Wageningen Environmental Research
Expressed Sequence Tags
Genetics
0303 health sciences
Expressed sequence tag
biology
qtl
Chromosome Mapping
food and beverages
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Oak
extraction d'adn
Microsatellite
Quercus petraea
marqueur moléculaire
Genome
Plant
Research Article
Biotechnology
Genetic Markers
microsatellite
lcsh:QH426-470
lcsh:Biotechnology
Computational biology
Quantitative trait locus
MESH: Expressed Sequence Tags
Quercus robur
03 medical and health sciences
pcr
Gene mapping
EST-SSR
lcsh:TP248.13-248.65
MESH: Quercus
MESH: Polymorphism
Genetic
Life Science
castanea
châtaignier
030304 developmental biology
Polymorphism
Genetic
MESH: Data Mining
quercus pedunculata
biology.organism_classification
lcsh:Genetics
Genetic marker
MESH: Minisatellite Repeats
Amplified fragment length polymorphism
MESH: Microsatellite Repeats
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
MESH: Chromosome Mapping
Microsatellite Repeats
010606 plant biology & botany
MESH: Cost-Benefit Analysis
Zdroj: BMC Genomics
BMC Genomics, BioMed Central, 2010, 11 (570), pp.570. ⟨10.1186/1471-2164-11-570⟩
BMC Genomics, BioMed Central, 2010, 11, pp.570. ⟨10.1186/1471-2164-11-570⟩
BMC Genomics, Vol 11, Iss 1, p 570 (2010)
BMC Genomics 11 (2010)
BMC Genomics, 11
BMC genomics 11 (2010): 570. doi:10.1186/1471-2164-11-570
info:cnr-pdr/source/autori:Durand J., Bodénès C., Chancerel E., Frigerio, J.M., Vendramin G., Sebastiani F., Buonamici A., Gailing O., Koelewijn H.P., Villani F., Mattioni, C., Cherubini M., Goicoechea P.G., Herrán A., Daruvar, Kremer A., Plomion. C./titolo:A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study./doi:10.1186%2F1471-2164-11-570/rivista:BMC genomics/anno:2010/pagina_da:570/pagina_a:/intervallo_pagine:570/volume:11
BMC genomics 11 (2010): 1–13. doi:10.1186/1471-2164-11-570
info:cnr-pdr/source/autori:J. Durand (1,2); C. Bodénès (1,2); E. Chancerel (1,2); J.-M. Frigerio (1,2); G. Vendramin (3);F. Sebastiani (3); A. Buonamici (3); O. Gailing (4,5); H.-P. Koelewijn (6); F. Villani (7); C. Mattioni (7); M. Cherubini (7); P. Goikoetxea (8); A. Herran (8) ; Z. Ikaran (8); C. Cabané (9); S. Ueno (1,2,10); F. Alberto (1,2); P.-Y. Dumoulin (1,2); E. Guichoux (1,2); A. de Daruvar (9); A.Kremer (1,2); C. Plomion (1,2)/titolo:A fast and cost-effective approach to develop and map EST-SSR markers: oakas a case study/doi:10.1186%2F1471-2164-11-570/rivista:BMC genomics/anno:2010/pagina_da:1/pagina_a:13/intervallo_pagine:1–13/volume:11
BMC Genomics 570 (11), 13 p.. (2010)
ISSN: 1471-2164
DOI: 10.1186/1471-2164-11-570⟩
Popis: Background Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.
Databáze: OpenAIRE
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