A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. - Archive ouverte HAL Access content directly
Journal Articles BMC Genomics Year : 2010

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

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Jérôme J. Durand
  • Function : Author
Emilie Chancerel
  • Function : Author
Jean-Marc Frigerio
  • Function : Author
  • PersonId : 868659
Giovanni Vendramin
  • Function : Author
Anna Buonamici
  • Function : Author
Oliver Gailing
  • Function : Author
Hans-Peter Koelewijn
  • Function : Author
Fiorella Villani
  • Function : Author
Claudia Mattioni
  • Function : Author
Marcello Cherubini
  • Function : Author
Pablo G Goicoechea
  • Function : Author
Ana Herrán
  • Function : Author
Ziortza Ikaran
  • Function : Author
Saneyoshi Ueno
  • Function : Author
  • PersonId : 914888
Florian Alberto
  • Function : Author
Pierre-Yves Dumoulin
  • Function : Author
Erwan Guichoux
  • Function : Author
Antoine Kremer

Abstract

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.
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hal-00645935 , version 1 (31-05-2020)

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Jérôme J. Durand, Catherine Bodénès, Emilie Chancerel, Jean-Marc Frigerio, Giovanni Vendramin, et al.. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.. BMC Genomics, 2010, 11 (570), pp.570. ⟨10.1186/1471-2164-11-570⟩. ⟨hal-00645935⟩
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