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BAC Libraries (available from the CNRGV)

Reference: Faivre-Rampant P, Lesur I, Boussardon C, Bitton F, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C (2011). Analysis of BAC end sequences in oak, providing insights into the composition of the genome of this keystone species. BMC Genomics 12: 292

 

SNP

  • get 7,576 SNPs from amplicon resequencing from the public repository of EVOLTREE (use the query builder, select fagaceae, select all, select SNP , scroll down to export data) and from NCBI dbSNP
  • get SNPs from in silico mining of ESTs (select in silico in column C of this file)

References:

  1. E Guichoux, P Garnier‐Géré, L Lagache, T Lang, C Boury, RJ Petit (2013) Outlier loci highlight the direction of introgression in oaksMolecular ecology 22: 450-462
  2. Lepoittevin C, Bodénès C, Chancerel E, Villate L, Lang T, Lesur I, Boury C, Ehrenmann F, Zelenica D, Boland A, Besse C, Garnier-Géré P, Plomion C, Kremer A (2015) Single-nucleotide polymorphism discovery and validation in high density SNP array for genetic analysis in European white oaks. Mol Ecol Res 15:1446-59
  3. Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse S, Quesneville H, Kremer A (2016) Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Res.
    16: 254-265

 

Unigene (available from Quercus portal)

Reference: Lesur I, Le Provost G, Bento P, Da Silva C, , Leplé JC, Murat F, Ueno S, Bartholomé J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Loustau ML, Léger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C (2015) The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 16:112

 

Genetic Map (available from Quercus portal)

References: 

  1. Bodénès C, Chancerel E, Murat F, Bagnoli F, Gailing O, Durand J, Koelewijn HP, Goicoechea P, Villani F, Roussel G, Salse S, Vendramin GG, Soularue JP, Boury C, Alberto F, Kremer A, Plomion C (2012) Comparative mapping in the Fagaceae and beyond using EST-SSRs. BMC Plant Biol 12:153
  2. Bodénès C, Chancerel E, Ehrenmann F, Kremer A, Plomion C (2016) High-density linkage mapping and distribution of segregation distortion regions in the oak genome. DNA Res 23:115-24.

 

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