@article {174,
	title = {Single-nucleotide polymorphism discovery and validation in high density SNP array for genetic analysis in European white oaks},
	journal = {Molecular Ecology Resources},
	year = {2015},
	pages = {n/a-n/a},
	abstract = {<p>An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered for SNP discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454 technology sequences from 5,112 contigs (6,542 putative in silico SNPs). The 7,913 SNPs were genotyped across the six parental individuals, full-sib progenies (one within each species and two interspecific crosses between Q. petraea and Q. robur), and three natural populations from south-western France that included two additional interfertile white oak species (Q. pubescens and Q. pyrenaica). The genotyping success rate in mapping populations was 80.4\% overall and 72.4\% for polymorphic SNPs. In natural populations, these figures were lower (54.8\% and 51.9\%, respectively). Illumina genotype clusters with compression (shift of clusters on the normalised X-axis) were detected in \&nbsp;25\% of the successfully genotyped SNPs, and may be due to the presence of paralogues. Compressed clusters were significantly more frequent for SNPs showing a priori incorrect Illumina genotypes, suggesting that they should be considered with caution or discarded. Altogether, these results show a high experimental error rate for the Infinium array (between 15\% to 20\% of SNPs potentially unreliable, and 10\% when excluding all compressed clusters), and recommendations are proposed when applying this type of high-throughput technique. Finally, results on diversity levels and shared polymorphisms across targeted white oaks and more distant species of the Quercus genus are discussed, and perspectives for future comparative studies are proposed. This article is protected by copyright. All rights reserved.</p>
},
	author = {Lepoittevin, C. and Bodenes, C. and Chancerel, E. and Villate, L. and Lang, T. and Lesur, I. and Boury, C. and Ehrenmann, F. and Zelenica, D. and Boland, A. and Besse, C. and Garnier-G{\'E}R{\'E}, P. and Plomion, C. and Kremer, A.}
}
@article {130,
	title = {Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak},
	journal = {BMC GenomicsBMC Genomics},
	volume = {11},
	number = {650},
	year = {2010},
	note = {Using Smart Source ParsingNov 23},
	pages = {650},
	abstract = {BACKGROUND: The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity. RESULTS: We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0\%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7\%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4\% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html. CONCLUSIONS: This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.},
	keywords = {Base Sequence, Cluster Analysis, Computational Biology/ methods, Contig Mapping, Expressed Sequence Tags, Gene Library, Genes, Plant/genetics, Microsatellite Repeats/genetics, Peptides/genetics, Polymorphism, Single Nucleotide/genetics, Quercus/ genetics, RNA, Messenger/genetics/metabolism, Sequence Analysis, DNA/ methods, Sequence Homology, Nucleic Acid, Software, Species Specificity, Temperature, Trees/ genetics},
	isbn = {1471-2164 (Electronic)1471-2164 (Linking)},
	author = {Ueno, S. and Le Provost, G. and Leger, V. and Klopp, C. and Noirot, C. and Frigerio, J. M. and Salin, F. and Salse, J. and Abrouk, M. and Murat, F. and Brendel, O. and Derory, J. and Abadie, P. and Leger, P. and Cabane, C. and Barre, A. and de Daruvar, A. and Couloux, A. and Wincker, P. and Reviron, M. P. and Kremer, A. and Plomion, C.}
}
@article {85,
	title = {A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isozyme and 5S rDNA markers},
	journal = {Theoretical and Applied Genetics},
	volume = {97},
	year = {1998},
	note = {doi:10.1007/s001220050996},
	month = {1998},
	pages = {1090 - 1103},
	author = {Barreneche, T. and Bodenes, C. and Lexer, C. and Trontin, J. and Fluch, S. and Streiff, R. and Plomion, C. and Roussel, G. and Steinkellner, H. and Burg, K. and Favre, J. and Glossl, J. and Kremer, A.}
}
