Single-nucleotide polymorphism discovery and validation in high density SNP array for genetic analysis in European white oaks

Publication Type:Journal Article
Year of Publication:2015
Authors:C. Lepoittevin, Bodenes, 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.
Journal:Molecular Ecology Resources

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  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.

Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith