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

CORC > 西双版纳热带植物园 > 中国科学院西双版纳热带植物园 > 2012年后新成立研究组

	Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks
	Lepoittevin, C. ; Bodenes, C. ; Chancerel, E. ; Villate, L. ; Lang, T. ; Lesur, I. ; Boury, C. ; Ehrenmann, F. ; Zelenica, D. ; Boland, A. ; Besse, C. ; Garnier-Gere, P. ; Plomion, C. ; Kremer, A.
刊名	MOLECULAR ECOLOGY RESOURCES
	2015
卷号	15 期号:6 页码:1446-1459
关键词	cluster compression genotyping genotyping error rates infinium oaks SNP detection
ISSN号	1755-098X
中文摘要	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 5112 contigs (6542 putative in silico SNPs). The 7913 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 normalized x-axis) were detected in similar to 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% and 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.
资助信息	European Union (EVOLTREE Network of Excellence) [016322]; EVOLTREE Project; ANR GENOAK Project [11-BSV6-009-01]; GENOAK EU FP7 Project; FORESTTRAC EU FP7 Project; FORGER EU FP7 Project
原文出处	10.1111/1755-0998.12407
语种	英语
公开日期	2015-11-19
内容类型	期刊论文
源URL	[http://ir.xtbg.org.cn/handle/353005/9344]
专题	西双版纳热带植物园_2012年后新成立研究组
推荐引用方式 GB/T 7714	Lepoittevin, C.,Bodenes, C.,Chancerel, E.,et al. Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks[J]. MOLECULAR ECOLOGY RESOURCES,2015,15(6):1446-1459.
APA	Lepoittevin, C..,Bodenes, C..,Chancerel, E..,Villate, L..,Lang, T..,...&Kremer, A..(2015).Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks.MOLECULAR ECOLOGY RESOURCES,15(6),1446-1459.
MLA	Lepoittevin, C.,et al."Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks".MOLECULAR ECOLOGY RESOURCES 15.6(2015):1446-1459.