Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)

A novel set of SNPs was derived from transcriptome data of ten Norway spruce (Picea abies) trees from the Bavarian Forest National Park in GermanyÂ (BaFoNP). SNPs were identified by mapping against a de-novo transcriptome assembly and against pre-mRNAs of predicted genes of the reference genome asse...

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Veröffentlicht in:	Conservation genetics resources 2016-06, Vol.8 (2), p.105-107
Hauptverfasser:	Heer, Katrin, Kristian K. Ullrich, Sascha Liepelt, Stefan A. Rensing, Jiabin Zhou, Birgit Ziegenhagen, Lars Opgenoorth
Format:	Artikel
Sprache:	eng
Schlagworte:	Animal Genetics and Genomics Biodiversity Biomedical and Life Sciences Conservation Biology/Ecology Divergence Ecology Evolutionary Biology forests Gene expression Gene mapping genes genome assembly genotyping Life Sciences National parks Picea abies Plant Genetics and Genomics Single-nucleotide polymorphism Technical Note transcriptome transcriptomics Trees
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Beschreibung
Zusammenfassung:	A novel set of SNPs was derived from transcriptome data of ten Norway spruce (Picea abies) trees from the Bavarian Forest National Park in GermanyÂ (BaFoNP). SNPs were identified by mapping against a de-novo transcriptome assembly and against pre-mRNAs of predicted genes of the reference genome assembly. This resulted in 111,849 and 366,577 SNPs, respectively. Out of these, 311 were either randomly selected or chosen because of their pronounced divergence between sampling sites and genotyped in 218 trees with an Illumina Infinium HD iSelect BeadChip.
ISSN:	1877-7252 1877-7260
DOI:	10.1007/s12686-016-0520-4