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

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Ullrich,  Kristian K.
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Heer, K., Ullrich, K. K., Liepelt, S., Rensing, S. A., Zhou, J., Ziegenhagen, B., et al. (2016). Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst). Conservation Genetics Resources, 8(2), 105-107. doi:10.1007/s12686-016-0520-4.


Cite as: http://hdl.handle.net/11858/00-001M-0000-002C-2D2B-B
Abstract
A novel set of SNPs was derived from transcriptome data of ten Norway spruce (Picea abies) trees from the Bavarian Forest National Park in Germany (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.