Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)
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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.
KeywordsRNA-seq Single nucleotide polymorphism Norway spruce Genotyping
We thank the Bavarian Forest National Park for funding the RNA-seq data. KH was funded by the ERAnet BiodivERsA project ‘TipTree’ (ANR-12-EBID-0003) funded by the German Federal Ministry of Education and Research (Grant 01LC1202A). Thanks to M Bacht und C Scherer (University of Marburg) for assistance with RNA extraction and to EM Sehr, M Stierschneider, E Wischnitzki and S Fluch (AIT) for coordinating the SNP genotyping. We thank the Team from congenie.org and plantgenie.org to host the phase corrected GFF file.
- Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57:289–300Google Scholar