1. bookVolume 64 (2015): Issue 1-6 (December 2015)
Journal Details
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Format
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eISSN
2509-8934
First Published
22 Feb 2016
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1 time per year
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English
access type Open Access

PCR-based detection of single sequence variants from a natural collection of the non-model tree species European Aspen Populus tremula (L.)

Published Online: 07 Jun 2017
Volume & Issue: Volume 64 (2015) - Issue 1-6 (December 2015)
Page range: 259 - 269
Received: 11 Nov 2015
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
Abstract

In the present study we present and discuss the identification of species-specific SNPs to rule out any experimental influence of species-specific primer design (Populus tremula vs. the closely related model-species Populus trichocarpa) on the detectability of SNPs. Applying a species-optimized method, partial sequences of 14 genes involved in xylem cell development, xylogenesis, pectin formation, and drought stress reaction were analyzed at the genomic level. About 3 Mb of sequence information were generated by Sanger sequencing technology and 258 sequence variants were identified. 15 out of these represent insertions /deletions located exclusively in non-coding regions and the remaining 243 are SNPs found in coding and non-coding regions of candidate genes.

The introduction of a species-specific SNP detection pipeline will help to detect nucleotide variants in P. tremula and to conduct association mapping in natural P. tremula populations.

Keywords

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