Applying targeted genotyping by sequencing with a new set of nuclear and plastid SNP and indel loci for Quercus robur and Quercus petraea

Bernd Degen,Svetlana Bakhtina,Hilke Schröder,Ruslan Ianbaev,Malte Mader,Yulai Yanbaev,Sabine Nürnberg,Celine Blanc-Jolivet

doi:10.1007/s12686-021-01207-6

Bernd Degen, Svetlana Bakhtina + Show 6 more

Open Access

https://doi.org/10.1007/s12686-021-01207-6

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Abstract

We used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically informative and polymorphic loci within Germany and Russia. We successfully screened a selected set of 431 nuclear single nucleotide polymorphism (nSNP), six nuclear Indel, six mitochondrial single nucleotide polymorphism (mtSNP) and ten chloroplast single nucleotide polymorphism (cpSNP) loci with a SeqSNP genotyping platform on 100 individuals Quercus petraea from 10 locations in Germany, 100 individuals Quercus robur from ten locations in Germany and 100 individuals Quercus robur from ten locations in Russia. The newly developed loci are useful for species identification and genetic studies on the genetic diversity and genetic differentiation of Quercus robur and Quercus petraea in Europe.

Highlights

In face of climate change both species Quercus robur and Quercus petraea are considered as alternatives compared to more drought sensitive tree species in Europe (Albert et al 2018)
For SNP and Indel discovery, we used leaf or cambium material from 95 Q. robur and Q. petraea trees originating from all Europe including Ukraine and Russia for the nuclear SNPs and additional 40 individuals from Europe (Q. robur) and Far East Russia (Q. mongolica) (Schroeder et al 2016) to check for plastid SNPs
For the selection of nuclear SNPs derived from Double Digest Restriction site associated DNA sequencing (Peterson et al 2012), we used the same samples and data described in Blanc-Jolivet et al (2020)

Summary

Introduction

In face of climate change both species Quercus robur and Quercus petraea are considered as alternatives compared to more drought sensitive tree species in Europe (Albert et al 2018). Keywords Quercus robur · Quercus petraea · Single nucleotide polymorphism · Indel · Targeted genotyping by sequencing Gene markers and especially large sets of SNPs play an important role to distinguish and identify different tree provenances (Blanc-Jolivet et al 2018; Pettenkofer et al 2020).

Results

Conclusion