A set of nuclear SNP loci derived from single sample double digest RAD and from pool sequencing for large-scale genetic studies in the European beech Fagus sylvatica

The large-scale spatial genetic structure of European beech, Fagus sylvatica, has been until now poorly studied. We conducted double digest RAD sequencing (ddRADseq) on 54 beech individuals stemming from 36 provenances to discover spatially informative nuclear SNP loci. In addition, two pools derived from 14 early and 14 late flushing individuals each were sequenced with Illumina HiSeq. From an initial amount of 5,464 loci detected by ddRADseq, we selected 559 informative loci. Further 27 additional loci showing significant allelic differences among early and late flushing individuals could be identified after a genotyping on 95 test individuals. The final selection of 578 loci was submitted to probe design for targeted genotyping by sequencing, which yielded 543 loci. The new set of SNP loci should be, after validation on a larger sample size, useful for large-scale genetic studies in this economically-important species.