Sequence capture of 15447 Q. robur targets tested on Q. suber and F. sylvatica.. Quercus robur

We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97X) for the detection of about 190 thousand SNPs evenly spread over the targeted regions. This dataset was then filtered, and 13 thousand SNPs were used to assess genetic relatedness between individuals, to estimate genomic inbreeding coefficients and to infer inbreeding depression from the correlation between fitness-related traits and inbreeding coefficients. Finally, we tested the transferability of the capture probes to related species/genera within the Fagaceae. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We were thus able to capture more than nine thousand SNPs in Q. suber and more than three thousand SNPs in Fagus sylvatica, demonstrating the efficacy of this sequence capture methodology for identifying orthologous genetic variants in related species in the absence of a reference genome.