Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand

Abstract

Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. 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 3 Mb 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 (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

“…Zhou et al 2014;Wang et al 2016), at the same time avoiding most of the above technical issues. TSC approaches will surely be encouraged and tailored to specific evolutionary research questions in oaks in the next decade, given the new Q. robur genome sequence availability (Plomion et al 2018;Lesur et al 2018 for the first TSC in oaks). However, the bioinformatics pipelines needed for validating haplotype-based or quality data for population genetics inferences also need constant reassessment according to research questions and chosen technology.…”

“…robur, Plomion et al 2016Q. robur, Plomion et al , 2018; Q. suber, Ramos et al 2018;Fagus sylvatica, Mishra et al 2018), and these provide great prospects for future evolutionary genomics studies (Petit et al 2013;Parent et al 2015;Cannon et al 2018;Lesur et al 2018).…”

“…These issues will be better addressed with genome-wide sequence data in many samples (Buerkle et al 2011), which will be facilitated in oaks by integrating the newly available genome sequence of Quercus robur to chosen HT resequencing methods e.g. Zhou and Holliday 2012;Lesur et al 2018 for the first target sequence capture in oaks).…”

In situestimation of genetic variation of functional and ecological traits inQuercus petraeaandQ.robur

“…We estimated pedigree relationship for all G2 individuals with at least one parent retrieved from parentage analysis, while results for individuals with both parents known are presented in appendix. Genomic relatedness was estimated among G1 individuals in a previous study (Lesur et al, 2018) following the method by Van Raden (2008) and using multiple SNP markers derived from target sequence capture. Relatedness was computed separately for each species and using 6 different sets of SNPs selected according to different thresholds of Minimum Allele Frequencies (MAF: 0.01, 0.05, 0.1, 0.15, 0.3 and 0.4) representing 33,000 to 1,500 markers (Appendix 4).…”

“…Accessing their genetic variation would allow to anticipate their respective ability to respond to ongoing selection pressures. In an earlier companion paper, we implemented a genomic capture approach to call thousands of SNPs and evaluate their use for recovering realized relatedness (Lesur et al, 2018). Estimates of realized relatedness were validated by comparing their values with known pedigree relationships.…”