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Development of target sequence capture and estimation of genomic relatedness in a mixed oak stand

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierHelixVenture
dc.contributor.authorLESUR KUPIN, Isabelle
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorALEXANDRE, Hermine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBOURY, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorCHANCEREL, Emilie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
dc.date.issued2018
dc.identifier.issn1664-462X
dc.description.abstractEnAnticipating 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 x) 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.
dc.language.isoen
dc.publisherFrontiers
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.title.enDevelopment of target sequence capture and estimation of genomic relatedness in a mixed oak stand
dc.typeArticle de revue
dc.identifier.doi10.3389/fpls.2018.00996
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalFrontiers in Plant Science
bordeaux.page1-16
bordeaux.volume9
bordeaux.peerReviewedoui
hal.identifierhal-02628743
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02628743v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Frontiers%20in%20Plant%20Science&rft.date=2018&rft.volume=9&rft.spage=1-16&rft.epage=1-16&rft.eissn=1664-462X&rft.issn=1664-462X&rft.au=LESUR%20KUPIN,%20Isabelle&ALEXANDRE,%20Hermine&BOURY,%20Christophe&CHANCEREL,%20Emilie&PLOMION,%20Christophe&rft.genre=article


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