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A new Genomic resource for Populus nigra and its deployment for genetic studies

hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorFAIVRE-RAMPANT, Patricia
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorJORGE, Véronique
hal.structure.identifierUniversità degli Studi di Udine - University of Udine [Italie]
dc.contributor.authorZAINA, Giusi
hal.structure.identifierIstituto di Genomica Applicata [IGA]
dc.contributor.authorGIACOMELLO, Stefania
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorSEGURA, Vincent
hal.structure.identifierIstituto di Genomica Applicata [IGA]
dc.contributor.authorSCALABRIN, Simone
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorGUÉRIN, Vanina
hal.structure.identifierIstituto di Genomica Applicata [IGA]
dc.contributor.authorDE PAOLI, Emanuele
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorALUOME, Christelle
hal.structure.identifierUniversity of Southampton
dc.contributor.authorVIGER, Maud
hal.structure.identifierIstituto di Genomica Applicata [IGA]
dc.contributor.authorCATTONARO, Federica
hal.structure.identifierUniversity of Southampton
dc.contributor.authorPAYNE, Adrienne
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorPAULSTEPHENRAJ, Pauline Sandra
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorLE PASLIER, Marie-Christine
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorBERARD, Aurélie
hal.structure.identifierUniversity of Southampton
dc.contributor.authorALLWRIGHT, Mike
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorVILLAR, Marc
hal.structure.identifierUniversity of Southampton
dc.contributor.authorTAYLOR, Gail
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorBASTIEN, Catherine
hal.structure.identifierUniversità degli Studi di Udine - University of Udine [Italie]
hal.structure.identifierIstituto di Genomica Applicata [IGA]
dc.contributor.authorMORGANTE, Michele
dc.date.issued2016
dc.date.conference2016-05-30
dc.description.abstractEnBlack poplar (Populus nigra L., Salicaceae) is an Eurasian native species distributed within fluvial corridors. As a pioneer species, P. nigra plays an important role in the establishment of riparian ecosystems. The species has important adaptive performances that have promoted Black poplar as a parental pool in interspecific breeding programs world-wide. Until recently, there is no genomic resource in black poplar to support genetic diversities studies and breeding. INRA, University of Southampton, University of Udine and IGA were collaborating to develop genomic resources and genetic tools for black poplar. SNPs were discovered using whole genome sequencing of 51 individuals relevant of the genetic diversity of an association population covering the range of the species in Western Europe. Four individuals were selected and sequenced at coverage > 25X and 47 at coverage <25X. We had two main objectives: to maximize the genetic variation among individuals and to identify informative SNPs. More than 189 000 SNPs were identified within 15 known QTL regions related to rust resistance, wood properties, water use efficiency and phenology, 2 916 expressional candidate genes for the same traits, and 1 732 genes spread out on the genome. Because many more SNPs were detected than needed, a set of stringent parameters was applied to filter 10 331 loci for the construction of a 12K Infinium BeadChip array (Faivre Rampant et al, 2016). This new array was employed to genotype more than 1 000 unrelated individuals and progenies. The high SNP call rate over 90% provided valuable information on population genetic structure. The structure pattern was consistent with the geographical distribution of the populations under study. However, admixture is an important feature in French populations. Moreover a high rate of clonality was found in populations from Netherlands and Germany. Most polymorphic SNPs had a Minor Allele Frequency greater than 0.05, showing that the array is suitable for association studies. The array data were also used to estimate linkage disequilibrium. The r2 fell to approximately one half of the initial value within 5 to 7 kb. This new information is important to develop further whole genome association in P. nigra. The 12K Infinium BeadChip array is the first genotyping resource for black poplar, and examples of current applications in diversity studies, pedigree validation, genetic mapping, genomic evaluation and natural-population-based genetic association will be presented. It is also considered as gold standard to fine-tune parameters for SNP calling from RNAseq and whole-genome sequencing data.
dc.language.isoen
dc.title.enA new Genomic resource for Populus nigra and its deployment for genetic studies
dc.typeCommunication dans un congrès
dc.subject.halSciences du Vivant [q-bio]/Biotechnologies
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.description.sponsorshipEuropeNovel tree breeding strategies
bordeaux.conference.titleIUFRO Genomics and Forest Tree Genetics
bordeaux.countryFR
bordeaux.conference.cityArcachon
bordeaux.peerReviewednon
hal.identifierhal-02743801
hal.version1
hal.invitednon
hal.conference.end2016-06-03
hal.popularnon
hal.audienceNationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02743801v1
bordeaux.COinSctx_ver=Z39.88-2004&amp;rft_val_fmt=info:ofi/fmt:kev:mtx:journal&amp;rft.date=2016&amp;rft.au=FAIVRE-RAMPANT,%20Patricia&amp;JORGE,%20V%C3%A9ronique&amp;ZAINA,%20Giusi&amp;GIACOMELLO,%20Stefania&amp;SEGURA,%20Vincent&amp;rft.genre=unknown


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