Personne : Isabel, Nathalie
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Faculté de foresterie et de géodésie, Université Laval
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- PublicationRestreintGene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations(Wiley-Blackwell Publishing Ltd., 2018-10-01) Giguère, Isabelle; Isabel, Nathalie; Ryan, Natalie; MacKay, John; Guy, Robert D. (Robert Dean); Prunier, Julien; Porth, IlgaGene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intraprovenance cross (north–north cross, 58th parallel) and an interprovenances cross (north–south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One‐to‐five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water‐use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast‐evolving pathogens.
- PublicationAccès libreGenomic diversity evaluation of populus trichocarpa germplasm for rare variant genetic association studies(Frontiers Media S.A, 2020-01-28) Isabel, Nathalie; Prunier, Julien; Porth, Ilga; Klápště, Jaroslav; Villarreal Aguilar, Juan Carlos; El-Kassaby, Yousry A.; Piot, AnthonyGenome-wide association studies are powerful tools to elucidate the genome-to-phenomerelationship. In order to explain most of the observed heritability of a phenotypic trait, asufficient number of individuals and a large set of genetic variants must be examined. Thedevelopment of high-throughput technologies and cost-efficient resequencing of completegenomes have enabled the genome-wide identification of genetic variation at large scale.As such, almost all existing genetic variation becomes available, and it is now possible toidentify rare genetic variants in a population sample. Rare genetic variants that were usuallyfiltered out in most genetic association studies are the most numerous genetic variationsacross genomes and hold great potential to explain a significant part of the missingheritability observed in association studies. Rare genetic variants must be identified withhigh confidence, as they can easily be confounded with sequencing errors. In this study,we used a pre-filtered data set of 1,014 purePopulus trichocarpaentire genomes toidentify rare and common small genetic variants across individual genomes. We comparedvariant calls betweenPlatypusandHaplotypeCallerpipelines, and we further applied strictqualityfilters for improved genetic variant identification. Finally, we only retained geneticvariants that were identified by both variant callers increasing calling confidence. Based onthese shared variants and after stringent qualityfiltering, we found high genomic diversity inP. trichocarpagermplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance ofgenomic diversity and the potential of rare defective genetic variants in explaining asignificant portion ofP. trichocarpa's phenotypic variability in association genetics. Theultimate goal is to associate both rare and common alleles with poplar's wood quality traitsto support selective breeding for an improved bioenergy feedstock.