Antoine Kremer

Publications (126) View all

• Article: Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing.

  Saneyoshi Ueno, Christophe Klopp, Jean Charles Leplé, Jérémy Derory, Céline Noirot, Valérie Léger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
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  ABSTRACT: BACKGROUND: In temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during which the plant is not growing, allows trees to avoid cold injury resulting from exposure to low temperatures. An understanding of the molecular machinery controlling the shift between these two phenological states is of key importance in the context of climatic change. The objective of this study was to identify genes upregulated during endo- and ecodormancy, the two main stages of bud dormancy. Sessile oak is a widely distributed European white oak species. A forcing test on young trees was first carried out to identify the period most likely to correspond to these two stages. Total RNA was then extracted from apical buds displaying endo- and ecodormancy. This RNA was used for the generation of cDNA libraries, and in-depth transcriptome characterization was performed with 454 FLX pyrosequencing technology. RESULTS: Pyrosequencing produced a total of 495,915 reads. The data were cleaned, duplicated reads removed, and sequences were mapped onto the oak UniGene data. Digital gene expression analysis was performed, with both R statistics and the R-Bioconductor packages (edgeR and DESeq), on 6,471 contigs with read numbers >= 5 within any contigs. The number of sequences displaying significant differences in expression level (read abundance) between endo- and ecodormancy conditions ranged from 75 to 161, depending on the algorithm used. 13 genes displaying significant differences between conditions were selected for further analysis, and 11 of these genes, including those for glutathione-S-transferase (GST) and dehydrin xero2 (XERO2) were validated by quantitative PCR. CONCLUSIONS: The identification and functional annotation of differentially expressed genes involved in the "response to abscisic acid", "response to cold stress" and "response to oxidative stress" categories constitutes a major step towards characterization of the molecular network underlying vegetative bud dormancy, an important life history trait of long-lived organisms.
  BMC Genomics 04/2013; 14(1):236. · 4.07 Impact Factor
• Article: Q(ST) ( ) < F(ST) As a signature of canalization.

  Jean-Baptiste Lamy, Christophe Plomion, Antoine Kremer, Sylvain Delzon
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  ABSTRACT: A key aim of evolutionary biology - inferring the action of natural selection on wild species - can be achieved by comparing neutral genetic differentiation between populations (F(ST) ) with quantitative genetic variation (Q(ST) ). Each of the three possible outcomes of comparisons of Q(ST) and F(ST) (Q(ST) ( ) > F(ST) , Q(ST) ( ) = F(ST) , Q(ST) ( ) < F(ST) ) is associated with an inference (diversifying selection, genetic drift, uniform selection, respectively). However, published empirical and theoretical studies have focused on the Q(ST) ( ) > F(ST) outcome. We believe that this reflects the absence of a straightforward biological interpretation of the Q(ST) < F(ST) pattern. We here report recent evidence of this neglected evolutionary pattern, provide guidelines to its interpretation as either a canalization phenomenon or a consequence of uniform selection and discuss the significant importance this issue will have for the area of evolutionary biology.
  Molecular Ecology 10/2012; · 5.52 Impact Factor
• Article: Comparative mapping in the Fagaceae and beyond with EST-SSRs.

  Catherine Bodénès, Emilie Chancerel, Oliver Gailing, Giovanni G Vendramin, Francesca Bagnoli, Jerome Durand, Pablo G Goicoechea, Carolina Soliani, Fiorella Villani, Claudia Mattioni, Hans Peter Koelewijn, Florent Murat, Jerome Salse, Guy Roussel, Christophe Boury, Florian Alberto, Antoine Kremer, Christophe Plomion
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  ABSTRACT: BACKGROUND: Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. RESULTS: We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. CONCLUSIONS: This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
  BMC Plant Biology 08/2012; 12(1):153. · 3.45 Impact Factor
• Article: What are the consequences of growth selection on wood density in the French maritime pine breeding programme?

  Laurent Bouffier, Annie Raffin, Philippe Rozenberg, Céline Meredieu, Antoine Kremer
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  ABSTRACT: Volume and stem straightness were the main selection criteria for the first two generations of the French maritime pine (Pinus pinaster Ait.) breeding programme. In this article, we investigate the consequences of this selection on wood quality. Wood density, as a predictor of wood quality, is studied both in the breeding populations and in commercial varieties. Phenotypic and genetic correlations between wood density and growth traits are investigated in successive breeding populations with three genetic field experiments of respectively 30, 29 and 12years old. Correlation estimates were either slightly negative or non-significantly different from zero depending on the test considered. Consequently, a low impact of growth selection on wood quality should be expected in improved seed sources. However, we observed a significant wood density decrease in two improved varieties as compared to unimproved seed sources at age 15. In addition to this first effect on wood density, growth improvement is also expected to reduce the rotation age and thus increase the proportion of juvenile wood, which is known as having a lower density than mature wood. This change was studied and quantified using a growth model. Finally, a wood density decrease reaching up to 6% was predicted in the improved varieties compared to unimproved material, when both the observed decrease in wood density and the predicted increase in juvenile wood proportion were taken into account. Implications for the breeding programme were considered.
  Tree Genetics & Genomes 04/2012; 5(1):11-25. · 2.34 Impact Factor
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  Available from: Antoine Kremer

  Article: Evidence of altitudinal increase in photosynthetic capacity: gas exchange measurements at ambient and constant CO2 partial pressures

  Caroline C. Bresson, Andrew S. Kowalski, Antoine Kremer, Sylvain Delzon
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  ABSTRACT: – • Because all microclimatic variables change with elevation, it is difficult to compare plant performance and especially photosynthetic capacity at different elevations. Indeed, most previous studies investigated photosynthetic capacity of low- and high-elevation plants using constant temperature, humidity and light but varying CO2 partial pressures (P CO 2). – • Using gas exchange measurements, we compared here maximum assimilation rates (A max) at ambient and constant-low-elevation P CO 2for two temperate tree species along an altitudinal gradient (100 to 1600 m) in the Pyrénées mountains. – • Significant differences in A max were observed between the CO2 partial pressure treatments for elevations above 600 m, the between-treatment differences increasing with elevation up to 4 μmol m−2 s−1. We found an increase in A max with increasing elevation at constant-low-elevation P CO 2 but not at ambient P CO 2 for both species. Given a 10% change in P CO 2, a proportionally higher shift in maximum assimilation rate was found for both species. – • Our results showed that high elevation populations had higher photosynthetic capacity and therefore demonstrated that trees coped with extreme environmental conditions by a combination of adaptation (genetic evolution) and of acclimation. Our study also highlighted the importance of using constant CO2 partial pressure to assess plant adaptation at different elevations. – • Les conditions microclimatiques étant très variables avec l’altitude, il est difficile de comparer les performances d’une espèce végétale à différentes altitudes, particulièrement la capacité photosynthétique. En effet, la plupart des études antérieures ont estimé le taux maximal d’assimilation à basses et hautes altitudes en maintenant la température, l’humidité de l’air et la lumière constantes mais en laissant varier la pression partielle de CO2 (P CO 2). – • Afin de comparer le taux maximum d’assimilation (A max) à pressions partielles de CO2 constantes de basse altitude et variables, nous avons effectué des mesures d’échanges gazeux sur deux espèces d’arbres tempérés le long d’un gradient altitudinal de 1600 m de dénivelé dans les Pyrénées françaises. – • La différence entre les deux traitements de P CO 2 est significative au-dessus de 600 m d’altitude et atteint un maximum de 4 μmol m−2 s−1. Pour les deux espèces, nous avons mis en évidence une augmentation de A max avec l’altitude à P CO 2 constantes mais pas à P CO 2 ambiantes. Pour une modification de P CO 2 de 10 %, le changement du taux maximum d’assimilation est proportionnellement supérieur chez les deux espèces. – • Nos résultats montrent que les populations de hautes altitudes possèdent une capacité photosynthétique supérieure, démontrant que les arbres font face aux conditions environnementales extrêmes grâce à des adaptations génétiques ou des acclimatations. Notre étude souligne ainsi l’importance de fixer la PCO 2 pour comparer l’adaptation des plantes à différentes altitudes. Keywordsadaptation–altitudinal gradient–acclimation–partial pressure–photosynthetic capacity Mots-clésadaptation–acclimatation–gradient altitudinal–pression partielle–capacité photosynthétique
  Annals of Forest Science 04/2012; 66(5):505-505. · 1.79 Impact Factor