Laurent Bouffier

French National Institute for Agricultural Research, Lutetia Parisorum, Île-de-France, France

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Publications (8)21.3 Total impact

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    ABSTRACT: The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (He) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of He across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species.
    BMC Genomics 03/2014; 15(1):171. · 4.40 Impact Factor
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    ABSTRACT: We assessed the adaptive potential of seed and leaf phenology in 10 natural populations of sessile oak (Quercus petraea) sampled along two altitudinal transects using common garden experiments. Population differentiation for both phenological traits was observed with high-altitude populations germinating and flushing later than low altitude ones. However, high genetic variation and heritability values were also maintained within populations, despite slightly decreasing for dates of leaf unfolding with increasing altitude. We suggest that biotic and abiotic fluctuating selection pressures within populations and high gene flow are the main mechanisms maintaining high genetic variation for these fitness related traits. Moreover, changes in selection intensity and/or selection pressures along the altitudinal gradient can explain the reduction in genetic variation observed for leaf phenology. We anticipate that the maintenance of high genetic variation will be a valuable resource for future adaptation of sessile oak populations undergoing an upslope shift caused by climate change.
    Journal of Evolutionary Biology 07/2011; 24(7):1442-54. · 3.48 Impact Factor
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    ABSTRACT: Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. We assessed cavitation resistance (P(50)), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F(ST)) and quantitative genetic differentiation (Q(ST)), for retrospective identification of the evolutionary forces acting on these traits. In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h(2) (ns) = 0.43±0.18, CV(A) = 4.4%). Q(ST) was significantly lower than F(ST), indicating uniform selection for P(50), rather than genetic drift. Putative mechanisms underlying Q(ST)<F(ST) are discussed.
    PLoS ONE 01/2011; 6(8):e23476. · 3.73 Impact Factor
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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 01/2009; 5(1):11-25. · 2.40 Impact Factor
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    L Bouffier, A Raffin, A Kremer
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    ABSTRACT: Directional selection impacts a trait distribution by shifting its mean and reducing its variance. The change of variance is of major importance as the response to selection in subsequent generations is highly dependent of the genetic variability available in the population. In this contribution, evolution of genetic variation was investigated through the first breeding populations of the French maritime pine (Pinus pinaster Ait.) breeding program. We considered three populations: P0 (the forest where plus trees were initially selected), G0 (the plus tree population) and G1 (the population composed of trees selected in the progenies of G0). Analyses focused on the following selected traits: total height (H), girth at 1.30 m (D) and stem deviation to verticality (S). More than 150,000 trees from 25 tests of three distinct populations were studied with an individual genetic model. Accurate genetic parameters were obtained by taking all relationships between trees into account. For H and D, we found a strong decrease of the genetic variation from P0 to G0 corresponding to the initial selection of plus trees, which constitutes the base population of the breeding program. Then, despite the second step of selection applied, no appreciable evolution arose from comparisons between G0 and G1 for these traits. For S, the evolution is less significant as phenotypic variation slightly increased, possibly due to changes of silvicultural practices.
    Heredity 08/2008; 101(2):156-65. · 4.11 Impact Factor
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    ABSTRACT: Growth and form are the two main traits used for genetic improvement of maritime pine (Pinus pinaster Ait.) in the southwest of France. In this paper, wood density is studied to answer two main questions: Is there a general trend for density variability throughout tree development and has selection indirectly reduced wood density variability over breeding populations, owing to genetic unfavourable correlation with growth? Wood density and its components were studied in three polycross tests, each representative of one of the successive breeding populations. Wood density was measured with an X-ray densitometer in approximately 50 families per test with >1900 trees. A preliminary study showed that bark-to-pith ring indexing allows for a better estimation of genetic effects than does pith-to-bark indexing. Genetic variability of wood density appears to be highly dependent on the year considered and no general pattern can be detected over time. Whereas the variability of selected traits is known to have decreased over breeding populations, no significant change was found for variability of wood density.La croissance et la rectitude sont les deux principaux critères utilisés pour l'amélioration génétique du Pin maritime (Pinus pinaster Ait.) dans le sud-ouest de la France. Dans cet article, la densité du bois a été étudiée pour répondre à deux questions principales : La variabilité de la densité du bois montre-t-elle une tendance générale au cours du développement de l'arbre et la variabilité de la densité a-t-elle été modifiée indirectement par la sélection en raison d'une corrélation défavorable entre la densité du bois et la croissance ? La densité du bois et ses composantes ont été analysées dans trois tests polycross représentant les populations d'amélioration successives. Au total environ 50 familles par test, soit plus de 1900 arbres, ont été mesurées par microdensitométrie. Une étude préliminaire a permis de montrer que l'annotation des cernes de l'écorce vers le cœur de l'arbre permet une meilleure estimation des effets génétiques par rapport à une annotation du cœur de l'arbre vers l'écorce. La variabilité génétique de la densité du bois apparaît fortement dépendante de l'année considérée mais notre étude ne révèle aucune tendance générale au cours des années. De plus, alors que la variabilité génétique des caractères sélectionnés a diminué au cours des populations d'amélioration, aucune évolution significative n'a été mise en évidence pour la variabilité de la densité du bois.
    Canadian Journal of Forest Research 07/2008; 38(8):2148-2158. · 1.56 Impact Factor
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    ABSTRACT: Growth and stem straightness are the two main selection criteria in the French maritime pine breeding programme. In this contribution, our objective was to study the possibility of selecting for wood density assessed at an early stage. We measured X-ray wood density, in three progeny tests, on more than 1 900 breast high increment cores. High relative expected genetic gain (from 3 to 9%) was found for wood density at mature stage. Juvenile and adult wood density estimations were well-correlated; the relative efficiency of early selection reached about 80% at 12 years old. As it would not be realistic to use the X-ray densitometer at an operational scale in a breeding programme, we tested the efficiency of using the Resistograph, an indirect method to assess wood density on live trees. High correlation between the Resistograph and density data ($R$$^{2}$ = 0.93 on familial data) was found, suggesting that wood density through Resistograph assessment could be soon integrated as a new selection criterion in our breeding programme. Peut-on efficacement sélectionner la densité du bois chez le pin maritime (Pinus pinaster Ait.) au stade juvénile ?. La croissance et la rectitude du tronc sont les deux principaux critères de sélection dans le programme d'amélioration génétique du pin maritime en France. Cette étude a pour objectif d'évaluer la possibilité de sélectionner la densité du bois au stade juvénile. Plus de 1 900 arbres, provenant de trois tests, ont été analysés par microdensitométrie. Des gains génétiques relatifs élevés ont été mis en évidence pour la densité du bois au stade adulte (3 à 9 %). Les estimations de la densité réalisées aux stades adulte et juvénile étant bien corrélées, l'efficacité relative de la sélection atteint environ 80 % à l'âge de 12 ans. Les mesures de densité par rayons X ne sont pas envisageables à grande échelle dans le cadre d'un programme d'amélioration, ainsi nous avons évalué l'efficacité de l'utilisation du Résistographe, une méthode indirecte pour estimer la densité du bois sur arbres debout. Des corrélations élevées ont été mises en évidence entre les données obtenues avec le Résistographe et celles obtenues par microdensitométrie ($R$$^{2}$ = 0.93 avec les données familiales). Il semble donc possible d'intégrer la densité du bois, estimée avec le Résistographe, comme nouveau critère de sélection dans notre programme d'amélioration.
    Annals of Forest Science 01/2008; · 1.63 Impact Factor
  • Laurent BOUFFIER, Annie RAFFIN, Antoine KREMER
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    ABSTRACT: The ‘Landes de Gascogne’ area in south west of France is covered mainly by a huge forest of planted maritime pine. The selective breeding program has achieved significant genetic gains in terms of both growth and stem straightness. A retrospective study shows that the chosen selection strategy allowed enough variability in selection criteria to continue the programme over several generations. However, altered social demands and future climate change require selection criteria and strategies to be adapted. Les Landes de Gascogne sont très majoritairement couvertes par une vaste forêt cultivée de Pin maritime. Le programme d’amélioration génétique a permis d’améliorer sensiblement à la fois la croissance et la rectitude basale des arbres. Une étude rétrospective montre que la stratégie de sélection suivie a maintenu suffisamment de variabilité sur les critères de sélection pour assurer la poursuite du programme sur plusieurs générations. Toutefois, l’évolution des demandes de la société et les changements climatiques à venir nécessitent une adaptation des critères et des méthodes de sélection.