Laurent Bouffier

Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range.

Background 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. Methodology 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. Results/Discussion 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 (h2 ns = 0.43±0.18, CVA = 4.4%). Q ST was significantly lower than F ST, indicating uniform selection for P 50, rather than genetic drift. Putative mechanisms underlying QST

Adaptive responses for seed and leaf phenology in natural populations of sessile oak along an altitudinal gradient.

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.

Can wood density be efficiently selected at early stage in maritime pine (Pinus pinaster Ait.)

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 (R2 = 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.RésuméLa 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 (R2 = 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.

Genomic selection in maritime pine.

A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM).

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

BackgroundThe 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.ResultsUsing 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.ConclusionsThese 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.

Performance of genomic prediction within and across generations in maritime pine

BackgroundGenomic selection (GS) is a promising approach for decreasing breeding cycle length in forest trees. Assessment of progeny performance and of the prediction accuracy of GS models over generations is therefore a key issue.ResultsA reference population of maritime pine (Pinus pinaster) with an estimated effective inbreeding population size (status number) of 25 was first selected with simulated data. This reference population (n = 818) covered three generations (G0, G1 and G2) and was genotyped with 4436 single-nucleotide polymorphism (SNP) markers. We evaluated the effects on prediction accuracy of both the relatedness between the calibration and validation sets and validation on the basis of progeny performance. Pedigree-based (best linear unbiased prediction, ABLUP) and marker-based (genomic BLUP and Bayesian LASSO) models were used to predict breeding values for three different traits: circumference, height and stem straightness. On average, the ABLUP model outperformed genomic prediction models, with a maximum difference in prediction accuracies of 0.12, depending on the trait and the validation method. A mean difference in prediction accuracy of 0.17 was found between validation methods differing in terms of relatedness. Including the progenitors in the calibration set reduced this difference in prediction accuracy to 0.03. When only genotypes from the G0 and G1 generations were used in the calibration set and genotypes from G2 were used in the validation set (progeny validation), prediction accuracies ranged from 0.70 to 0.85.ConclusionsThis study suggests that the training of prediction models on parental populations can predict the genetic merit of the progeny with high accuracy: an encouraging result for the implementation of GS in the maritime pine breeding program.

Wood density variability in successive breeding populations of maritime pine

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 decre...