[Show abstract][Hide abstract] ABSTRACT: Polycross mating systems are widely used in forest tree breeding for genetic testing. Backward selection based on polycross testing assumes equal male reproductive success and true half-sib progeny. The main objectives of this study were, firstly, to investigate the departure from these assumptions in a maritime pine polycross trial and, secondly, to evaluate the consequences for heritability and breeding values estimations. A total of 984 offspring from 98 half-sib families was genotyped with single nucleotide polymorphism markers to recover the full pedigree. Paternity was assigned successfully for 89 % of the offspring at a 99 % confidence level. We thus concluded there was an 11 % pollen contamination rate, assuming contamination when no genotype from the polymix composition could be identified as a father. The paternal contribution to the offspring varied among the males, but the departure from half-sib assumption was moderate since the average genetic correlation within the family was 0.26. Heritability and breeding values for girth at breast height and stem sweep were estimated using individual-tree mixed models with either partial or full pedigree information. The results highlighted a minor bias in heritability estimation due to unknown paternity, as well as a high correlation for estimated breeding values between the partial and full pedigree models, suggesting that the genetic merit of the parental generation for backward selection was adequately predicted using the partial pedigree model. Finally, pedigree recovery was also discussed in a perspective of forward selection.
Full-text · Article · Oct 2015 · Tree Genetics & Genomes
[Show abstract][Hide abstract] ABSTRACT: Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly-multiplexed single-nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from i) a three-generation inbred (F2) pedigree, ii) the French breeding population, and iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2,052 / 8,410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5,016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3,981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. This article is protected by copyright. All rights reserved.
[Show description][Hide description] DESCRIPTION: First genomic selection study in a maritime breeding population (n=661).
The overall intra-chromosomal linkage disequilibrium was low (r2 = 0.01).
The predictive ability of markers for growth and stem quality ranged from 0.43 to 0.49.
GBLUP, Bayesian Ridge, Bayesian LASSO regression models had similar predictive power.
[Show abstract][Hide abstract] ABSTRACT: Key message This review highlights some of the discoveries and applications made possible by " omics " technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology. & Context A decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of the structure, functioning, and evolution of forest tree genomes. & Aims and methods This review highlights some of the discoveries and applications that " omics " technologies have made possible for forest trees over the past 10 years. & Results In this review, we start by our current understanding of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiot-ic stresses. We then skim over advances in interactome analysis and epigenomics, the knowledge of the extent of genetic variation within and between species, revealing micro-and macro-evolutionary processes and species history, together with the complex architecture of quantitative traits. We finally end with applications in genetic resource conservation and breeding. & Conclusion The knowledge gained through the use of these technologies has a huge potential impact for adapting forests to the main challenges they will have to face: changing demand from ecosystem services with potentially conflicting
Full-text · Article · Jun 2015 · Annals of Forest Science
[Show abstract][Hide abstract] ABSTRACT: For the most part, molecular markers and detection of quantitative trait loci have been developed for forest tree species in view to performing marker-assisted selection (MAS). However, MAS has not been applied to forest trees until now. In parallel, some success stories of MAS in crop breeding have been reported. Recently, genotyping techniques have undergone a tremendous increase in throughput, moving the trend from MAS to genomic selection. We analyzed 250 papers reporting the use of MAS in plant breeding and found that the most popular schemes used were gene pyramiding and marker-assisted backcross manipulating a single or very few genomic regions which have a major impact on crop value. We reviewed theoretical and simulation studies to identify the parametric space in which MAS is expected to bring about significant advantages over phenotypic selection. Then, we tried to explain why MAS has not been applied to forest trees and discuss the opportunities offered by recent advances in these species.
Full-text · Article · Aug 2014 · Tree Genetics & Genomes
[Show abstract][Hide abstract] ABSTRACT: To meet the increasing demand of wood biomass worldwide in the context of climate change, developing improved forest tree
varieties for high productivity in water-limited conditions is becoming a major issue. This involves breeding for genotypes
combining high growth and moderate water loss and thus high water-use efficiency (WUE). The present work provides original
data about the genetics of intrinsic WUE (the ratio between net CO2 assimilation rate and stomatal conductance, also estimated by carbon isotope composition of plant material; δ13C) and its relation to growth in Pinus pinaster Ait. First, heritability for δ13C was estimated (0.29) using a 15-year-old progeny trial (Landes provenance), with no significant differences among three
sites contrasting in water availability. High intersite correlations (0.63–0.91) and significant but low genotype–environment
interactions were detected. Secondly, the genetic architectures of δ13C and growth were studied in a three-generation inbred pedigree, introducing the genetic background of a more-drought-adapted
parent (Corsican provenance), at ages of 2 years (greenhouse) and 9 years (plantation). One of the quantitative trait loci
(QTLs) identified in the field experiment, explaining 67% of the phenotypic variance, was also found among the QTLs detected
in the greenhouse experiment, where it colocalized with QTLs for intrinsic WUE and stomatal conductance. This work was able
to show that higher WUE was not genetically linked to less growth, allowing thus genetic improvement of water use. As far
as is known, the heritability and QTL effects estimated here are based on the highest number of genotypes measured to date.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: Maritime pine (Pinus pinaster Ait.) is the main plantation species in France with nearly one million hectare of cultivated forests in South Western France. A breeding program has been implemented since the early 1960s using a recurrent selection scheme. The breeding strategy combines two successive experimental designs: polymix crossing to evaluate parental breeding values and full-sib crossing from which selections are made for the next generation of breeding. This strategy was efficient both to increase genetic gains (maritime pine varieties reach 30% expected gain in volume and in stem straightness) and to maintain genetic variability in the breeding populations (Bouffier et al., 2008).
Future improved varieties must be adapted to environmental evolutions (climate change, development of some pests) and to wood industry diversification. In that changing context, forest tree breeding programs have to integrate more and more selection criteria and to propose different varieties adapted to various environments and diversified uses. Then it appears of first importance to accelerate the selection cycles in order to often renew variety composition. Fast development of molecular genetic tools and their cost drop-off can be of great help to cope with these challenges. Shortening selection cycle could be reached by polymix breeding with parental analysis of progeny as proposed by Lambeth et al. (2001) instead of the current breeding strategy of fullsib breeding and testing.
In that perspective, a maritime pine polymix progeny trial is currently under study. Trees have been highly phenotyped for various traits relative to growth (diameter, height), wood quality (stem straightness, spiral grain, wood density) and adaptation (water use efficiency). We are now genotyping this population with 60 SNPs (Sequenom technology) to recover the paternity identity. The poster will present first results of this study which aims to answer the following questions: Is there a differential reproductive success among pollen donors? What is the gain for breeding value accuracy when analyses are carried out with the full pedigree instead of with only the mother identity? Which new breeding strategies integrated the pedigree recovery can be implemented?
Bouffier, L., Raffin, A., Kremer, A. 2008. Evolution of genetic variation for selected traits in successive breeding populations of maritime pine. Heredity 101:156-165.
Lambeth, C., Lee, B.C., O’Malley, D., Wheeler, N. 2001. Polymix breeding with parental analysis of progeny: an alternative to full-sib breeding and testing. Theor Appl Genet 103:930-943.
[Show abstract][Hide abstract] ABSTRACT: Maritime pine is a major species for the French industry covering over 1 million hectares with a total production of 9 million m3 representing about 25% of total pulpwood and softwood timber and an annual turnover of 2.5 billion €. Most of this production is localized in the Aquitania forest in SouthWestern France. As the main intensively managed conifer in France, maritime pine is subjected to advanced forestry and genetic breeding since the early sixties. After 40 years research, a 40% cumulated genetic gain is expected by the third round of selection; but there are also limitations to improvement progress, i.e. quite long generation time, large genetic loads and high genetic redundancy within breeding population. Sudden and drastic changes in market value and environmental constraints in recent years (2 heavy storms during the last decade, increased drought and biotic stress) would need a significant paradigm shift in current breeding technology to deliver suitable tested tree varieties in plantation forestry (i.e. multivarietal forestry targeting a wide range of end-products through various silvicultural regimes). Field comparison of vegetative propagules is a key towards individual selection and efficient capture of the best genetic stocks. Clonal propagation is also required for scaling up production of improved varieties. Somatic embryogenesis (SE) is considered as the key technology to fulfil such requirements in maritime pine. As SE initiation from mature trees is still challenging in pine and other conifers, we are developing in maritime pine the classical SE approach for postponed propagation of tested trees involving SE initiation from immature zygotic embryos and stable cryopreservation of juvenile embryogenic tissue. Genotype captures at both SE initiation and maturation steps are key issues for successful implementation of this technology. The species, characterized by low vegetative propagation ability (cutting production is very difficult and particularly expensive, at least in Europe, compared to some other pine species). At the initiation step, family effect was confirmed to be highly significant. However with a mean genotype capture within family of 77% the variation among genetic backgrounds is now established within acceptable limits and has huge practical implications for our breeding program. The maturation step is currently more problematic but recent progress resulted in about 40% genotype capture. Major findings will be synthesized from 10 years maturation experiments at both FCBA and INRA.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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
No preview · Article · Jan 2009 · Tree Genetics & Genomes
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
No preview · Article · Jul 2008 · Canadian Journal of Forest Research
[Show abstract][Hide abstract] 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.
Full-text · Article · Jan 2008 · Annals of Forest Science