Leopoldo Sanchez

Somatic embryogenesis in forestry with a focus on Europe: state-of-the-art, benefits, challenges and future direction

Vegetative propagation of forest trees offers advantages to both tree breeders and the forest industry. This review will describe benefits, type of vegetative propagation, and its integration into breeding programmes. Of all of the different methods for vegetative propagation, only rooted cuttings and somatic embryogenesis (and the combined use of both) offer any practical methods for large-scale commercial use. However, it is very difficult to fully appreciate the overall level of activity of the research and application of somatic embryogenesis of forest trees. Publications and reports only highlight a small fraction of the ongoing work. To this end, a survey was conducted across Europe (under EU Research Infrastructure Concerted Action “Treebreedex”) to document the species involved, the state-of-the-art of somatic embryogenesis, its stage of development and its application in tree improvement programmes and to commercial forestry. The results of this survey are presented and discussed. In addition, this review presents the challenges (biological, economic, public acceptance and regulatory) and their relationships to European forestry. Finally, a strategy to promote the use of this technology is proposed.

Genomic selection prediction accuracy in a perennial crop: case study of oil palm (Elaeis guineensis Jacq.).

Key messageGenomic selection empirically appeared valuable for reciprocal recurrent selection in oil palm as it could account for family effects and Mendelian sampling terms, despite small populations and low marker density.AbstractGenomic selection (GS) can increase the genetic gain in plants. In perennial crops, this is expected mainly through shortened breeding cycles and increased selection intensity, which requires sufficient GS accuracy in selection candidates, despite often small training populations. Our objective was to obtain the first empirical estimate of GS accuracy in oil palm (Elaeis guineensis), the major world oil crop. We used two parental populations involved in conventional reciprocal recurrent selection (Deli and Group B) with 131 individuals each, genotyped with 265 SSR. We estimated within-population GS accuracies when predicting breeding values of non-progeny-tested individuals for eight yield traits. We used three methods to sample training sets and five statistical methods to estimate genomic breeding values. The results showed that GS could account for family effects and Mendelian sampling terms in Group B but only for family effects in Deli. Presumably, this difference between populations originated from their contrasting breeding history. The GS accuracy ranged from −0.41 to 0.94 and was positively correlated with the relationship between training and test sets. Training sets optimized with the so-called CDmean criterion gave the highest accuracies, ranging from 0.49 (pulp to fruit ratio in Group B) to 0.94 (fruit weight in Group B). The statistical methods did not affect the accuracy. Finally, Group B could be preselected for progeny tests by applying GS to key yield traits, therefore increasing the selection intensity. Our results should be valuable for breeding programs with small populations, long breeding cycles, or reduced effective size.

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).

Potential for marker-assisted selection for forest tree breeding: lessons from 20 years of MAS in crops

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.

Gain and diversity in advanced generation coastal Douglas-fir selections for seed production populations

Sublines are used in the third-generation breeding and testing of coastal Douglas-fir in British Columbia, with the original intent of selecting only one genotype per subline for production populations (e.g., seed orchards) to eliminate relatedness among parents (therein called “1/SL”). We evaluated three additional selection scenarios that did not consider the subline structure. One of the scenarios strictly selected on the basis of the highest breeding values of the trees (“TOP”); another scenario used the TOP selections, but assigned the number of ramets per selection proportionally to the selection breeding value (“LIND”); lastly, a simulated annealing technique was applied to maximize gain under explicit constraints on coancestry (“OPTS”). All three alternative selection scenarios resulted in some relatedness and coancestry among selections, but the last two provided increases in average breeding values compared to those obtained by the 1/SL scenario. Effective population sizes (and consequently inbreeding coefficients) varied among the three selection scenarios. Effects of the various selections on merchantable volume at rotation age were determined using a linear regression model based on an individual tree model (TASS), which was first run to determine the relationship between merchantable volume and inbreeding (f). LIND and TOP selections yielded the highest breeding values but, due to the increased coancestry among selections, paid a penalty in the merchantable volume determination. OPTS maximized merchantable volume at rotation age 60 after including more than 13 selections with an increase of around 3% over that obtained by the 1/SL selection scenario, with an associated increase in Ne of 50%. Other implications of the three alternative selection scenarios are discussed.

Genetic control of the tree-ring response of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) to the 2003 drought and heat-wave in France

The genetic control of tree ring growth in Douglas-fir in response to the drought and heat-wave that occurred in 2003 in Europe was studied with microdensity profiles in three clonal experiments located in three different French regions. The drought and heat-wave significantly affected Douglas-fir wood formation. The Chassenoix site (Northeast of Massif-Central) was more severely affected that the other two: the 2003 year-ring was narrower and less dense than in the other sites and than the previous (2002) and following (2004) year-rings in the same site: ring growth stopped earlier and latewood did not develop completely. The year-rings 2004 and 2002 were very similar in this site. There was a significant genetic control for all ring parameters in the three sites and during the three years. The heritability was highly variable between years and among sites, without any clear pattern in this variability, except in Chassenoix where it was slightly lower in the 2003 year-ring. Variables measuring the response of trees to the 2003 event, i.e., the difference in ring width between 2002 and 2003, or between 2003 and 2004, showed a very variable degree of genetic control, from very low to relatively high. Douglas-fir seemed plastic enough to acclimate to the drought and heat-wave and then to recover during 2004. Furthermore the level of heritability estimated demonstrates that Douglas-fir has an adaptive potential that could be useful for multi-generation long-term response.RésuméLa réponse du douglas à la canicule de 2003 en France a été étudiée à l’aide de profils microdensitométriques obtenus sur des arbres de 3 tests clonaux situés dans 3 régions différentes. La canicule a significativement affecté la formation du bois du douglas. Les arbres du site de Chassenoix, situé dans le Morvan, ont réagi plus fortement que ceux des 2 autres : le cerne de l’année de la canicule est plus étroit et moins dense que le même cerne dans les 2 autres sites et plus étroit et moins dense que les cernes immédiatement antérieur (2002) et postérieur (2004) dans le même site; la formation du bois s’est arrêtée plus tôt et le bois final ne s’est pas complètement développé. À Chassenoix, le cerne de l’année 2004 ressemble plus au cerne 2002 qu’au cerne 2003, ce qui traduit une récupération. Nous mettons en évidence un contrôle génétique significatif pour toutes les variables intra-cernes dans les 3 sites, pour les 3 années 2002, 2003 et 2004. Les héritabilités sont très variables entre caractères, sites et années, sans structure particulière, sauf à Chassenoix où ces héritabilités sont légèrement plus faibles durant l’année de la canicule. Des variables décrivant la réponse des arbres entre 2002 et 2003 puis 2003 et 2004 sont très irrégulièrement contrôlées génétiquement, avec des héritabilités allant de 0 à près de 0,5. Le douglas semble avoir été suffisamment plastique pour s’acclimater à la sécheresse et canicule puis pour récupérer en 2004 une croissance proche de celle de 2002. De plus, son potentiel génétique démontré par le niveau d’héritabilité estimé lui donne également une capacité adaptative multi-génération à plus long terme.

Gametic models for multitrait selection schemes to study variance of response and drift under adverse genetic correlations

A major issue faced by breeders is how to effectively manage adverse correlations in breeding programs. We present results of a Monte Carlo allele-based simulation of the changes in response and variance of response under adverse genetic correlations by using the examples of two contrasting selection methods: the ‘Smith-Hazel’ selection index (SH) and independent culling (IC). We assumed several gene models, which included linkage and antagonistic pleiotropy as the primary drivers of adverse genetic correlations. The different behaviors of these selection methods allowed us to identify the mechanism behind the generation of uncertainty under antagonistic trait selection: IC had the properties of stabilizing selection, while SH behaved more similar to disruptive selection. Although SH outperformed IC in terms of genetic gain, this advantage happened at the cost of higher variance of response and loss of heterozygosity. Using an optimum selection algorithm (OS) to prevent the loss of heterozygosity through a constraint on inbreeding in SH/OS increased marginally the reliability, remaining still below that of IC under equal conditions. However, SH/OS had lower inbreeding (ΔF) than IC for equivalent levels of genetic gain, so a compromise between high selection reliability, low ΔF, and gain must be made by a breeder under antagonistic trait selection even with the use of optimization tools.

Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population

AbstractKey messageExplicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657–1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (<0.07), although the number of ancestors was overestimated and the selfing rate could be biased. Simulations also showed that linkage disequilibrium between markers and departure from the Hardy–Weinberg equilibrium in the founder population did not affect the efficiency of the method. Real oil palm data confirmed the simulation results, with a high correlation between the true and estimated genealogical coancestry (>0.9) and a low RMSE (<0.08) using 38 markers. The method was applied to the Deli oil palm population for which pedigree data were scarce. The estimated genealogical coancestries were highly correlated (>0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0.

Effect of Selection Method on Genetic Correlation and Gain in a Two-trait Selection Scheme

Summary Adverse genetic correlations between wood volume and quality traits are one of the main constraints in advancing radiata pine and other pine breeding programs. To overcome or deal with adverse genetic correlation in radiata pine and other conifer breeding programs, a Monte Carlo simulation study for the adversely correlated traits DBH and wood density was conducted using allele-based models. Two allelic models were generated for the study: a mixed-loci model using independent and pleiotropic loci (i.e. each locus affecting more than one trait) for adversely correlated traits and an all-antagonistic-pleiotropic-loci model. Selection was conducted for three scenarios: the first was based on a single trait, the second on index selection for two adversely correlated traits (DBH and wood density) with equal or, third, unequal economic weights. Results indicated that: 1. Adverse genetic correlation tends to increase under pleiotropic models with selection. 2. Genetic gains for adversely correlated traits (such as DBH and wood density) could be made for many generations with selective breeding if there are independent loci for individual traits. 3. New alleles (from infusion or mutation) with less antagonistic effect are required for further genetic gain in the two adversely correlated traits simultaneously if all independent alleles are fixed (i.e. without allelic variation) and pleiotropic loci with antagonistic effects are not fixed. 4. For short-term genetic gain in adversely correlated traits, selection based on two traits simultaneously is more effective than selection based on a single trait. Developing economic weights through breeding objectives is a sound approach for short-term breeding programs. Economic weights will influence genetic gain for individual traits and genetic correlation between traits. 5. For long-term genetic gain, dissecting the genetic basis of traits using a large association population is recommended. When the genetic mechanisms controlling adversely correlated traits are better understood, an allele model could be developed to study optimal strategies under different gene actions.

Douglas-Fir ( Pseudotsuga menziesii (Mirb.) Franco)

Douglas fir (Pseudotsuga menziesii (Mirb.) Franco) is native to the Pacific coast range and along the Rocky Mountains through Canada and USA. In the early 19th nineteenth century, it was introduced to Western Europe, where nowadays it covers almost 800,000 ha. Despite this considerable extent, the relatively recent introduction to Europe means this exotic species is still a minor forest species for several European countries. This status may be revised notably in the context of climate change, considering the high adaptability potential of the species.