Philippe Vigneron

Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus

BackgroundEucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly improve growth performance and wood properties (WPs). In this study, an interspecific cross between Eucalyptus urophylla and E. grandis was used to identify major genomic regions (Quantitative Trait Loci, QTL) controlling the variability of WPs.ResultsLinkage maps were generated for both parent species. A total of 117 QTLs were detected for a series of wood and end-use related traits, including chemical, technological, physical, mechanical and anatomical properties. The QTLs were mainly clustered into five linkage groups. In terms of distribution of QTL effects, our result agrees with the typical L-shape reported in most QTL studies, i.e. most WP QTLs had limited effects and only a few (13) had major effects (phenotypic variance explained > 15%). The co-locations of QTLs for different WPs as well as QTLs and candidate genes are discussed in terms of phenotypic correlations between traits, and of the function of the candidate genes. The major wood property QTL harbours a gene encoding a Cinnamoyl CoA reductase (CCR), a structural enzyme of the monolignol-specific biosynthesis pathway.ConclusionsGiven the number of traits analysed, this study provides a comprehensive understanding of the genetic architecture of wood properties in this Eucalyptus full-sib pedigree. At the dawn of Eucalyptus genome sequence, it will provide a framework to identify the nature of genes underlying these important quantitative traits.

Structure of the specific combining ability between two species of Eucalyptus. I. RAPD data

Abstract Within the context of the reciprocal recurrent selection scheme developed in 1989 by CIRAD-Forêt on Eucalyptus, RAPD essays were performed to assess the genetic diversity in the two species E. urophylla and E. grandis. The molecular markers were split into two parts: the specific markers (present with different frequencies in the two species) and the common markers (present with similar frequencies in the two species). The study analyses the structure of genetic diversity within and between the two species of Eucalyptus. Different genetic distances are worked out for use in prediction equations of the individual tree trunk volume of hybrids at 38 months. Each distance is expressed as the sum of the general genetic distance and the specific genetic distance. The general genetic distance based on the double presence plus the double absence of bands seems to be an interesting co-variate to use in a factor regression model. Through this model the distance calculated between species explains the general combining ability (GCA) and the specific combining ability (SCA) of the phenotypic character with a global coefficient of determination of 81.6%.

A candidate gene for lignin composition in #Eucalyptus#: #Cinnamoyl-CoA reductase# (CCR)

Lignin content and composition are considered as mandatory traits of eucalyptus breeding programs, especially for pulp, paper, and bioenergy production. In this article, we used 33 Eucalyptus urophylla full-sib families of an 8 × 8 factorial design to provide estimates of genetic parameters for lignin- and growth-related traits. Secondly, from the sequencing of the 16 unrelated founders, we described the nucleotide and haplotype variability of cinnamoyl-CoA reductase (CCR), a candidate gene for lignin-related traits encoding the cinnamoyl-CoA reductase. Finally, we tested the association between CCR polymorphisms and trait variation using a mixed linear model. A high value of narrow sense heritability was obtained for lignin content (h² = 0.85) and S/G ratio (h² = 0.62) indicating that these traits are under strong genetic control. High levels of nucleotide (θπ = 0.0131) and haplotype (Hd = 0.958) diversity were detected for CCR. From an initial set of 152 biallelic single nucleotide polymorphisms (SNPs), a subset of 65 nonredundant loci was selected. Three intronic SNPs were found to be associated to the variation of S/G ratio after multiple testing correction. In the line of what has been obtained in forest trees, these SNPs explained between 2.45% and 2.87% of the genetic variance of the trait. This study demonstrates the interest of the candidate gene approach for quantitative trait nucleotide detection in Eucalyptus and paves the way to gene assisted selection of lignin composition in E. urophylla.

Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: prediction accuracy implications.

Hybrids are broadly used in plant breeding and accurate estimation of variance components is crucial for optimizing genetic gain. Genome-wide information may be used to explore models designed to assess the extent of additive and non-additive variance and test their prediction accuracy for the genomic selection. Ten linear mixed models, involving pedigree- and marker-based relationship matrices among parents, were developed to estimate additive (A), dominance (D) and epistatic (AA, AD and DD) effects. Five complementary models, involving the gametic phase to estimate marker-based relationships among hybrid progenies, were developed to assess the same effects. The models were compared using tree height and 3303 single-nucleotide polymorphism markers from 1130 cloned individuals obtained via controlled crosses of 13 Eucalyptus urophylla females with 9 Eucalyptus grandis males. Akaike information criterion (AIC), variance ratios, asymptotic correlation matrices of estimates, goodness-of-fit, prediction accuracy and mean square error (MSE) were used for the comparisons. The variance components and variance ratios differed according to the model. Models with a parent marker-based relationship matrix performed better than those that were pedigree-based, that is, an absence of singularities, lower AIC, higher goodness-of-fit and accuracy and smaller MSE. However, AD and DD variances were estimated with high s.es. Using the same criteria, progeny gametic phase-based models performed better in fitting the observations and predicting genetic values. However, DD variance could not be separated from the dominance variance and null estimates were obtained for AA and AD effects. This study highlighted the advantages of progeny models using genome-wide information.

Plasticity of primary and secondary growth dynamics in Eucalyptus hybrids: a quantitative genetics and QTL mapping perspective

BackgroundThe genetic basis of growth traits has been widely studied in forest trees. Quantitative trait locus (QTL) studies have highlighted the presence of both stable and unstable genomic regions accounting for biomass production with respect to tree age and genetic background, but results remain scarce regarding the interplay between QTLs and the environment. In this study, our main objective was to dissect the genetic architecture of the growth trajectory with emphasis on genotype x environment interaction by measuring primary and secondary growth covering intervals connected with environmental variations.ResultsThree different trials with the same family of Eucalyptus urophylla x E. grandis hybrids (with different genotypes) were planted in the Republic of Congo, corresponding to two QTL mapping experiments and one clonal test. Height and radial growths were monitored at regular intervals from the seedling stage to five years old. The correlation between growth increments and an aridity index revealed that growth before two years old (r = 0.5; 0.69) was more responsive to changes in water availability than late growth (r = 0.39; 0.42) for both height and circumference. We found a regular increase in heritability with time for cumulative growth for both height [0.06 - 0.33] and circumference [0.06 - 0.38]. Heritabilities for incremental growth were more heterogeneous over time even if ranges of variation were similar (height [0-0.31]; circumference [0.19 to 0.48]). Within the trials, QTL analysis revealed collocations between primary and secondary growth QTLs as well as between early growth increments and final growth QTLs. Between trials, few common QTLs were detected highlighting a strong environmental effect on the genetic architecture of growth, validated by significant QTL x E interactions.ConclusionThese results suggest that early growth responses to water availability determine the genetic architecture of total growth at the mature stage and highlight the importance of considering growth as a composite trait (such as yields for annual plants) for a better understanding of its genetic bases.

Age trends of microfibril angle inheritance and their genetic and environmental correlations with growth, density and chemical properties in Eucalyptus urophylla S.T. Blake wood

Abstract• ContextThe genetic and environmental control of microfibril angle (MFA) and its genetic correlations with other wood and growth traits are still not well established in Eucalyptus sp.• AimsTo determine the narrow-sense heritability estimates (h2) of MFA, wood density (D), Klason lignin (KL) content, syringyl to guaiacyl (S/G) ratio and growth traits, their variation from pith to cambium and their genetic correlations.• MethodsHeritability and correlations were assessed in 340 control-pollinated progenies of 14-year-Eucalyptus urophylla S.T. Blake using near infrared spectroscopic models.• ResultsModerate to high heritability were found for MFA (h2 = 0.43), D (h2 = 0.61), S/G (h2 = 0.71) and LK (h2 = 0.76). The genetic control of D and MFA and the genetic and residual correlation between chemical and growth traits varied with age. The genetic correlation C × D was always strongly negative (r < −0.80) while the correlation D × MFA remained constant and positive in the juvenile wood (r = 0.7), before disappearing in the mature wood. These results could be explained by gene pleiotropic effect, low microfibril angle compensating for low wood density and fast growth or by linkage disequilibrium induced by sampling. Variations in MFA and KL in the mature wood were also genetically controlled.• ConclusionsThese findings provide the opportunity for developing breeding strategies for pulpwood, fuelwood and sawntimber production in Eucalyptus sp.

What factors influence the stem taper of Eucalyptus: growth, environmental conditions, or genetics?

Abstract• IntroductionStem taper equations have been widely used for volume estimation to varied top diameter limits or for biomass calculations. However, their main drawback is that specific calibration is often necessary for each species or clone, and accounting for genetic and environmental effects is often a challenge.• MethodsIn order to investigate this point, we decided to study the stem shape of several clones growing in Congo and to build an equation which should (1) be simple and have a good predictive quality, (2) have explicit parameters, and (3) be generic enough so as to be transposable to other species or to other eucalyptus clones. A sample of 1,623 trees, representing 16 genetically different clones selected for their contrasting growth patterns, was used.• ResultsEven though these clones had different stem shapes, we successfully developed a single equation using the triplet (height/diameter at breast height/age) for all the clones.• ConclusionsThe study also indicates that both growth environmental conditions and genetics have an impact on the stem shape, but that the genetic effect was fully realized through tree growth. The root mean square error for the over-bark diameter was 7 mm, allowing its use over the whole plantation area.

Using B-splines for growth curve classification: applications to selection of eucalypt clones

Abstract The cumulative growth of a tree is the result of genotypic and environmental effects and their interaction. In tree breeding and selection, assessment of genetic effects over time is an important task. To address this, we focused on volume growth of 77 clones of eucalypt hybrids Eucalyptus urophylla×Eucalyptus grandis measured in a clonal test. A new methodology of growth modeling using B-splines is introduced and applied to this population. Classification of the curves is made using a hierarchical robust clustering on B-spline function coefficients. Clusters obtained from this method can be interpreted as representing different strategies of growth. It allows selection of clones in an easy and graphical way. The accuracy of the B-splines method, clone selection strategy, and the perspective for the breeding program are discussed in the frame of the eucalypt genetic improvement program of the Congo.

Determining the optimal age for selection by modelling the age-related trends in genetic parameters in #Eucalyptus# hybrid populations

Abstract Ten factorial mating designs using a combined total of 88 females, 107 males, 684 families and 37,206 individual trees were used to model the age-related trends in genetic parameters and genetic gain between four and 65 months in the Eucalyptus urophylla x grandis breeding population in Republic of Congo. Selection was either of pure species (as parents for continued breeding) or individual hybrids for commercial plantations based on clonal varieties. The variance components were significantly different from zero for female, male and female-by-male interaction effects for volume. The age-related trends in additive, dominance and environmental variances, modelled by nonlinear functions, showed three phases corresponding to different stages of competition and growth. Male and female narrow sense heritabilities were high (h2 Am= 0.70 and h2 Af = 0.90, respectively for highest estimates) compared with individual broad sense heritability (h2 ind= 0.45). They were modelled by polynomial functions that did not display specific trends with age. The age-age correlations, modelled by a response surface, were higher than 0.8 after 36 months. A similar trend with age was observed for additive and total genetic effects. Genetic gain was calculated by combining the different models. The genetic gain was higher for female than for male. Considerable gains can be achieved by clone selection. The efficiency of selection indicated an optimal age of 54 months for juvenile selection of males and females and a mature age for ortets. The trend in efficiency of selection per time unit showed that juvenile selection for volume is much more efficient than adult selection whatever the age.

Structure of the specific combining ability between two species of Eucalyptus.II. A clustering approach and a multiplicative model

Abstract The Eucalyptus breeding program of URPPI (a partnership between CIRAD-Forêt, Centre National de la Recherche Forestière du Congo, and Unité d’Aforestation Industrielle du Congo) consists of a reciprocal recurrent selection scheme developed in the Congo between the two species Eucalyptus urophylla and Eucalyptus grandis. Two approaches are proposed in order to model and predict the specific combining ability (SCA) between these species. The clustering approach uses a simultaneous clustering procedure of the two species based on SCA and reveals heterotic groups coherent with the geographical origins of E. urophylla genotypes. The second approach uses a multiplicative model to partition the SCA into three multiplicative terms explaining 95% of the interaction.