Jean-Marc Bouvet

Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago

We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatellite loci. The number of alleles per locus ranged from 3 to 33 and the observed heterozygosity per population ranged from 0.01 in Maré to 0.74 in Ile des Pins. The genetic diversity was lowest in the most recent islands, the Loyautés, and highest in the oldest island, Grande Terre, as well as the nearby small Ile des Pins. Significant departures from panmixia were observed for some loci–population combinations (per population FIS = 0–0.03 on Grande‐Terre and Ile des Pins, and 0–0.67 on Loyautés). A strong genetic differentiation among all islands was observed (FST = 0.22), and the amount of differentiation increased with geographic distance in Iles Loyauté and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average FIS that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occurred extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum.

Near Infrared Spectroscopy for High-Throughput Characterization of Shea Tree (Vitellaria paradoxa) Nut Fat Profiles

The Shea tree (Vitellaria paradoxa) is a major tree species in African agroforestry systems. Butter extracted from its nuts offers an opportunity for sustainable development in Sudanian countries and an attractive potential for the food and cosmetics industries. The purpose of this study was to develop near-infrared spectroscopy (NIRS) calibrations to characterize Shea nut fat profiles. Powders prepared from nuts collected from 624 trees in five African countries (Senegal, Mali, Burkina Faso, Ghana and Uganda) were analyzed for moisture content, fat content using solvent extraction, and fatty acid profiles using gas chromatography. Results confirmed the differences between East and West African Shea nut fat composition: eastern nuts had significantly higher fat and oleic acid contents. Near infrared reflectance spectra were recorded for each sample. Ten percent of the samples were randomly selected for validation and the remaining samples used for calibration. For each constituent, calibration equations were developed using modified partial least squares (MPLS) regression. The equation performances were evaluated using the ratio performance to deviation (RPD(p)) and R(p)(2) parameters, obtained by comparison of the validation set NIR predictions and corresponding laboratory values. Moisture (RPD(p) = 4.45; R(p)(2) = 0.95) and fat (RPD(p) = 5.6; R(p)(2) = 0.97) calibrations enabled accurate determination of these traits. NIR models for stearic (RPD(p) = 6.26; R(p)(2) = 0.98) and oleic (RPD(p) = 7.91; R(p)(2) = 0.99) acids were highly efficient and enabled sharp characterization of these two major Shea butter fatty acids. This study demonstrated the ability of near-infrared spectroscopy for high-throughput phenotyping of Shea nuts.

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.

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%.

Small effect of fragmentation on the genetic diversity of Dalbergia monticola, an endangered tree species of the eastern forest of Madagascar, detected by chloroplast and nuclear microsatellites

BACKGROUND AND AIMS The oriental forest ecosystem in Madagascar has been seriously impacted by fragmentation. The pattern of genetic diversity was analysed on a tree species, Dalbergia monticola, which plays an important economic role in Madagascar and is one of the many endangered tree species in the eastern forest. METHODS Leaves from 546 individuals belonging to 18 small populations affected by different levels of fragmentation were genotyped using eight nuclear (nuc) and three chloroplast (cp) microsatellite markers. KEY RESULTS For nuclear microsatellites, allelic richness (R) and heterozygosity (H(e,nuc)) differed between types of forest: R = 7.36 and R = 9.55, H(e,nuc) = 0.64 and H(e,nuc) = 0.80 in fragmented and non-fragmented forest, respectively, but the differences were not significant. Only the mean number of alleles (N(a,nuc)) and the fixation index F(IS) differed significantly: N(a,nuc) = 9.41 and N(a,nuc) = 13.18, F(IS) = 0.06 and F(IS) = 0.15 in fragmented and non-fragmented forests, respectively. For chloroplast microsatellites, estimated genetic diversity was higher in non-fragmented forest, but the difference was not significant. No recent bottleneck effect was detected for either population. Overall differentiation was low for nuclear microsatellites (F(ST,nuc) = 0.08) and moderate for chloroplast microsatellites (F(ST,cp) = 0.49). A clear relationship was observed between genetic and geographic distance (r = 0.42 P < 0.01 and r = 0.42 P = 0.03 for nuclear and chloroplast microsatellites, respectively), suggesting a pattern of isolation by distance. Analysis of population structure using the neighbor-joining method or Bayesian models separated southern populations from central and northern populations with nuclear microsatellites, and grouped the population according to regions with chloroplast microsatellites, but did not separate the fragmented populations. CONCLUSIONS Residual diversity and genetic structure of populations of D. monticola in Madagascar suggest a limited impact of fragmentation on molecular genetic parameters.

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.

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.

Molecular data reveal isolation by distance and past population expansion for the shea tree (Vitellaria paradoxa C.F. Gaertn) in West Africa.

While the genetic structure of many tree species in temperate, American and Asian regions is largely explained by climatic oscillations and subsequent habitat contractions and expansions, little is known about Africa. We investigated the genetic diversity and structure of shea tree (Vitellaria paradoxa,) in Western Africa, an economically important tree species in the Sudano‐Sahelian zone. Eleven nuclear microsatellites (nuc) were used to genotype 673 trees selected in 38 populations. They revealed moderate to high within‐population diversity: allelic richness ranged from Rnuc = 3.99 to 5.63. This diversity was evenly distributed across West Africa. Populations were weakly differentiated (FSTnuc = 0.085; P < 0.0001) and a pattern of isolation by distance was noted. No phylogeographic signal could be detected across the studied sample. Additionally, two chloroplast microsatellite loci, leading to 11 chlorotypes, were used to analyse a sub‐set of 370 individuals. Some variation in chloroplast allelic richness among populations could be detected (Rcp = 0.00 to 4.36), but these differences were not significant. No trend with latitude and longitude were observed. Differentiation was marked (GSTcp = 0.553; P < 0.0001), but without a significant phylogeographical signal. Population expansion was detected considering the total population using approximate Bayesian computation (nuclear microsatellites) and mismatch distribution (chloroplast microsatellites) methods. This expansion signal and the isolation by distance pattern could be linked to the past climatic conditions in West Africa during the Pleistocene and Holocene which should have been favourable to shea tree development. In addition, human activities through agroforestry and domestication (started 10 000 bp) have probably enhanced gene flow and population expansion.