Nicolas Marron

Bud set in poplar – genetic dissection of a complex trait in natural and hybrid populations

• The seasonal timing of growth events is crucial to tree distribution and conservation. The seasonal growth cycle is strongly adapted to the local climate that is changing because of global warming. We studied bud set as one cornerstone of the seasonal growth cycle in an integrative approach. • Bud set was dissected at the phenotypic level into several components, and phenotypic components with most genetic variation were identified. While phenotypic variation resided in the timing of growth cessation, and even so more in the duration from growth cessation to bud set, the timing of growth cessation had a stronger genetic component in both natural and hybrid populations. • Quantitative trait loci (QTL) were identified for the most discriminative phenotypic bud-set components across four poplar pedigrees. The QTL from different pedigrees were recurrently detected in six regions of the poplar genome. • These regions of 1.83-4.25 Mbp in size, containing between 202 and 394 genes, form the basis for further molecular-genetic dissection of bud set.

Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

BackgroundHybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions.ResultsFour leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like ‘ripening’ and ‘adventitious roots development’.ConclusionBeyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.

Genomic regions involved in productivity of two interspecific poplar families in Europe. 1. Stem height, circumference and volume

Interspecific hybrids of Populus species are known for their superior growth. In this study, we examined the effect of the genetic background and contrasting environmental conditions on growth and searched for quantitative trait loci (QTL) affecting growth traits. To this end, two hybrid poplar families resulting from controlled crosses, Populus deltoides ‘S9-2’ × P. nigra ‘Ghoy’ (D × N, 180 F1) and P. deltoides ‘S9-2’ × P. trichocarpa ‘V24’ (D × T, 182 F1), were grown at two contrasting sites, Northern Italy and Central France. At the end of the second growing season, tree dimensions (stem height, circumference, and volume) were assessed. The performances of both families significantly differed within and between sites. Tree volume was significantly larger at the Italian site as compared to the French site. Genotype by environment interactions were significant but low for both families and for all growth traits. Tight correlations among the individual growth traits indicated that there may be a common genetic mechanism with pleiotropic effects on these growth traits. In line with previous studies, linkage groups I, VII, IX, X, XVI, XVII, and XIX appeared to have genomic regions with the largest effects on growth traits. This study revealed that (1) both families have high potential for selection of superior poplar hybrids due to the pronounced heterosis (hybrid vigor) and the large genetic variability in terms of growth and (2) the choice of site is crucial for poplar cultivation.

Variability in Populus leaf anatomy and morphology in relation to canopy position, biomass production, and varietal taxon

Twelve poplar (Populus) genotypes, belonging to different taxa and to the sections Aigeiros and Tacamahaca, were studied during the third growing season of the second rotation of a high density coppice culture. With the objective to highlight the relationships between leaf traits, biomass production and taxon as well as the influence of canopy position, anatomical and morphological leaf characteristics (i.e. thickness of epidermis, of palisade and spongy parenchyma layers, density and length of stomata, leaf area, specific leaf area (SLA) and nitrogen concentration) were examined for mature leaves from all genotypes and at two canopy positions (upper and lower canopy). Above ground biomass production, anatomical traits, stomatal and morphological leaf characteristics varied significantly among genotypes and between canopy positions. The spongy parenchyma layer was thicker than the palisade parenchyma layer for all genotypes and irrespective of canopy position, except for genotypes belonging to the P. deltoides × P. nigra taxon (section Aigeiros). Leaves at the upper canopy position had higher stomatal density and thicker anatomical layers than leaves at the lower canopy position. Leaf area and nitrogen concentration increased from the bottom to the top of the canopy, while SLA decreased. Positive correlations between biomass production and abaxial stomatal density, as well as between biomass production and nitrogen concentration were found. A principal component analysis (PCA) showed that genotypes belonging to the same taxon had similar anatomical characteristics, and genotypes of the same section also showed common leaf characteristics. However, Wolterson (P. nigra) differed in anatomical leaf characteristics from other genotypes belonging to the same section (section Aigeiros). Hybrids between the two sections (Aigeiros × Tacamahaca) expressed leaf characteristics intermediate between both sections, while their biomass production was low.RésuméDouze génotypes de peuplier (Populus), appartenant à différents taxa ainsi qu’aux sections Aigeiros et Tacamahaca, ont été étudiés durant la troisième saison de croissance de la deuxième rotation d’une plantation à forte densité. L’objectif de l’expérience était de mettre en évidence les relations entre les caractères foliaires, la production de biomasse et le taxon, ainsi que l’influence de la position des feuilles dans la canopée. Pour ce faire, diverses caractéristiques anatomiques et morphologiques des feuilles (épaisseur des épidermes et des parenchymes palissadique et lacuneux, densité et longueur des stomates, surface foliaire, surface foliaire spécifique (SLA) et teneurs en azote) ont été déterminées pour des feuilles matures de tous les génotypes et à deux hauteurs dans la canopée (haute et basse). La production de biomasse aérienne et les caractères foliaires anatomiques et morphologiques variaient significativement entre génotypes et entre positions dans la canopée. Le parenchyme lacuneux était plus épais que le parenchyme palissadique pour tous les génotypes et quel que soit la hauteur dans la canopée, excepté pour les génotypes appartenant au taxon P. deltoides × P. nigra (section Aigeiros). Les feuilles du sommet de la canopée présentaient des densités de stomates et des épaisseurs de tissus plus importantes que les feuilles de la base de la canopée. La surface des feuilles et leurs teneurs en azote augmentaient de la base vers le sommet de la canopée, tandis que les SLA diminuaient. Des corrélations positives entre la production aérienne de biomasse et la densité de stomates abaxiale ainsi qu’entre la production de biomasse et la teneur en azote foliaire ont été mises en évidence. Une analyse en composantes principales (ACP) a montré que les génotypes appartenant au même taxon présentaient des caractéristiques anatomiques similaires, et que les génotypes de la même section montraient également des caractéristiques foliaires communes. Wolterson (P. nigra) était cependant différent des autres génotypes de la même section (section Aigeiros) en termes de caractères anatomiques. Les hybrides entre les deux sections (Aigeiros × Tacamahaca) présentaient des caractéristiques foliaires intermédiaires entre les sections, alors que leur production de biomasse était faible.

Is the ranking of poplar genotypes for leaf carbon isotope discrimination stable across sites and years in two different full-sib families?

Introduction Because of its vigorous growth, poplar can play an important role for sustainable production of woody biomass to cover renewable energy needs. Hence, the selection of suitable genotypes has to be based on relevant traits, among which intrinsic water use efficiency (Wi, estimated through leaf carbon isotope discrimination, Δ) may be a key trait. Besides a large genetic variation in Δ among the frequently planted poplar hybrids, the use of Δ in deployment or breeding programmes requires insights in the robustness of the genotype ranking for Δ across environments and years.Methods Two F1 full-sib families of poplar (Populus deltoides × Populus nigra and Populus deltoides × Populus trichocarpa) were grown at two sites in Europe, i.e. northern Italy and central France. For each family, leaf samples from 31 F1 genotypes collected during different field studies were used (1) to assess the effect of genotype, site and year on Δ in leaves, as well as their mutual interactions, and (2) to elucidate the relationships between Δ, leaf morphology and tree dimensions.Results Under the well-watered conditions of our study, a low to moderate genetic variability was observed in the two poplar families. Within-family broad-sense heritability values ranged from 0 to 0.49. The ranking of genotypes for Δ was more stable between years than between sites.Conclusions The study confirmed the occurrence of some degree of genetic variability of Δ in the studied poplar families and the possibility to identify genotypes with low, stable Δ values across years. However, the significant genotype-by-site interactions in our study suggest that selection for larger water use efficiency or lower Δ in these families has to consider specific responses in different environments.

Genomic regions involved in productivity of two interspecific poplar families in Europe. 2. Biomass production and its relationships with tree architecture and phenology

Short-rotation coppice of hybrid poplar is a promising renewable feedstock for biofuel production. Breeding for high biomass in short-rotation coppice has started only recently. Two hybrid poplar families were grown at two sites in Europe and phenotyped for a variety of biomass-related traits (1) to examine the extent of phenotypic and genetic variation in biomass production, ramification, resprouting, and phenology, (2) to search for genomic regions involved in productivity, and (3) to determine the effect of the environment on the expression of these traits. The performance of both families differed within and among sites. A pronounced heterosis was observed in most cases. Moderate to high heritability values were found. Seventeen quantitative trait loci (QTL) for biomass production, 13 for ramification, ten for resprouting, 21 for bud burst, and ten for bud set were identified. Genetic correlations and QTL colocation showed that high wood production was associated with high allocation of wood into branches and with high production of resprouts after coppicing. Correlations and QTL colocation between biomass production and phenology traits were weak. Our study provides valuable information on genomic regions involved in biomass production, ramification, and phenology and on phenotypic and genetic relationships among these three trait categories.

Augmenter le niveau de production de biomasse des cultures ligneuses dédiées ou semi-dédiées. Principaux enseignements du projet SYLVABIOM

L’utilisation de cultures en rotations courtes d’arbres à croissance rapide, dédiées en tout ou partie à la production de biomasse, est une des voies envisageables pour contribuer aux objectifs fixés par l’Union européenne en matière de développement des énergies renouvelables (Bastien et al., 2011). Malgré leur potentiel pour la production de biomasse ligneuse, l’étude de ces systèmes a été un peu délaissée en France depuis la fin du siècle dernier. Il apparaît néanmoins important de bien comprendre les interactions entre la nature et les propriétés du matériel végétal et les conditions de culture (pédoclimat, densité de plantation) afin d’optimiser l’adéquation entre ces paramètres et augmenter les chances de réussite des plantations. Dans le cadre de l’appel à projets ANR-BIO-E 2008, le projet SYLVABIOM a mobilisé un large consortium pluridisciplinaire autour de l’étude des facteurs génétiques et environnementaux déterminant la production de biomasse par des espèces ligneuses cultivées en plantations à rotations courtes. Le projet intégratif portait à la fois sur des aspects appliqués (évaluation des potentialités de croissance, comparaison de clones) et des aspects fondamentaux ayant des conséquences appliquées (efficiences d’utilisation de l’eau et de l’azote, contrôle épigénétique de la plasticité phénotypique). Le projet était organisé en deux tâches relativement indépendantes correspondant à deux itinéraires culturaux : — Taillis à courte et très courte rotation : Quatre sites ateliers installés dans des stations écologiquement contrastées avec trois espèces (Peuplier, Saule, Robinier) cultivées en taillis à courte ou à très courte rotation (TCR ou TTCR) ont permis d’évaluer les potentialités de croissance des arbres et l’efficacité avec laquelle ils utilisent l’eau et l’azote en fonction des conditions de culture. Des données relatives au taux de méthylation de l’ADN et à sa pertinence en tant que marqueur précoce de la productivité, ont également été recueillies. — Futaie à courte révolution : Les réseaux d’essais forestiers de l’INRA et de FCBA ont été réévalués sous l’angle de la production de biomasse totale. Les essences les plus performantes ont pu faire l’objet de nouvelles mesures de croissance et biomasse totale compartimentée (bois, écorce, branches, feuilles).

Winter-dormant shoot apical meristem in poplar trees shows environmental epigenetic memory

The winter-dormant shoot apical meristem of the tree species Populus keeps an epigenetic memory of environmental variations that arose during the preceding vegetative period.