Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

<p>Abstract</p> <p>Background</p> <p>One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it>Quercus robur</it>, its characterization and an analysis of BAC end sequences.</p> <p>Results</p> <p>The <it>Eco</it>RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it>ab initio </it>repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it>Arabidopsis thaliana</it>, <it>Vitis vinifera </it>and <it>Populus trichocarpa</it>. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it>V. vinifera.</it></p> <p>Conclusions</p> <p>This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p

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

Background: Eucalyptus 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. Results: Linkage 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 &gt; 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. Conclusions: Given 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. (Résumé d'auteur

Diagnostic sédimentaire de la Loire en amont de Nantes par modélisation physique à fond mobile et analyse dynamique des dunes en similitude de Shields

Le modèle physique construit par la Compagnie Nationale du Rhône a pour but d’étudier l’efficacité d’un aménagement sur la Loire. Une première phase, constituée de 52 essais, a permis d’établir un diagnostic sédimentaire sur 15 ans. Un engraissement naturel de la Loire s’établit sur cette période, cette tendance oscille cependant autour d’un équilibre. La géométrie et la dynamique des dunes sur le modèle sont analogues aux mesures observées sur la Loire. Ainsi, la similitude de Shields entraine une bonne représentation du charriage sur la Loire. Ces premiers essais constituent des points de référence pour la seconde phase d’essais avec l’aménagement

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Cause–effect relationship among morphological adaptations, growth, and gas exchange response of pedunculate oak seedlings to waterlogging

International audience& Context In response to waterlogging, pedunculate oak is known to develop adventitious roots and hypertrophied lenti-cels. However, to date, a link between these adaptations and the ability to maintain net CO 2 assimilation rates and growth has not been demonstrated. & Aims The aim of this study was to explore the cause–effect relationship between the ability to form morphological adap-tations (hypertrophied lenticels and adventitious roots) and the capacity to maintain high assimilation rate and growth. & Methods The occurrence of morphological adaptations and the parameters of photosynthesis were monitored over 20 days of waterlogging in 5-week-old pedunculate oak seedlings presenting similar morphological development. & Results Based on the development or not of morphological adaptations, the following three categories of responses were identified: development of hypertrophied lenticels and adven-titious roots, development of hypertrophied lenticels alone, and the lack of development of adaptive structures. These categories, ranked in the order given, corresponded to decreas-ing levels of initial net CO 2 assimilation rate growth and photosynthesis parameters observed during waterlogging. & Conclusion We observed a two-way cause–effect relationship between the capacity to form adaptive structures and the assim-ilation rate. Indeed, the initial assimilation rate determined the occurrence of hypertrophied lenticels and growth during stress, and then the development of morphological adaptations en-hanced the ability to maintain assimilation levels during the stress

Production of micro-cuttings from acorns to test the plasticity of response to contrasting soil water regimes

International audienceWe collected acorns from selected Quercusrobur and Quercus petraea mother trees growing at stationswith different depths to the water table. We producedpairs of micro-cuttings from these single acorns. Theobtained pairs of cuttings represented phenotypes of highsimilarity according to photosynthetic parameters. Thesepairs of cuttings were used to test the plasticity of responseto contrasting water regimes. For each pair, one cutting wassubmitted to drought and the other was submitted towaterlogging. Drought response was recorded according togas exchange traits (stomatal closure and water use efficiency).The response to waterlogging was recordedaccording to the capacity to form hypertrophied lenticelsand to maintain the CO2 assimilation rate. Intermediaryphenotypes presenting both high water use efficiency andthe capacity to develop hypertrophied lenticels wereexpected

Apports de la modélisation physique avec distorsions pour l'analyse des cours d'eau sableux : exemple de la Loire aval

Création de 700 épis dans le dernier siècle, extractions massives de sable réalisées pour les besoins de l'industrie … ces actions anthropiques ont eu des conséquences graves sur le fonctionnement de la Loire : enfoncement du lit, et mauvaise alimentation des annexes fluviales notamment. Dans le cadre du plan Loire IV (2014–2020) financé notamment par l'Union européenne, et dont la maîtrise d'ouvrage est en partie portée par Voies Navigables de France (VNF), la réalisation d'un ouvrage de correction sédimentaire a été proposée au voisinage de Nantes, avec l'objectif d'engendrer un remous solide régressif. Pour les études conception morpho-sédimentaires, la Compagnie Nationale du Rhône (CNR) a proposé une modélisation hybride ou composite, qui s'appuie notamment sur un modèle numérique 2D hydro-sédimentaire ainsi qu'un modèle physique de grande dimension : 1/100 pour l'échelle de longueur avec un facteur 2 de distorsion verticale, 1/33 pour l'échelle de densité des matériaux. Ce modèle à fond mobile a été conçu pour satisfaire à deux lois de similitudes dont la combinaison produit des distorsions géométriques et de densité des matériaux. La complexité d'un tel modèle impose un grand nombre de vérifications par l'expérience qu'il faut confronter aux approches théoriques de dimensionnement : du comportement granulaire aux macro-phénomènes (dunes). Un jeu de 341 dunes formées en laboratoire pendant plus de 50 essais a été analysé selon deux axes : le premier concerne la caractérisation géométrique (hauteur, longueur) grâce à la disponibilité de Modèles Numériques de Terrain capturés par un procédé de photogrammétrie submergée, et le second est focalisé sur la vitesse de migration des dunes par Large Scale Particle Image Velocimetry (LSPIV). L'ensemble des analyses réalisées a montré la très bonne adéquation entre les résultats de laboratoire et les phénomènes ligériens de transport de sable

Light acclimation and photosynthetic response of beech (Fagus sylvatica L.) saplings under artificial shading or natural mediterranean conditions

Acclimation of beech (Fagus sylvatica L.) to different light conditions was studied in natural regeneration below black pine canopies (Pinus nigra ssp. nigricans) in Mont-Ventoux (Vaucluse, France) and with potted saplings - from the same origin - under shaded tunnels in southern France (Avignon, Vaucluse), and north-eastern France (Nancy, Meurthe-et-Moselle). Leaf mass to area ratio and leaf carbon content per unit mass increased, while leaf nitrogen content per unit mass (Nm) remained constant, with increasing relative irradiance (RI). Maximum carboxylation rate (Vcmax) and maximum electron transport flux (Jmax) increased with RI and were higher in the natural regeneration than in the potted saplings. These two parameters were higher for the potted saplings in north-eastern France than for those in southern France. Leaf nitrogen allocation to carboxylation (Pr) or bioenergetics (Pb) did not vary with RI. Pr and Pb were higher in the natural regeneration than in the potted saplings, whereas Nm was lower in the natural regeneration than in the fertilised potted saplings. Seasonal time course of these parameters in the natural regeneration in Mont-Ventoux, from bud burst to the beginning of summer drought, showed that after the leaf expansion period, leaf composition and photosynthetic parameters remain globally constant