Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin. (Résumé d'auteur

Coffee quality, in the present context of overproduction worldwide, has to be considered as a main selection criterion for coffee improvement. After a definition of quality, and an overview of the non genetic factors affecting its variation, this review focuses on the genetic factors involved in the control of coffee quality variation. Regarding the complexity of this trait, the different types of quality are first presented. Then, the great variation within and between coffee species is underlined, mainly for biochemical compounds related to quality (caffeine, sugars, chlorogenic acids, lipids). The ways for breeding quality traits for cultivated species, Coffea arabica and Coffea canephora are discussed, with specific challenges for each species. For C. arabica, maintaining a good quality in F 1 intraspecific hybrids, introgressed lines from Timor hybrid, and grafted varieties are the main challenges. For C. canephora, the improvement is mainly based on intraspecific and interspecific hybrids, using the whole genetic variability available within this species. An improvement is obtained for bean size, with significant genetic gains in current breeding programmes. The content in biochemical compounds related to cup quality is another way to improve Robusta quality. Finally, ongoing programmes towards the understanding of the molecular determinism of coffee quality, particularly using coffee ESTs, are presented. Key words: Coffea spp., biochemical compounds, candidate genes, ESTs, genetic breeding, marker-assisted selection, quality. Genética da qualidade do café:No contexto do excedente de produção mundial, a qualidade do café tem sido considerada o principal critério de seleção no melhoramento dessa cultura. Após definir qualidade e fazer considerações sobre os fatores não genéticos afetando sua variação, esta revisão se concentra sobre os fatores genéticos envolvidos no controle da variação da qualidade do café. Em relação à complexidade desta característica, os diferentes tipos de qualidade são apresentados. Então, a grande variação dentro e entre as espécies de café é discutida, principalmente em relação aos caracteres bioquímicos relacionados com qualidade (cafeína, açúcares, ácidos clorogênicos, lipídeos). As maneiras para melhorar estes caracteres relacionados à qualidade nas espécies cultivadas Coffea arabica e Coffea canephora são discutidas, assim como os desafios específicos a cada espécie. Para C. arabica, manutenção da boa qualidade em híbridos interespecíficos F 1 , linhagens geradas por introgressão a partir do Híbrido do Timor, e enxertia de variedades são os principais desafios. Para C. canephora, o melhoramento é principalmente baseado em híbridos intra e interespecíficos, usando a variabilidade genética disponível nesta espécie. Um avanço é obtido com o tamanho da semente, com significante ganho genético em programas de melhoramento. O conteúdo de compostos bioquímicos relacionados com a qualidade da bebida é uma outra maneira de melhorar a qualidade do café Robusta. Finalmente, são comentados...

Pedunculate oak and sessile oak are two sympatric interfertile species that exhibit leaf morphological differences. We aimed to detect quantitative trait loci (QTLs) of these traits in order to locate genomic regions involved in species differentiation. A total of 15 leaf morphological traits were assessed in a mixed forest stand composed of Quercus petraea and Q. robur and in a full-sib pedigree of Q. robur. The progeny of the full-sib family were vegetatively propagated in two successive experiments comprising 174 and 216 sibs, and assessments were made on two leaves collected on each of the 1080 and 1530 cuttings corresponding to the two experiments. Traits that exhibited strong species differences in the mixed stand tended also to have higher repeatability values in the mapping population, thus indicating higher genetic control. A genetic map was constructed for QTL detection. Composite interval mapping with the one QTL model was used for QTL detection. From one to three QTLs were detected for 13 traits. In-depth analysis of the QTLs, controlling the five morphological traits that exhibited the highest interspecific differences in the mixed stand, indicated that they were distributed on six linkage groups, with two clusters comprising QTLs of at least two discriminant traits. These results were reinforced when error 1 for QTL detection was set at 5% at the chromosome level, as up to nine clusters could be identified. In conclusion, traits involved in interspecific differentiation of oaks are under polygenic control and widespread in clusters across the genome.

Sucrose metabolism and the role of sucrose synthase were investigated in the fruit tissues (pericarp, perisperm, and endosperm) of Coffea arabica during development. Acid invertase, sucrose phosphate synthase, and sucrose synthase activities were monitored and compared with the levels of sucrose and reducing sugars. Among these enzymes, sucrose synthase showed the highest activities during the last stage of endosperm and pericarp development and this activity paralleled closely the accumulation of sucrose in these tissues at this stage. Carbon partitioning in fruits was studied by pulse-chase experiments with (14)C-sugars and revealed high rates of sucrose turnover in perisperm and endosperm tissues. Additional feeding experiments with (14)CO(2) showed that leaf photosynthesis contributed more to seed development than the pericarp in terms of photosynthate supply to the endosperm. Sugar analysis, feeding experiments, and histological studies indicated that the perisperm plays an important role in this downloading process. It was observed that the perisperm presents a transient accumulation of starch which is degraded as the seed develops. Two full-length cDNAs (CaSUS1 and CaSUS2) and the complete gene sequence of the latter were also isolated. They encode sucrose synthase isoforms that are phylogenetically distinct, indicating their involvement in different physiological functions during cherry development. Contrasting expression patterns were observed for CaSUS1 and CaSUS2 in perisperm, endosperm, and pericarp tissues: CaSUS1 mRNAs accumulated mainly during the early development of perisperm and endosperm, as well as during pericarp growing phases, whereas those of CaSUS2 paralleled sucrose synthase activity in the last weeks of pericarp and endosperm development. Taken together, these results indicate that sucrose synthase plays an important role in sugar metabolism during sucrose accumulation in the coffee fruit.

Classical quantitative genetics and quantitative trait dissection analysis (QTL) approaches were used in order to investigate the genetic determinism of wood cellulose carbon isotope composition ( δ δ δ δ 13 C, a time integrated estimate of water use efficiency) and of diameter growth and their relationship on adult trees (15 years) of a forest tree species (maritime pine). A half diallel experimental set-up was used to (1) estimate heritabilities for δ δ δ δ 13 C and ring width and (2) to decompose the phenotypic δ δ δ δ 13 C/growth correlation into its genetic and environmental components. Considerable variation was found for δ δ δ δ 13 C (range of over 3‰) and for ring width (range of over 5 mm) and significant heritabilities (narrow sense 0·17/0·19 for δ δ δ δ 13 C and ring width, respectively, 100% additivity). The significant phenotypic correlation between δ δ δ δ 13 C and ring width was not determined by the genetic component, but was attributable to environmental components. Using a genetic linkage map of a full-sib family, four significant and four suggestive QTLs were detected for δ δ δ δ 13 C, the first for δ δ δ δ 13 C in a forest tree species, as far as known to the authors. Two significant and four suggestive QTLs were found for ring width. No co-location of QTLs was found between δ δ δ δ 13 C and growth.

-Wood is one of our most important natural resources and has been exploited for many hundreds of years as fuel, building material and a source of paper. Its composition is variable among and within species. The ability to monitor the intra-specific variability is a prerequisite to improve wood and end-products properties. This paper describes a study of the genetic control of a large set of wood properties, including growth, timber quality traits, wood chemical composition, kraft pulp production parameters and pulp properties, in a 12 × 12 half diallel of maritime pine (Pinus pinaster Ait.). While relatively high (h ns 2 > 0.3) narrow-sense heritabilities were observed for density heterogeneity, lignin content, alpha-cellulose content and coarseness, no significant genetic effect was detected for hemi cellulose, water extractives, kraft pulp production parameters and pylodin. Slightly lower heritabilities (0.15 < h ns 2 < 0.3) were also obtained for wood density and fibre properties (length, width, curl, zero span). As a consequence and considering the phenotypic coefficient of variation obtained for these traits, improvement by selection of trees with outstanding wood quality is feasible. Nevertheless, it seems obvious that wood quality breeding can not be done without taking into account growth, and the only way to manage this constraint (negative correlation between growth and density) will be the constitution of elite "wood quality" populations in a already growth improved genetic population.wood quality / heritability / genetic correlation / tree breeding / Pinus pinaster Ait.Résumé -Déterminisme génétique des propriétés du bois impliquées dans la production papetière et la qualité du bois d'oeuvre chez le Pin maritime (Pinus pinaster Ait.). Le bois, une des ressources naturelles les plus importantes, est exploité depuis des centaines d'années comme combustible, matériau de construction et source de papier. Sa composition est très variable, non seulement entre espèces mais aussi au niveau intra spécifique. La compréhension de cette variabilité intra spécifique est un pré-requis de l'amélioration des propriétés des produits à base de bois. L'objectif de l'étude présentée ici est la compréhension du déterminisme génétique de plusieurs caractères impliqués dans la composition chimique et les propriétés du bois (caractéristiques physiques, paramètres de production industrielle et propriétés de la pâte) grâce à l'étude d'un demi diallèle 12 × 12. Bien que des héritabilités au sens strict relativement élevées (h ns 2 > 0,3) aient été obtenues pour l'hétérogénéité de la densité, les contenus en lignine et en alpha-cellulose et la masse linéique, aucun effet génétique significatif n'a été mis en évidence pour le contenu en hémi-cellulose, les extractibles, les paramètres de production de pâtes kraft, et la densité estimée grâce au pilodyn. Des héritabilités plus faibles (0,15 < h ns 2 < 0,3) ont quant à elles été obtenues pour la densité du bois et les propriétés des fibres (longueur, largeur, courbure, ri...

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.

Coffee fruits grown in shade are characterized by larger bean size than those grown under full-sun conditions. The present study assessed the effects of shade on bean characteristics and sugar metabolism by analyzing tissue development, sugar contents, activities of sucrose metabolizing enzymes and expression of sucrose synthase-encoding genes in fruits of coffee (Coffea arabica L.) plants submitted to full-sun (FS) and shade (SH) conditions. Evolution of tissue fresh weights measured in fruits collected regularly from flowering to maturation indicated that this increase is due to greater development of the perisperm tissue in the shade. The effects of light regime on sucrose and reducing sugar (glucose and fructose) contents were studied in fresh and dry coffee beans. Shade led to a significant reduction in sucrose content and to an increase in reducing sugars. In pericarp and perisperm tissues, higher activities of sucrose synthase (EC 2.4.1.13) and sucrose-phosphate synthase (SPS: EC 2.4.1.14) were detected at maturation in the shade compared with full sun. These two enzymes also had higher peaks of activities in developing endosperm under shade than in full sun. It was also noted that shade modified the expression of SUS-encoding genes in coffee beans; CaSUS2 gene transcripts levels were higher in SH than in FS. As no sucrose increase accompanied these changes, this suggests that sucrose metabolism was redirected to other metabolic pathways that need to be identified.