UMR QualiSud

The sequencing and analysis of the banana genome is reported; these results inform plant phylogenetic relationships and genome evolution, and provide a resource for future genetic improvement of this important crop species. Bananas (Musa spp.) are a staple food and a major source of income in many tropical and subtropical countries. This paper reports the sequencing and analysis of the banana genome. This is the first non-grass monocotyledon to have its genome sequenced, providing an important bridge for comparative genome analysis in plants. Global banana production is under threat from increasingly well-adapted pests and diseases, so the availability of the genome sequence is an important resource for future crop development and improvement. Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3,4. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence.

Fleshy fruit acidity is an important component of fruit organoleptic quality and is mainly due to the presence of malic and citric acids, the main organic acids found in most ripe fruits. The accumulation of these two acids in fruit cells is the result of several interlinked processes that take place in different compartments of the cell and appear to be under the control of many factors. This review combines analyses of transcriptomic, metabolomic, and proteomic data, and fruit process-based simulation models of the accumulation of citric and malic acids, to further our understanding of the physiological mechanisms likely to control the accumulation of these two acids during fruit development. The effects of agro-environmental factors, such as the source:sink ratio, water supply, mineral nutrition, and temperature, on citric and malic acid accumulation in fruit cells have been reported in several agronomic studies. This review sheds light on the interactions between these factors and the metabolism and storage of organic acids in the cell.

Summary Physicochemical and morphological properties of açai powder produced with different carrier agents were evaluated in this work. Powders were produced by spray drying, using maltodextrin 10DE, maltodextrin 20DE, gum arabic and tapioca starch as carrier agents. Powder characterisation included analysis of moisture content, water activity, solubility, hygroscopicity, particle size distribution, morphology, total polyphenolics and antioxidant activity. Results showed that the samples produced with maltodextrin 20DE and gum arabic presented the smallest size and highest hygroscopicity. The powder produced with tapioca starch exhibited the lowest hygroscopity and solubility, and the highest mean diameter. With regard to morphology, all particles exhibited spherical and shrivelled surfaces, except those produced with tapioca starch, which exhibited rounded and smooth surfaces. Powders produced with maltodextrins and gum arabic showed high polyphenolic retention and antioxidant activity preservation after storage at 40 °C for 15 days, while for the particles produced with tapioca starch, this protective effect was less pronounced.

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published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destine au dpt et la diffusion de documents scientifiques de niveau recherche, publis ou non, manant des tablissements d'enseignement et de recherche franais ou trangers, des laboratoires publics ou privs.

Chocolate is a widely consumed product worldwide due to its exquisite flavor, which comes from the unique and fascinating cocoa flavor. This flavor depends on little controllable variables such as the genotype and the agroecological niche, and on the other side, on postharvest operations: (1) cocoa transformation from seeds to beans that comprises cocoa seeds preconditioning, fermentation, and drying, and (2) the production of chocolate from the bean in which roasting is highlighted. Postharvest transformation operations are critically important because during these, cocoa flavor is formed, allowing the differentiation of two categories: bulk and specialty cocoa. In this sense, this article presents an overview of cocoa postharvest operations, the variables and phenomena that influence and control the physical and biochemical transformation from seeds to cocoa beans, and their relation to the formation of chocolate flavor. Moreover, research perspectives in terms of control and management of postharvest practices in order to obtain cocoa with differentiated and specialty characteristics "from bean to bar" are discussed.

Iron deficiency is the most frequent nutritional deficiency in the world with an estimated 1.4 billion people affected. The usual way to fight iron deficiency is iron fortification, but this approach is not always effective and can have undesirable side effects including an increase in the growth and virulence of gut bacterial pathogens responsible for diarrhea and gut inflammation. Iron is mainly absorbed in the duodenum and is tightly regulated in mammals. Unabsorbed iron enters the colonic lumen where many microorganisms, referred to as gut microbiota, reside. Iron is essential for these bacteria, and its availability consequently affects this microbial ecosystem. The aim of this review is to provide further insights into the complex relationship between iron and gut microbiota. Given that overcoming anemia caused by iron deficiency is still a challenge today, gut microbiota could help identify more efficient ways to tackle this public health problem.

Water deficit (WD) is expected to increase in intensity, frequency and duration in many parts of the world as a consequence of global change, with potential negative effects on plant gas exchange and growth. We review here the parameters that can be derived from measurements made on leaves, in the field, and that can be used to assess the effects of WD on the components of plant photosynthetic rate, including stomatal conductance, mesophyll conductance, photosynthetic capacity, light absorbance, and efficiency of absorbed light conversion into photosynthetic electron transport. We also review some of the parameters related to dissipation of excess energy and to rerouting of electron fluxes. Our focus is mainly on the techniques of gas exchange measurements and of measurements of chlorophyll a fluorescence (ChlF), either alone or combined. But we put also emphasis on some of the parameters derived from analysis of the induction phase of maximal ChlF, notably because they could be used to assess damage to photosystem II. Eventually we briefly present the non-destructive methods based on the ChlF excitation ratio method which can be used to evaluate non-destructively leaf contents in anthocyanins and flavonols.

Among other fermentation processes, lactic acid fermentation is a valuable process which enhances the safety, nutritional and sensory properties of food. The use of starters is recommended compared to spontaneous fermentation, from a safety point of view but also to ensure a better control of product functional and sensory properties. Starters are used for dairy products, sourdough, wine, meat, sauerkraut and homemade foods and beverages from dairy or vegetal origin. Among lactic acid bacteria, Lactobacillus, Lactococcus, Leuconostoc, Streptococcus and Pediococcus are the majors genera used as starters whereas Weissella is not. Weissella spp. are frequently isolated from spontaneous fermented foods and participate to the characteristics of the fermented product. They possess a large set of functional and technological properties, which can enhance safety, nutritional and sensory characteristics of food. Particularly, Weissella cibaria and Weissella confusa have been described as high producers of exo-polysaccharides, which exhibit texturizing properties. Numerous bacteriocins have been purified from Weissella hellenica strains and may be used as bio-preservative. Some Weissella strains are able to decarboxylate polymeric phenolic compounds resulting in a better bioavailability. Other Weissella strains showed resistance to low pH and bile salts and were isolated from healthy human feces, suggesting their potential as probiotics. Despite all these features, the use of Weissella spp. as commercial starters remained non-investigated. Potential biogenic amine production, antibiotic resistance pattern or infection hazard partly explains this neglecting. Besides, Weissella spp. are not recognized as GRAS (Generally Recognized As Safe). However, Weissella spp. are potential powerful starters for food fermentation as well as Lactococcus, Leuconostoc or Lactobacillus species.

Abstract Cassava ( Manihot esculenta Crantz) is one of the most important sources of starch in the tropics. There is limited and contradictory information regarding cassava starch characteristics. The International Center for Tropical Agriculture (CIAT) holds in trust FAO's cassava germplasm collection. Starches from 3272 landraces (including 12 wild relatives) and 772 improved clones were extracted and analyzed over a period of several years. In most cases only one starch sample per genotype was analyzed. Average cyanogenic potential was 327 ppm but considerably higher in the landraces (340 ppm) than in improved clones (267 ppm). Average total and reducing sugars were slightly higher in improved clones (4.06 and 1.56%, respectively) than in landraces (3.68 and 1.25%, respectively). Amylose content was similar in both types of germplasm with an average of 20.7%. Average pasting temperature was 65.3°C. Maximum viscosity was 777.5 mPa s, breakdown was 298.1 mPa s, consistency was 155.8 mPa s and setback was ‐144.5 mPa s. The large sample of starches analyzed provides very robust information regarding the actual characteristics of cassava starch.

There are more than 1300 articles in scientific literature dealing with positive impacts of Ultrasound-Assisted Extraction (UAE) such as reduction of extraction time, diminution of solvent and energy used, enhancement in yield and even selectivity, intensification of diffusion, and eliminating wastes. This present study aims to understand what are the mechanism(s) behind these positive impacts which will help to design a decision tool for UAE of natural products. Different microscopic observations (Scanning Electron Microscopy (SEM), Environmental Scanning Electron Microscopy (e-SEM), Cyto-histochemistry) have been used for spacial and temporal localization of metabolites in rosemary leaves, which is one of the most studied and most important plant for its antioxidant metabolites used in food industry, during conventional and ultrasound extraction. The study permits to highlight that ultrasound impacted rosemary leaves not by a single or different mechanisms in function of ultrasound power, as described by previous studies, but by a chain detexturation mechanism in a special order: local erosion, shear forces, sonoporation, fragmentation, capillary effect, and detexturation. These detexturation impacts followed a special order during ultrasound treatment leading at the end to the total detexturation of rosemary leaves. These mechanisms and detexturation impacts were identified in glandular trichomes, non-glandular-trichomes and the layer adaxial and abaxial cuticle. Modelling metabolites diffusion phenomenon during conventional and ultrasound extraction with the second Fick's law allowed the estimation of diffusivities and solvent penetration into the inner tissues and in meantime to accelerate the release of valuable metabolites.

Numerous traditional low-alcohol fermented beverages produced from fruit or vegetables are described around the world. Fruit and vegetables and lactic fermented products both present nutritional benefits, which give reasons for the recent expansion of non-dairy lactic fermented juices on the market. In addition, fruit and vegetable juices are new carriers for probiotic bacteria. Specific phenotypic traits of lactic acid bacteria (LAB) are required so that LAB can effectively grow in fruit or vegetable juices, increase their safety and improve their sensory and nutritional quality. From the diversity of microbiota of spontaneous fermentations, autochthonous starters can be selected, and their higher performance than allochthonous LAB was demonstrated. Achieving long-term storage and constant high quality of these beverages requires additional processing steps, such as heat treatment. Alternatives to conventional treatments are investigated as they can better preserve nutritional properties, extract bioactive compounds and promote the growth and metabolism of LAB. Specific processing approaches were shown to increase probiotic viability of fruit and vegetable juices. More knowledge on the metabolic activity of lactic acid bacterium consortium in fruit or vegetable juices has become a bottleneck for the understanding and the prediction of changes in bioactive compounds for functional beverages development. Hopefully, the recent developments of metabolomics and methods to describe enzymatic machinery can result in the reconstruction of fermentative pathways.

Consumption of dietary ellagitannins (ETs) has been associated with different health benefits. Nonetheless, ETs are not bioavailable as such and are metabolized in vivo. They are partially converted into ellagic acid (EA) in the upper gastrointestinal (GI) tract, but this first metabolite is also poorly bioavailable. In the lower GI tract, EA and residual ETs are metabolized by gut microbiota to produce urolithins, which, together with their conjugate relatives, persist at relatively high concentrations in plasma and urine for days after ingestion of dietary ETs. Thus, ETs and EA may exert local health benefits on the GI tract but systemic health benefits are more likely to result from urolithins. Cellular models suggest that, at physiological concentration, urolithins are active against chronic degenerative diseases. Health benefits have been proven in animal models and during clinical studies. Even so, the crucial involvement of gut microbiota in ET bioconversion induces important variability of physiological response among humans, giving rise to the concept of high and low urolithin producers. This variability among consumers in obtaining potential health benefits from dietary ETs raises new challenges for the functional food industry. Different research perspectives are discussed to tackle this significant issue for nutritionists, food technologists, and consumers.

Lipid oxidation is a major concern in the food, cosmetic, and pharmaceutical sectors. The degradation of unsaturated lipids affects the nutritional, physicochemical, and organoleptic properties of products and can lead to off-flavors and to the formation of potentially harmful oxidation compounds. To prevent or slow down lipid oxidation, different antioxidant additives are used alone or in combination to achieve the best possible efficiency with the minimum possible quantities. In manufactured products, that is, heterogeneous systems containing lipids as emulsions or bulk phase, the efficiency of an antioxidant is determined not only by its chemical reactivity, but also by its physical properties and its interaction with other compounds present in the products. The antioxidants most widely used on the industrial scale are probably tocopherols, either as natural extracts or pure synthetic molecules. Considerable research has been conducted on their antioxidant activity, but results regarding their efficiency are contradictory. Here, we review the known mechanisms behind the antioxidant activity of tocopherols and discuss the chemical and physical features that determine their efficacy. We first describe their chemical reactivity linked with the main factors that modulate it between efficient antioxidant capacity and potential prooxidant effects. We then describe their chemical interactions with other molecules (phenolic compounds, metals, vitamin C, carotenes, proteins, and phospholipids) that have potential additive, synergistic, or antagonist effects. Finally, we discuss other physical parameters that influence their activity in complex systems including their specific interactions with surfactants in emulsions and their behavior in the presence of association colloids in bulk oils.

Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

Abstract One of cadmium’s major exposure routes to humans is through rice consumption. The concentrations of cadmium in the global polished (white), market rice supply-chain were assessed in 2270 samples, purchased from retailers across 32 countries, encompassing 6 continents. It was found on a global basis that East Africa had the lowest cadmium with a median for both Malawi and Tanzania at 4.9 μg/kg, an order of magnitude lower than the highest country, China with a median at 69.3 μg/kg. The Americas were typically low in cadmium, but the Indian sub-continent was universally elevated. In particular certain regions of Bangladesh had high cadmium, that when combined with the high daily consumption rate of rice of that country, leads to high cadmium exposures. Concentrations of cadmium were compared to the European Standard for polished rice of 200 μg/kg and 5% of the global supply-chain exceeded this threshold. For the stricter standard of 40 μg/kg for processed infant foods, for which rice can comprise up to 100% by composition (such as rice porridges, puffed rice cereal and cakes), 25% of rice would not be suitable for making pure rice baby foods. Given that rice is also elevated in inorganic arsenic, the only region of the world where both inorganic arsenic and cadmium were low in grain was East Africa.

ABSTRACT Improving total carotenoids content (TCC) in cassava roots is an important strategy to reduce vitamin A deficiency in human populations that rely on cassava as a source of energy in their diets. The high heritability for TCC in the roots allowed the International Center for Tropical Agriculture to implement a rapid cycling recurrent selection approach that reduced the standard length of each cycle from the ordinary 8 yr to 3. Data from successive evaluation nurseries suggested that gains have been made through time. However, no comparison of different cycles of selection has been made when representatives of each cycle were grown together. This study compares 4 to 5 clones representative of cycles of selection from 2004 to 2009. Results demonstrated significant gains for TCC as well as for total β‐carotene (TBC) expressed both in a fresh and dry weight basis. Although dry matter content (DMC) was not a selection criterion during the selection process, it increased with the successive cycles of selection. This suggests that indeed, simultaneous gains for TCC, TBC, and DMC are feasible. This finding is relevant for the important ongoing efforts at the International Institute of Tropical Agriculture and African National Programs to release biofortified cassava clones in Africa with adequate levels of dry matter content.

Abstract Mahogany is one of the most valuable woods and was widely used until it was included in Appendix II of the Convention on International Trade in Endangered Species as endangered species. Mahogany wood sometimes is traded under different names. Also, some similar woods belonging to the Meliaceae family are traded as “mahogany” or as being of a “mahogany pattern”. To investigate the feasibility of the use of near infrared spectroscopy for wood discrimination, the mahogany ( Swietenia macrophylla King.), andiroba or crabwood ( Carapa guianensis Aubl.), cedar ( Cedrela odorata L.), and curupixá ( Micropholis melinoniana Pierre) woods were examined. Four discrimination models based on partial least squares-discriminant analysis were developed based on a calibration set composed of 88 samples and a test set with 44 samples. Each model corresponds to the discrimination of a wood species from the others. Optimization of the model was performed by means of the OPUS ® software followed by statistical analysis software (Matlab ® ). The observed root mean square errors of predictions were 0.14, 0.09, 0.12, and 0.06 for discriminations of mahogany, cedar, andiroba, and curupixá, respectively. The separations of the species obtained based on the difference in the predicted values was at least 0.38. This makes it possible to perform safe discriminations with a very low probability of misclassifying a sample. This method can be considered accurate and fast.

* The genomic era facilitates the understanding of how transcriptional networks are interconnected to program seed development and filling. However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm. Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin. * The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids. For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling. * Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides. * Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue.

EID:2-s2.0-33846224803