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1. Role of PRMT1 and PRMT5 in Breast Cancer

Author

Sébastien Martinez, Stéphanie Sentis, Coralie Poulard, Olivier Trédan, and Muriel Le Romancer

Subjects
PRMT1, PRMT5, arginine methylation, breast cancer, transcriptional regulation, cell signaling, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

Breast cancer is the most common cancer diagnosed in women worldwide. Early-stage breast cancer is curable in ~70–80% of patients, while advanced metastatic breast cancer is considered incurable with current therapies. Breast cancer is a highly heterogeneous disease categorized into three main subtypes based on key markers orientating specific treatment strategies for each subtype. The complexity of breast carcinogenesis is often associated with epigenetic modification regulating different signaling pathways, involved in breast tumor initiation and progression, particularly by the methylation of arginine residues. Protein arginine methyltransferases (PRMT1-9) have emerged, through their ability to methylate histones and non-histone substrates, as essential regulators of cancers. Here, we present an updated overview of the mechanisms by which PRMT1 and PRMT5, two major members of the PRMT family, control important signaling pathways impacting breast tumorigenesis, highlighting them as putative therapeutic targets.

Published
2024
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2. SoREn, How Dynamic Software Update Tools Can Help Cybersecurity Systems to Improve Monitoring and Actions

Author

Sébastien Martinez, Christophe Gransart, Olivier Stienne, Virginie Deniau, and Philippe Bon

Subjects
dynamic software updating, dynamic reconfiguration, Electronic computers. Computer science, QA75.5-76.95
Abstract

Because stopping a service to apply updates raises issues, Dynamic Software Updating studies the application of updates on programs without disrupting the services they provide. This is acheived using specific mechanisms operating updating tasks such as the modification of the program state. To acheive transparency, Dynamic Software Updating systems use pre-selected and pre-configured mechanisms. Developers provide patches that are transparently converted to dynamic updates. The cost of such transparency is often that applied patches cannot modify the general semantic of the updated program. Allowing dynamic modification of the general semantic of a running program is rarely considered.In the context of protection of communications between moving vehicles and uncontrolled infrastructure, SoREn (Security REconfigurable Engine) is designed to be dynamically reconfigurable. Its semantics can transparently be modified at runtime to change the security policy it enforces. Administrators can supply new policies to trigger a reconfiguration, without developing new components. This paper details and discusses the design of SoREn, its meta-model linked to cybersecurity business concepts and its automatic reconfiguration calculator allowing transparent application of reconfigurations.

Published
2022
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3. Multi-scale high-throughput phenotyping of apple architectural and functional traits in orchard reveals genotypic variability under contrasted watering regimes

Author

Aude Coupel-Ledru, Benoît Pallas, Magalie Delalande, Frédéric Boudon, Emma Carrié, Sébastien Martinez, Jean-Luc Regnard, and Evelyne Costes

Subjects
Botany, QK1-989, Plant culture, SB1-1110
Abstract

High-throughput phenotyping for plants A high-throughput method for determining plant characteristics offers a viable way to track competitive traits in the field. Increasingly difficult agricultural conditions are spurring plant breeding programs to prioritize plants with strong adaptations for healthy metabolism, but no current technologies can rapidly assess plant traits in the field. Now, Benoît Pallas, of the French National Institute for Agricultural Research, and his team have adapted tools such as infrared and laser-light scanning, and drone imagery, to take define and correlate metrics of 1000 apple trees, such as measurements of volume, leaf area, photosynthetic activity, and water usage. With these results and prior knowledge of the trees’ genotype, the team was able to group the trees into six classes with distinct physical and functional trait combinations. These techniques may open doors for discovering the genetic bases of plant traits.

Published
2019
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4. Impact of Within-Tree Organ Distances on Floral Induction and Fruit Growth in Apple Tree: Implication of Carbohydrate and Gibberellin Organ Contents

Author

Fares Belhassine, Sébastien Martinez, Sylvie Bluy, Damien Fumey, Jean-Jacques Kelner, Evelyne Costes, and Benoît Pallas

Subjects
leaf/fruit removal, floral induction, fruit weight, non-structural carbohydrates, source-sink relationships, shoot/branch autonomy, Plant culture, SB1-1110
Abstract

In plants, organs are inter-dependent for growth and development. Here, we aimed to investigate the distance at which interaction between organs operates and the relative contribution of within-tree variation in carbohydrate and hormonal contents on floral induction and fruit growth, in a fruit tree case study. Manipulations of leaf and fruit numbers were performed in two years on “Golden delicious” apple trees, at the shoot or branch scale or one side of Y-shape trees. For each treatment, floral induction proportion and mean fruit weight were recorded. Gibberellins content in shoot apical meristems, photosynthesis, and non-structural carbohydrate concentrations in organs were measured. Floral induction was promoted by leaf presence and fruit absence but was not associated with non-structural content in meristems. This suggests a combined action of promoting and inhibiting signals originating from leaves and fruit, and involving gibberellins. Nevertheless, these signals act at short distance only since leaf or fruit presence at long distances had no effect on floral induction. Conversely, fruit growth was affected by leaf presence even at long distances when sink demands were imbalanced within the tree, suggesting long distance transport of carbohydrates. We thus clarified the inter-dependence and distance effect among organs, therefore their degree of autonomy that appeared dependent on the process considered, floral induction or fruit growth.

Published
2019
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5. Genetic Variation of Morphological Traits and Transpiration in an Apple Core Collection under Well-Watered Conditions: Towards the Identification of Morphotypes with High Water Use Efficiency.

Author

Gerardo Lopez, Benoît Pallas, Sébastien Martinez, Pierre-Éric Lauri, Jean-Luc Regnard, Charles-Éric Durel, and Evelyne Costes

Subjects
Medicine, Science
Abstract

Water use efficiency (WUE) is a quantitative measurement which improvement is a major issue in the context of global warming and restrictions in water availability for agriculture. In this study, we aimed at studying the variation and genetic control of WUE and the respective role of its components (plant biomass and transpiration) in a perennial fruit crop. We explored an INRA apple core collection grown in a phenotyping platform to screen one-year-old scions for their accumulated biomass, transpiration and WUE under optimal growing conditions. Plant biomass was decompose into morphological components related to either growth or organ expansion. For each trait, nine mixed models were evaluated to account for the genetic effect and spatial heterogeneity inside the platform. The Best Linear Unbiased Predictors of genetic values were estimated after model selection. Mean broad-sense heritabilities were calculated from variance estimates. Heritability values indicated that biomass (0.76) and WUE (0.73) were under genetic control. This genetic control was lower in plant transpiration with an heritability of 0.54. Across the collection, biomass accounted for 70% of the WUE variability. A Hierarchical Ascendant Classification of the core collection indicated the existence of six groups of genotypes with contrasting morphology and WUE. Differences between morphotypes were interpreted as resulting from differences in the main processes responsible for plant growth: cell division leading to the generation of new organs and cell elongation leading to organ dimension. Although further studies will be necessary on mature trees with more complex architecture and multiple sinks such as fruits, this study is a first step for improving apple plant material for the use of water.

Published
2015
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6. Overexpression of the Promigratory and Prometastatic PTK7 Receptor Is Associated with an Adverse Clinical Outcome in Colorectal Cancer.

Author

Anne-Catherine Lhoumeau, Sébastien Martinez, Jean-Marie Boher, Geneviève Monges, Rémy Castellano, Armelle Goubard, Marie Doremus, Flora Poizat, Bernard Lelong, Cécile de Chaisemartin, Florence Bardin, Patrice Viens, Jean-Luc Raoul, Thomas Prebet, Michel Aurrand-Lions, Jean-Paul Borg, and Anthony Gonçalves

Subjects
Medicine, Science
Abstract

Biomarkers and novel therapeutic targets are urgently needed in colorectal cancer (CRC). The pseudo tyrosine kinase receptor 7 (PTK7) is involved in planar cell polarity and it is deregulated in various malignancies, including CRC. Yet, little is known about its protein expression in human CRC, or about a possible correlation of its expression with clinical endpoints. Using a clinically annotated Tissue MicroArray (TMA) produced from from 192 consecutive CRC patients treated by initial surgery, we examined PTK7 expression by immunohistochemistry in tumoral tissue and matched normal mucosae, and correlated its expression with clinico-pathological features and patient outcome. PTK7 depletion by specific shRNA in HCT116 and HCT15 CRC cell lines was found to affect cell proliferation, resistance to drugs and cell migration. Tumor growth and metastatic phenotype were investigated in vivo using a xenograft mouse model of CRC cells with modulated expression of PTK7 levels. PTK7 was significantly up-regulated in CRC tissue as compared to matched healthy mucosae, and significant overexpression was found in 34% of patients. PTK7 overexpression was significantly associated with a reduced metastasis-free survival in non-metastatic patients. In HCT116 and HCT15 cells, shRNA PTK7 reduced migration but did not affect cell proliferation and resistance to drugs. In a xenograft mouse of HCT15 cells, downregulation of PTK7 led to reduced tumor growth, whereas its overexpression in PTK7-negative cancer cells led to increased metastatic events. PTK7 expression thus represents a potential prognostic biomarker and a novel therapeutic target in CRC.

Published
2015
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7. Fruit self-thinning: a trait to consider for genetic improvement of apple tree.

Author

Jean-Marc Celton, Jean-Jacques Kelner, Sébastien Martinez, Abdel Bechti, Amina Khelifi Touhami, Marie José James, Charles-Eric Durel, François Laurens, and Evelyne Costes

Subjects
Medicine, Science
Abstract

In apple (Malus×domestica Borkh), as in many fruiting crops, fruit maintenance vs abscission is a major criteria for production profitability. Growers routinely make use of chemical thinning agents to control total fruit load. However, serious threats for the environment lead to the demand for new apple cultivars with self-thinning properties. In this project, we studied the genetic determinism of this trait using a F1 progeny derived from the cross between the hybrid INRA X3263, assumed to possess the self-thinning trait, and the cultivar 'Belrène'. Both counting and percentage variables were considered to capture the fruiting behaviour on different shoot types and over three consecutive years. Besides low to moderate but significant genetic effects, mixed models showed considerable effects of the year and the shoot type, as well as an interaction effect. Year effect resulted mainly from biennial fruiting. Eight Quantitative Trait Locus (QTL) were detected on several linkage groups (LG), either independent or specific of the year of observation or the shoot type. The QTL with highest LOD value was located on the top third of LG10. The screening of three QTL zones for candidate genes revealed a list of transcription factors and genes involved in fruit nutrition, xylem differentiation, plant responses to starvation and organ abscission that open new avenues for further molecular investigations. The detailed phenotyping performed revealed the dependency between the self-thinning trait and the fruiting status of the trees. Despite a moderate genetic control of the self-thinning trait, QTL and candidate genes were identified which will need further analyses involving other progenies and molecular investigations.

Published
2014
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10. A genotype-specific architectural and physiological profile is involved in the flowering regularity of apple trees

Author

Fares Belhassine, Benoît Pallas, Sylvie Pierru-Bluy, Sébastien Martinez, Damien Fumey, and Evelyne Costes

Subjects
Cytokinins, Genotype, Physiology, Malus, Starch, Flowers, Plant Science, Gibberellins, Trees
Abstract

In polycarpic plants, meristem fate varies within individuals in a given year. In perennials, the proportion of floral induction (FI) in meristems also varies between consecutive years and among genotypes of a given species. Previous studies have suggested that FI of meristems could be determined by the within-plant competition for carbohydrates and by hormone signaling as key components of the flowering pathway. At the genotypic level, variability in FI was also associated with variability in architectural traits. However, the part of genotype-dependent variability in FI that can be explained by either tree architecture or tree physiology is still not fully understood. This study aimed at deciphering the respective effect of architectural and physiological traits on FI variability within apple trees by comparing six genotypes with contrasted architectures. Shoot type demography as well as the flowering and fruit production patterns were followed over 6 years and characterized by different indexes. Architectural morphotypes were then defined based on architectural traits using a clustering approach. For two successive years, non-structural starch content in leaf, stem and meristems, and hormonal contents (gibberellins, cytokinins, auxin and abscisic acid) in meristems were quantified and correlated to FI within-tree proportions. Based on a multi-step regression analysis, cytokinins and gibberellins content in meristem, starch content in leaves and the proportion of long shoots in tree annual growth were shown to contribute to FI. Although the predictive linear model of FI was common to all genotypes, each of the explicative variables had a different weight in FI determination, depending on the genotype. Our results therefore suggest both a common determination model and a genotype-specific architectural and physiological profile linked to its flowering behavior.

Published
2022

11. CD9 mediates the uptake of extracellular vesicles from cancer-associated fibroblasts that promote pancreatic cancer cell aggressiveness

Author

Jérémy Nigri, Julie Leca, Sarah-Simha Tubiana, Pascal Finetti, Fabienne Guillaumond, Sébastien Martinez, Sophie Lac, Juan L. Iovanna, Stéphane Audebert, Luc Camoin, Sophie Vasseur, François Bertucci, and Richard Tomasini

Subjects
Pancreatic Neoplasms, Extracellular Vesicles, Mice, Cancer-Associated Fibroblasts, Animals, Cell Biology, Molecular Biology, Biochemistry, Carcinoma, Pancreatic Ductal
Abstract

In pancreatic ductal adenocarcinoma (PDAC), signaling from stromal cells is implicated in metastatic progression. Tumor-stroma cross-talk is often mediated through extracellular vesicles (EVs). We previously reported that EVs derived from cancer-associated stromal fibroblasts (CAFs) that are abundant in annexin A6 (ANXA6 + EVs) support tumor cell aggressiveness in PDAC. Here, we found that the cell surface glycoprotein and tetraspanin CD9 is a key component of CAF-derived ANXA6 + EVs for mediating this cross-talk. CD9 was abundant on the surface of ANXA6 + CAFs isolated from patient PDAC samples and from various mouse models of PDAC. CD9 colocalized with CAF markers in the tumor stroma, and CD9 abundance correlated with tumor stage. Blocking CD9 impaired the uptake of ANXA6 + EVs into cultured PDAC cells. Signaling pathway arrays and further analyses revealed that the uptake of CD9 + ANXA6 + EVs induced mitogen-activated protein kinase (MAPK) pathway activity, cell migration, and epithelial-to-mesenchymal transition (EMT). Blocking either CD9 or p38 MAPK signaling impaired CD9 + ANXA6 + EV–induced cell migration and EMT in PDAC cells. Analysis of bioinformatic datasets indicated that CD9 abundance was an independent marker of poor prognosis in patients with PDAC. Our findings suggest that CD9-mediated stromal cell signaling promotes PDAC progression.

Published
2022

12. In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer

Author

Sebastien Martinez, Shifei Wu, Michael Geuenich, Ahmad Malik, Ramona Weber, Tristan Woo, Amy Zhang, Gun Ho Jang, Dzana Dervovic, Khalid N. Al-Zahrani, Ricky Tsai, Nassima Fodil, Philippe Gros, Steven Gallinger, G. Gregory Neely, Faiyaz Notta, Ataman Sendoel, Kieran Campbell, Ulrich Elling, and Daniel Schramek

Subjects
Science
Abstract

Abstract Functionally characterizing the genetic alterations that drive pancreatic cancer is a prerequisite for precision medicine. Here, we perform somatic CRISPR/Cas9 mutagenesis screens to assess the transforming potential of 125 recurrently mutated pancreatic cancer genes, which revealed USP15 and SCAF1 as pancreatic tumor suppressors. Mechanistically, we find that USP15 functions in a haploinsufficient manner and that loss of USP15 or SCAF1 leads to reduced inflammatory TNFα, TGF-β and IL6 responses and increased sensitivity to PARP inhibition and Gemcitabine. Furthermore, we find that loss of SCAF1 leads to the formation of a truncated, inactive USP15 isoform at the expense of full-length USP15, functionally coupling SCAF1 and USP15. Notably, USP15 and SCAF1 alterations are observed in 31% of pancreatic cancer patients. Our results highlight the utility of in vivo CRISPR screens to integrate human cancer genomics and mouse modeling for the discovery of cancer driver genes with potential prognostic and therapeutic implications.

Published
2024
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13. Towards safe and secure computer based railway interlocking systems

Author

Philippe Bon, Sébastien Martinez, Matthieu Perin, Dalay Israel de Almeida Pereira, and Simon Collart Dutilleul

Subjects
business.industry, Computer science, Automotive Engineering, Computer based, Transportation, Software engineering, business, Formal methods, Interlocking, Civil and Structural Engineering
Published
2020

15. Summer drought impacts annual shoot growth dynamics in apple tree: a comparative study on three cultivars

Author

Benoît Pallas, Evelyne Costes, D. Chen, Sébastien Martinez, Y. Wang, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Northwest A&F University, and Institute of Soil and Water Conservation

Subjects
0106 biological sciences, période estivale, ramification, pommier, Apple tree, Horticulture, Biology, 010603 evolutionary biology, 01 natural sciences, Shoot growth dynamics, cycle de croissance, Tree architecture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cultivar, Malus x domestica, malus domestica, Vegetal Biology, architecture de l'arbre, Drought, déficit hydrique, fungi, food and beverages, dynamique de croissance, 15. Life on land, Rhythmic growth, Shoot, Biologie végétale, 010606 plant biology & botany
Abstract

Plants respond to drought by adjusting different growth and developmental processes. This study investigated the impact of a summer water deficit on shoot growth dynamics, comparatively in three apple cultivars, in their second and third year of growth. Trees were differentially irrigated to induce water stress (WS) or well - watered conditions (WW). WS effects were evaluated on long shoots in either terminal or lateral position, by observing metamer appearance rate, growth duration and arrest time. In the three cultivars, WS promoted growth cessations (GC) during summer leading to bicyclic shoots. These GC occurred early in the season, when WS conditions were mild. Consistently with tree ontogeny, the number of shoots that resumed growth after summer arrest decreased between the two consecutive years, but more in WS than WW conditions. In both monocyclic and bicyclic shoots, WS provoked a more precocious GC at the end of the growth season. Even though WS impact slightly differed among cultivars, a reduction in shoot neoformation and an increase in summer arrest appeared as a common response of apple tree to water deficit. This can be interpreted as an avoidance strategy to reduce the tree leaf area, leading to a modification of the within - tree shoot demography in favor of medium and short shoots.

Published
2020

16. Unravelling the responses of different apple varieties to water constraints by continuous field thermal monitoring

Author

David Gómez-Candón, Vincent Mathieu, Sébastien Martinez, Sylvain Labbé, Magalie Delalande, Jean-Luc Regnard, Producció Vegetal, and Ús Eficient de l'Aigua en Agricultura

Subjects
Horticulture
Abstract

This research aimed at analyzing the response of apple tree varieties subjected to soil water deficit and atmospheric drought in a field phenotyping platform located in the Mediterranean area. The main assumption of the study was that seasonal and daily stomatal behavior can be monitored by continuous measurement of canopy surface temperature (Ts) as a proxy of stomatal closure. To achieve the study objectives, thermal monitoring of 6 pre-commercial apple varieties was simultaneously carried out throughout one season by nadir-oriented thermo-radiometers placed 1.50 m over the tree top canopy. Two water regimes were applied to each variety during a 4-week summer period: normal irrigation (WW) vs progressive water deficit (WS). The maximum difference in Ts between water regimes was recorded daily between 11:00 and 14:20 GMT, with an earlier closure of stomata in WS trees. During the day, a more negative stem water potential (Ψstem) and a higher diurnal Ts (+1° to +2 °C) were observed on WS trees, resulting in a significant limitation of fruit growth. Tree water stress was caused by both edaphic and atmospheric droughts, in the medium and short terms respectively, with inter-varietal and inter-regime differences highlighting distinct stomatal closure behaviors. Results suggest that some of the varieties studied are well adapted to stressful summer conditions, as long as irrigation needs are met, while other varieties show a particular sensitivity to the mid-day evaporative demand, which may limit their extension. Although these results are not comprehensive enough to predict the optimal performance of varieties under different stress scenarios, the proposed methodology allows to assess the dynamics of tree response to water constraints using non-invasive thermal sensors. It opens up new perspectives for the phenotyping of apple cultivars under abiotic stress, achievable through the quantified study of their transpiration flux in response to stress scenarios. These prospects will require further in planta measurements to dissect varietal differences. info:eu-repo/semantics/acceptedVersion

Published
2022

17. Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

Author

YiQing Lü, Tiffany Cho, Saptaparna Mukherjee, Carmen Florencia Suarez, Nicolas S Gonzalez-Foutel, Ahmad Malik, Sebastien Martinez, Dzana Dervovic, Robin Hyunseo Oh, Ellen Langille, Khalid N Al-Zahrani, Lisa Hoeg, Zhen Yuan Lin, Ricky Tsai, Geraldine Mbamalu, Varda Rotter, Patricia Ashton-Prolla, Jason Moffat, Lucia Beatriz Chemes, Anne-Claude Gingras, Moshe Oren, Daniel Durocher, and Daniel Schramek

Subjects
Genome-wide CRISPR Screening, Mutant p53, p53 Stability, Breast Cancer, Fluorescence-based Stability Reporter, Biology (General), QH301-705.5, Medicine (General), R5-920
Abstract

Abstract Tumor suppressor p53 (TP53) is frequently mutated in cancer, often resulting not only in loss of its tumor-suppressive function but also acquisition of dominant-negative and even oncogenic gain-of-function traits. While wild-type p53 levels are tightly regulated, mutants are typically stabilized in tumors, which is crucial for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. Most regulators of wild-type p53 also regulate p53 mutants, except for p53 R337H regulators, which are largely private to this mutant. Mechanistically, FBXO42 emerged as a positive regulator for a subset of p53 mutants, working with CCDC6 to control USP28-mediated mutant p53 stabilization. Additionally, C16orf72/HAPSTR1 negatively regulates both wild-type p53 and all tested mutants. C16orf72/HAPSTR1 is commonly amplified in breast cancer, and its overexpression reduces p53 levels in mouse mammary epithelium leading to accelerated breast cancer. This study offers a network perspective on p53 stability regulation, potentially guiding strategies to reinforce wild-type p53 or target mutant p53 in cancer.

Published
2024
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19. Spatial variability in carbon- and nitrogen-related traits in apple trees: the effects of the light environment and crop load

Author

Benoît Pallas, Jérôme Ngao, André Marquier, Brigitte Saint-Joanis, Sébastien Martinez, Sylvie Bluy, Evelyne Costes, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-14-CE35-0001,AlternApp,Genetic mechanisms underlying alternate cropping in apple (Malus x domestica)(2014), ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, Carbohydrate content, Nonstructural Carbon, Perennial plant, Light Microclimate, Physiology, Nitrogen, chemistry.chemical_element, Plant Science, Biology, Photosynthesis, 01 natural sciences, Sink (geography), 03 medical and health sciences, Leaf Photosynthesis, Carbon assimilation, Spatial Variability, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 2. Zero hunger, High rate, geography, geography.geographical_feature_category, Light Harvesting, 15. Life on land, Carbon, Plant Leaves, 030104 developmental biology, Agronomy, chemistry, Fruit, Malus, Source-Sink Relationships, Spatial variability, 010606 plant biology & botany
Abstract

Photosynthetic carbon assimilation rates are highly dependent on environmental factors such as light availability and on metabolic limitations such as the demand for carbon by sink organs. The relative effects of light and sink demand on photosynthesis in perennial plants such as trees remain poorly characterized. The aim of the present study was therefore to characterize the relationships between light and fruit load on a range of leaf traits including photosynthesis, non-structural carbohydrate content, leaf structure, and nitrogen-related variables in fruiting (‘ON’) and non-fruiting (‘OFF’) ‘Golden Delicious’ apple trees. We show that crop status (at the tree scale) exerts a greater influence over leaf traits than the local light environment or the local fruit load. High rates of photosynthesis were observed in the ON trees. This was correlated with a high leaf nitrogen content. In contrast, little spatial variability in photosynthesis rates was observed in the OFF trees. The lack of variation in photosynthesis rates was associated with high leaf non-structural carbohydrate content at the tree level. Taken together, these results suggest that low carbon demand leads to feedback limitation on photosynthesis resulting in a low level of within-tree variability. These findings provide new insights into carbon and nitrogen allocations within trees, which are heavily dependent on carbon demand.

Published
2020

20. Analysis of the impact of carbon source-sink relationships on flowering patterns reveals that apple tree growth and functioning are determined by mechanisms occurring at the tree and shoot scales

Author

Sébastien Martinez, S. Bluy, J.-J. Kelner, Evelyne Costes, J. Ngao, J.-B. Durand, and Benoît Pallas

Subjects
0106 biological sciences, 0301 basic medicine, geography, geography.geographical_feature_category, Apple tree, Horticulture, Biology, 01 natural sciences, Sink (geography), 03 medical and health sciences, 030104 developmental biology, Shoot, Carbon source, 010606 plant biology & botany
Published
2018

21. Water stress assessment at tree scale: high-resolution thermal UAV imagery acquisition and processing

Author

Jorge Torres-Sánchez, David Gómez-Candón, Audrey Jolivot, Sylvain Labbé, Jean-Luc Regnard, Sébastien Martinez, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Domaine expérimental de Melgueil (MONTP MELGUEIL UE), Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Agropolis Fondation through the 'Investissements d'Avenir' program [ANR-10-LABX-0001-01, 1202-070], ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, thermal imagery, [SDV]Life Sciences [q-bio], Population, Image processing, Horticulture, Noon, 01 natural sciences, drought assessment, Altitude, unmanned aerial vehicle, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, stress indices, education, Image resolution, Malus x domestica, Remote sensing, education.field_of_study, Contextual image classification, 04 agricultural and veterinary sciences, Geography, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Radiometry, Scale (map), 010606 plant biology & botany
Abstract

VIII International Symposium on Irrigation of Horticultural Crops., Water stress assessment can be performed by analyzing thermal images taken onboard Unmanned Aerial Vehicles (UAVs). This study focuses on the acquisition and data extraction of high-resolution UAV-sensed thermal images. The datasets obtained, through computation of spectral indices and image classification, allowed to assess the response to drought of an apple hybrid population submitted to different water regimes. Studies were performed in an experimental apple orchard located in southern France. Flights were planned at solar noon on four successive dates during summer 2013 (40 m altitude, 0.10 m spatial resolution) and at five successive hours of the day, once water stress was established. The high temporal and spatial resolution of images allowed acquiring data at canopy and intra-canopy scales, with a short revisit time. As the miniaturized uncooled thermal camera carried onboard the UAV needs careful correction of radiometry, this was performed by continuous reference to ground thermal targets, while an automatized image processing was carried out. Thanks to the high resolution of the remote images obtained, and the capacity to efficiently delineate each individual tree within the whole trial, it was possible to analyze inter- and intra-canopy thermal variations. Indices extracted from thermal images showed significantly higher canopy temperatures in water restricted trees compared to well-irrigated ones. These differences were related to the severity of water deficit. However, responses also varied significantly according to the genotype. The image-based variables in apple trees constitute a basis for a further finely tuned analysis of the differential response to water stress.

Published
2017

22. Neoformation and summer arrest are common sources of tree plasticity in response to water stress of apple cultivars

Author

Sébastien Martinez, Youke Wang, Evelyne Costes, Dianyu Chen, Benoît Pallas, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Northwest A&F University, Institute of Soil and Water Conservation, and China Scholarship Council (CSC)

Subjects
0106 biological sciences, Ontogeny, Adaptation, Biological, Apple tree, Plant Science, Biology, Plasticity, 010603 evolutionary biology, 01 natural sciences, Shoot growth dynamics, Trees, Shoot expansion, Species Specificity, Polycyclism, Tree architecture, Malus × domestica, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Stress avoidance, Cultivar, Drought, Water stress, fungi, Water, food and beverages, Original Articles, 15. Life on land, Horticulture, Malus, Shoot, Rhythmic growth, Plant Shoots, Decreased growth, 010606 plant biology & botany
Abstract

International audience; Background and Aims: Depending on the species, water stress affects different growth and developmental processes, mainly due to changes in hydraulic properties and hormonal signalling. This study compared the impact of water stress on tree development and organ growth in three apple cultivars. Methods: Trees were differentially irrigated to induce water stress or to provide well-watered conditions in their second and third years of growth. Effects of water stress were evaluated at tree scale by shoot number and proportions of the different types of shoots, and at shoot scale by metamer appearance rate, growth duration and arrest time, as well as organ size. Key Results: Water stress promoted early growth cessation, prolonged summer arrests and decreased growth resumptions, thus modifying within-tree shoot demography in favour of short shoots. Growth cessations occurred in mild water stress conditions before any difference in stem water potential appeared. No major impact was observed on organ size. Consistently with tree ontogeny, the number of shoots that resumed growth after summer arrest decreased with years, but more in water-stressed than well-watered conditions. Conclusions: Even though the impact of water stress differed slightly among cultivars, the reduction in neoformation and increase in summer arrest played a common role in apple tree morphological responses and led to stress avoidance by early reduction of tree leaf area.

Published
2019

23. Assessing T-LiDAR technology for high throughput phenotyping apple tree topological and architectural traits

Author

Frédéric Boudon, Sébastien Martinez, Olivier Simler, Evelyne Costes, Benoît Pallas, Emma Carrie, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Population, pommier, Apple tree, Geometry, 02 engineering and technology, Horticulture, Topology, digitalisation 3 d, surface foliaire, 01 natural sciences, Branching (linguistics), Leaf area, High throughput phenotypic, phénotypage, 0202 electrical engineering, electronic engineering, information engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Throughput (business), Mathematics, topologie, education.field_of_study, Vegetal Biology, Structure reconstruction, architecture de l'arbre, 020207 software engineering, Branching points, Tree (data structure), Lidar, Allometry, Biologie végétale, 010606 plant biology & botany
Abstract

We aim at extending methodologies based on T-Lidar scans for providing a description of individual apple tree topology and architecture. Experiments were performed on 2- and 3-year-old trees belonging to a core collection of French apple cultivars. In 2016, ten trees were precisely scanned in winter to assess our ability to extract topological traits. In 2017, the whole core-collection was scanned to estimate tree leaf areas at the end of the summer period. Topological reconstructions on 2016 data were performed with Plantscan3D software using existing algorithms whereas an allometric relationship depending on tree alpha hull volumes was used for estimating tree leaf areas on 2017 data. Topological traits extracted from T-LiDAR data were compared to digitizing data of the same trees and the estimated total leaf areas were compared to manual measurements on a sample of twenty trees displaying large variability in vegetative development. In 2016, topological reconstructions gave promising results with R² values higher than 0.90 for the total number of axes and growth units pet tree and for their mean length when T-Lidar were compared to digitizing data. However, a significant number of short axes or growth units were not detected by the T-Lidar. Comparisons between T-LiDAR and digitizing data showed g ood adequacy if axes were classified depending on their branching order suggesting that our method was relevant for evaluating the number of branching points in the structure. Regarding data collected on leafy trees in 2017, the total leaf area estimated from T-LiDAR was also highly correlated (R²= 0.83) with manual measurements. Forthcoming works are undergoing for improving topological reconstruction algorithms in order to extract topological traits and new variables related to vegetative development on the whole population. Nevertheless this first study suggests that this method could be adapted for phenotypic architectural traits on large tree population on which genetic analyses could be performed.

Published
2018

24. Assessing the robustness of leaf fluorescence parameters for phenotyping the genotypic variability in photosynthesis across hundreds of apple tree cultivars

Author

Benoît Pallas, Luigi Manfrini, Brunella Morandi, Stefano Tartarini, Aude Coupel-Ledru, Sébastien Martinez, Jean-Luc Regnard, Magalie Delalande, Evelyne Costes, L. Corelli Grappadelli, Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Coupel-Ledru A., Regnard J.L., Pallas B., Martinez S., Delalande M., Morandi B., Manfrini L., Tartarini S., Corelli Grappadelli L., and Costes E.

Subjects
0106 biological sciences, 2. Zero hunger, 0303 health sciences, Fluorimetry, [SDV]Life Sciences [q-bio], Robustness (evolution), Apple tree, 15. Life on land, Horticulture, Biology, Photosynthesis, 01 natural sciences, 03 medical and health sciences, Photosynthesi, Malus × domestica, Cultivar, Core-collection, Water deficit, 030304 developmental biology, 010606 plant biology & botany
Abstract

International audience; To cope with increasing water scarcity, breeding programs targeting for more efficient crop require comprehensive knowledge of carbon- and water use-related processes, including photosynthesis, the regulation of transpiration (by stomatal closure) and water use efficiency (the ratio of carbon gain to water use). These questions have been scarcely studied in fruit trees, yet are of major economic importance. A main limitation results from the lack of high-throughput techniques to characterize the physiological variability in these processes for hundreds of trees in the field as required to performing genetic analyses. We screened the European apple diversity for photosynthesis, by unique combination of high-throughput and in planta measurements applied on two core-collections in Montpellier (France) and Bologna (Italy), respectively. A progressive soil water deficit was ensured and continuously monitored in both orchards, through summer irrigation withholding, in order to evaluate the genotypic variability in response to drought. We tested the relevance and applicability of the semi-empirical IPL index, computed from chlorophyll fluorescence measurements, as a high-throughput indicator of leaf photosynthesis. The validity of this proxy was assessed through fine measurements of photosynthesis on 6 cultivars common to both collections. We validated the robustness of IPL through model calibration across sites, days and periods of measurements. We then undertook IPL measurements in the whole collections (>250 cultivars). A large variability of IPL was observed with highly significant effects of the genotype and watering scenario (well-watered vs. water deficit). These results pave the way to genome wide association studies (GWAS) to identify the genomic regions controlling the variations detected.

Published
2018

25. In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer

Author

Dzana Dervovic, Ahmad A. Malik, Edward L. Y. Chen, Masahiro Narimatsu, Nina Adler, Somaieh Afiuni-Zadeh, Dagmar Krenbek, Sebastien Martinez, Ricky Tsai, Jonathan Boucher, Jacob M. Berman, Katie Teng, Arshad Ayyaz, YiQing Lü, Geraldine Mbamalu, Sampath K. Loganathan, Jongbok Lee, Li Zhang, Cynthia Guidos, Jeffrey Wrana, Arschang Valipour, Philippe P. Roux, Jüri Reimand, Hartland W. Jackson, and Daniel Schramek

Subjects
Science
Abstract

Abstract How the genetic landscape governs a tumor’s response to immunotherapy remains poorly understood. To assess the immune-modulatory capabilities of 573 genes associated with altered cytotoxicity in human cancers, here we perform CRISPR/Cas9 screens directly in mouse lung cancer models. We recover the known immune evasion factors Stat1 and Serpinb9 and identify the cancer testis antigen Adam2 as an immune modulator, whose expression is induced by KrasG12D and further elevated by immunotherapy. Using loss- and gain-of-function experiments, we show that ADAM2 functions as an oncogene by restraining interferon and TNF cytokine signaling causing reduced presentation of tumor-associated antigens. ADAM2 also restricts expression of the immune checkpoint inhibitors PDL1, LAG3, TIGIT and TIM3 in the tumor microenvironment, which might explain why ex vivo expanded and adoptively transferred cytotoxic T-cells show enhanced cytotoxic efficacy in ADAM2 overexpressing tumors. Together, direct in vivo CRISPR/Cas9 screens can uncover genetic alterations that control responses to immunotherapies.

Published
2023
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26. Il metodo rivoluzionario per una memoria infallibile

Author

Sébastien Martinez and Sébastien Martinez

Abstract

Bestseller in Francia Il modo più semplice e geniale per non dimenticare più nulla Tecniche infallibili per potenziare la memoria e non dimenticare più nulla Non ricordiamo il titolo di un film o il nome di un regista? Non ci sforziamo neppure di ricordarlo, prendiamo lo smartphone e il nome desiderato compare sul display. Una soluzione facile, ma che in realtà impoverisce le nostre capacità mnemoniche. Molti studi scientifici hanno dimostrato invece quanto sia importante tenere in allenamento la memoria, per migliorare le capacità cognitive e la biochimica cerebrale. La paura di terribili e noiosi esercizi, però, farebbe scappare anche i più determinati. Siamo dunque destinati a non ricordare il nome delle persone che incontriamo nella vita e sul lavoro, a fare figuracce con il capo o con gli amici? No, la soluzione c'è ed è facile e divertente. Seguendo i consigli e gli stratagemmi spiegati in questo libro, chiunque sarà in grado di imparare le mille parole alla base di una lingua straniera in meno di un mese, recitare qualunque poesia senza incertezze, memorizzare i testi per un esame, ricordarsi esattamente i dati da sciorinare in riunione senza l'aiuto di internet. Sébastien Martinez, campione di memoria, invita ad abbandonare il monotono metodo della ripetizione e ad abbracciare l'arte della memorizzazione veloce, ispirata alle tecniche degli antichi greci e romani, dove fantasia e creatività sono elementi fondamentali e dove tutto è possibile. Un viaggio iniziatico per potenziare l'attenzione e non dimenticare più niente. «Martinez, campione francese di memoria, sostiene che imparare a ricordare sia il miglior modo per essere liberi, e dunque felici.» Libération «In questo libro molto divertente, Sébastien Martinez ci accompagna con entusiasmo alla scoperta delle tecniche di memorizzazione, dalle più semplici alle meno note. Uno strumento prezioso per tutti.» Le Parisien Magazine Sébastien Martinezè nato nel sud della Francia nel 1987 e ha cominciato ad appassionarsi alle tecniche della memorizzazione mentre studiava per diventare ingegnere minerario. Ha sperimentato svariati metodi fino a svilupparne uno suo che, dopo la laurea, ha deciso di mettere a disposizione di tutti. Ha partecipato ai campionati della memoria svoltisi nel novembre 2015 aggiudicandosi il titolo di Campione di Francia. Il suo credo è: «Siamo tutti geni, le capacità del nostro cervello sono infinite».

Published
2017

27. Growth and carbon balance are differently regulated by tree and shoot fruiting contexts: an integrative study on apple genotypes with contrasted bearing patterns

Author

Jérôme Ngao, Sébastien Martinez, Evelyne Costes, Sylvie Bluy, Anne Clément-Vidal, Benoît Pallas, Jean-Jacques Kelner, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
Fructification, 0106 biological sciences, 0301 basic medicine, Physiology, F62 - Physiologie végétale - Croissance et développement, Plant Science, 01 natural sciences, F30 - Génétique et amélioration des plantes, Trees, Malus × domestica Borkh, Multiplication végétative, Architecture, Photosynthesis, Bourgeon, biology, food and beverages, Plant physiology, Horticulture, Non-structural carbohydrates, Malus, Shoot, Carbohydrate Metabolism, Gibberellin, France, Phénologie, Génotype, Plant Shoots, Genotype, F60 - Physiologie et biochimie végétale, Context (language use), Flowers, Biennial bearing, Crop, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Croissance, fungi, Crop load, 15. Life on land, biology.organism_classification, Carbon, Plant Leaves, 030104 developmental biology, Fruit, Cycle du carbone, 010606 plant biology & botany
Abstract

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières; International audience; In plants, carbon source–sink relationships are assumed to affect their reproductive effort. In fruit trees, carbon source–sink relationships are likely to be involved in their fruiting behavior. In apple, a large variability in fruiting behaviors exists, from regular to biennial, which has been related to the within-tree synchronization vs desynchronization of floral induction in buds. In this study, we analyzed if carbon assimilation, availability and fluxes as well as shoot growth differ in apple genotypes with contrasted behaviors. Another aim was to determine the scale of plant organization at which growth and carbon balance are regulated. The study was carried out on 16 genotypes belonging to three classes: (i) biennial, (ii) regular with a high production of floral buds every year and (iii) regular, displaying desynchronized bud fates in each year. Three shoot categories, vegetative and reproductive shoots with or without fruits, were included. This study shows that shoot growth and carbon balance are differentially regulated by tree and shoot fruiting contexts. Shoot growth was determined by the shoot fruiting context, or by the type of shoot itself, since vegetative shoots were always longer than reproductive shoots whatever the tree crop load. Leaf photosynthesis depended on the tree crop load only, irrespective of the shoot category or the genotypic class. Starch content was also strongly affected by the tree crop load with some adjustments of the carbon balance among shoots since starch content was lower, at least at some dates, in shoots with fruits compared with the shoots without fruits within the same trees. Finally, the genotypic differences in terms of shoot carbon balance partly matched with genotypic bearing patterns. Nevertheless, carbon content in buds and the role of gibberellins produced by seeds as well as the distances at which they could affect floral induction should be further analyzed.

Published
2017

28. High-throughput phenotyping of an apple core collection: identification of genotypes with high water use efficiency

Author

Jean-Luc Regnard, Benoît Pallas, Gerardo Lopez, Charles-Eric Durel, Pierre-Eric Lauri, Evelyne Costes, Sébastien Martinez, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ARCHITECTURE (IRISA-D3), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Pushing Architecture and Compilation for Application Performance (PACAP), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-ARCHITECTURE (IRISA-D3), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)

Subjects
0106 biological sciences, Malus, Irrigation, Water stress, [SDV]Life Sciences [q-bio], Biomass, soil water restriction, drought, Horticulture, 01 natural sciences, Malus × domestica Borkh, Plant breeding, Genetic variation, Genotype, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, plant transpiration, Water-use efficiency, [SDV.BDD]Life Sciences [q-bio]/Development Biology, plant biomass, Transpiration, 2. Zero hunger, biology, 04 agricultural and veterinary sciences, biology.organism_classification, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, 010606 plant biology & botany
Abstract

International audience; To detect genotypes with high water use efficiency (WUE) in apple (Malus × domestica), 193 genotypes from an INRA core collection were evaluated in 2014. Eight grafted replicates per genotype grown as one-year-old scions were studied in a high-throughput phenotyping platform (PhenoArch). Individual pot weight was recorded twice a day and irrigation was scheduled for 46 days according to two irrigation treatments: well-watered (WW), maintaining soil water content (SWC) at 1.4 g g-1; and water stress (WS), reducing SWC until 0.7 g g-1 and maintaining this value for ten days. For each genotype, half of the replicates were WW while the other half were grown under WS. Plant 3D images were automatically acquired every two days. Analysis of images and pot weight differences allowed the estimation of the accumulated whole-plant biomass (A_Bio) and transpiration (Plant_T) during the experiment. WUE was calculated as the ratio A_Bio/Plant_T. A_Bio and WUE had a higher genetic variation than Plant_T under WW and WS conditions. The genetic variation in WUE is a promising result, indicating that available genetic resources such as the INRA core collection could be useful to improve apple plant material for the use of water. WS reduced A_Bio and Plant_T but the reduction was less evident in WUE. Some genotypes had similar WUE values under WW and WS conditions. We identified of a group of 38 genotypes with high WUE under WW and WS. The existence of genotypes with high WUE whatever the water regime in apple may encourage apple breeders to consider the use of these genotypes as potential parents for improving apple plant material for the use of water.

Published
2017

29. Heritability and genetic variation of plant biomass, transpiration, and water use efficiency for an apple core-collection

Author

Evelyne Costes, Benoît Pallas, Sébastien Martinez, Pierre-Eric Lauri, Gabriela F López, Charles-Eric Durel, Jean-Luc Regnard, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), ARCHITECTURE (IRISA-D3), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Pushing Architecture and Compilation for Application Performance (PACAP), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-ARCHITECTURE (IRISA-D3), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, European Project: 265582,EC:FP7:KBBE,FP7-KBBE-2010-4,FRUIT BREEDOMICS(2011), and Pallas, Benoit

Subjects
0106 biological sciences, 0301 basic medicine, Irrigation, Malus, [SDV]Life Sciences [q-bio], Biomass, Horticulture, Biology, 01 natural sciences, complex mixtures, Malus × domestica Borkh, Plant breeding, physiologie végétale, 03 medical and health sciences, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Water-use efficiency, high-throughput phenotyping, plant breeding, plant images, Transpiration, 2. Zero hunger, Vegetal Biology, plant image, fungi, food and beverages, Heritability, biology.organism_classification, variation génétique, 030104 developmental biology, Agronomy, High-throughput phenotyping, Biologie végétale, 010606 plant biology & botany
Abstract

International audience; To study the heritability and genetic variation of plant biomass, transpiration and water use efficiency (WUE) in apple (Malus × domestica Borkh.), 193 genotypes from an INRA apple core-collection were evaluated in 2014. Four grafted replicates per genotype grown as one-year-old scions were studied in a high-throughput phenotyping platform (PhenoArch). Individual pot weight was recorded twice a day and irrigation was scheduled to maintain constant soil water content (SWC) and avoid any water stress during 46 days. Plant 3D pictures were automatically taken every two days. Analysis of pictures and pot weights differences allowed the estimation of whole-plant biomass and transpiration during the experiment. WUE was calculated as the ratio of accumulated biomass to transpiration. For each trait, we tested nine mixed models to account for the genetic effect and spatial variability inside PhenoArch. The Best Linear Unbiased Predictors (BLUPs) of genetic values were estimated after model selection. For each trait, broad-sense heritability (H2) was calculated from variance estimates. Plant biomass, transpiration and WUE had H2 values of 0.76, 0.54, and 0.73, respectively. The H2 value of WUE is high enough to consider that this trait is under genetic control in apple. The genetic variation of WUE indicated that apple genetic resources such as the INRA core-collection could be extremely useful to improve apple plant material for the use of water.

Published
2017

30. The impact of long-term water stress on tree architecture and production is related to changes in transitions between vegetative and reproductive growth in the ‘Granny Smith’ apple cultivar

Author

Jean-Baptiste Durand, Benoît Pallas, Weiwei Yang, Sébastien Martinez, Evelyne Costes, Mingyu Han, SWSAF, College of horticulture, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Modelling and Inference of Complex and Structured Stochastic Systems (MISTIS), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut National Polytechnique de Grenoble (INPG), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Modelling and Inference of Complex and Structured Stochastic Systems (MISTIS ), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, 0301 basic medicine, Perennial plant, Physiology, Vegetative reproduction, Ontogeny, variable-order Markov chain, Plant Science, Biology, 01 natural sciences, Trees, 03 medical and health sciences, water stress, Stress, Physiological, Malus × domestica Borkh, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Axillary bud, Botany, branching, Cultivar, 2. Zero hunger, Reproduction, Water stress, fungi, bearing behavior, Biennial bearing, Water, food and beverages, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, bud fate, 030104 developmental biology, Tree architecture, Fruit, Malus, Plant Shoots, 010606 plant biology & botany
Abstract

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières; International audience; Water stress (WS) generates a number of physiological and morphological responses in plants that depend on the intensity and duration of stress as well as the plant species and development stage. In perennial plants, WS may affect plant development through cumulative effects that modify plant functions, architecture and production over time. Plant architecture depends on the fate of the terminal and axillary buds that can give rise, in the particular case of apple, to reproductive or vegetative growth units (GUs) of different lengths. In this study, the impact of long-term WS (7 years) on the fate of terminal and axillary buds was investigated in relation to flowering occurrence and production pattern (biennial vs regular) in the ‘Granny Smith’ cultivar. It was observed that WS decreased the total number of GUs per branch, regardless of their type. Conversely, WS did not modify the timing of the two successive developmental phases characterized by the production of long and medium GUs and an alternation of floral GUs over time, respectively. The analysis of GU successions over time using a variable-order Markov chain that included both the effects of the predecessor and water treatment revealed that WS reduced the transition towards long and medium GUs and increased the transition toward floral, short and dead GUs. WS also slightly increased the proportion of axillary floral GUs. The higher relative frequency of floral GUs compared with vegetative ones reduced the tendency to biennial bearing under WS. The accelerated ontogenetic trend observed under WS suggests lower vegetative growth that could, in turn, be beneficial to floral induction and fruit set.

Published
2016

31. Cancer-associated fibroblast-derived annexin A6+ extracellular vesicles support pancreatic cancer aggressiveness

Author

Jean-Baptiste Bachet, Jérémy Nigri, Pascale Zimmermann, Nelson Dusetti, Juan L. Iovanna, Daniel Pietrasz, Marie-Noëlle Lavaut, Véronique Secq, Sophie Vasseur, Christian Bressy, Celine Loncle, Sophie Lac, Richard Tomasini, Marion Rubis, Julie Leca, Stéphane Garcia, Samuel Granjeaud, Julie Roques, Christine Brun, Mehdi Ouaissi, Arnauld Sergé, Corinne Bousquet, Sébastien Martinez, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), service hospitalier d'anatomie et cytologie pathologique humaine, APHM, Marseille, Assistance Publique - Hôpitaux de Marseille (APHM), Médecine Personnalisée, Pharmacogénomique, Optimisation Thérapeutique (MEPPOT - U1147), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches en Oncologie biologique et Oncopharmacologie (CRO2), Aix Marseille Université (AMU)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d'Hépato-Gastro-Entérologie [CHU Pitié-Salpêtrière], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre National de la Recherche Scientifique (CNRS), Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium., Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de chirurgie digestive et Hépatobiliaire, Groupe Hospitalier Pitié Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, APHP, Service d'Hépato-Gastroentérologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Centre de Recherche en Cancérologie de Marseille ( CRCM ), Aix Marseille Université ( AMU ) -Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Assistance Publique - Hôpitaux de Marseille ( APHM ), Médecine Personnalisée, Pharmacogénomique, Optimisation Thérapeutique ( MEPPOT - U1147 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre de Recherche en Cancérologie de Toulouse ( CRCT ), Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherches en Oncologie biologique et Oncopharmacologie ( CRO2 ), Aix Marseille Université ( AMU ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], Centre National de la Recherche Scientifique ( CNRS ), Technologies avancées pour le génôme et la clinique ( TAGC ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), and Katholieke Universiteit Leuven ( KU Leuven )

Subjects
Male, 0301 basic medicine, congenital, hereditary, and neonatal diseases and abnormalities, Stromal cell, health care facilities, manpower, and services, education, Cell, Mice, Nude, Cell Communication, medicine.disease_cause, Metastasis, Mice, 03 medical and health sciences, 0302 clinical medicine, Stroma, Cell-Derived Microparticles, health services administration, Pancreatic cancer, Thrombospondin 1, Biomarkers, Tumor, medicine, Animals, Humans, Annexin A6, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Chemistry, General Medicine, Fibroblasts, medicine.disease, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Neoplasm Proteins, Pancreatic Neoplasms, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Cancer research, Female, Carcinogenesis, Low Density Lipoprotein Receptor-Related Protein-1, Annexin A2, Research Article, Carcinoma, Pancreatic Ductal
Abstract

The intratumoral microenvironment, or stroma, is of major importance in the pathobiology of pancreatic ductal adenocarcinoma (PDA), and specific conditions in the stroma may promote increased cancer aggressiveness. We hypothesized that this heterogeneous and evolving compartment drastically influences tumor cell abilities, which in turn influences PDA aggressiveness through crosstalk that is mediated by extracellular vesicles (EVs). Here, we have analyzed the PDA proteomic stromal signature and identified a contribution of the annexin A6/LDL receptor-related protein 1/thrombospondin 1 (ANXA6/LRP1/TSP1) complex in tumor cell crosstalk. Formation of the ANXA6/LRP1/TSP1 complex was restricted to cancer-associated fibroblasts (CAFs) and required physiopathologic culture conditions that improved tumor cell survival and migration. Increased PDA aggressiveness was dependent on tumor cell-mediated uptake of CAF-derived ANXA6+ EVs carrying the ANXA6/LRP1/TSP1 complex. Depletion of ANXA6 in CAFs impaired complex formation and subsequently impaired PDA and metastasis occurrence, while injection of CAF-derived ANXA6+ EVs enhanced tumorigenesis. We found that the presence of ANXA6+ EVs in serum was restricted to PDA patients and represents a potential biomarker for PDA grade. These findings suggest that CAF-tumor cell crosstalk supported by ANXA6+ EVs is predictive of PDA aggressiveness, highlighting a therapeutic target and potential biomarker for PDA.

Published
2016

32. Impact of long term water deficit on production and flowering occurrence in the ‘Granny Smith’ apple tree cultivar

Author

Benoit Pallas, Weiwei Yang, Jean-Baptiste Durand, Sébastien Martinez, Evelyne Costes, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), College of horticulture, Northwest Agriculture and Forestry University, Modelling and Inference of Complex and Structured Stochastic Systems (MISTIS ), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Durand, Jean-Baptiste, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), SWSAF, Modelling and Inference of Complex and Structured Stochastic Systems (MISTIS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut National Polytechnique de Grenoble (INPG), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Prof. Dr. Luca Corelli-Grappadelli, Department of Agricultural Sciences, Università di Bologna, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
malus domestica, Vegetal Biology, Water stress, variété granny smith, fungi, alternance de production, food and beverages, composante du rendement, fructification, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Biennal bearing, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics, Flowering, biennial bearing, Yield components, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Architecture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, stress hydrique, relation croissance fructification, croissance végétative, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], Biologie végétale, architecture de la plante
Abstract

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières; International audience; Apple trees are usually irrigated to avoid yield losses due to water deficit but the shortage of water has become a critical problem in apple orchards. Nevertheless, most of the studies that have been conducted on tree responses to water stress have focused on shoot, leaf and fruit growth during a single growing season. This study presents the results of an experiment performed over 8 years on Granny Smith trees subjected to well watered and water stressed conditions. The yearly production of growth units along branches and the yield components (number of fruit, yield and individual fruit weight) were recorded over the experimental period. Statistical indexes adapted from the biennial bearing index were computed to analyze the impact of water stress on biennial bearing. Trees subjected to water stress did not display any significant decrease in total yield. Nevertheless, water stress increased crop load (number of fruit per trunk cross sectional area) and the total number of harvested fruit over the experimental period. Conversely, water stress decreased the individual fruit weight whatever the year. The increase in the cumulative number of harvested fruit and crop load were mainly associated with a higher proportion of floral GUs under water stress, especially in OFF years, this leading to reduce biennial bearing in this condition. The observed increase in the transition probability towards flowering along branches was hypothesized to be related to a decrease in vegetative growth under water stress that can favor floral induction in the meristems. The decrease in individual fruit weight under water stress was interpreted as the result of the increase in crop load. This study showed that water stress affects yield components by modifying the equilibrium between vegetative and reproductive growth. Forthcoming works will further analyze the effect of water stress taking into account the genotypic variability.

Published
2016

33. Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

Author

Erica A. Di Pierro, Mario Di Guardo, Sébastien Martinez, Marco C. A. M. Bink, Jean-Jacques Kelner, Evelyne Costes, François Laurens, Eric van de Weg, Alix Allard, Jean Michel Legave, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Biometris, Wageningen University and Research Centre [Wageningen] (WUR), Research and Innovation Centre, Edmund Mach Foundation (FEM), Wageningen UR Plant Breeding, Department of Biosciences, University of Milan, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, European Project: 265582, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Wageningen University and Research [Wageningen] (WUR), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Università degli Studi di Milano = University of Milan (UNIMI), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Costes, Evelyne, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, 0301 basic medicine, Candidate gene, dormancy, genetic structures, Physiology, QTL, approche gène candidat, Plant Science, 01 natural sciences, Laboratorium voor Plantenveredeling, Climate change, date de floraison, Phenology QTL, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Genetics, education.field_of_study, changement climatique, Vegetal Biology, biology, Biologie du développement, food and beverages, Single Nucleotide, PE&RC, Development Biology, Pedigree, Biometris, DAM genes, Dormancy, Flowering genes, Malus×domestica (Borkh), Pedigree-based analysis, Malus, flowering genes, Trait, PBR Biodiversity and genetic variation, Research Paper, Population, Quantitative Trait Loci, Single-nucleotide polymorphism, Flowers, Quantitative trait locus, Genes, Plant, Polymorphism, Single Nucleotide, phenology, Genetic determinism, 03 medical and health sciences, PBR Biodiversiteit en Genetische Variatie, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Allele, Polymorphism, education, arbre fruitier, fungi, Malus×domestica (Borkh), pedigree-based analysis, Haplotypes, Plant Breeding, Plant, biology.organism_classification, dormance, Malusà domestica (Borkh), 030104 developmental biology, Genes, 13. Climate action, malus domestica borkh, EPS, Biologie végétale, 010606 plant biology & botany
Abstract

Highlight QTLs and candidate genes for the regulation of budbreak and flowering time reveal new hypotheses on temperature perception in growth resumption at spring time in apple., In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6–21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase.

Published
2016

34. Contribution de l'imagerie infrarouge thermique infrarouge à haute résolution à un phénotypage sur site à haut débit d'une progéniture de pomme soumise à des contraintes hydriques

Author

Nicolas Virlet, Jean-Luc Regnard, Sébastien Martinez, Evelyne Costes, Audrey Jolivot, Pierre-Eric Lauri, David Gómez-Candón, Sylvain Labbé, Valentine Lebourgeois, Science du sol et environnement (MONTP UMR SOL ENVI), Institut National de la Recherche Agronomique (INRA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Montpellier SupAgro, Languedoc-Roussillon Region, Telerieg (Interreg IV) : SOE1/P2/E082, HiriFAP (Agropolis Fondation) : ANR-10-LABX-0001-01, Agreenium EcoHort programme, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)

Subjects
0106 biological sciences, IMAGERIE, variabilité génétique, 01 natural sciences, high spatial resolution, remote sensing, Evapotranspiration, Image resolution, malus domestica, Vegetal Biology, température de la feuille, [SDE.IE]Environmental Sciences/Environmental Engineering, déficit hydrique, télédétection aéroportée, drought stress, 04 agricultural and veterinary sciences, Vegetation, agriculture de précision, Agricultural sciences, photographie aérienne, Geography, Field trial, imagery, F60 - Physiologie et biochimie végétale, Apple tree, Horticulture, analyse d'image, Normalized Difference Vegetation Index, stress du à la sécheresse, Altitude, [SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture, DEFICIT EN EAU, irrigation à la parcelle, TELEDETECTION, Remote sensing, STRESS HYDRIQUE, TEMPERATURE DE SURFACE, canopy surface temperature, genetic variability, image resolution, Malus × domestica, transpiration, water deficit index, Pixel, INFRAROUGE THERMIQUE, 15. Life on land, HAUTE RESOLUTION SPATIALE, transpiration des feuilles, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, imagerie haute resolution, H50 - Troubles divers des plantes, U30 - Méthodes de recherche, Biologie végétale, Sciences agricoles, 010606 plant biology & botany
Abstract

International audience; The genetic variability of fruit trees in response to drought stress is scarcely studied. As adaptation of scion cultivars to abiotic constraints constitutes a new challenge for fruit production, in particular where water scarcity is likely to occur, development of high-throughput phenotyping strategies applicable in the field to assess the tree response to soil drought among large populations is needed, overcoming the limitations of usual in-planta measurements. In this research, remotely sensed images were acquired by ultra-light aircraft (ULA) and an unmanned aerial vehicle (UAV) during 4 years in a field trial where an apple progeny (122 hybrids) was studied under contrasted summer irrigation regimes. Ortho-images were simultaneously acquired in visible (RGB), near-infrared (NIR) and thermalinfrared (TIR) bands. After rthorectification, georeferencing and mosaicking, RGB and NIR images were used to compute different vegetation indices over the field trial, while TIR imaging allowed extraction of the vegetation surface temperature (Ts), which was calibrated at ground level by using hot and cold reference targets. The Morans'f water deficit index (WDI), which combines the surface minus air temperature (Ts-Ta) and the normalized difference vegetation index (NDVI), was used as a stress phenotypic variable. WDI estimates the ratio of actual to maximal evapotranspiration (WDI=1.ETact/ETmax) in discontinuous plant covers. Like the Ts-Ta variable, it significantly discriminated the tree water statuses and genotypes. On the basis of different plant- and image-based indices, individual tree behaviour trends (isohydric vs. anisohydric) can be distinguished among the progeny, irrespective of tree vigour. This opens potential applications for plant breeding, and genetic bases of apple tree response to water stress are currently investigated through quantitative trait locus (QTL) detection. Making use of ULA with flights performed at 40-60 m altitude made it possible to strongly improve the TIR image resolution ('10 cm) and to limit the number of vegetation/soil mixed pixels. However, it will require careful image posttreatment, possibly including classification and/or segmentation.

Published
2016

35. Genetic variability and phenotypic plasticity of apple morphological responses to soil water restriction in relation with leaf functions and stem xylem conductivity

Author

Jean-Luc Regnard, Pierre-Eric Lauri, Tete Severien Barigah, Marco Zibordi, Pasquale Losciale, Luigi Manfrini, Evelyne Costes, Gerardo Lopez, Sébastien Martinez, Luca Corelli-Grappadelli, Lauri, Pierre-Éric, Barigah, Têtè Sévérien, Lopez, Gerardo, Martinez, Sébastien, Losciale, Pasquale, Zibordi, Marco, Manfrini, Luigi, Corelli-Grappadelli, Luca, Costes, Evelyne, Regnard, Jean-Luc, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Dipartimento Scienze Agrarie, University of Bologna, Research Unit for Agriculture in Dry Environments, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), ARIMNET research program APMed (Apple and Peach in Mediterranean orchards-Integrating tree water status and irrigation management for coping with water scarcity and aphid control), European Project: 265582, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Bologna/Università di Bologna, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Council for Agricultural Research and Economics (CREA), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, 0301 basic medicine, Stomatal conductance, Plasticity, Physiology, [SDV]Life Sciences [q-bio], variabilité génétique, pommier, Apple tree, Plant Science, Biology, 01 natural sciences, water stress, 03 medical and health sciences, Soil drought stre, Botany, Genetic variation, plasticité de l'architecture, apple tree, Genetic variability, Transpiration, Phenotypic plasticity, Ecology, Soil drought stress, fungi, adaptation au stress, Apple, Xylem, food and beverages, Forestry, 15. Life on land, Horticulture, 030104 developmental biology, 13. Climate action, Plant morphology, Shoot growth, Iso-anisohydry, croissance des arbres, stress hydrique, écophysiologie végétale, 010606 plant biology & botany
Abstract

In drought-stressed apple, leaf area decrease and stem growth cessation increase are key determinants of drought avoidance. Both the genotype and its possible phenotypic plasticity contribute to the variability of responses. Under soil water restriction, plant growth is impaired by the indirect negative impact on plant carbon balance of stomata closure and hydraulic failure. The relative contributions of these two phenomena have been scarcely explored in trees under different drought-stress intensities, and even less work is published which accounts for genetic variability and phenotypic plasticity. Working on 21 apple genotypes from the same progeny, we assessed the effects of two consecutive periods of soil drought, moderate and severe, on growth and functional patterns of leaf and stem. Leaf area decreased while temporary stem growth cessation increased under drought with strong variations depending on the genotype. These results suggested that both reduction of transpiring leaf area and leaf organogenesis are key determinants for drought avoidance in the apple. Results also confirmed the pivotal role of stomatal conductance (g s) in maintaining percent loss of conductivity of the stem xylem (PLC) under values for runaway embolism (ca. 14 % under severe drought). The sorting of genotypes according to their morphological response to drought showed that genotypes with high reduction of growth were characterized by similar g s but lower PLC than genotypes with medium and low reduction of growth. This suggests that for a given level of stomatal closure the drought-related reduction of leaf area could also limit the progression of cavitation in stem xylem. As a whole, the variability of morphological responses of apple genotypes to contrasted drought conditions indicated that both genetic variability and phenotypic plasticity are involved in the range of iso-anisohydry documented for this species.

Published
2016

36. Genetic Variation of Morphological Traits and Transpiration in an Apple Core Collection under Well-Watered Conditions: Towards the Identification of Morphotypes with High Water Use Efficiency

Author

Benoît Pallas, Pierre-Eric Lauri, Evelyne Costes, Gerardo Lopez, Sébastien Martinez, Jean-Luc Regnard, Charles-Eric Durel, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, BAP-INRA department, Marie-Curie FP7 COFUND People Programme AgreenSkills’ fellowship grant number: 267196, European Project: 265582, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Perennial plant, Water Wells, lcsh:Medicine, Biomass, 01 natural sciences, transpiration, Trees, lcsh:Science, morphotype, Transpiration, 0303 health sciences, Vegetal Biology, architecture de l'arbre, Multidisciplinary, food and beverages, Spatial heterogeneity, plateforme de phénotypage, Phenotype, Malus, core collection, efficience d'utilisation de l'eau, Research Article, Genotype, pommier, Plant Development, Context (language use), Biology, 03 medical and health sciences, Genetic variation, biomasse, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, classification hiérarchique ascendante, Water-use efficiency, coefficient d'heritabilité, 030304 developmental biology, lcsh:R, Genetic Variation, Water, Plant Transpiration, 15. Life on land, Heritability, Plant Leaves, Agronomy, Seedlings, lcsh:Q, Biologie végétale, contrôle génétique, 010606 plant biology & botany
Abstract

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresData Availability: The relevant DOIs/accession numbers required to access raw data in Zenodo is: http://dx.doi.org/10.5281/zenodo.35030 (doi: 10.5281/zenodo.35030).; Water use efficiency (WUE) is a quantitative measurement which improvement is a major issue in the context of global warming and restrictions in water availability for agriculture. In this study, we aimed at studying the variation and genetic control of WUE and the respective role of its components (plant biomass and transpiration) in a perennial fruit crop. We explored an INRA apple core collection grown in a phenotyping platform to screen one-year-old scions for their accumulated biomass, transpiration and WUE under optimal growing conditions. Plant biomass was decompose into morphological components related to either growth or organ expansion. For each trait, nine mixed models were evaluated to account for the genetic effect and spatial heterogeneity inside the platform. The Best Linear Unbiased Predictors of genetic values were estimated after model selection. Mean broad-sense heritabilities were calculated from variance estimates. Heritability values indicated that biomass (0.76) and WUE (0.73) were under genetic control. This genetic control was lower in plant transpiration with an heritability of 0.54. Across the collection, biomass accounted for 70% of the WUE variability. A Hierarchical Ascendant Classification of the core collection indicated the existence of six groups of genotypes with contrasting morphology and WUE. Differences between morphotypes were interpreted as resulting from differences in the main processes responsible for plant growth: cell division leading to the generation of new organs and cell elongation leading to organ dimension. Although further studies will be necessary on mature trees with more complex architecture and multiple sinks such as fruits, this study is a first step for improving apple plant material for the use of water.

Published
2015

37. Genetic determinism of anatomical and hydraulic traits within an apple progeny

Author

Catherine Trottier, Marc Lartaud, Xavier Bry, Pierre-Eric Lauri, Sébastien Martinez, Véronique Ripetti, Hervé Cochard, Evelyne Costes, Olivier Gorza, and Jean-Marc Celton

Subjects
0106 biological sciences, 0303 health sciences, Water transport, Physiology, Apple tree, Xylem, Plant Science, 15. Life on land, Biology, Quantitative trait locus, Heritability, 01 natural sciences, 03 medical and health sciences, Horticulture, Botany, Principal component analysis, Genetic variability, Fruit tree, 030304 developmental biology, 010606 plant biology & botany
Abstract

The apple tree is known to have an isohydric behaviour, maintaining rather constant leaf water potential in soil with low water status and/or under high evaporative demand. However, little is known on the xylem water transport from roots to leaves from the two perspectives of efficiency and safety, and on its genetic variability. We analysed 16 traits related to hydraulic efficiency and safety, and anatomical traits in apple stems, and the relationships between them. Most variables were found heritable, and we investigated the determinism underlying their genetic control through a quantitative trait loci (QTL) analysis on 90 genotypes from the same progeny. Principal component analysis (PCA) revealed that all traits related to efficiency, whether hydraulic conductivity, vessel number and area or wood area, were included in the first PC, whereas the second PC included the safety variables, thus confirming the absence of trade-off between these two sets of traits. Our results demonstrated that clustered variables were characterized by common genomic regions. Together with previous results on the same progeny, our study substantiated that hydraulic efficiency traits co-localized with traits identified for tree growth and fruit production.

Published
2011

38. The PTK7 and ROR2 Protein Receptors Interact in the Vertebrate WNT/Planar Cell Polarity (PCP) Pathway *

Author

Virginie Thomé, Anne-Catherine Lhoumeau, Laurent Kodjabachian, Sébastien Martinez, Pierluigi Scerbo, Avais M. Daulat, Jean-Paul Borg, Marilyn Giordano, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), BORG, Jean-Paul, Aix Marseille Université (AMU)-Institut Paoli-Calmettes, and Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Embryo, Nonmammalian, planar cell polarity, [SDV.BC.IC] Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Xenopus Proteins, migration, Biochemistry, Receptor tyrosine kinase, Xenopus laevis, 0302 clinical medicine, Cell polarity, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Morphogenesis, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Wnt Signaling Pathway, ROR2, Orphan receptor, 0303 health sciences, Wnt signaling pathway, Cadherins, xenopus, PTK7, [SDV.BDD.MOR] Life Sciences [q-bio]/Development Biology/Morphogenesis, 3. Good health, Cell biology, protein-tyrosine kinase (tyrosine kinase), cell polarity, 030220 oncology & carcinogenesis, WNT5A, Tyrosine kinase, Active Transport, Cell Nucleus, Wnt pathway, Receptor tyrosine kinase-like orphan receptor, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Receptor Tyrosine Kinase-like Orphan Receptors, Wnt-5a Protein, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, Animals, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, development, 030304 developmental biology, Cell Nucleus, Receptor Protein-Tyrosine Kinases, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Cell Biology, Protocadherins, Wnt Proteins, body regions, HEK293 Cells, biology.protein, JNK
Abstract

Background: The planar cell polarity pathway plays important roles in morphogenetic processes. Results: PTK7 and ROR2 form a heterodimeric complex and bind to WNT5A, promoting JNK phosphorylation and regulating expression of paraxial protocadherin. Conclusion: PTK7 and ROR2 promote cell movement in mammalian cells and coordinate cell polarity during morphogenetic movements. Significance: We reveal new mechanisms of action of PTK7 in WNT/PCP signaling., The non-canonical WNT/planar cell polarity (WNT/PCP) pathway plays important roles in morphogenetic processes in vertebrates. Among WNT/PCP components, protein tyrosine kinase 7 (PTK7) is a tyrosine kinase receptor with poorly defined functions lacking catalytic activity. Here we show that PTK7 associates with receptor tyrosine kinase-like orphan receptor 2 (ROR2) to form a heterodimeric complex in mammalian cells. We demonstrate that PTK7 and ROR2 physically and functionally interact with the non-canonical WNT5A ligand, leading to JNK activation and cell movements. In the Xenopus embryo, Ptk7 functionally interacts with Ror2 to regulate protocadherin papc expression and morphogenesis. Furthermore, we show that Ptk7 is required for papc activation induced by Wnt5a. Interestingly, we find that Wnt5a stimulates the release of the tagged Ptk7 intracellular domain, which can translocate into the nucleus and activate papc expression. This study reveals novel molecular mechanisms of action of PTK7 in non-canonical WNT/PCP signaling that may promote cell and tissue movements.

Published
2015

39. Safe reconfiguration of Coqcots and Pycots components

Author

Fabien Dagnat, Jérémy Buisson, Sébastien Martinez, Elena Leroux, ArchWare, Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec, Centre de Recherche des Ecoles de St-Cyr Coëtquidan (CREC), Ecoles de St-Cyr Coëtquidan, Département informatique (INFO), Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT), Process for Adaptative Software Systems (PASS), Télécom Bretagne-LANGAGE ET GÉNIE LOGICIEL (IRISA-D4), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Rennes 1 (UR1), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), LANGAGE ET GÉNIE LOGICIEL (IRISA-D4), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA)

Subjects
ACM: D.: Software/D.2: SOFTWARE ENGINEERING/D.2.11: Software Architectures, Correctness, Coqcots, Computer science, Dynamic software updating, Distributed computing, ACM: D.: Software/D.2: SOFTWARE ENGINEERING/D.2.4: Software/Program Verification, 02 engineering and technology, dynamic software updating, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], component model, Software, User experience design, runtime evolution, 0202 electrical engineering, electronic engineering, information engineering, Coq, DSU, Software system, ACM: D.: Software/D.2: SOFTWARE ENGINEERING/D.2.7: Distribution, Maintenance, and Enhancement, computer.programming_language, business.industry, Control reconfiguration, 020207 software engineering, computer.file_format, Python (programming language), Dynamic reconfiguration, Hardware and Architecture, Middleware, ACM: D.: Software/D.2: SOFTWARE ENGINEERING, 020201 artificial intelligence & image processing, Executable, business, computer, Information Systems, Python
Abstract

Dynamic reconfiguration without suspending components.Integration of dynamic software updating and dynamic architecture reconfiguration.Coq proof mode as an interactive development environment for reconfigurations.Bidirectional translation between middleware and Coq-based abstract component model. Display Omitted Software systems have to face evolutions of their running context and users. Therefore, the so-called dynamic reconfiguration has been commonly adopted for modifying some components and/or the architecture at runtime. Traditional approaches typically stop the needed components, apply the changes, and restart the components. However, this scheme is not suitable for critical systems and degrades user experience. This paper proposes to switch from the stop/restart scheme to dynamic software updating (DSU) techniques. Instead of stopping a component, its implementation is replaced by another one specifically built to apply the modifications while maintaining the best quality of service possible. The major contributions of this work are: (i) the integration of DSU techniques in a component model; (ii) a reconfiguration development process including specification, proof of correctness using Coq, and; (iii) a systematic method to produce the executable script. In this perspective, the use of DSU techniques brings higher quality of service when reconfiguring component-based software. Moreover, the formalization allows ensuring the safety and consistency of the reconfiguration process.

Published
2015

40. The PTK7 Receptor Family

Author

Anne-Catherine Lhoumeau, Sébastien Martinez, Thomas Prebet, and Jean-Paul Borg

Subjects
Transmembrane domain, Chemistry, ROR1, Extracellular, PTK7, Matrix metalloproteinase, Ligand (biochemistry), Neuron-derived orphan receptor 1, Domain (software engineering), Cell biology
Abstract

PTK7 represents the only member of its family. It has a classical RTK structure with an extracellular domain, a transmembrane domain, and an intracellular domain. However, this domain lacks catalytic activity and therefore PTK7 also belongs to the pseudokinase group. PTK7 is processed by metalloproteinases MT1-MPP and ADAMs and sequentially by γ-secretase. No ligand has been identified to date.

Published
2015

41. Plasticity in vegetative growth over contrasted growing sites of an F1 Olive tree progeny during its juvenile phase

Author

Nathalie Moutier, Bouchaib Khadari, Lorenzo León, Sébastien Martinez, Evelyne Costes, Gilbert Garcia, Angelina Belaj, Inès Ben Sadok, Raúl de la Rosa, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de l’olivier de Sfax, Ctr Alameda Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, phase juvénile, media_common.quotation_subject, lcsh:Medicine, Biology, 01 natural sciences, 03 medical and health sciences, olivier, Olea, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant breeding, Gene–environment interaction, lcsh:Science, 030304 developmental biology, media_common, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Vegetal Biology, architecture de l'arbre, Models, Genetic, Ecology, lcsh:R, 15. Life on land, Heritability, Olive trees, interaction génotype environnement, Plant Breeding, Tree (data structure), Seedlings, Trait, croissance des arbres, Gene-Environment Interaction, lcsh:Q, Habit, adaptation au changement climatique, Fruit tree, Biologie végétale, Research Article, 010606 plant biology & botany
Abstract

Climatic changes impact fruit tree growth and severely limit their production. Investigating the tree ability to cope with environmental variations is thus necessary to adapt breeding and management strategies in order to ensure sustainable production. In this study, we assessed the genetic parameters and genotype by environment interaction (GxE) during the early tree growth. One hundred and twenty olive seedlings derived from the cross 'Olivière' x 'Arbequina' were examined across two sites with contrasted environments, accounting for ontogenetic trends over three years. Models including the year of growth, branching order, environment, genotype effects, and their interactions were built with variance function and covariance structure of residuals when necessary. After selection of a model, broad sense heritabilities were estimated. Despite strong environmental effect on most traits, no GxE was found. Moreover, the internal structure of traits co-variation was similar in both sites. Ontogenetic growth variation, related to (i) the overall tree form and (ii) the growth and branching habit at growth unit scale, was not altered by the environment. Finally, a moderate to strong genetic control was identified for traits at the whole tree scale and at internode scale. Among all studied traits, the maximal internode length exhibited the highest heritability (H2 = 0.74). Considering the determinant role of this trait in tree architecture and its stability across environments, this study consolidates its relevance for breeding.

Published
2015

42. Multispectral airborne imagery in the field reveals genetic determinisms of morphological and transpiration traits of an apple tree hybrid population in response to water deficit

Author

Jean-Jacques Kelner, Nicolas Virlet, Jean-Luc Regnard, Evelyne Costes, Sébastien Martinez, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
0106 biological sciences, Physiology, Genetic Linkage, QTL, Multispectral image, Plant Science, Multispectral imagery, 01 natural sciences, Trees, index de végétation, modèle linéaire, imagerie multispectrale à haute résolution, Vegetation index, vegetation index, Thermal infrared, Transpiration, malus domestica, 0303 health sciences, education.field_of_study, Vegetal Biology, déficit hydrique, Malus×domestica, Surface temperature, food and beverages, Vegetation, Droughts, Phenotype, Malus, Seasons, Rootstock, Research Paper, déterminisme génétique, Population, Quantitative Trait Loci, Apple tree, Quantitative trait locus, Biology, quantitative trait locus (QTL), 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, 030304 developmental biology, Water, Plant Transpiration, 15. Life on land, Heritability, Agronomy, Fruit, Remote Sensing Technology, acquisition d'image, Biologie végétale, 010606 plant biology & botany
Abstract

Highlight This research successfully used image-based spectral indices acquired in the field to assess variability of response to drought in a tree mapping population and to detect the related genetic determinisms., Genetic studies of response to water deficit in adult trees are limited by low throughput of the usual phenotyping methods in the field. Here, we aimed at overcoming this bottleneck, applying a new methodology using airborne multispectral imagery and in planta measurements to compare a high number of individuals. An apple tree population, grafted on the same rootstock, was submitted to contrasting summer water regimes over two years. Aerial images acquired in visible, near- and thermal-infrared at three dates each year allowed calculation of vegetation and water stress indices. Tree vigour and fruit production were also assessed. Linear mixed models were built accounting for date and year effects on several variables and including the differential response of genotypes between control and drought conditions. Broad-sense heritability of most variables was high and 18 quantitative trait loci (QTLs) independent of the dates were detected on nine linkage groups of the consensus apple genetic map. For vegetation and stress indices, QTLs were related to the means, the intra-crown heterogeneity, and differences induced by water regimes. Most QTLs explained 15−20% of variance. Airborne multispectral imaging proved relevant to acquire simultaneous information on a whole tree population and to decipher genetic determinisms involved in response to water deficit.

Published
2015

43. Erratum to: Genetic variability and phenotypic plasticity of apple morphological responses to soil water restriction in relation with leaf functions and stem xylem conductivity

Author

Pierre-Éric Lauri, Têtè Sévérien Barigah, Gerardo Lopez, Sébastien Martinez, Pasquale Losciale, Marco Zibordi, Luigi Manfrini, Luca Corelli-Grappadelli, Evelyne Costes, and Jean-Luc Regnard

Subjects
010504 meteorology & atmospheric sciences, Ecology, Physiology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Forestry, 04 agricultural and veterinary sciences, Plant Science, 01 natural sciences, 0105 earth and related environmental sciences
Published
2016

44. Author Correction: In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer

Author

Dzana Dervovic, Ahmad A. Malik, Edward L. Y. Chen, Masahiro Narimatsu, Nina Adler, Somaieh Afiuni-Zadeh, Dagmar Krenbek, Sebastien Martinez, Ricky Tsai, Jonathan Boucher, Jacob M. Berman, Katie Teng, Arshad Ayyaz, YiQing Lü, Geraldine Mbamalu, Sampath K. Loganathan, Jongbok Lee, Li Zhang, Cynthia Guidos, Jeffrey Wrana, Arschang Valipour, Philippe P. Roux, Jüri Reimand, Hartland W. Jackson, and Daniel Schramek

Subjects
Science
Published
2023
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45. Coqcots & Pycots: non-stopping components for safe dynamic reconfiguration

Author

Sébastien Martinez, Everton Calvacante, Jérémy Buisson, Elena Leroux, Fabien Dagnat, ArchWare, Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec, Ecoles de Saint-Cyr Coëtquidan [Guer], Université de Bretagne Sud (UBS), Departamento de Informática e Matemática Aplicada [Natal] (DIMAp), Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Process for Adaptative Software Systems (PASS), Télécom Bretagne-LANGAGE ET GÉNIE LOGICIEL (IRISA-D4), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Rennes 1 (UR1), Département informatique (INFO), Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Université de Rennes 1 (UR1), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), and LANGAGE ET GÉNIE LOGICIEL (IRISA-D4)

Subjects
Correctness, Coqcots, business.industry, Computer science, dynamic reconfiguration, Quality of service, Distributed computing, Dynamic software updating, Control reconfiguration, computer.file_format, dynamic software updating, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], component model, Pycots, D.2.11, Software, User experience design, runtime evolution, Coq, DSU, Software system, Executable, business, computer, Python
Abstract

International audience; Software systems have to face evolutions of their running context and users. Therefore, the so-called dynamic reconfiguration has been commonly adopted for modifying some components and/or the architecture at runtime. Traditional approaches typically stop the needed components, apply the changes, and restart the components. However, this scheme is not suitable for critical systems and degrades user experience. This paper proposes to switch from the stop/restart scheme to dynamic software updating (DSU) techniques. Instead of stopping a component, its implementation is replaced by another one specifically built to apply the modifications while maintaining the best quality of service possible. The major contributions of this work are: (i) the integration of DSU techniques in a component model, and; (ii) a reconfiguration development process including specification, proof of correctness using Coq, and a systematic method to produce the executable script. In this perspective, the use of DSU techniques brings higher quality of service when reconfiguring component-based software and the formalization allows ensuring the safety and consistency of the reconfiguration process.

Published
2014

46. Stress indicators based on airborne thermal imagery for field phenotyping a heterogeneous tree population for response to water constraints

Author

Valentine Lebourgeois, Sébastien Martinez, Nicolas Virlet, Jean-Luc Regnard, Sylvain Labbé, Evelyne Costes, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
Physiology, [SDV]Life Sciences [q-bio], Multispectral image, Phénotype, F62 - Physiologie végétale - Croissance et développement, Plant Science, drought, surface temperature, Trees, remote sensing, Evapotranspiration, Statistics, Range (statistics), Température de l'air, education.field_of_study, Ecology, Indice de surface foliaire, Temperature, phenomics, Vegetation, F70 - Taxonomie végétale et phytogéographie, Fruits tempérés, Droughts, Physiologie végétale, water deficit index (WDI), Bilan hydrique, Imagerie, temperate fruit species, Research Paper, vegetation index, Stress dû à la sécheresse, Télédétection, Population, evapotranspiration, Malus × domestica Borkh, education, Culture fruitière, 15. Life on land, Évapotranspiration, Quantile regression, Malus pumila, Environmental science, Plant cover, H50 - Troubles divers des plantes, Quantile
Abstract

Highlight text Thermal infrared imagery contributes to the phenotyping of crop response to water stress. Based on multispectral images, the Vegetation Index–Temperature (VIT) concept constitutes a relevant approach., As field phenotyping of plant response to water constraints constitutes a bottleneck for breeding programmes, airborne thermal imagery can contribute to assessing the water status of a wide range of individuals simultaneously. However, the presence of mixed soil–plant pixels in heterogeneous plant cover complicates the interpretation of canopy temperature. Moran’s Water Deficit Index (WDI = 1–ETact/ETmax), which was designed to overcome this difficulty, was compared with surface minus air temperature (T s–T a) as a water stress indicator. As parameterization of the theoretical equations for WDI computation is difficult, particularly when applied to genotypes with large architectural variability, a simplified procedure based on quantile regression was proposed to delineate the Vegetation Index–Temperature (VIT) scatterplot. The sensitivity of WDI to variations in wet and dry references was assessed by applying more or less stringent quantile levels. The different stress indicators tested on a series of airborne multispectral images (RGB, near-infrared, and thermal infrared) of a population of 122 apple hybrids, under two irrigation regimes, significantly discriminated the tree water statuses. For each acquisition date, the statistical method efficiently delineated the VIT scatterplot, while the limits obtained using the theoretical approach overlapped it, leading to inconsistent WDI values. Once water constraint was established, the different stress indicators were linearly correlated to the stem water potential among a tree subset. T s–T a showed a strong sensitivity to evaporative demand, which limited its relevancy for temporal comparisons. Finally, the statistical approach of WDI appeared the most suitable for high-throughput phenotyping.

Published
2014

47. Fruit self-thinning: a trait to consider for genetic improvement of apple tree

Author

Marie José James, Evelyne Costes, Amina Khelifi Touhami, Charles-Eric Durel, François Laurens, Jean-Jacques Kelner, Sébastien Martinez, Jean-Marc Celton, Abdel Bechti, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Pépinières et Roseraies G. Delbard, department BAP (Plant Biology and Breeding), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Costes, Evelyne

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, Heredity, Genetic Linkage, Ingénierie des aliments, lcsh:Medicine, Plant Science, Plant Genetics, Trees, Contig Mapping, [SDV.IDA]Life Sciences [q-bio]/Food engineering, lcsh:Science, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 2. Zero hunger, Vegetal Biology, auto-éclaircie, Multidisciplinary, biology, Biologie du développement, food and beverages, Agriculture, Genomics, Plants, Trait Locus, Development Biology, environnement, Agricultural sciences, rentabilité, Horticulture, Phenotypes, Phenotype, Inflorescence, Malus, Alimentation et Nutrition, Trait, Research Article, déterminisme génétique, Genotype, conduite de la plante, Quantitative Trait Loci, Apple tree, Crops, Quantitative trait locus, Genes, Plant, Fruits, Abscission, Xylem, Botany, Genetics, Food engineering, Food and Nutrition, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant breeding, Biology, Crosses, Genetic, arboriculture, Models, Genetic, Quantitative Traits, fungi, lcsh:R, 15. Life on land, biology.organism_classification, Sustainable Agriculture, Plant Breeding, Fruit, éclaircissage chimique, malus domestica borkh, lcsh:Q, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Sciences agricoles, Biologie végétale, Developmental Biology
Abstract

In apple (Malus x domestica Borkh), as in many fruiting crops, fruit maintenance vs abscission is a major criteria for production profitability. Growers routinely make use of chemical thinning agents to control total fruit load. However, serious threats for the environment lead to the demand for new apple cultivars with self-thinning properties. In this project, we studied the genetic determinism of this trait using a F1 progeny derived from the cross between the hybrid INRA X3263, assumed to possess the self-thinning trait, and the cultivar ‘Belre`ne’. Both counting and percentage variables were considered to capture the fruiting behaviour on different shoot types and over three consecutive years. Besides low to moderate but significant genetic effects, mixed models showed considerable effects of the year and the shoot type, as well as an interaction effect. Year effect resulted mainly from biennial fruiting. Eight Quantitative Trait Locus (QTL) were detected on several linkage groups (LG), either independent or specific of the year of observation or the shoot type. The QTL with highest LOD value was located on the top third of LG10. The screening of three QTL zones for candidate genes revealed a list of transcription factors and genes involved in fruit nutrition, xylem differentiation, plant responses to starvation and organ abscission that open new avenues for further molecular investigations. The detailed phenotyping performed revealed the dependency between the self-thinning trait and the fruiting status of the trees. Despite a moderate genetic control of the self-thinning trait, QTL and candidate genes were identified which will need further analyses involving other progenies and molecular investigations.

Published
2014

48. Correction: QTL Mapping of Flowering and Fruiting Traits in Olive

Author

Bouchaib Khadari, Ahmed Rebai, Gilbert Garcia, Laila Essalouh, Jean-Marc Celton, Amal Zine El Aabidine, Sébastien Martinez, Evelyne Costes, Inès Ben Sadok, and Naziha Grati-Kamoun

Subjects
Multidisciplinary, Science, lcsh:R, Correction, lcsh:Medicine, Quantitative trait locus, Biology, Bioinformatics, Evolutionary biology, Medicine, lcsh:Q, lcsh:Science
Abstract

Only a portion of Figure 5 is included in the article. Please find a full version of Figure 5 here

Published
2014

49. Abstract A61: CAF-derived ANXA6+-exosomes support pancreatic cancer aggressiveness and serve as a circulating biomarker

Author

Marion Rubis, Daniel Pietrasz, Samuel Granjeaud, Pascale Zimmermann, Sébastien Martinez, Juan L. Iovanna, Christine Brun, Celine Loncle, Mehdi Ouaissi, Jérémy Nigri, Jean-Baptiste Bachet, Julie Leca, Stéphane Garcia, Richard Tomasini, Véronique Secq, Nelson Dusetti, Sophie Vasseur, Julie Roques, and Sophie Lac

Subjects
Oncology, Cancer Research, medicine.medical_specialty, Circulating biomarkers, business.industry, Internal medicine, Pancreatic cancer, medicine, medicine.disease, business, Microvesicles
Abstract

Pancreatic ductal adenocarcinoma (PDA) is one of deadliest human malignancies with a median survival barely reaching 6 months post-diagnosis. Such epidemiologic data highlight the urgent need to refine current therapies by integrating recent available knowledge on PDA biology. The malignant progression of PDA is characterized by the presence of an exuberant intra-tumoral microenvironment mainly composed of cancer associated fibroblasts (CAFs) and immune cells. This compartment interacts with pancreatic tumor cells surrounded by dense matrix and hypoxic areas, and affects their behavior through a poorly understood network. Indeed, cellular crosstalk between stromal and tumor cells is of major importance in pancreatic ductal adenocarcinoma (PDA). Here, by analyzing the proteomic stromal signature of human PDA, we highlight a possible contribution of the ANXA6/LRP1/TSP1 complex in such crosstalk. Following in vivo validations and stromal localization of each three candidates, we demonstrated that the formation of this complex is restricted to cancer associated fibroblasts (CAFs) cultured under physiopathological conditions (co-culture with macrophages, under hypoxia and lipid deprivation). Increased PDA aggressiveness is dependent on the uptake by tumor cells of CAFs-derived ANXA6+-exosomes. Targeting of ANXA6, and the relevant complex, in CAFs impairs PDA and metastasis occurrence while injection of ANXA6+-exosomes enhances tumorigenesis. Detection of ANXA6+-exosomes in serum is restricted to PDA patients and can distinguish PDA grade. Our data reveal a new CAF-tumor cell crosstalk supported by ANXA6+-exosomes and highlight a therapeutic target and an interesting biomarker for PDA. Citation Format: Julie Leca, Sebastien Martinez, Sophie Lac, Jeremy Nigri, Veronique Secq, Marion Rubis, Nelson Dusetti, Celine Loncle, Julie Roques, Daniel Pietrasz, Stéphane Garcia, Samuel Granjeaud, Mehdi Ouaissi, Jean-Baptiste Bachet, Christine Brun, Juan L. Iovanna, Pascale Zimmermann, Sophie Vasseur, Richard Tomasini.{Authors}. CAF-derived ANXA6+-exosomes support pancreatic cancer aggressiveness and serve as a circulating biomarker. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A61.

Published
2016

50. ShadObf: A C-Source Obfuscator Based on Multi-objective Optimisation Algorithms

Author

Benoit Bertholon, Sébastien Varrette, and Sébastien Martinez

Subjects
Reverse engineering, Theoretical computer science, Source code, Computer science, business.industry, media_common.quotation_subject, Evolutionary algorithm, Cloud computing, Python (programming language), computer.software_genre, Evolutionary computation, Obfuscation (software), Heuristics, business, computer, media_common, computer.programming_language
Abstract

The development of the new Cloud Computing paradigm as lead to a reevaluation of the security issues. When running a private code on a Public Cloud or on any remote machine, its owner has no guarantees that the code cannot be reverse engineered, understood and modified. One of the solutions for the code owner in order to protect his intellectual property is to obfuscate his algorithms. The obfuscation of source code is a mechanism to modify a source code to make it unintelligible by humans even with the help of computing resources. More precisely, the objective is to conceal the purpose of a program or its logic without altering its functionality, thus preventing the tampering or the reverse engineering of the program. Obfuscation is usually performed by applying transformations to the initial source code, but it reveals many open questions: what transformation should be chosen? In which order should the obfuscator apply them? How can we quantify the obfuscation capacity of a given program? In order to answer these questions, we propose here ShadObf, an obfuscation framework based on evolutionary heuristics designed to optimise for a given input C program, the sequence of transformations that should be applied to the source code to improve its obfuscation capacity. This last measure involves the combination of well known metrics, coming from the Software Engineering area, which are optimised simultaneously thanks to Multi Objective Evolutionary Algorithms. We have validated our approach over a classical matrix multiplication program - experiments on other applications are still in progress.

Published
2013

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