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2. The PPILOW project: Innovations improving welfare in low input and organic pig and poultry farms

Author

Collin, Anne, Meloni, Giuditta, Bonnefous, Claire, Re, Martina, van Vooren, Laura, Niemi, Jarkko, Väre, Minna, Lähtinen, Katja, Tuyttens, Frank A.M., Graat, Evelien, Vanden Hole, Charlotte, Rodenburg, Tb (bas), Kliphuis, Saskia, Giersberg, Mona, Tavares, Olivia, Desaint, Brieuc, Steenfeldt, Sanna, Pedersen, Lene, Engberg, Ricarda M., Almadani Mohamad, Isam, Carelli, Riccardo, Sciarretta, Marlene, Guilloteau, Laurence, Réhault-Godbert, Sophie, Gautron, Joël, Le Bihan-Duval, Elisabeth, Mignon-Grasteau, Sandrine, Berri, Cécile, Guettier, Elodie, Baéza, Elisabeth, Chartrin, Pascal, Bordeau, Thierry, Raynaud, Emilie, Couroussé, Nathalie, Cailleau-Audouin, Estelle, Crochet, Sabine, Tourneur, Léa, Guichaoua, Adrien, van den Brand, Henry, Castellini, Cesare, Reverchon, Maxime, Sourdioux, Michel, Akakpo, Roland, Rangel Pedersen, Ninfa, Schepens, Rene, Almind, Maria, Grenier, Katia, Dubuc, David, Le Lann, Marie-Véronique, Ponzio, Raffaella, Mainardi, Marina, Accotto, Caterina, Coletta, Monica, Guesdon, Vanessa, Leruste, Hélène, Billiard, Bérangère, Ferreira, Vitor Hugo Bessa, Baldinger, Lisa, Pluschke, Helen, Delanoue, Elsa, Laura, Warin, Pertusa, Marion, Stomp, Mathilde, Travel, Angelique, Bouvarel, Isabelle, Germain, Karine, Ravon, Laure, Calandreau, Ludovic, Labas, Valérie, Prunier, Armelle, Merlot, Elodie, Tallet, Céline, Perruchot, Marie-Hélène, Louveau, Isabelle, van Milgen, Jaap, Dessauge, Frederic, Clouard, Caroline, Lebret, Bénédicte, Montagne, Lucile, Faure, Justine, Zuliani, Anna, Venezia, Pietro, Canario, Laurianne, Ferchaud, Stéphane, Cozma, Vasile, Spinu, Marina, Horia Bǎieş, Mihai, Courboulay, Valérie, Roguet, Christine, Gaudré, Didier, Chevillon, Patrick, Alibert, Laurent, Decruyenaere, Virginie, Wavreille, José, Vanggaard, Pia, Vanggaard, Jan, Micheloni, Cristina, Thobe, Petra, Lombard, Sarah, Caillaud, Laura, Bernardet, Nelly, Collet, Julie, Molenaar, Roos, Mattioli, Simona, Hill, Nigel, Cadudal, François, Quentin, Maxime, Leterrier, Christine, Teixeira-Gomes, Ana-Paula, Uzbekova, Svetlana, Maugrion, Emilie, Rocchi, Lucia, Biologie des Oiseaux et Aviculture (BOA), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli Studi di Perugia = University of Perugia (UNIPG), Associazione Italiana per l'Agricoltura Biologica (AIAB), Scuela Santa Anna (SSSA), Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP), BioForum Vlaanderen, Natural Resources Institute Finland (LUKE), Research Institute for Agricultural, Fisheries and Food (ILVO), Utrecht University [Utrecht], Institut Technique de l'Agriculture Biologique (ITAB), Aarhus University [Aarhus], Thuenen Institute of Farm Economics, European Association for Animal Production (EAAP), Les instituts techniques agricoles (Acta), Wageningen University and Research [Wageningen] (WUR), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Fermentation Experts, Équipe Micro et nanosystèmes HyperFréquences Fluidiques (LAAS-MH2F), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Équipe DIagnostic, Supervision et COnduite (LAAS-DISCO), Slow Food Biodiversity, JUNIA (JUNIA), Université catholique de Lille (UCL), Thuenen-Institute of Organic Farming, ITAVI, Elevage Alternatif et Santé des Monogastriques (UE EASM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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), SIVtro VSF Italia, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Expérimentale Elevages Porcins Innovants (GenESI), USAMV Cluj-Napoca, Institut du Porc (IFIP), Centre Wallon de Recherches Agronomiques (CRA-W), Vanggaard Staldmontage, Harper Adams University, EAAP, PPILOW, and European Project: 816172,H2020-EU.3.2.1.1. - Increasing production efficiency and coping with climate change, while ensuring sustainability and resilience ,PPILOW (2019)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SCCO]Cognitive science, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, [SHS]Humanities and Social Sciences
Abstract

International audience; The PPILOW project aims to co-construct innovations to improve Poultry and Pig Welfare in Low-input outdoor and Organic farming systems through a multi-actor approach. PPILOW implements a participatory approach for proposing and studying welfare-improvement levers. It will provide a combination of practical solutions that can be applied at a pan-European level with specific adjustments depending on citizen’s expectations and the target market. The multi-actor approach consists in involving end-users including farmers, breeding companies, feed producers, consumer associations, retailers, advisers, processors, and scientists in National Practitioner Groups (NPG) in six participating countries. PPILOW partners facilitate the groups by connecting NPG at European level, transferring scientific information, interacting with partners engaged in animal experiments, and co-creating innovations rising from NPG-specific demands. They co-build with PPILOW partners welfare self-assessment tools (development of the PIGLOW app for pigs and refinement of the EBENE® app for poultry), and innovative breeding, feeding, and rearing strategies and techniques to improve the welfare of animals. They co-design protocols, test innovations on farm, and disseminate the results. In turn, they receive insights on methods and scientific results, and inputs from other NPG reinforcing the value of the expected outcomes. Approaches focus on avoiding physical damage and the elimination of layer male chicks, on reducing boar taint of intact male pigs, promoting positive behaviours, animal health, and robustness through field studies with pigs and poultry. Multicriteria analyses of the most effective levers of welfare improvement will be performed to evaluate their economic, social, and environmental impacts based on the ‘One Welfare’ concept; economic and business models will also be developed. To ensure the rapid uptake of the project results by end-users, the close involvement of PPILOW’s NPG throughout the EU will ensure disseminationactivities and the facilitation of change. The PPILOW project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement N°816172. www.ppilow.eu.

Published
2022

5. Yam genomics supports West Africa as a major cradle of crop domestication

Author

Scarcelli, Nora, Cubry, Philippe, Akakpo, Roland, Thuillet, Anne-Céline, Obidiegwu, Jude, Baco, Mohamed N., Otoo, Emmanuel, Sonké, Bonaventure, Dansi, Alexandre, Djedatin, Gustave, Mariac, Cédric, Couderc, Marie, Causse, Sandrine, Alix, Karine, Chaïr, Hâna, François, Olivier, Vigouroux, Yves, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), National Root Crops Research Institute, Université de Parakou (UP), Centre for Scientific and Industrial Research, Partenaires INRAE, University of Yaoundé [Cameroun], National University of Sciences, Technologies, Engineering and Mathematics of Abomey, 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), Université de Montpellier (UM), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Agence Nationale de la Recherche (ANR) : AFRICROP ANR-13-BSV7-0017, ANR : ANR-10-INBS-09, ARCAD project - Agropolis foundation, FEDER program, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
Crops, Agricultural, Pennisetum, Séquence nucléotidique, [SDV]Life Sciences [q-bio], Forests, Polymorphism, Single Nucleotide, F30 - Génétique et amélioration des plantes, génomique, Domestication, Evolution, Molecular, Rivers, Igname, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, B50 - Histoire, Research Articles, Histoire naturelle, Evolutionary Biology, Models, Statistical, Base Sequence, Whole Genome Sequencing, Dioscorea, Domestication des plantes, SciAdv r-articles, Agriculture, Oryza, F70 - Taxonomie végétale et phytogéographie, Genomics, Plant Leaves, Africa, Western, Provenance, Genome, Plant, Research Article
Abstract

Yam, a tuber crop, was domesticated alongside some African cereals and defines a cradle of domestication in West Africa., While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.

Published
2019
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6. African yam domestication in light of the NGS revolution

Author

Scarcelli, Nora, Cubry, Philippe, Akakpo, Roland, Thuillet, Anne-Céline, Obidiegwu, Jude, Baco, Mohamed N., Otoo, Emmanuel, Sonké, Bonaventure, Dansi, Alexandre, Djedatin, Gustave, Mariac, Cédric, Couderc, Marie, Causse, Sandrine, Alix, Karine, Chaïr, Hâna, François, Olivier, and Vigouroux, Yves

Abstract

Yam (Dioscorea sp.) produces a starchy tuber cultivated for human consumption. It is a backbone for food security in tropical countries, especially in West Africa. The most cultivated species, D. rotundata, originated from Africa. However, due to the lack of archaeological data and genetic tools, very little is known about yam domestication. Currently, the wild progenitor of yam is unclear and the geographical origin of yam cultivation has not been elucidated. Here, we took advantage of the recent sequencing of the D. rotundata genome and the development of new powerful analyses to get new insights into the domestication process of African yam. We analyzed a large sampling of cultivated yam and its two closest wild relatives, the savannah species D. abyssinica and the forest species D. praehensilis, collected in West Africa and Cameroon. Whole genome resequencing produced more than 3 million good quality SNPs and revealed a strong genetic structure between the three species, as well as between Cameroon and West African countries. Using coalescent models, we showed that cultivated yam was domesticated from the forest species D. praehensilis. Spatially explicit models inferred an origin of yam culture expansion in the Niger River basin, in a region located in north Benin.

Published
2019

7. Etude de la domestication et de l’adaptation de l’igname (Dioscorea spp) en Afrique par des approches génomiques

Author

Akakpo, Roland, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Agence Nationale de la Recherche (ANR), Université Paris Saclay (COmUE), Karine Alix-Jenczewski, Yves Vigouroux, Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and STAR, ABES

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Domestication, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Génomique des populations, Dioscorea spp, NGS, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Adaptation, Population genomics, Transposable elements, Eléments transposables
Abstract

Yam (Dioscorea spp) is a major staple for more than 100 million people in Africa. The main objectives of the present PhD project were to study yam genomic diversity, its domestication, and to characterize the genomic determinism of its adaptation to different climatic zones. We investigated the genetic basis of yam domestication in a comparative genomic approach between the cultivated species D. rotundata and two wild close relatives D. praehensilis and D. abyssinica, by exploiting NGS sequencing data. We demonstrated that genes from the starch biosynthesis were selected during yam domestication. Genes related to tuber morphology or phototropism ability, as well as genes of the NADH dehydrogenase complex were also under selection. The same NADH-DH complex was also identified when assessing adaptation to climate variability. We also created the first de novo database of yam transposable elements (TEs). The study we performed on these repeat elements (REs) highlighted a strong correlation between the variability in relative abundances of numerous REs and climatic variability. Finally, we were able to propose an hypothesis on the origin of the cultivated yam D. rotundata. Our hypothesis identifies the origin of yam in the forest areas, with the species D. praehensilis as the putative progenitor. Our results question the generally admitted hypothesis of savannah origins for crops and agriculture in Africa., L’igname (Dioscorea spp) est un aliment de base de plus de 100 millions de personnes en Afrique. L’objectif de cette thèse était d'étudier la diversité génomique de l'igname, comprendre les bases génétiques de sa domestication, et d'étudier son adaptation à différentes zones climatiques. L’étude du processus de domestication de l’igname a été menée par une approche de génomique comparée entre l’espèce cultivée D. rotundata et deux espèces sauvages apparentées D. praehensilis et D. abyssinica, en utilisant des données de séquençage NGS génomique. Nous avons mis en évidence des sélections fortes de gènes de la voie de biosynthèse de l’amidon. Des gènes impliqués dans la morphologie des tubercules ou l’aptitude au phototropisme, ainsi que des gènes du complexe NADH deshydrogenase ont également été identifiés comme sélectionnés durant la domestication. Ce même complexe NADH-DH a également été identifié lors de la recherche de gènes associés à la distribution d’une collection d’ignames selon la variabilité climatique. Nous avons aussi créé la première banque de novo d’éléments transposables (ET) de l’igname. L’étude que nous avons menée sur les éléments répétés (ER) du génome de l’igname nous a permis d’identifier une forte corrélation entre la variabilité des abondances relatives d’un grand nombre d’ERs et la variabilité climatique. Enfin, nous avons pu proposer une hypothèse quant à l’origine de l’igname cultivée D. rotundata. La domestication de l'igname dériverait de l'espèce inféodée au milieu forestier, D. praehensilis. Ces résultats remettent en cause l’hypothèse d’une origine stricte en zone de savane pour les espèces cultivées et l’agriculture en Afrique de l'Ouest.

Published
2018

8. Additional file 1: of Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

Author

Akakpo, Roland, Scarcelli, Nora, Chaïr, Hana, Dansi, Alexandre, Djedatin, Gustave, Anne-Céline Thuillet, Rhoné, Bénédicte, François, Olivier, Alix, Karine, and Vigouroux, Yves

Abstract

We assess if the mapping of genomic DNA reads on a transcriptome reference could impact SNP calling in our special case. Table S1. Summary of mapping and SNP calling using simulated data. (DOCX 15 kb)

Published
2017
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9. Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

Author

Akakpo, Roland, Scarcelli, Nora, Chaïr, Hâna, Dansi, Alexandre, Djedatin, Gustave, Thuillet, Anne-Céline, Rhoné, Bénédicte, François, Olivier, Alix, Karine, Vigouroux, Yves, Akakpo, Roland, Scarcelli, Nora, Chaïr, Hâna, Dansi, Alexandre, Djedatin, Gustave, Thuillet, Anne-Céline, Rhoné, Bénédicte, François, Olivier, Alix, Karine, and Vigouroux, Yves

Abstract

Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication.

Published
2017

10. Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

Author

Akakpo, Roland, primary, Scarcelli, Nora, additional, Chaïr, Hana, additional, Dansi, Alexandre, additional, Djedatin, Gustave, additional, Thuillet, Anne-Céline, additional, Rhoné, Bénédicte, additional, François, Olivier, additional, Alix, Karine, additional, and Vigouroux, Yves, additional

Published
2017
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11. CIRAD, IRD and INRA Yam genomic initiatives: unlocking genetic diversity and accelerating yam breeding. [W902]

Author

Chaïr, Hâna, Scarcelli, Nora, Arnau, Gemma, Pavis, Claudie, Akakpo, Roland, Dansi, Alexandre, Petro, Dalila, Alix, Karine, Lebot, Vincent, Vigouroux, Yves, Chaïr, Hâna, Scarcelli, Nora, Arnau, Gemma, Pavis, Claudie, Akakpo, Roland, Dansi, Alexandre, Petro, Dalila, Alix, Karine, Lebot, Vincent, and Vigouroux, Yves

Abstract

The fast development of new sequencing technologies allows unlocking diversity of tropical crops. The French institutes CIRAD, IRD and INRA have worked together the last 7 years to improve the yam's genomics toolkit. Using RNASeq from leaves and flower tissues, we have assembled the transcriptomes of three yam cultivated species: Dioscorea rotundata, D. alata and D. trifida. Genotyping by sequencing approaches are currently used to develop a genetic map from four half-sibling families of D. alata. Such tools will allow refining genome assembly and identifying QTL related to anthracnose resistance. The study of genomics diversity of D. alata using sampling covering the four continents Asia, Pacific, Africa and America is currently underway. Using similar approaches, we obtained 600K SNPs in D. rotundata, D. abyssinica and D. praehensilis. We will present result of this study documenting both the relationship and diversity in these three African species and the detection of genes under selection, genes that may be of importance for yam improvement. We further investigated the important role of wild to cultivated gene flow between D. nummularia/D. alata and D. abyssinica/D. praehensilis/D. rotundata could play in yam improvement. (Texte intégral)

Published
2016

12. CIRAD, IRD and INRA Yam genomic initiatives: unlocking genetic diversity and accelerating yam breeding. [W902]

Author

Chaïr, Hâna, Scarcelli, Nora, Gemma ARNAU, Pavis, Claudie, Akakpo, Roland, Dansi, Alexandre, Petro, Dalila, Alix, Karine, Lebot, Vincent, and Vigouroux, Yves

Subjects
F60 - Physiologie et biochimie végétale, F70 - Taxonomie végétale et phytogéographie, F30 - Génétique et amélioration des plantes
Abstract

The fast development of new sequencing technologies allows unlocking diversity of tropical crops. The French institutes CIRAD, IRD and INRA have worked together the last 7 years to improve the yam's genomics toolkit. Using RNASeq from leaves and flower tissues, we have assembled the transcriptomes of three yam cultivated species: Dioscorea rotundata, D. alata and D. trifida. Genotyping by sequencing approaches are currently used to develop a genetic map from four half-sibling families of D. alata. Such tools will allow refining genome assembly and identifying QTL related to anthracnose resistance. The study of genomics diversity of D. alata using sampling covering the four continents Asia, Pacific, Africa and America is currently underway. Using similar approaches, we obtained 600K SNPs in D. rotundata, D. abyssinica and D. praehensilis. We will present result of this study documenting both the relationship and diversity in these three African species and the detection of genes under selection, genes that may be of importance for yam improvement. We further investigated the important role of wild to cultivated gene flow between D. nummularia/D. alata and D. abyssinica/D. praehensilis/D. rotundata could play in yam improvement. (Texte intégral)

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