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Génétique Quantitative et Évolution - Le Moulon

GEvAD - Genomics, Evolution and Adaptation of Domesticated plants

photo de l'équipe

From the characterization of patterns of genomic diversity of domesticated plants and their wild relatives : we study the demographic and selective histories that have accompanied the emergence and diffusion of crops; we examine the dynamics of their genomes; we characterize the molecular bases of their adaptations and their biotic interactions; we investigate the consequences of interspecific hybridization at the origin of many allopolyploid crops; we study gene flow between wild and domestic forms both from an adaptive introgression and a reproductive isolation perspective. We use an integrative approach combining bioinformatics, molecular tools, phenotype measurements and statistical modeling. Professors of the team teach courses in evolution, population genetics and quantitative, plant genomics, plant breeding, biostatistics at AgroParisTech and Université Paris-Saclay.

Méthodologies

Emergence and diffusion of crops

Local adaptation - How to define adaptive syndromes? Which are the locus displaying footrpints of spatialy-varying selection? Are these loci associated to phenotypic, transcriptomic, epigenetic variation?
Pangenomics and adaptation - What are the molecular mechanisms at the origin of structural variants (transposable elements, presence-absence of genes/large genomic regions)? How do they evolve? What is their role in adaptive processes? What is the function of dispensable genes?
DNA Methylation and Adaptive Responses - What is the impact of environmental constraints on the methylome? Which regulatory pathways are involved? How do DNA methylation perturbations translate at the phenotype level? Response to divergent selection - What is the dynamic of the adaptive response in small populations submitted to artificial selection? How do gene networks respond to this selection? What is the link between network structure and phenotypic response?

Impact of human-mediated selection on biotic interactions

Local adaptation of pathogens to their hosts ("Projet ATIP Avenir") - What are the ecological factors and genomic bases driving local adaptation of a pest to its host?
Reproductive success of floral morphs - How does floral dimorphism impact plant-pollinator interactions, plant mating system and fitness?

Crosstalks between wild and domesticates

Genomic consequences of interspecific hybridization - What is molecular response to allopolyploidy (activation of transposable elements, gene and small non-coding RNA expression)? What is the impact of allopolyploidy-triggered structural variations on the repertoire of micro RNAs? Can we characterize the relationships between structural and functional changes?
Adaptive introgression between wild and cultivated forms - How did introgressions between forms shape their genomes? What is the genomic architecture of these introgressions? What is the contribution of TEs to genomic structure of species complex?
Reproductive isolation between wild and cultivated forms - What is the extent of reproductive barriers? What are the links between these barriers and the levels of historical, genomic, phenotypic divergence? What are their molecular determinants?


GEvAD is attached to the LabEx SPS, Sciences des Plantes de Saclay.

Members

  • Karine Alix Professor (AgroParisTech)
  • Kévin Baudry Postdoctoral Fellow (INRAE)
  • Xilong Chen Postdoc (CNRS)
  • Amandine Cornille Junior Investigator (CNRS)
  • Hélène Corti (INRAE)
  • Noémie Delprouve (INRAE)
  • Maud Fagny Postdoctoral Fellow (INRAE)
  • Justine Floret (INRAE)
  • Pierre Gérard Assistant Professor (AgroParisTech)
  • Jehanne Hilairet (INRAE)
  • Johann Joets Engineer (INRAE)
  • Thomas Kaczmarek (INRAE)
  • Martine Le Guilloux (CNRS)
  • Jeanne Liger (INRAE)
  • Domenica Manicacci Assistant Professor (Université Paris-Saclay)
  • Maeva Mollion Postdoctoral fellow (INRAE)
  • Agnès Rousselet (INRAE)
  • Maud Tenaillon Research Director (CNRS)
  • Sergio Vasquez PhD Student (INRAE)
  • Anthony Venon (INRAE)
  • Clémentine Vitte Junior Investigator (CNRS)

Publications

Jabbour F, Pasquier PED, Chazalviel L, Guilloux ML, Condee Silva N, Deveaux Y, Manicacci D, Galipot P, Heiss AG, Damerval C. (2020) Evolution of the distribution area of the Mediterranean Nigella damascena and a likely multiple molecular origin of its perianth dimorphism. Flora, 151735
Lorant A, Ross-Ibarra J, Tenaillon M, Dutheil JY. (2020) Genomics of Long- and Short-Term Adaptation in Maize and Teosintes. , 289-311
Aguirre‐Liguori JA, Gaut BS, Jaramillo‐Correa JP, Tenaillon MI, Montes‐Hernández S, García‐Oliva F, Hearne SJ, Eguiarte LE. (2019) Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana ). Mol Ecol, 11 (28) 2814-2830
Cornille A, Antolín F, Garcia E, Vernesi C, Fietta A, Brinkkemper O, Kirleis W, Schlumbaum A, Roldán-Ruiz I. (2019) A Multifaceted Overview of Apple Tree Domestication. Trends in Plant Science, 8 (24) 770 - 782
Courret C, Gérard PR, Ogereau D, Falque M, Moreau L, Montchamp-Moreau C. (2019) X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression. Heredity, 6 (122) 906-915
Fustier MA, Martínez-Ainsworth NE, Aguirre-Liguori JA, Venon A, Corti H, Rousselet A, Dumas F, Dittberner H, Camarena MG, Grimanelli D, Ovaskainen O, Falque M, Moreau L, Meaux J, Montes-Hernández S, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. (2019) Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude. PLOS Genetics, 12 (15) e1008512
Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T. (2019) Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. Annu. Rev. Phytopathol., 1 (57) annurev-phyto-082718-095947
Liu S, Cornille A, Decroocq S, Tricon D, Chague A, Eyquard JP, Liu WS, Giraud T, Decroocq V. (2019) The complex evolutionary history of apricots: species divergence, gene flow and multiple domestication events. Mol Ecol, mec.15296
Mabire C, Duarte J, Darracq A, Pirani A, Rimbert H, Madur D, Combes V, Vitte C, Praud S, Rivière N, Joets J, Pichon JP, Nicolas SD. (2019) High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics, 1 (20) 848
Martinez Palacios P, Jacquemot MP, Tapie M, Rousselet A, Diop M, Remoué C, Falque M, Lloyd A, Jenczewski E, Lassalle G, Chévre AM, Lelandais C, Crespi M, Brabant P, Joets J, Alix K. (2019) Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids. Mol Biol Evol, 4 (36) 709-726
Martinez N, 25/10/2019, Characterizing the genomic determinants and phenotypic responses to altitudinal adaptation in teosintes (Zea mays ssp. parviglumis and ssp. mexicana)
Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. (2019) Apple whole genome sequences: recent advances and new prospects. Hortic Res, 1 (6) 59
Ruhsam M, Jessop W, Cornille A, Renny J, Worrell R. (2019) Crop-to-wild introgression in the European wild apple Malus sylvestris in Northern Britain. Forestry (Lond), 1 (92) 85-96
Scarcelli N, Cubry P, Akakpo R, Thuillet AC, Obidiegwu J, Baco MN, Otoo E, Sonké B, Dansi A, Djedatin G, Mariac C, Couderc M, Causse S, Alix K, Chaïr H, François O, Vigouroux Y. (2019) Yam genomics supports West Africa as a major cradle of crop domestication. Sci. Adv., 5 (5) eaaw1947
Volk GM, Cornille A, Korban SS. (2019) Genetic Diversity and Domestication History in Pyrus. , 51-62
Akakpo R, 2018-05-16 16/05/18, Étude de la domestication et de l’adaptation de l’igname (Dioscorea spp) en Afrique par des approches génomiques
Amirchakhmaghi N, Yousefzadeh H, Hosseinpour B, Espahbodi K, Aldaghi M, Cornille A. (2018) First insight into genetic diversity and population structure of the Caucasian wild apple (Malus orientalis Uglitzk.) in the Hyrcanian forest (Iran) and its resistance to apple scab and powdery mildew. Genet Resour Crop Evol, 4 (65) 1255-1268
Besnard G, Terral JF, Cornille A. (2018) On the origins and domestication of the olive: a review and perspectives. Annals of botany, 3 (121) 385-403
Dard-Dascot C, Naquin D, d'Aubenton-Carafa Y, Alix K, Thermes C, van Dijk E. (2018) Systematic comparison of small RNA library preparation protocols for next-generation sequencing. BMC genomics, 1 (19) 118
Darracq A, Vitte C, Nicolas S, Duarte J, Pichon JP, Mary-Huard T, Chevalier C, Bérard A, Le Paslier MC, Rogowsky P, Charcosset A, Joets J. (2018) Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics, 1 (19) 119
Käfer J, Betancourt A, Villain AS, Fernandez M, Vignal C, Marais GAB, Tenaillon MI. (2018) Progress and Prospects in Gender Visibility at SMBE Annual Meetings. Genome Biol Evol, 3 (10) 901-908
Lorant A, Ross-Ibarra J, Tenaillon MI, Dutheil JY. (2018) Genomics of long- and short- term adaptation in maize and teosintes. , (accepted) in press
Lorant A, 2018-03-28 28/03/18, Plasticité et adaptation génétique comme contributeurs de l'histoire évolutive du maïs cultivé et des formes sauvages apparentées
Odonkor S, Choi S, Chakraborty D, Martinez-Bello L, Wang X, Bahri BA, Tenaillon MI, Panaud O, Devos KM. (2018) QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica. Front. Plant Sci., (9)
Tenaillon MI, Sedikki K, Mollion M, Guilloux ML, Marchadier E, Ressayre A, Dillmann C. (2018) Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network. bioRxiv, 461947
Aguirre‐Liguori JA, Tenaillon MI, Vázquez‐Lobo A, Gaut BS, Jaramillo‐Correa JP, Montes‐Hernandez S, Souza V, Eguiarte LE. (2017) Connecting genomic patterns of local adaptation and niche suitability in teosintes. Molecular Ecology, 16 (26) 4226-4240
Akakpo R, Scarcelli N, Chaïr H, Dansi A, Djedatin G, Thuillet AC, Rhoné B, François O, Alix K, Vigouroux Y. (2017) Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes. BMC Genomics, 1 (18) 782
Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JSP. (2017) Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. Ann Bot, 2 (120) 183-194
Brandenburg JT, Mary-Huard T, Rigaill G, Hearne SJ, Corti H, Joets J, Vitte C, Charcosset A, Nicolas SD, Tenaillon MI. (2017) Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLOS Genetics, 3 (13) e1006666
Feurtey A, Cornille A, Shykoff JA, Snirc A, Giraud T. (2017) Crop‐to‐wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe. Evolutionary Applications, 2 (10) 180-188
Fustier MA, Brandenburg JT, Boitard S, Lapeyronnie J, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. (2017) Signatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples. Molecular Ecology, 10 (26) 2738-2756
Petit E, Silver C, Cornille A, Gladieux P, Rosenthal L, Bruns E, Yee S, Antonovics J, Giraud T, Hood ME. (2017) Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Molecular Ecology, 7 (26) 1877-1890
Berthouly‐Salazar C, Thuillet AC, Rhoné B, Mariac C, Ousseini IS, Couderc M, Tenaillon MI, Vigouroux Y. (2016) Genome scan reveals selection acting on genes linked to stress response in wild pearl millet. Molecular Ecology, 21 (25) 5500-5512
Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright SI, Lascoux M. (2016) Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris). Molecular Ecology, 2 (25) 616–629
Decroocq S, Cornille A, Tricon D, Babayeva S, Chague A, Eyquard JP, Karychev R, Dolgikh S, Kostritsyna T, Liu S, Liu W, Geng W, Liao K, Asma BM, Akparov Z, Giraud T, Decroocq V. (2016) New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Molecular Ecology, 19 (25) 4712–4729
Feurtey A, Gladieux P, Hood ME, Snirc A, Cornille A, Rosenthal L, Giraud T. (2016) Strong phylogeographic co-structure between the anther-smut fungus and its white campion host. New Phytologist, 3 (212) 668-679
Fustier MA, 2016-06-16 16/06/16, Adaptation locale des téosintes Zea mays ssp. parviglumis et Zea mays ssp. mexicana le long de gradients altitudinaux
Kryvokhyzha D, Holm K, Chen J, Cornille A, Glémin S, Wright S, Lagercrantz U, Lascoux M. (2016) The influence of demographic history on gene expression variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). , 1106-21
Martinez-Ainsworth NE, Tenaillon MI. (2016) Superheroes and masterminds of plant domestication. Comptes rendus biologies, 7-8 (339) 268-73
Tenaillon MI, Manicacci D, Nicolas SD, Tardieu F, Welcker C. (2016) Testing the link between genome size and growth rate in maize. PeerJ, (4) e2408
Cornille A, Feurtey A, Gélin U, Ropars J, Misvanderbrugge K, Gladieux P, Giraud T. (2015) Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples. Evolutionary Applications, n/a-n/a
Durand E, Tenaillon MI, Raffoux X, Thépot S, Falque M, Jamin P, Bourgais A, Ressayre A, Dillmann C. (2015) Dearth of polymorphism associated with a sustained response to selection for flowering time in maize. BMC Evol Biol, 1 (15) 103
Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel CE, Branca A. (2015) Genomic basis of the differences between cider and dessert apple varieties. Evolutionary Applications, 7 (8) 650-661
Yao JL, Xu J, Cornille A, Tomes S, Karunairetnam S, Luo Z, Bassett H, Whitworth C, Rees-George J, Ranatunga C, Snirc A, Crowhurst R, de Silva N, Kumar S, Chagne D, Bus V, Volz R, Rikkerink E, Gardiner SE, Giraud T, Newcomb R, MacDiarmid R, Gleave AP. (2015) A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal, 417-427
Cornille A, Giraud T, Smulders MJM, Roldán-Ruiz I, Gladieux P. (2014) The domestication and evolutionary ecology of apples. Trends in Genetics, 2 (30) 57-65
Martinez-Palacios P, 2014-03-28 28/03/14, Réponse des agents non codants du génome – éléments transposables et petits ARN – à un événement d'allopolyploïdie : le génome du colza (Brassica napus) comme modèle d'étude
Muñoz Diez C, Meca E, Tenaillon MI, Gaut BS. (2014) Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome. PLoS genetics, 4 (10) e1004298
Nougué O, Corbi J, Ball SG, Manicacci D, Tenaillon MI. (2014) Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway. BMC evolutionary biology, (14) 103
Schnitzler A, Arnold C, Cornille A, Bachmann O, Schnitzler C. (2014) Wild European Apple (Malus sylvestris (L.) Mill.) Population Dynamics: Insight from Genetics and Ecology in the Rhine Valley. Priorities for a Future Conservation Programme. PLoS ONE, 5 (9) e96596
Vitte C, Fustier MA, Alix K, Tenaillon MI. (2014) The bright side of transposons in crop evolution. Briefings in functional genomics, 4 (13) 276-95
Yuan JH, Cornille A, Giraud T, Cheng FY, Hu YH. (2014) Independent domestications of cultivated tree peonies from different wild peony species. Molecular Ecology, 1 (23) 82-95
Alix K, 2013-03-26 26/03/13, Allopolyploïdie et éléments transposables : contribution à l’étude de la dynamique évolutive du génome des Brassica
Cornille A, Gladieux P, Giraud T. (2013) Crop-to-wild gene flow and spatial genetic structure in the wild closest relatives of the cultivated apple. Evolutionary Applications, 5 (6) 737-748
Cornille A, Giraud T, Bellard C, Tellier A, Le Cam B, Smulders MJM, Kleinschmit J, Roldan-Ruiz I, Gladieux P. (2013) Post-glacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple. Molecular Ecology, 8 (22) 2249-63
Jenczewski E, Chèvre AM, Alix K, Chen ZJ, Birchler JA. (2013) Chromosomal and gene expression changes in Brassica allopolyploids. , 171-186
Muñoz Diez C, Vitte C, Ross-Ibarra J, Gaut BS, Tenaillon MI, Grandbastien MA, Casacuberta J, Hohmann S. (2013) Using next generation sequencing to investigate genome size variation and transposable element content. , 41-58
Muñoz Diez C, Gaut BS, Meca E, Scheinvar E, Montes-Hernandez S, Eguiarte LE, Tenaillon MI. (2013) Genome size variation in wild and cultivated maize along altitudinal gradients. The New phytologist, (199) 264-276
Sarilar V, Martinez-Palacios P, Rousselet A, Ridel C, Falque M, Eber F, Chevre AM, Joets J, Brabant P, Alix K. (2013) Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids. The New phytologist, 2 (198) 593-604
Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhajarvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nature genetics, 7 (44) 803-7
Corbi J, Dutheil JY, Damerval C, Tenaillon MI, Manicacci D. (2012) Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation. Annals of botany, 4 (109) 693-708
Cornille A, Underhill JG, Cruaud A, Hossaert-McKey M, Johnson SD, Tolley KA, Kjellberg F, van Noort S, Proffit M. (2012) Floral volatiles, pollinator sharing and diversification in the fig–wasp mutualism: insights from Ficus natalensis, and its two wasp pollinators (South Africa). Proceedings of the Royal Society of London B: Biological Sciences, 1734 (279) 1731-1739
Cornille A, Gladieux P, Smulders MJ, Roldan-Ruiz I, Laurens F, Le Cam B, Nersesyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenaillon MI, Giraud T. (2012) New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS genetics, 5 (8) e1002703
Durand E, Bouchet S, Bertin P, Ressayre A, Jamin P, Charcosset A, Dillmann C, Tenaillon MI. (2012) Flowering time in maize: linkage and epistasis at a major effect locus. Genetics, 4 (190) 1547-62
Hufford MB, Martinez-Meyer E, Gaut BS, Eguiarte LE, Tenaillon MI. (2012) Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight. PloS one, 11 (7) e47659
Khobragade A, 2012-03-23 23/03/12, Combining linkage analysis and association genetics to finely map loci involved in maize grain production and maturation -- Cartographie fine de locus impliqués dans la production et la maturation du grain chez le maïs par une approche conjointe de linkage et de génétique d’association
Lê Van A, Gladieux P, Lemaire C, Cornille A, Giraud T, Durel CE, Caffier V, Le Cam B. (2012) Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host. Evolutionary Applications, 7 (5) 694-704
Zerjal T, Rousselet A, Mhiri C, Combes V, Madur D, Grandbastien MA, Charcosset A, Tenaillon MI. (2012) Maize genetic diversity and association mapping using transposable element insertion polymorphisms. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 8 (124) 1521-37
Becker A, Alix K, Damerval C. (2011) The evolution of flower development: current understanding and future challenges. Annals of botany, 9 (107) 1427-31
Corbi J, Debieu M, Rousselet A, Montalent P, Le Guilloux M, Manicacci D, Tenaillon MI. (2011) Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme. Theor Appl Genet, 4 (122) 705-22
Sarilar V, Marmagne A, Brabant P, Joets J, Alix K. (2011) BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space. Plant molecular biology, 1-2 (77) 59-75
Tenaillon MI, Charcosset A. (2011) A European perspective on maize history. Comptes rendus biologies, 3 (334) 221-8
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. (2011) Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome biology and evolution, (3) 219-29
Tenaillon MI, Manicacci D, Prioul JL, Thévenot C, Molnar T, Mike Burrel . (2011) Maize origins: an old question under the spotlights. , 89-110
Virlouvet L, Jacquemot MP, Gerentes D, Corti H, Bouton S, Gilard F, Valot B, Trouverie J, Tcherkez G, Falque M, Damerval C, Rogowsky P, Perez P, Noctor G, Zivy M, Coursol S. (2011) The ZmASR1 protein influences branched-chain amino acid biosynthesis and maintains kernel yield in maize under water-limited conditions. Plant physiology, 2 (157) 917-36