GEvAD - Genomics, Evolution and Adaptation of Domesticated plants

Genomics, Evolution and Adaptation of Domesticated plants

We characterize genomic diversity patterns of domesticated plants and their wild relatives to study:

We use an integrative approach combining bioinformatics and molecular tools, phenotype measurements, population genomics, statistical modeling and systems biology. The team’s Professors teach courses in evolution, population and quantitative genetics, plant genomics, plant breeding, biostatistics at AgroParisTech and Université Paris-Saclay.

Méthodologies

Emergence, evolution and diffusion of domesticated plants

Karine Alix, Harry Belcram, Pierre Gérard, Martine Le Guilloux , Domenica Manicacci, Agnès Rousselet, Maud Tenaillon

Domestication syndrome at the phenotypic and molecular scales
Arthur Wojcik

  • How have the wild and domesticated compartments evolved?
  • What is the impact of human-driven selection on genetic correlations between characters, gene co-expression patterns, gene regulatory networks?
  • What is the contribution of TEs to genomic structure of species complex?

Reproductive isolation between wild and cultivated forms
Arthur Wojcik

  • What is the extent of reproductive barriers?
  • What are the links between these barriers and the levels of historical, genomic and phenotypic divergence?
  • What are their molecular determinants? \

Genomic consequences of interspecific hybridization

  • What are the molecular responses 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?

Domestication of interspecific interactions (maize-bean coculture)
Noa Vazeux-Blumental

  • What are the American origins of intercropped maize and bean landraces that are nowadays cultivated in Europe?
  • What are the genetic determinants of the success of this crop association (complementarity and facilitation)?

Gene regulation, structural variations and polygenic adaptation.

Karine Alix, Maud Fagny, Johann Joets, Clémentine Vitte

Pangenomics and adaptation
We study the accessory (present-absent) genes and their contribution to the plant development and its response to the environment.

  • What are the structural and functional characteristics of accessry genes compared to core genes?
  • What is the contribution of accessory genes to adaptation?
  • Which evolutionnary forces are driving the accessory genome?

Transposable elements, cis-regulatory elements and gene expression regulation
We are studying the contribution of transposable elements to the evolution of the genes’ expression.

  • To what extend do transposable elements contribute to cis-regulatory elements regulating gene expression?
  • Which biological functions do they regulate?
  • Are they important in regulating the plant’s response to the environment?
  • What is the impact of transposable elements-led structural variation on gene expression regulation?

Adaptive responses of gene expression regulatory networks
Thomas-Sylvestre Michau
We are studying the response of gene expression regulatory networks to the environment, and their role in crops adaptation.

  • To which extent are the gene expression regulatory networks rewired in response to environmental constraints?
  • What is the link between gene regulatory network rewiring and crops phenotypic response?
  • Does the gene regulatory network structure constrain or facilitate the adaptation of polygenic characters to the environment?

To tackle these questions, we use maize development and response to abiotic stresses (mainly to water deficit) as a model. We generate genomic (genome assembly, panels resequencing), epigenomic (methylome and ATAC-seq), and transcriptomic (RNA-seq) data, that we analyze using tools and approaches from bioinformatics, biostatistics and systems biology.

Funded projects

  • Projet H2020, Topic SFS-28-01-2019: ‘GenRes and pre-breeding communities” (INCREASE, 2020-2026) H2020 project Page

  • ANR Générique ‘Domestication as a step towards reproductive isolation – DomIsol’ (DOMISOL, 2020-2026) ANR DomIsol Page

  • ANR PRC “Homoeologous Exchanges as Drivers for Innovation in Brassica napus” (EDIn, 2023−2026) ANR EDIn Page

  • ANR JCJC “Characterizing Network Wirings of Maize Water Deficit Tolerance for Genomic Selection Enhancement” (NETWITS 2024-2028) ANR NETWITS PAGE

  • ANR PRC “Transposable elements evolution as driver for plant gene regulation” (SATURN, 2025-2028)

Members

Former members

Martine Le Guilloux AI CNRS (1982-2024), Hélène Corti Technician (2012-2021), Abirami Soundiramourtty Master2 (2019), Natalia Martinez-Ainsworth PhD (2015-2019), Margaux-Alison Fustier PhD (2012-2016), Jean-Tristan Brandenburg CDD Recherche (2013-2016), Eleonore Durand PhD student (2008-2011), Jonathan Corbi PhD (2006-2010), Tatiana Zerjal PhD (2006-2008)

Publications

  • Stone K., Platig J., Quackenbush J., Fagny M. . (2024) Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network. Systems Biology,
  • Burban E., Tenaillon M. , Glémin S.. (2023) RIDGE, a tool tailored to detect gene flow barriers across species pairs. Evolutionary Biology,
  • Chen X., Avia K., Forler A., Remoué C., Venon A., Rousselet A. , Lucas G., Kwarteng AO., Rover R., Le Guilloux M., Belcram H. , Combes V., Corti H., Olverà-Vazquez S., Falque M., Alins G., Kirisits T., Ursu TM., Roman A., Volk GM., Bazot S., Cornille A.. (2023) Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [ Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple. Annals of Botany, 6 (131) 1025-1037
  • Conde E Silva N., Leguilloux M., Bellec A., Rodde N., Aubert J., Manicacci D. , Damerval C., Berges H., Deveaux Y.. (2023) A MITE insertion abolishes the AP3-3 self-maintenance regulatory loop in apetalous flowers of Nigella damascena. Journal of Experimental Botany, 5 (74) 1448-1459
  • Desbiez-Piat A., Ressayre A., Marchadier E., Noly A., Remoue C., Vitte C. , Belcram H. , Bourgais A., Galic N., Guilloux ML., Tenaillon M. , Dillmann C.. (2023) Pervasive GxE interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics, (in press) 2023.01.13.523786
  • Moissiard G., Mirouze M., Carles CC., Vitte C. . (2023) Editorial: Plant epigenetics and chromatin dynamics - EPIPLANT 2021-2022. Front. Plant Sci., (14) 1260391
  • Papalini S., Di Vittori V., Pieri A., Allegrezza M., Frascarelli G., Nanni L., Bitocchi E., Bellucci E., Gioia T., Pereira LG., Susek K., Tenaillon M. , Neumann K., Papa R.. (2023) Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies. Plants, 19 (12) 3452
  • Tenaillon M. , Burban E., Huynh S., Wojcik A. , Thuillet AC., Manicacci D. , Gérard P. , Alix K. , Belcram H. , Cornille A., Brault M., Stevens R., Lagnel J., Dogimont C., Vigouroux Y., Glémin S.. (2023) Crop domestication as a step toward reproductive isolation. American Journal of Botany, 7 (110) e16173
  • Tittes, S., Lorant, A., McGinty, S., Holland, J.B., Sanchez-Gonzalez, JJ, Seetharam, A., Tenaillon, M.I., Ross-Ibarra, J.. (2023) Not so local: the population genetics of convergent adaptation in maize and teosinte. eLife, RP92405 (12)
  • Bastide H., Ogereau D., Montchamp-Moreau C., Gérard P. . (2022) The fate of a suppressed X-linked meiotic driver: experimental evolution in Drosophila simulans. Chromosome Res, 2-3 (30) 141-150
  • Ben Guebila M., Weighill D., Lopes-Ramos CM., Burkholz R., Pop RT., Palepu K., Shapoval M., Fagny M. , Schlauch D., Glass K., Altenbuchinger M., Kuijjer ML., Platig J., Quackenbush J.. (2022) An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nat Methods, 5 (19) 511-513
  • Bina H., Yousefzadeh H., Venon A., Remoué C., Rousselet A. , Falque M., Faramarzi S., Chen X., Samanchina J., Gill D., Kabaeva A., Giraud T., Hosseinpour B., Abdollahi H., Gabrielyan I., Nersesyan A., Cornille A.. (2022) Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool. Molecular Ecology, 21 (31) 5581-5601
  • Burban E., Tenaillon M. , Le Rouzic A.. (2022) Gene network simulations provide testable predictions for the molecular domestication syndrome. Genetics, 2 (220) iyab214
  • Fagny M. , Glass K., Kuijjer ML.. (2022) Editorial: Applications and Methods in Genomic Networks. Front. Genet., (13) 936015
  • Fréville H., Montazeaud G., Forst E., David J., Papa R., Tenaillon M. . (2022) Shift in beneficial interactions during crop evolution. Evolutionary Applications, 6 (15) 905-918
  • Gaynor SM., Fagny M. , Lin X., Platig J., Quackenbush J.. (2022) Connectivity in eQTL networks dictates reproducibility and genomic properties. Cell Reports Methods, 5 (2) 100218
  • Speck A., Trouvé JP., Enjalbert J., Geffroy V., Joets J. , Moreau L.. (2022) Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax (Linum usitatissimum L.). Front. Plant Sci., (13) 871633
  • Barrera-Redondo J., Sánchez-de la Vega G., Aguirre-Liguori JA., Castellanos-Morales G., Gutiérrez-Guerrero YT., Aguirre-Dugua X., Aguirre-Planter E., Tenaillon M. , Lira-Saade R., Eguiarte LE.. (2021) The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative. Hortic Res, 1 (8) 109
  • Bellucci E., Mario Aguilar O., Alseekh S., Bett K., Brezeanu C., Cook D., De la Rosa L., Delledonne M., Dostatny DF., Ferreira JJ., Geffroy V., Ghitarrini S., Kroc M., Kumar Agrawal S., Logozzo G., Marino M., Mary‐Huard T., McClean P., Meglič V., Messer T., Muel F., Nanni L., Neumann K., Servalli F., Străjeru S., Varshney RK., Vasconcelos MW., Zaccardelli M., Zavarzin A., Bitocchi E., Frontoni E., Fernie AR., Gioia T., Graner A., Guasch L., Prochnow L., Oppermann M., Susek K., Tenaillon M. , Papa R.. (2021) The INCREASE project: Intelligent Collections of food‐legume genetic resources for European agrofood systems. The Plant Journal, 3 (108) 646-660
  • Desbiez-Piat A., Le Rouzic A., Tenaillon M. , Dillmann C.. (2021) Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations. Genetics, 2 (219)
  • Desbiez-Piat, 2021, The Dynamics of the Response to Selection under High Drift-High Selection: Insights from Saclay’s Divergent Selection Experiments for Flowering Time in Maize, PhD Thesis, Université Paris-Saclay
  • Deveaux Y., Conde e Silva N., Manicacci D. , Le Guilloux M., Brunaud V., Belcram H. , Joets J. , Soubigou-Taconnat L., Delannoy E., Corti H., Balzergue S., Caius J., Nadot S., Damerval C.. (2021) Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L.. Front. Plant Sci., (12) 660803
  • Fagny M. , Kuijjer ML., Stam M., Joets J. , Turc O., Rozière J., Pateyron S., Venon A., Vitte C. . (2021) Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. Frontiers in Genetics, (11) 1703
  • Jabbour F., Pasquier PED., Chazalviel L., Guilloux ML., Conde e Silva N., Deveaux Y., Manicacci D. , Galipot P., Heiss AG., Damerval C.. (2021) Evolution of the distribution area of the Mediterranean Nigella damascena and a likely multiple molecular origin of its perianth dimorphism. Flora, (274) 151735
  • Kalendar R., Sabot F., Rodriguez F., Karlov GI., Natali L., Alix K. . (2021) Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools. Front. Plant Sci., (12) 735134
  • Olvera-Vazquez SG., Remoué C., Venon A., Rousselet A. , Grandcolas O., Azrine M., Momont L., Galan M., Benoit L., David GM., Alhmedi A., Beliën T., Alins G., Franck P., Haddioui A., Jacobsen SK., Andreev R., Simon S., Sigsgaard L., Guibert E., Tournant L., Gazel F., Mody K., Khachtib Y., Roman A., Ursu TM., Zakharov IA., Belcram H. , Harry M., Roth M., Simon JC., Oram S., Ricard JM., Agnello A., Beers EH., Engelman J., Balti I., Salhi-Hannachi A., Zhang H., Tu H., Mottet C., Barrès B., Degrave A., Razmjou J., Giraud T., Falque M., Dapena E., Miñarro M., Jardillier L., Deschamps P., Jousselin E., Cornille A.. (2021) Large-scale geography survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa. Peer Community Journal, (1)
  • Chaix R., Fagny M. , Cosin-Tomás M., Alvarez-López M., Lemee L., Regnault B., Davidson RJ., Lutz A., Kaliman P.. (2020) Differential DNA methylation in experienced meditators after an intensive day of mindfulness-based practice: Implications for immune-related pathways. Brain, Behavior, and Immunity, (84) 36-44
  • Fagny M. , Platig J., Kuijjer ML., Lin X., Quackenbush J.. (2020) Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. Br J Cancer, 4 (122) 569-577
  • Le Corre V., Siol M., Vigouroux Y., Tenaillon M. , Délye C.. (2020) Adaptive introgression from maize has facilitated the establishment of a teosinte as a noxious weed in Europe. Proc. Natl. Acad. Sci. U.S.A., 41 (117) 25618-25627
  • Lopes-Ramos CM., Chen CY., Kuijjer ML., Paulson JN., Sonawane AR., Fagny M. , Platig J., Glass K., Quackenbush J., DeMeo DL.. (2020) Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports, 12 (31) 107795
  • Lorant A., Ross-Ibarra J., Tenaillon M. , Dutheil JY.. (2020) Genomics of Long- and Short-Term Adaptation in Maize and Teosintes. Springer Link, 289-311
  • Aguirre‐Liguori JA., Gaut BS., Jaramillo‐Correa JP., Tenaillon M. , 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 P. , 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
  • Cuello, C., Baldy, A., Brunaud, V., Joets, J., Jacquemot, M.P., Coursol, S.. (2019) A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PlosOne, 12 (14) e0227011
  • Damerval C., Citerne H., Conde E Silva N., Deveaux Y., Delannoy E., Joets J. , Simonnet F., Staedler Y., Schönenberger J., Yansouni J., Le Guilloux M., Sauquet H., Nadot S.. (2019) Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. Front Plant Sci, (10) 18
  • 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 M. . (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
  • Martínez Ainsworth NE., 2019-10, Characterizing the genomic determinants and phenotypic responses to altitudinal adaptation in teosintes (Zea mays ssp. parviglumis and ssp. mexicana), Theses, Université Paris Saclay (COmUE)
  • 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
  • Tenaillon M. , Seddiki K., Mollion M., Guilloux ML., Marchadier E., Ressayre A., Dillmann C.. (2019) Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network. bioRxiv, 461947
  • Volk GM., Cornille A., Korban SS.. (2019) Genetic Diversity and Domestication History in Pyrus. Springer Link, 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, PhD thesis, Université Paris-Saclay
  • Bennetzen J., Flint-Garcia S., Hirsch C., Tuberosa R., Joets J. , Vitte C. , Charcosset A.. (2018) Draft Assembly of the F2 European Maize Genome Sequence and Its Comparison to the B73 Genome Sequence: A Characterization of Genotype-Specific Regions. DOI.org (Crossref), 3-12
  • 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 M. . (2018) Progress and Prospects in Gender Visibility at SMBE Annual Meetings. Genome Biol Evol, 3 (10) 901-908
  • Lorant A., Ross-Ibarra J., Tenaillon M. , Dutheil JY.. (2018) Genomics of long- and short- term adaptation in maize and teosintes. , (accepted) in press
  • Lorant A., 2018-03, Plasticity and genetic adaptation as contributors to the evolutionary history of cultivated maize and its wild relatives, Theses, Université Paris Saclay (COmUE)
  • Odonkor S., Choi S., Chakraborty D., Martinez-Bello L., Wang X., Bahri BA., Tenaillon M. , Panaud O., Devos KM.. (2018) QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica. Front. Plant Sci., (9)
  • Richard MMS., Gratias A., Thareau V., Kim KD., Balzergue S., Joets J. , Jackson SA., Geffroy V.. (2018) Genomic and epigenomic immunity in common bean: the unusual features of NB-LRR gene family. DNA Res, 2 (25) 161-172
  • Aguirre‐Liguori JA., Tenaillon M. , 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 P. , 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 M. . (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 M. . (2017) Signatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples. Molecular Ecology, 10 (26) 2738-2756
  • Ousseini IS., Bakasso Y., Kane NA., Couderc M., Zekraoui L., Mariac C., Manicacci D. , Rhoné B., Barnaud A., Berthouly-Salazar C., Assoumane A., Moussa D., Moussa T., Vigouroux Y.. (2017) Myosin XI is associated with fitness and adaptation to aridity in wild pearl millet. Heredity, 2 (119) 88-94
  • 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 M. , 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, Adaptation locale des téosintes Zea mays ssp. parviglumis et Zea mays ssp. mexicana le long de gradients altitudinaux, Theses, Université Paris Saclay (COmUE)
  • 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 M. . (2016) Superheroes and masterminds of plant domestication. Comptes rendus biologies, 7-8 (339) 268-73
  • Tenaillon M. , 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 M. , 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
  • Jabbour F., Udron M., Le Guilloux M., Goncalves B., Manicacci D. , Nadot S., Damerval C.. (2015) Flower development schedule and AGAMOUS-like gene expression patterns in two morphs of Nigella damascena (Ranunculaceae) differing in floral architecture. Bot J Linn Soc, 4 (178) 608-619
  • 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
  • Muñoz Diez C., Meca E., Tenaillon M. , 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 M. . (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 M. . (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, HDR, Université Paris-Sud
  • Cornille A., Gladieux P., Giraud T.. (2013) Crop‐to‐wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple. Evol Appl, 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) Postglacial recolonization history of the European crabapple ( Malus sylvestris Mill.), a wild contributor to the domesticated apple. Mol Ecol, 8 (22) 2249-2263
  • Jenczewski E., Chèvre AM., Alix K. , Chen ZJ., Birchler JA.. (2013) Chromosomal and gene expression changes in Brassica allopolyploids. , 171-186
  • Muñoz Diez C., Gaut BS., Meca E., Scheinvar E., Montes-Hernandez S., Eguiarte LE., Tenaillon M. . (2013) Genome size variation in wild and cultivated maize along altitudinal gradients. The New phytologist, (199) 264-276
  • Muñoz Diez C., Vitte C. , Ross-Ibarra J., Gaut BS., Tenaillon M. , Grandbastien MA., Casacuberta J., Hohmann S.. (2013) Using next generation sequencing to investigate genome size variation and transposable element content. , 41-58
  • 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 M. , 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 M. , 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 M. , 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 M. . (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 M. . (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, PhD thesis, AgroParisTech
  • 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 M. . (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 M. . (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 M. , Charcosset A.. (2011) A European perspective on maize history. Comptes rendus biologies, 3 (334) 221-8
  • Tenaillon M. , 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 M. , 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