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Génétique Quantitative et Évolution - Le Moulon

GEvAD - Genomics, Evolution and Adaptation of Domesticated plants

Genomics, Evolution and Adaptation of Domesticated plants

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; we investigate gene flow between wild and domestic forms, as well as the consequences of interspecific hybridization at the origin of many allopolyploid crops. We use an integrative approach combining bioinformatics, molecular tools, phenotype measurements, population genomics 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? What are the loci displaying footprints of spatially-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?
Adaptive responses of gene regulatory networks - What is the dynamic of the adaptive response of populations undergoing a combination of environmental constraints ? What is the impact of selection on the rewiring of gene regulatory networks? What is the link between network structures and phenotypic responses? \

Impact of human-mediated selection on cooperative biotic interactions

Reproductive success of floral morphs - How does floral dimorphism impact plant-pollinator interactions, plant mating system and fitness?
Maize-Bean coculture - What are the American origins of intercropped maize and bean landraces in Europe? What are the genetic determinants of the success of this crop association? \

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)
  • Harry Belcram Ingénieur d'étude (INRAE)
  • Noémie Delpouve (INRAE)
  • Maud Fagny Junior Investigator (INRAE)
  • Pierre Gérard Maître de Conférence (AgroParisTech)
  • Johann Joets Engineer (INRAE)
  • Martine Le Guilloux Technician (CNRS)
  • Domenica Manicacci Assistant Professor (Université Paris-Saclay)
  • Thomas-Sylvestre Michau PhD student (INRAE)
  • Agnès Rousselet Technician (INRAE)
  • Maud Tenaillon Research Director (CNRS)
  • Noa Vazeux-Blumental PhD student (Université Paris-Saclay)
  • Clémentine Vitte Junior Investigator (CNRS)
  • Arthur Wojcik PhD student (Université Paris-Saclay)

Former members

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

  • 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
  • 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
  • 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
  • Burban E., Tenaillon M. , Le Rouzic A.. (2022) Gene network simulations provide testable predictions for the molecular domestication syndrome. Genetics, 2 (220) iyab214
  • Conde E Silva N., Leguilloux M., Bellec A., Rodde N., Aubert J., Manicacci D. , Damerval C., Berges H., Deveaux Y., Bartlett M.. (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
  • 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
  • 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)
  • 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
  • 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 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
  • 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. , 51-62
  • Achour Z., 2018-05-15 15/05/18, Réponse du méthylome suite à l’exposition au froid chez une espèce à génome complexe : le maïs (Zea mays ssp. mays), PhD thesis, Université Paris-Saclay
  • 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
  • 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
  • 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. , 3-12
  • 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 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)
  • 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., 2016-06-16 16/06/16, Adaptation locale des téosintes Zea mays ssp. parviglumis et Zea mays ssp. mexicana le long de gradients altitudinaux, PhD thesis, Université Paris-Sud
  • 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
  • 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, PhD thesis, Université Paris Sud
  • 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
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