GEvAD - Genomics, Evolution and Adaptation of Domesticated plants
08/10/2024 -
GQE
Investigating the mechanisms that have accompanied the evolution of crops from their domestication to their diffusion and adaptation to a diversity of environments
Head :
Maud Tenaillon (CNRS)
Head :
Maud Tenaillon (CNRS)
We characterize genomic diversity patterns of domesticated plants and their wild relatives to study:
- the evolutionnary processes that have accompanied the emergence and diffusion of crops outside the location of their domestication ( Emergence, evolution and diffusion of domesticated plants );
- the molecular bases of crop adaptation, with a focus on the regulation of gene expression ( Gene regulation, structural variations and polygenic adaptation ).
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.
Emergence, evolution and diffusion of domesticated plants
Karine Alix, , Pierre Gérard, Martine Le Guilloux, , Agnès Rousselet, Maud Tenaillon
Domestication syndrome at the phenotypic and molecular scales
- 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
- 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)
- 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
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
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Projet H2020, Topic SFS-28-01-2019: ‘GenRes and pre-breeding communities” (INCREASE, 2020-2026) H2020 project Page
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ANR Générique ‘Domestication as a step towards reproductive isolation – DomIsol’ (DOMISOL, 2020-2026) ANR DomIsol Page
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ANR PRC “Homoeologous Exchanges as Drivers for Innovation in Brassica napus” (EDIn, 2023−2026) ANR EDIn Page
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ANR JCJC “Characterizing Network Wirings of Maize Water Deficit Tolerance for Genomic Selection Enhancement” (NETWITS 2024-2028) ANR NETWITS PAGE
Members
- Karine Alix, Professor (AgroParisTech)
- Maud Fagny, INRAE, Junior Researcher (INRAE)
- Pierre Gérard, Maître de Conférence (AgroParisTech)
- Johann Joets, Engineer (INRAE)
- Martine Le Guilloux, Technician (CNRS)
- Agnès Rousselet, Technician (INRAE)
- Maud Tenaillon, Research Director (CNRS)
- Clémentine Vitte, Principal Investigator (CNRS)
Publications
- Stone K., Platig J., Quackenbush J., Fagny M. . (2024) Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network. bioRxiv, 2024.02.27.582063
- 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
- Desbiez-Piat A., Ressayre A., Marchadier E., Noly A., Bourgais A., Galic N., Le Guilloux M. , Tenaillon M. , Dillmann C.. (2023) The coupling between mutations effects and environment guides the exploration of phenotypic space as evidenced in artificial selection experiments. DOI.org (Crossref),
- 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. Plant J, 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)
- 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)
- 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. 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
- 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 N., 25/10/2019, Characterizing the genomic determinants and phenotypic responses to altitudinal adaptation in teosintes (Zea mays ssp. parviglumis and ssp. mexicana), PhD thesis, Université Paris-Saclay
- 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
- 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. 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
- 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 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., 2018-03-28 28/03/18, Plasticité et adaptation génétique comme contributeurs de l'histoire évolutive du maïs cultivé et des formes sauvages apparentées, PhD thesis, Université Paris-Saclay
- 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)
- Tenaillon M. , 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 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
- 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