last updated 04/01/2023 -   +33 (0)1 69 33 23 34
 Genomics, Evolution and Adaptation of Domesticated plants
 CNRS, Research Director
 publications - orcid 

My research focuses on understanding how evolutionary forces shape genetic variation of plant genomes. I have a specific interest for the domestication process. This process has resulted in a loss of diversity due to population bottleneck and selection at target loci. During my PhD, I addressed questions such as: What are the locus involved in the domestication syndrome in millet? What is the influence of the reproductive system on the organization of domestication genes? Since then, I’ve been focusing mainly on maize as a model species. I investigated the influence of recombination and selection in shaping diversity patterns in this species. I have worked both at a small scale to understand the interference between selective sweeps, and at a multilocus scale to model the demographic impact of domestication on diversity and linkage disequilibrium. I used a coalescent model to detect locus under selection in maize. In parallel, I studied the evolution of multigene families encoding enzymes of the starch biosynthesis pathway, the increase of which was a domestication target.

More recently, I have been working on questions related to variation in genome size within and between species in the Zea genus, both from a genomic - Transposable Element (TE) content - and from an ecological perspective (correlation with environmental variables). I also focused on the characterisation on the demographic and adaptive history of European maize, which underwent two independent introductions from the American continent. Admixture between Southern and Northern lineages has triggered adaptation to mid-latitudes in these two continents. Interestingly, we discovered genomic regions with unusual level of residual heterozygosity which we interpreted as the result of selection against inbreeding depression.


Ongoing projects

  • Local adaptation of teosintes along altitudinal gradients This work has consisted in collecting natural populations of teosintes, obtaining high-throughput sequencing data at the population level, describing TE content of teosinte genomes, discovering loci targeted by selection, characterizing an adaptative syndrome using common gardens experiments, undertaking association mapping to link genotypic to phenotypic variation.

  • Experimental evolution in maize We conducted two divergent selection experiments for flowering date in two homogenous genetic backgrounds (inbreds) over 20 generations. The resulting populations display marked shifts in floral transition. We described a significant and continuous response to selection, that is caused by both selection on residual heterozygosity and new mutations. This response translates at the transcriptomic level with evidence for genetic convergence between maize lines. We are now investigating dynamics of fixation and effects of mutations by combining simulations and association mapping. We are also questioning the impact of such phenological shifts on the root microbiome.

  • Reproductive isolation between wild and domesticates Here we are adressing questions such as: What is the extent of reproductive barriers between wild and domesticates? What are the links between reproductive barriers, historical, genomic and phenotypic divergence? What are the molecular determinants of these barriers?

  • Maize-Bean intercropping
    Unlike natural and human selection, which has acted for millennia in a multi-specific assemblage context, biotic interactions are minimized in modern agroecosystems. We focus on maize and bean, two crops that are still associated in some traditional European agricultural systems. We seek the potential benefits of this biological partnership which could result from complementarity and/or facilitation processes. We integrate field surveys, agronomic measures, genetic tools to study the evolutionary history and the determinants of maize-bean intercropping. More generally, through the INCREASE project (   , we want to promote the description, preservation and use of the genetic resources of food legumes. Learn more about a really cool experiment on beans Citizen Science Experiment   .


Position and Education Full CV

  • CNRS researcher, GQE-Le Moulon (2002-present)
  • Awarded by the CNRS bronze medal in 2011
  • Visiting researcher in the Gaut lab at UC Irvine CA (2009-2011)
  • HDR defended 2009 (University Paris-Sud)
  • Postdoctoral fellow in the Gaut lab at UC Irvine CA (1999-2002)
  • Master and PhD student, Dpt. Evolution and Systematics, University Paris-Sud (1995-1999)


Publication list  


  • 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. (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 PR., 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
  • Burban E., Tenaillon M. , Le Rouzic A.. (2022) Gene network simulations provide testable predictions for the molecular domestication syndrome. Genetics, 2 (220) iyab214
  • 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
  • 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)
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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