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The V.A.S.T lab

Variation and Abiotic Stress Tolerance


   Arabidopsis RILs  
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              Here is a list of our publications since 2002.


  Marchadier E., Hanemian M., Tisné S., Bach L., Bazakos C., Gilbault E., Haddadi P., Virlouvet L., Loudet O. (2019)

  The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana.

  PLoS Genetics  15:e1007954




  Tang N., Shahzad Z., Lonjon F., Loudet O., Vailleau F., Maurel M. (2018)

  Natural variation at XYLEM NAC DOMAIN 1 impacts root hydraulics and trade-off for stress responses in Arabidopsis.

  Nature Communications  9:3884




  Michael T.P., Jupe F., Bemm F., Motley S.T., Sandoval J.P., Lanz C., Loudet O., Weigel D., Ecker J.R. (2018)

  High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.

  Nature Communications  9:541




  Bazakos C., Hanemian M., Trontin C., Jiménez-Gómez J.M., Loudet O. (2017)

  New strategies and tools in quantitative genetics: how to go from the phenotype to the genotype.

  Annual Review of Plant Biology 68:435-455




  Agorio A., Durand S., Fiume E., Brousse C., Gy I., Simon M., Anava S., Rechavi O., Loudet O., Camilleri C., Bouché N. (2017)

  An Arabidopsis natural epiallele maintained by a feed-forward silencing loop between histone and DNA.

  PLoS Genetics 13:e1006551




  Viaud G., Loudet O., Cournède P-H. (2017)

  Leaf segmentation and tracking in Arabidopsis thaliana combined to an organ-scale plant model for genotypic differentiation.

  Frontiers in Plant Science 7: 2057 doi: 10.3389/fpls.2016.02057




  Nijveen H., Ligterink W., Keurentjes J.J.B., Loudet O., Long J., Sterken M.G., Prins P., Hilhorst H.W., de Ridder D., Kammenga J.E., Snoek B.L. (2017)

  AraQTL - Workbench and archive for systems genetics in Arabidopsis thaliana.

  The Plant Journal 89: 1225-1235




  Shahzad Z., Canut M., Tournaire-Roux C., Martinière A., Boursiac Y., Loudet O., Maurel C. (2016)

  A potassium-dependent oxygen sensing pathway regulates plant root hydraulics.

  Cell   167: 87-98  Supp. Material




  Müller NA, Wijnen CL, Srinivasan A, Ryngajllo M, Ofner I, Lin T, Ranjan A, West D, Maloof JN, Sinha NR, Huang S, Zamir D, Jiménez-Gómez JM. (2016)

  Domestication selected for deceleration of the circadian clock in cultivated tomato.

  Nature Genetics  48(1): 89-93




  Cubillos F.A., Stegle O., Grondin C., Canut M., Tisné S., Gy I., Loudet O. (2014)

  Extensive cis-regulatory variation robust to environmental perturbation in A. thaliana.

  The Plant Cell  26: 4298-4310   Supp. Info    Supp. Dataset 1    Supp. Dataset 2




  Schmalenbach I, Zhang L, Ryngajllo M, Jiménez-Gómez JM. (2014)

  Functional analysis of the Landsberg erecta allele of FRIGIDA.

  BMC Plant Biology  14(1): 218




  Téoulé E., Géry C. (2014)

  Mapping of quantitative trait loci (QTL) associated with plant freezing tolerance and cold acclimation.

  Methods in Molecular Biology  1166: 43-64




  Gloggnitzer J, Akimcheva S, Srinivasan A, Kusenda B, Riehs N, Stampfl H, Bautor J, Dekrout B, Jonak C, Jiménez-Gómez JM, Parker JE, Riha K. (2014)

  Nonsense-mediated mRNA decay modulates immune receptor levels to regulate plant antibacterial defense.

  Cell Host & Microbe  16(3): 376-390




  Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. (2014)

  The genome of the stress-tolerant wild tomato species Solanum pennellii.

  Nature Genetics  46(9): 1034-1038




  Trontin C., Kiani S., Corwin J.A., Hématy K., Yansouni J., Kliebenstein D.J., Loudet O. (2014)

  A pair of receptor-like kinases is responsible for natural variation in shoot growth response to mannitol treatment in Arabidopsis thaliana.

  The Plant Journal  78(1): 121-133  Supp. Material  /  Supp. Tables




  Jiménez-Gómez JM. (2014)

  Network types and their application in natural variation studies in plants.

  Current Opinion in Plant Biology  18: 80-86




  Saez-Aguayo S., Rondeau-Mouro C., Macquet A., Kronholm I., Ralet M.-C., Berger A., Sallé C., Poulain D.,

  Granier F., Botran L., Loudet O., de Meaux J., Marion-Poll A., North H.M. (2014)

  Local evolution of seed flotation in Arabidopsis.

  PLoS Genetics 10(3): e1004221  Paper eLink




  Coustham V., Vlad D., Deremetz A., Gy I., Cubillos F.A., Kerdaffrec E., Loudet O., Bouché N. (2014)

  SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1.

  PLoS ONE  9(1): e84687  Paper eLink  /  Supp. Figures  /  Supp. Tables




  Koprivova A., Giovannetti M., Baraniecka P., Lee B.R., Grondin C., Loudet O., Kopriva S. (2013)

  Natural variation in ATPS1 isoform of ATP Sulfurylase contributes to control of sulfate levels in Arabidopsis.

  Plant Physiology  163(3): 1133-1141   Supp. Material




  Chardon F., Bedu M., Calenge F., Klemens P.A.W., Spinner L., Clement G., Chietera G., Léran S.,

  Ferrand M., Lacombe B., Loudet O., Dinant S., Bellini C., Neuhaus H.E., Daniel-Vedele F., Krapp A. (2013)

  Leaf fructose content is controlled by the vacuolar transporter SWEET17 in Arabidopsis.

  Current Biology  23(8): 697-702   Supp. Material




  Silveira A.B., Trontin C., Cortijo S., Barau J., Vieira Del Bem L.E., Loudet O., Colot V., Vincentz M. (2013)

  Extensive natural epigenetic variation at a de novo originated gene.

  PLoS Genetics  9(4): e1003437   Paper eLink   /   Supp. Figures




  Tisné S., Serrand Y., Bach L., Gilbault E., Ben Ameur R., Balasse H., Voisin R., Bouchez D., Durand-Tardif M.,

  Guerche P., Chareyron G., Da Rugna J., Camilleri C., Loudet O. (2013)

  PHENOSCOPE: an automated large-scale phenotyping platform offering high spatial homogeneity.

  The Plant Journal  74: 534-544   Supp. Material




  Pineau C., Loubet S., Lefoulon C., Chalies C., Fizames C., Lacombe B., Ferrand M., Loudet O., Berthomieu P., Richard O. (2012)

  Natural variation at the FRD3 MATE transporter locus reveals cross-talk between Fe homeostasis and Zn tolerance in Arabidopsis thaliana.

  PLoS Genetics  8(12): e1003120   Paper eLink   /   Supp. Figures & Tables




  Jasinski S., Lecureuil A., Miquel M., Loudet O., Raffaele S., Froissard M., Guerche P. (2012)

  Natural variation in seed very long chain fatty acid content is controlled by a new isoform of KCS18 in Arabidopsis thaliana.

  PLoS ONE  7: e49261   Paper eLink




  Poormohammad Kiani S., Trontin C., Andreatta M., Simon M., Robert T., Salt D.E., Loudet O. (2012)

  Allelic heterogeneity and trade-off shape natural variation for response to soil micronutrient.

  PLoS Genetics  8(7): e1002814   Paper eLink   /   Supp. Figures   /   Supp. Tables




  Cubillos F.A., Yansouni J., Khalili H., Balzergue S., Elftieh S., Martin-Magniette M.L., Serrand Y., Lepiniec L., Baud S.,

  Dubreucq B., Renou J.P., Camilleri C., Loudet O. (2012)

  Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures.

  BMC Genomics  13: 117   Supp. Text&Figures   /   Supp. Tables   /   The QTL Store




  Routaboul J.M., Dubos C., Beck G., Marquis C., Bidzinski P., Loudet O., Lepiniec L. (2012)

  Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis.

  Journal of Experimental Botany  63: 3749-3764   Supp. Data




  Bouteillé M., Rolland G., Balsera C., Loudet O., Muller B. (2012)

  Disentangling the intertwined genetic bases of root and shoot growth in Arabidopsis.

  PLoS ONE  7, e32319   Paper eLink




  Durand S., Bouché N., Perez Strand E., Loudet O., Camilleri C. (2012)

  Rapid establishment of genetic incompatibility through natural epigenetic variation.

  Current Biology  22: 326-331   Supp. Data




  Cubillos F.A., Coustham V., Loudet O. (2012)

  Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants.

  Current Opinion in Plant Biology  15: 192-198




  Simon M., Simon A., Martins F., Botran L., Tisné S., Granier F., Loudet O., Camilleri C. (2011)

  DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions.

  The Plant Journal  69: 1094-1101   Supp. Fig.  /   Supp. Tab.   /   Cluster   /   ANATool




  Trontin C., Tisné S., Bach L., Loudet O. (2011)

  What does Arabidopsis natural variation teach us (and does not teach us) about adaptation in plants?

  Current Opinion in Plant Biology  14: 225-231




  Lefebvre V., Fortabat M-N., Ducamp A., North H.M., Maia-Grondard A., Trouverie J., Boursiac Y., Mouille G., Durand-Tardif M. (2011)

  ESKIMO1 disruption in Arabidopsis alters vascular tissue and impairs water transport.

  PLoS ONE  6(2): e16645   Paper eLink




  Géry C., Zuther E., Schulz E., Legoupi J., Chauveau A., McKhann H., Hincha D. K., Téoulé E. (2011)

  Natural variation in the freezing tolerance of Arabidopsis thaliana: effects of RNAi-induced CBF depletion and QTL localisation vary among accessions.

  Plant Science   180(1): 12-23




  Vlad D., Rappaport F., Simon M., Loudet O. (2010)

  Gene transposition causing natural variation for growth in Arabidopsis thaliana.

  PLoS Genetics  6(5): e1000945   Paper eLink  /  Supp. Fig.  /  Supp. Tab.




  Kronholm I., Loudet O., de Meaux J. (2010)

  Influence of mutation rate on estimators of genetic differentiation - lessons from Arabidopsis thaliana.

  BMC Genetics  11:33




  Platt A., Horton M., Huang Y.S., Li Y., Anastasio A.E., Wayan Mulyati N., Ågren J., Bossdorf O., Byers D., Donohue K., Dunning M., Holub E.B.,

  Hudson A., Le Corre V., Loudet O., Roux F., Warthmann N., Weigel D., Rivero L., Scholl R., Nordborg M., Bergelson J., Borevitz J.O. (2010)

  The scale of population structure in Arabidopsis thaliana

  PLoS Genetics  6(2): e1000843   Paper eLink




  Bikard D., Patel D., Le Metté C., Giorgi V., Camilleri C., Bennett M.J., Loudet O. (2009)

  Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana

  Science  323: 623-626    Supp. Data  /  High Res. Figures  /  Free Full Text




  Balasubramanian S., Schwartz C., Singh A., Warthmann N., Kim M.C., Maloof J.N., Loudet O., Trainer G.T., Dabi T., Borevitz J.O., Chory J., Weigel D. (2009)

  QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines.

  PLoS ONE  4(2): e4318   Paper eLink




  Bouchabke O., Quashie M-L., Seoane-Redondo J., Fortabat M-N., Gery C., Yu A., Linderme D., Trouverie J., Granier F., Téoulé E. , Durand-Tardif. M. (2008)

  Eskimo1 is a key gene involved in water economy as well as cold acclimation and salt tolerance

  BMC Plant Biology  8: 125    Supp. Data




  Loudet O., Michael T.P., Burger B.T., Le Metté C., Mockler T.C., Weigel D., Chory J. (2008)

  A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana

  Proc. Natl. Acad. Sci. USA (PNAS)  105: 17193-17198   PNAS Supp. Data  /  Supplementary Tables




  Simon M., Loudet O., Durand S., Bérard A., Brunel D., Sennesal F.-X., Durand-Tardif M., Pelletier G., Camilleri C. (2008)

  QTL mapping in five new large RIL populations of Arabidopsis thaliana genotyped with consensus SNP markers.

  Genetics  178: 2253-2264   Supp. Data




  Bouchabke O., Chang F., Simon M., Voisin R., Pelletier G., Durand-Tardif M. (2008)

  Natural variation in Arabidopsis thaliana as a tool for highlighting differential drought responses.

  PLoS ONE  3(2): e1705   Paper eLink




  Sicard O., Loudet O., Keurentjes J. J. B., Candresse T., Le Gall O., Revers F., Decroocq V. (2008)

  Identification of quantitative trait loci controlling symptom development during viral infection in Arabidopsis thaliana.

  Molecular Plant-Microbe Interaction  21: 198-207




  Meng P.-H., Macquet A., Loudet O., Marion-Poll A., North H.M. (2008)

  Analysis of natural allelic variation controlling Arabidopsis thaliana seed germinability in response to cold and dark: identification of three major quantitative trait loci.

  Molecular Plant  1: 145-154




  Macquet A., Ralet M.-C., Loudet O., Kronenberger J., Mouille G., Marion-Poll A., North H.M. (2007)

  A naturally occurring mutation in an Arabidopsis accession affects a b-D-galactosidase that increases the hydrophilic potential of rhamnogalacturonan I in seed mucilage.

  The Plant Cell  19: 3990-4006




  Loudet O., Saliba-Colombani V., Camilleri C., Calenge F., Gaudon V., Koprivova A., North K.A., Kopriva S., Daniel-Vedele F. (2007)

  Natural variation for sulfate content in Arabidopsis is highly controlled by APR2.

  Nature Genetics  39: 896-900   Supp. Data




  Perchepied L., Kroj T., Tronchet M., Loudet O., Roby D. (2006)

  Natural variation in partial resistance to Pseudomonas syringae is controlled by two major QTLs in Arabidopsis thaliana.

  PLoS ONE  1(1): e123   Paper eLink




  Calenge F., Saliba-Colombani V., Mahieu S., Loudet O., Daniel-Vedele F., Krapp A. (2006)

  Natural variation for carbohydrate content in Arabidopsis thaliana: interaction with complex traits dissected by quantitative genetics.

  Plant Physiology  141: 1630-1643




  Kliebenstein D.J., West M.A.L., van Leeuwen H., Loudet O., Doerge R.W., St.Clair D.A. (2006)

  Identification of QTLs controlling gene expression networks defined a priori.

  BMC Bioinformatics  7: 308




  Barrière Y., Denoue D., Briand M., Simon M., Jouanin L., Durand-Tardif M. (2006)

  Genetic variations of cell wall digestibility related traits in floral stems of Arabidopsis thaliana accessions as a basis for the improvement of the feeding value in maize and forage plants.

  Theoretical and Applied Genetics  113: 163-75




  Mouille G., Witucka-Wall H., Bruyant M.P., Loudet O., Rihouey C., Lerouxel O., Lerouge P., Hofte H., Pauly M. (2006)

  QTL analysis of primary cell wall composition in Arabidopsis thaliana.

  Plant Physiology  141: 1035-1044




  Diaz C., Saliba-Colombani V., Loudet O., Belluomo P., Moreau L., Daniel-Vedele F., Morot-Gaudry J.-F., Masclaux-Daubresse C. (2006)

  Leaf yellowing and anthocyanin accumulation are two genetically independent strategies in response to nitrogen limitation in Arabidopsis thaliana.

  Plant and Cell Physiology  47: 74-83




  Reymond M., Svistoonoff S., Loudet O., Nussaume L., Desnos T. (2006)

  Identification of QTL controlling root growth response to phosphate starvation in Arabidopsis thaliana.

  Plant, Cell and Environment  29:115-125




  Loudet O., Gaudon V., Trubuil A., Daniel-Vedele F. (2005)

  Quantitative trait loci controlling root growth and architecture in Arabidopsis thaliana confirmed by heterogeneous inbred family.

  Theoretical and Applied Genetics  110: 742-753




  Wolyn D., Borevitz J., Loudet O., Schwartz C., Maloof J., Ecker J., Berry C., Chory J. (2004)

  Light-response Quantitative Trait Loci identified with composite interval and eXtreme Array Mapping in Arabidopsis thaliana.

  Genetics  167: 907-917




  Loudet O., Chaillou S., Krapp A., Daniel-Vedele F. (2003)

  Quantitative Trait Loci analysis of water and anion contents in interaction with nitrogen availability in Arabidopsis thaliana.

  Genetics  163: 711-722




  Loudet O., Chaillou S., Merigout P., Talbotec J., Daniel-Vedele F. (2003)

  Quantitative Trait Loci analysis of nitrogen use efficiency in Arabidopsis.

  Plant Physiology  131: 345-358




  Loudet O., Chaillou S., Camilleri C., Bouchez D., Daniel-Vedele F. (2002)

  Bay-0 x Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis.

  Theoretical and Applied Genetics  104: 1173-1184




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