Variation and Abiotic Stress Tolerance

Goelzer A, Rajjou L, Chardon F, Loudet O, Fromion V (2024). Resource allocation modeling for autonomous prediction of plant cell phenotypes. Metab Eng, S1096-7176(24)00054-5. PubMed | DOI

Shahzad Z, Tournaire-Roux C, Canut M, Adamo M, Roeder J, Verdoucq L, Martiniere A, Amtmann A, Santoni V, Grill E, Loudet O, Maurel C (2023). Protein kinase SnRK2.4 is a key regulator of aquaporins and root hydraulics in Arabidopsis. Plant J, 117: 264-279. PubMed | DOI

Elfarargi AF, Gilbault E, Döring N, Neto C, Fulgione A, Weber APM, Loudet O, Hancock AM (2023). Genomic basis of adaptation to a novel precipitation regime. Mol Biol Evol, msad031. PubMed | DOI

Géry C, Téoulé E (2022). Cold acclimation diversity in Arabidopsis thaliana: CRISPR/Cas9 as a tool to fine analysis of Tandem Gene Arrays, application to CBF genes. Dev Genes Evol. PubMed | DOI

Xiang Y, Sapir T, Rouillard P, Ferrand M, Jiménez-Gómez JM (2022). Interaction between photoperiod and variation in circadian rhythms in tomato. BMC Plant Biol, 22(1):187. PubMed | DOI

Baduel P, Leduque B, Ignace A, Gy I, Gil J Jr, Loudet O, Colot V, Quadrana L (2021). Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biol, 22(1):138. PubMed | DOI

Jiao WB, Patel V, Klasen J, Liu F, Pecinkova P, Ferrand M, Gy I, Camilleri C, Effgen S, Koornneef M, Pecinka A, Loudet O, Schneeberger K (2021). The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Mol Biol Evol, 38(4):1225-1240. PubMed | DOI

Hanemian M, Vasseur F, Marchadier E, Gilbault E, Bresson J, Gy I, Violle C, Loudet O (2020). Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana. Nat Commun, 11(1):4140. PubMed | DOI

Téoulé E, Géry C (2020). Mapping of Quantitative Trait Loci (QTL) Associated with Plant Freezing Tolerance and Cold Acclimation. Methods Mol Biol, 2156:61-84. PubMed | DOI

Van Dooren TJM, Silveira AB, Gilbault E, Jiménez-Gómez JM, Martin A, Bach L, Tisne S, Quadrana L, Loudet O, Colot V (2020). Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects. J Exp Bot, 71:3588-3602. PubMed | DOI

Deremetz A, Le Roux C, Idir Y, Brousse C, Agorio A, Gy I, Parker JE, Bouché N (2019). Antagonistic Actions of FPA and IBM2 Regulate Transcript Processing from Genes Containing Heterochromatin. Plant Physiol, 180:392-403. PubMed | DOI

Marchadier E, Hanemian M, Tisne 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 Genet, 15:e1007954. PubMed | DOI

Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker JR (2018). High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun, 9:541. PubMed | DOI

Tang N, Shahzad Z, Lonjon F, Loudet O, Vailleau F, Maurel C (2018). Natural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis. Nat Commun, 9:3884. PubMed | DOI

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 Genet, 13:e1006551. PubMed | DOI

Bazakos C, Hanemian M, Trontin C, Jiménez-Gómez JM, Loudet O (2017). New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype. Annu Rev Plant Biol, 68:435-455. PubMed | DOI

Nijveen H, Ligterink W, Keurentjes JJ, Loudet O, Long J, Sterken MG, Prins P, Hilhorst HW, De Ridder D, Kammenga JE, Snoek BL (2017). AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana. Plant J, 89:1225-1235. PubMed | DOI

Bar M, Israeli A, Levy M, Ben Gera H, Jiménez-Gómez JM, Kouril S, Tarkowski P, Ori N (2016). CLAUSA Is a MYB Transcription Factor That Promotes Leaf Differentiation by Attenuating Cytokinin Signaling. Plant Cell, 28:1602-1615. PubMed | DOI

Lopez-Obando M, Hoffmann B, Géry C, Guyon-Debast A, Téoulé E, Rameau C, Bonhomme S, Nogué F (2016). Simple and Efficient Targeting of Multiple Genes Through CRISPR-Cas9 in Physcomitrella patens. G3, 6:3647-3653. PubMed | DOI

Mosquera T, Alvarez MF, Jiménez-Gómez JM, Muktar MS, Paulo MJ, Steinemann S, Li J, Draffehn A, Hofmann A, Lubeck J, Strahwald J, Tacke E, Hofferbert HR, Walkemeier B, Gebhardt C (2016). Targeted and Untargeted Approaches Unravel Novel Candidate Genes and Diagnostic SNPs for Quantitative Resistance of the Potato (Solanum tuberosum L.) to Phytophthora infestans Causing the Late Blight Disease. PLoS One, 11:e0156254. PubMed | DOI

Muller NA, Jiménez-Gómez JM (2016). Analysis of Circadian Leaf Movements. Methods Mol Biol, 1398:71-79. PubMed | DOI

Muller 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. Nat Genet, 48:89-93. PubMed | DOI

Perea-Resa C, Carrasco-Lopez C, Catala R, Tureckova V, Novák O, Zhang W, Sieburth L, Jiménez-Gómez JM, Salinas J (2016). The LSM1-7 Complex Differentially Regulates Arabidopsis Tolerance to Abiotic Stress Conditions by Promoting Selective mRNA Decapping. Plant Cell, 28:505-520. PubMed | DOI

Shahzad Z, Canut M, Tournaire-Roux C, Martiniere A, Boursiac Y, Loudet O, Maurel C (2016). A Potassium-Dependent Oxygen Sensing Pathway Regulates Plant Root Hydraulics. Cell, 167:87-98 e14. PubMed | DOI

Srinivasan A, Jiménez-Gómez JM, Fornara F, Soppe WJ, Brambilla V (2016). Alternative splicing enhances transcriptome complexity in desiccating seeds. J Integr Plant Biol, 58:947-958. PubMed | DOI

Viaud G, Loudet O, Cournede PH (2016). Leaf Segmentation and Tracking in Arabidopsis thaliana Combined to an Organ-Scale Plant Model for Genotypic Differentiation. Front Plant Sci, 7:2057. PubMed | DOI

Bensussan M, Lefebvre V, Ducamp A, Trouverie J, Gineau E, Fortabat MN, Guillebaux A, Baldy A, Naquin D, Herbette S, Lapierre C, Mouille G, Horlow C, Durand-Tardif M (2015). Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis. Plant Physiol, 168:452-463. PubMed | DOI

Le Hir R, Spinner L, Klemens PA, Chakraborti D, De Marco F, Vilaine F, Wolff N, Lemoine R, Porcheron B, Géry C, Téoulé E, Chabout S, Mouille G, Neuhaus HE, Dinant S, Bellini C (2015). Disruption of the Sugar Transporters AtSWEET11 and AtSWEET12 Affects Vascular Development and Freezing Tolerance in Arabidopsis. Mol Plant, 8:1687-1690. PubMed | DOI

Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sorensen 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-Gómez JM, Ryngajllo M, Kimura S, Kumar Ra, 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. Nat Genet, 46:1034-1038. PubMed | DOI

Bomblies K, Loudet O (2014). Genome studies and molecular genetics: Genomic approaches to understanding evolution, development and the plant phenome. Curr Opin Plant Biol, 18:v-vi. PubMed | DOI

Coustham V, Vlad D, Deremetz A, Gy I, Cubillos FA, Kerdaffrec E, Loudet O, Bouché N (2014). SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1. PLoS One, 9:e84687. PubMed | DOI

Cubillos FA, Stegle O, Grondin C, Canut M, Tisne S, Gy I, Loudet O (2014). Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. Plant Cell, 26:4298-4310. PubMed | DOI

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, 16:376-390. PubMed | DOI

Jiménez-Gómez JM (2014). Network types and their application in natural variation studies in plants. Curr Opin Plant Biol, 18:80-86. PubMed | DOI

Saez-Aguayo S, Rondeau-Mouro C, Macquet A, Kronholm I, Ralet MC, Berger A, Sallé C, Poulain D, Granier F, Botran L, Loudet O, De Meaux J, Marion-Poll A, North HM (2014). Local evolution of seed flotation in Arabidopsis. PLoS Genet, 10:e1004221. PubMed | DOI

Schmalenbach I, Zhang L, Reymond M, Jiménez-Gómez JM (2014). The relationship between flowering time and growth responses to drought in the Arabidopsis Landsberg erecta x Antwerp-1 population. Front Plant Sci, 5:609. PubMed | DOI

Schmalenbach I, Zhang L, Ryngajllo M, Jiménez-Gómez JM (2014). Functional analysis of the Landsberg erecta allele of FRIGIDA. BMC Plant Biol, 14:218. PubMed | DOI

Téoulé E, Géry C (2014). Mapping of quantitative trait loci (QTL) associated with plant freezing tolerance and cold acclimation 2014. Methods Mol Biol, 1166:43-64. PubMed | DOI

Trontin C, Kiani S, Corwin JA, Hématy K, Yansouni J, Kliebenstein DJ, Loudet O (2014). A pair of receptor-like kinases is responsible for natural variation in shoot growth response to mannitol treatment in Arabidopsis thaliana. Plant J, 78:121-133. PubMed | DOI

Chardon F, Bedu M, Calenge F, Klemens PA, Spinner L, Clément G, Chietera G, Leran S, Ferrand M, Lacombe B, Loudet O, Dinant S, Bellini C, Neuhaus HE, Daniel-Vedele F, Krapp A (2013). Leaf fructose content is controlled by the vacuolar transporter SWEET17 in Arabidopsis. Curr Biol, 23:697-702. PubMed | DOI

Koprivova A, Giovannetti M, Baraniecka P, Lee BR, Grondin C, Loudet O, Kopriva S (2013). Natural variation in the ATPS1 isoform of ATP sulfurylase contributes to the control of sulfate levels in Arabidopsis. Plant Physiol, 163:1133-1141. PubMed | DOI

Silveira AB, Trontin C, Cortijo S, Barau J, Del Bem LE, Loudet O, Colot V, Vincentz M (2013). Extensive natural epigenetic variation at a de novo originated gene. PLoS Genet, 9:e1003437. PubMed | DOI

Tisne 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. Plant J, 74:534-544. PubMed | DOI

Bouteille 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. PubMed | DOI

Cubillos FA, Coustham V, Loudet O (2012). Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants. Curr Opin Plant Biol, 15:192-198. PubMed | DOI

Cubillos FA, Yansouni J, Khalili H, Balzergue S, Elftieh S, Martin-Magniette ML, Serrand Y, Lepiniec L, Baud S, Dubreucq B, Renou JP, Camilleri C, Loudet O (2012). Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures. BMC Genomics, 13:117. PubMed | DOI

Durand S, Bouché N, Perez Strand E, Loudet O, Camilleri C (2012). Rapid establishment of genetic incompatibility through natural epigenetic variation. Curr Biol, 22:326-331. PubMed | DOI

Jasinski S, Lécureuil 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. PubMed | DOI

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 Genet, 8:e1003120. PubMed | DOI

Poormohammad Kiani S, Trontin C, Andreatta M, Simon M, Robert T, Salt DE, Loudet O (2012). Allelic heterogeneity and trade-off shape natural variation for response to soil micronutrient. PLoS Genet, 8:e1002814. PubMed | DOI