We are studying the genomes of the grass species wheat, barley and rice to analyze genome evolution in cereals. Plant genomes generally evolve much more rapidly than animal genomes and we want to understand  the underlying molecular mechanisms. These studies in evolutionary genomics have already given surprising results: for the genomic regions analyzed to date, we found complete restructuring of the intergenic regions within 1 to 3 million years, a much faster and dramatic evolution than previously assumed.

The wheat genome is very large (5x the size of the human genome) and complex. The knowledge on cereal genome structure is used in our group for the molecular isolation of agronomically important genes from wheat and barley. We have recently isolated the first two resistance genes against the fungal diseases leaf rust and powdery mildew of wheat. We are now studying their activity and the evolution of resistance at the molecular level. 

The different projects conducted in the research group strongly depend on the use of genomic technologies as well as advanced bioinformatics.

• From laboratory to the field: biological control of Fusarium graminearum on infected maize crop residues
  Gimeno, A.; Kagi, A.; Drakopoulos, D.; Banziger, I.; Lehmann, E.; Forrer, H. -R.; Keller, B; Vogelgsang, S
  Journal Of Applied Microbiology  10.1111/jam.14634  Early Access: APR 2020
• Cross-Kingdom RNAi of Pathogen Effectors Leads to Quantitative Adult Plant Resistance in Wheat
  Schaefer, Luisa Katharina; Parlange, Francis; Buchmann, Gabriele; Jung, Esther; Wehrli, Andreas; et al.
  Frontiers In Plant Science  DOI: 10.3389/fpls.2020.00253 Published: MAR 10 2020
• Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
  Cossarizza, Andrea; Chang, Hyun-Dong; Radbruch, Andreas; Acs, Andreas; Adam, Dieter; et al.
  European Journal Of Immunology,  DOI: 10.1002/eji.201970107
• TaqMan qPCR for Quantification of Clonostachys rosea Used as a Biological Control Agent Against Fusarium graminearum
  Gimeno, A; Sohlberg, E; Pakula, T; Limnell, J; Keller, B; Laitila, A; Vogelgsang, S
  FRONTIERS IN MICROBIOLOGY, 10 10.3389/fmicb.2019.01627 JUL 16 2019
• Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34
  Krattinger, SG; Kang, J; Braunlich, S; Boni, R; Chauhan, H; Selter, LL; Robinson, MD; Schmid, MW; Wiederhold, E; Hensel, G; Kumlehn, J; Sucher, J; Martinoia, E; Keller, B
  NEW PHYTOLOGIST, 223 (2):853-866; 10.1111/nph.15815 JUL 2019
• The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat
  Bourras, S; Kunz, L; Xue, MF; Praz, CR; Muller, MC; Kalin, C; Schlafli, M; Ackermann, P; Fluckiger, S; Parlange, F; Menardo, F; Schaefer, LK; Ben-David, R; Roffler, S; Oberhaensli, S; Widrig, V; Lindner, S; Isaksson, J; Wicker, T; Yu, DZ; Keller, B
  NATURE COMMUNICATIONS, 10 10.1038/s41467-019-10274-1 MAY 23 2019
• Worldwide phylogeography and history of wheat genetic diversity
  Balfourier, F; Bouchet, S; Robert, S; De Oliveira, R; Rimbert, H; Kitt, J; Choulet, F; Appels, R; Feuillet, C; Keller, B; Praud, S; Baumann, U; Budak, H; Rogers, J; Eversole, K; Alaux, M; Bejar, B; Lafarge, S; Lagendijk, E; Derory, J; Le Gouis, J; Paux, E
  Group Author(s): Int Wheat Genome Sequencing Consor; BreedWheat Consortium
  SCIENCE ADVANCES, 5 (5):10.1126/sciadv.aav0536 MAY 2019
• Tracing the ancestry of modern bread wheats
  Pont, C; Leroy, T; Seidel, M; Tondelli, A; Duchemin, W; Armisen, D; Lang, D; Bustos-Korts, D; Goue, N; Balfourier, F; Molnar-Lang, M; Lage, J; Kilian, B; Ozkan, H; Waite, D; Dyer, S; Letellier, T; Alaux, M; Russell, J; Keller, B; van Eeuwijk, F; Spannagl, M; Mayer, KFX; Waugh, R; Stein, N; Cattivelli, L; Haberer, G; Charmet, G; Salse, J; Group Author(s): Wheat Barley Legacy Breeding
  NATURE GENETICS, 51 (5):905-+; 10.1038/s41588-019-0393-z MAY 2019
• Contribution of recent technological advances to future resistance breeding
  Sanchez-Martin, J; Keller, B
  THEORETICAL AND APPLIED GENETICS, 132 (3):713-732; SI 10.1007/s00122-019-03297-1 MAR 2019
• The evolutionary roles of hybridization and introgression: investigating species and genomic boundaries using the model plant system Primula (Primulaceae)
  Stubbs, RL; Theodoridis, S; Keller, B; Conti, E
  INTEGRATIVE AND COMPARATIVE BIOLOGY, 59 E417-E417; 1 MAR 2019
• A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew
  Muller, MC; Praz, CR; Sotiropoulos, AG; Menardo, F; Kunz, L; Schudel, S; Oberhansli, S; Poretti, M; Wehrli, A; Bourras, S; Keller, B; Wicker, T
  NEW PHYTOLOGIST, 221 (4):2176-2189; 10.1111/nph.15529 MAR 2019
• Genebank genomics highlights the diversity of a global barley collection
  Milner, SG; Jost, M; Taketa, S; Mazon, ER; Himmelbach, A; Oppermann, M; Weise, S; Knupffer, H; Basterrechea, M; Konig, P; Schuler, D; Sharma, R; Pasam, RK; Rutten, T; Guo, GG; Xu, DD; Zhang, J; Herren, G; Muller, T; Krattinger, SG; Keller, B; Jiang, Y; Gonzalez, MY; Zhao, YS; Habekuss, A; Farber, S; Ordon, F; Lange, M; Borner, A; Graner, A; Reif, JC; Scholz, U; Mascher, M; Stein, N
  NATURE GENETICS, 51 (2):319-+; 10.1038/s41588-018-0266-x FEB 2019
• Field grown transgenic Pm3e wheat lines show powdery mildew resistance and no fitness costs associated with high transgene expression
  Koller, T; Brunner, S; Herren, G; Sanchez-Martin, J; Hurni, S; Keller, B
  TRANSGENIC RESEARCH, 28 (1):9-20; 10.1007/s11248-018-0099-5 FEB 2019
• Convergent evolution of a metabolic switch between aphid and caterpillar resistance in cereals
  Li, B; Forster, C; Robert, CAM; Zust, T; Hu, L; Machado, RAR; Berset, JD; Handrick, V; Knauer, T; Hensel, G; Chen, W; Kumlehn, J; Yang, P; Keller, B; Gershenzon, J; Jander, G; Kollner, TG; Erb, M
  SCIENCE ADVANCES, 4 (12):10.1126/sciadv.aat6797 DEC 2018
• Cereal powdery mildew effectors: a complex toolbox for an obligate pathogen
  Bourras, S; Praz, CR; Spanu, PD; Keller, B
  CURRENT OPINION IN MICROBIOLOGY, 46 26-33; 10.1016/j.mib.2018.01.018 DEC 2018
• Evolutionary divergence of the rye Pm17 and Pm8 resistance genes reveals ancient diversity
  Singh, SP; Hurni, S; Ruinelli, M; Brunner, S; Sanchez-Martin, J; Krukowski, P; Peditto, D; Buchmann, G; Zbinden, H; Keller, B
  PLANT MOLECULAR BIOLOGY, 98 (3):249-260; 10.1007/s11103-018-0780-3 OCT 2018
• The wheat ABC transporter Lr34 modifies the lipid environment at the plasma membrane
  Deppe, JP; Rabbat, R; Hortensteiner, S; Keller, B; Martinoia, E; Lopez-Marques, RL
  JOURNAL OF BIOLOGICAL CHEMISTRY, 293 (48):18667-18679; 10.1074/jbc.RA118.002532 NOV 30 2018
• Shifting the limits in wheat research and breeding using a fully annotated reference genome
  Appels, R; Eversole, K; Feuillet, C; Keller, B; … Wicker, T; …; Uauy, C
  SCIENCE, 361 (6403):661-+; 10.1126/science.aar7191 AUG 17 2018
• Advances in Wheat and Pathogen Genomics: Implications for Disease Control
  Keller, Beat; Wicker, Thomas; Krattinger, Simon G. Edited by: Leach JE; Lindow SE
  ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56, 56 67-87; 10.1146/annurev-phyto-080516-035419 2018
• Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars
  Thind, AK; Wicker, T; Muller, T; Ackermann, PM; Steuernagel, B; Wulff, BBH; Spannagl, M; Twardziok, SO; Felder, M; Lux, T; Mayer, KFX; Keller, B; Krattinger, SG
  Group Author(s): Int Wheat Genome Sequencing
  GENOME BIOLOGY, 19 10.1186/s13059-018-1477-2 AUG 17 2018
• Infection conditions of Fusarium graminearum in barley are variety specific and different from those in wheat
  Schoneberg, T; Musa, T; Forrer, HR; Mascher, F; Bucheli, TD; Bertossa, M; Keller, B; Vogelgsang, S
  EUROPEAN JOURNAL OF PLANT PATHOLOGY, 151 (4):975-989; 10.1007/s10658-018-1434-7 AUG 2018
• A new player in race-specific resistance
  Keller, Beat; Krattinger, Simon G.
  NATURE PLANTS, 4 (4):197-198; 10.1038/s41477-018-0126-9 APR 2018
• Transcriptional profiling reveals no response of fungal pathogens to the durable, quantitative Lr34 disease resistance gene of wheat
  Sucher, J; Menardo, F; Praz, CR; Boni, R; Krattinger, SG; Keller, B
  PLANT PATHOLOGY, 67 (4):792-798; https://doi.org/10.1111/ppa.12797 MAY 2018
• Comparative Transcriptomics Reveals How Wheat Responds to Infection by Zymoseptoria tritici
  Authors: Ma, X; Keller, B; McDonald, BA; Palma-Guerrero, J; Wicker, T
  MOLECULAR PLANT-MICROBE INTERACTIONS, 31 (4):420-431; https://doi.org/10.1094/MPMI-10-17-0245-R APR 2018
• Pyramiding of transgenic Pm3 alleles in wheat results in improved powdery mildew resistance in the field
  Koller, Teresa; Brunner, Susanne; Herren, Gerhard; et al.
  THEORETICAL AND APPLIED GENETICS  131(4): 861-871, https://doi.org/10.1007/s00122-017-3043-9   APR 2018
• Distinct domains of the AVRPM3(A2/F2) avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function
  McNally, Kaitlin Elyse; Menardo, Fabrizio; Luthi, Linda; et al.
  NEW PHYTOLOGIST, 218(2):681-695, https://doi.org/10.1111/nph.15026   APR 2018
• Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen 
  Praz, Coraline R.; Menardo, Fabrizio; Robinson, Mark D.; et al. 
  FRONTIERS IN PLANT SCIENCE, 9: JAN 30 2018
• Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt 
  Mueller, Thomas; Schierscher-Viret, Beate; Fossati, Dario; et al. 
  THEORETICAL AND APPLIED GENETICS, 131 (2): 407-416 FEB 2018
• …

• Fungal disease resistance in cereals
• Structure and evolution of plant genomes
• Molecular basis of agronomically important traits
• Root hair development

• Evolutionary genomics
• Molecular Agronomy and Plant Breeding
• Plant Pathology