Publications

Names of our group members are in bold font. For individual publication lists of lab members see their individual pages on the Team page.

2023

• Kersten, S., Rabanal, F.A., Herrmann, J., Hess, M., Kronenberg, Z.N., Schmid, K., and Weigel, D. Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing. Plant Biotechnology Journal. DOI:10.1111/pbi.14033. Journal Preprint

• Lozano-Isla, F., Apaza, J.-D., Mujica Sanchez, A., Blas Sevillano, R., Haussmann, B.I.G., and Schmid, K. (2023) Enhancing quinoa cultivation in the Andean highlands of Peru: a breeding strategy for improved yield and early maturity adaptation to climate change using traditional cultivars. Euphytica 219, 26. Journal

• Latzel, V., Fischer, M., Groot, M., Gutzat, R., Lampei, C., Ouborg, J., Parepa, M., Schmid, K., Vergeer, P., Zhang, Y., and Bossdorf, O. (2023) Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana. New Phytologist 237, 1014–1023. Journal.

2022

• Patiranage, D.S., Rey, E., Emrani, N., Wellman, G., Schmid, K., Schmöckel, S.M., Tester, M., and Jung, C. (2022). Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history. eLife 11, e66873. Journal

• Maldonado-Taipe, N., Barbier, F., Schmid, K., Jung, C., and Emrani, N. (2022). High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (/Chenopodium quinoa/ Willd.). Frontiers in Plant Science 13:Article916067 Journal

• Haupt, M and Schmid, K (2022) Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions. bioRxiv 2022.02.18.480989 Preprint

• Baturaygil, A and Schmid, K (2022) Characterization of Flowering Time in Genebank Accessions of Grain Amaranths and Their Wild Relatives Reveals Signatures of Domestication and Local Adaptation. Agronomy 2, 505 Journal

• Chang, C.-W., Fridman, E., Mascher, M., Himmelbach, A., and Schmid, K. (2022). Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (Hordeum vulgare L. ssp. spontaneum) in the Southern Levant. Heredity 128, 107–119. Journal Preprint

2021

• Kersten, S., Chang, J., Huber, C.D., Voichek, Y., Lanz, C., Hagmaier, T., Lang, P., Lutz, U., Hirschberg, I., Lerchl, J., Porri A., Van de Peer, Y., Schmid, K. Weigel, D., Rabanal, F. A. (2021). Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass. bioRxiv 2021.12.14.472587. Preprint

• Latzel, V., Fischer, M., Groot, M., Gutzat, R., Lampei, C., Ouborg, J., Parepa, M., Schmid, K., Vergeer, P., Zhang, Y., & Bossdorf, O. (2021). Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana bioRxiv. Preprint

• Zimmermann, B., …, K. Schmid, … Bahrs, E. (2021). Mineral-Ecological Cropping Systems—A New Approach to Improve Ecosystem Services by Farming without Chemical Synthetic Plant Protection. Agronomy, 11, 1710. Journal

• Colque-Little, C., Abondano, M. C., Lund, O. S., Amby, D. B., Piepho, H. P., Andreasen, C., Schöckel, S. & Schmid, K. (2021). Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa). BMC Plant Biology, 21(1), 1-19. Journal

• Baturaygil, A., Stetter, M. G., & Schmid, K. (2021). Breeding Amaranth for Biomass: Evaluating Dry Matter Content and Biomass Potential in Early and Late Maturing Genotypes. Agronomy, 11(5), 970. Journal

• Kienbaum, L., Abondano, M. C., Blas, R., & Schmid, K. (2021). DeepCob: Precise and high-throughput analysis of maize cob geometry using deep learning with an application in genebank phenomics. Plant Methods, 17,91 Journal Preprint

• Böndel, K. B., & Schmid, K. J. (2021). Quinoa Diversity and Its Implications for Breeding. In The Quinoa Genome (pp. 107-118). Springer, Cham. Journal

2020

• Vidal-Villarejo, M., Freund, F., Hanekamp, H., von Tiedemann, A., & Schmid, K. J. (2021). Population genomic evidence for a repeated introduction and rapid expansion in Europe of a maize fungal pathogen. bioRxiv. Preprint

• Patirange, D. S., Rey, E., Emrani, N., Wellman, G., Schmid, K., Schmöckel, S. M., Tester, M. & Jung, C. (2020). Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history. bioRxiv. Preprint

• Puglia, G. D., Prjibelski, A. D., Vitale, D., Bushmanova, E., Schmid, K. J., & Raccuia, S. A. (2020). Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.). BMC Genomics, 21(1), 1-17. Journal

• Max Haupt, Karl Schmid (2020) Combining focused identification of germplasm and core collection strategies to identify genebank accessions for central European soybean breeding.Plant, Cell & Environment, 43(6), 1421-1436. Journal Preprint

• Waldvogel, A.‐M., Feldmeyer, B., Rolshausen, G., Exposito‐Alonso, M., Rellstab, C., Kofler, R., Mock, T., Schmid, K., Schmitt, I., Bataillon, T., Savolainen, O., Bergland, A., Flatt, T., Guillaume, F. and Pfenninger, M. (2020) Evolutionary genomics can improve prediction of species’ responses to climate change. Evolution Letters. doi:10.1002/evl3.154. Journal

2019

• Freund, F. (2019) Cannings models, populations size changes and multiple-merger coalescents. Preprint

• Freund, F. and Siri-Jégousse, A. (2019) Distinguishing coalescent models - which statistics matter most? Preprint

• Freund, F. and Siri-Jégousse, A. (2019) The minimal observable clade size of exchangeable coalescents. Preprint

• Menardo, F., Gagneux, S. and Freund, F. (2019) Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis. Preprint

• Christian Lampei, Jörg Wunder, Thomas Wilhalm, Karl J Schmid (2019) Microclimate predicts frost hardiness of alpine Arabidopsis thaliana populations better than elevation. Ecology and Evolution 9, Vol. 23:13017-13029. Journal

• Eyal Bdolach, Manas Ranjan Prusty, Adi Faigenboim‐Doron, Tanya Filichkin, Laura Helgerson, Karl J Schmid, Stephan Greiner, Eyal Fridman (2019) Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley. Plant, cell & environment 42, Vol 11:3105-3120. Journal

• Markus G Stetter, Mireia Vidal-Villarejo, Karl J Schmid (2019) Parallel seed color adaptation during multiple domestication attempts of an ancient new world grain. Molecular Biology and Evolution, msz304. Journal

2018

• Lampei, C. (2018) Multiple simultaneous treatments change plant response from adaptive parental effects to within-generation plasticity in Arabidopsis thaliana. Oikos. Journal

• Eldon, B. and Freund, F. (2018) Genealogical properties of subsamples in highly fecund populations. Journal of Statistical Physics. read-only version for non-subscribers{:target=“_blank”} Journal

• Schmid K., Kilian B., Russell J. (2018) Barley Domestication, Adaptation and Population Genomics. In: Stein N., Muehlbauer G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. Journal

• Patrick Thorwarth, Eltohamy A. A. Yousef and Karl J. Schmid (2018) Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower. G3: Genes, Genomes, Genetics vol. 8 no. 2 707-718. doi: 10.1534/g3.117.300199. Journal

• Eltohamy AA Yousef, Thomas Mueller, Andreas Boerner, Karl J Schmid (2018) Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks. PLoS ONE 13(2): e0192062. Journal

2017

• F. Freund and M. Möhle (2017) On the size of the block of 1 for Ξ-coalescents with dust. Modern Stochastics: Theory and Applications 4(4), 407-425. Journal

• Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colome-Tatche M, Durka W, Engelhardt J, Gaspar B, Gogol-Doring A, Grosse I, van Gurp TP, Heer K, Kronholm I, Lampei C, Latzel V, Mirouze M, Opgenoorth L, Paun O, Prohaska S, Rensing SA, Stadler P, Trucchi E, Ullrich K, Verhoeven KJF (2017) Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecology Letters, 20:1576–1590. Journal Preprint

• Thorwarth P, Ahlemeyer J, Bochard A-M, Krumnacker K, Blümel H, Laubach E, Knöchel N, Cselényi L, Ordon F, Schmid KJ (2017) Genomic prediction ability for yield-related traits in German winter barley elite material. Theoretical and Applied Genetics 130, pages1669–1683. Journal

• Groot MP, Kubisch A, Ouborg NJ, Pagel J, Schmid KJ, Vergeer P, Lampei C (2017) Transgenerational effects of mild heat in Arabidopsis thaliana show strong genotype specificity that is explained by climate at origin. New Phytologist. Journal PDF

• M.G. Stetter and K.J.Schmid (2017) Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop. Molecular Phylogenetics and Evolution 109: 80-92. Journal Preprint

• M.G. Stetter, T. Müller and K.J. Schmid (2017) Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus). Molecular Ecology. doi:10.1111/mec.13974. Journal Preprint

• Lampei C, Metz J and Tielbörger K (2017) Clinal population divergence in an adaptive parental environmental effect that adjusts seed banking. New Phytologist, 214:1230-1244. doi:10.1111/nph.14436. Journal

2016

• Jacquemin, Julie, et al. (2016) Levels and patterns of genetic diversity differ between two closely related endemic Arabidopsis species. bioRxiv: 048785. Preprint

• Taiji Kawakatsu, …, Karl Schmid, …(2016) Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell, Volume 166, Issue 2, Pages 492-505. doi:10.1016/j.cell.2016.06.044. Journal

• Bauer, E., Schmutzer, T., Barilar, I., Mascher, M., Gundlach, H., Martis, M. M., Twardziok, S. O., Hackauf, B., Gordillo, A., Wilde, P., Schmidt, M., Korzun, V., Mayer, K. F.X., Schmid, K., Schön, C.-C. and Scholz, U. (2016), Towards a whole-genome sequence for rye (Secale cereale L.). Plant J. Journal

• Novikova, P. Y., Hohmann, N., Nizhynska, V., Tsuchimatsu, T., Ali, J., Muir, G., Guggisberg, A., Paape, T., Schmid, K. and Fedorenko, O., Holm, S., Säll, T., Schlötterer, C., Marhold, K., Widmer, A., Sese, J., Shimizu K. K., Weigel, D., Krämer U., Koch Marcus A.,, Nordborg, M. (2016). Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics, 48, 1077–1082. Journal

• M. G. Stetter​, L. Zeitler, A. Steinhaus, K. Kroener, M. Biljecki and K. J. Schmid (2016) Crossing methods and cultivation conditions for rapid production of segregating populations in three grain amaranth species. Frontiers in Plant Science DOI:10.3389/flps.2016.00819. Journal Preprint

• T. Günther,C. Lampei, I. Barilar and K. J. Schmid (2016) Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps. Molecular Ecology DOI: 10.1111/mec.13705 Journal Preprint

• Toni I Gossmann, Dounia Saleh, Marc W Schmid, Michael A Spence, Karl J Schmid (2016) Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes. Mol. Biol. Evol. 33:1669–1678 Journal

• The Arabidopsis 1001 Genomes Consortium (2016) 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell doi:10.1016/j.cell.2016.05.063. 1001 Genomes Website{:target=“_blank”} Journal

• Russell, J., Mascher, M., Dawson, I.K., Kyriakidis, S., Calixto, C., Freund, F., Bayer, M., Milne, I., Marshall-Griffiths, T., Heinen, S., Hofstad, A., Sharma, R., Himmelbach, A., Knauft, M., van Zonneveld, M., Brown, J.W.S., Schmid, K., Kilian, B., Muehlbauer, G.J., Stein, N. and Waugh, R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nature Genetics 48,1024-1030. Journal

2015

• W. Gebrelassie, B. Lakew, B. I. G. Haussmann, K. J. Schmid (2015) Ethiopian barley landraces show higher yield stability and comparable yield to improved varieties in multi-environment field trials. J. Plant Breeding Crop Sci. 7:275-291 DOI: 10.5897/JPBCS2015.0524. Journal PDF

• S. Hübner, A. B. Korol and K. J. Schmid (2015) RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum. BMC Plant Biology 15:134. Journal Data

• M. G. Stetter, K. J. Schmid and U. Ludewig (2015) Uncovering genes and ploidy involved in the high diversity in root hair density, length and response to local scarce phosphate in Arabidopsis thaliana. PLOS ONE. Journal

• I. Gawenda, P. Thorwarth, T. Günther, F. Ordon and K. J. Schmid (2015) Genome-wide association studies in elite varieties of German winter barley using single-marker and haplotype-based methods. Plant Breeding 134,28–39. Journal

• B. Eldon, M. Birkner, J. Blath, and F. Freund. (2015) Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents? Genetics 199(3), 841-856. Journal

2014

• T. Müller, F. Freund, H. Wildhagen and K. J. Schmid (2014) Targeted re-sequencing of five Douglas-fir provenances reveals population structure and putative target genes of positive selection. Tree Genetics & Genomes. Journal

• G Bedada, A Westerbergh, T Müller, E Galkin, E Bdolach, M Moshelion, E Fridman and K J Schmid (2014) Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts. BMC Genomics.2014, 15:995. Journal

• Eltohamy A. A. Yousef, Christian Lampei, Karl J. Schmid (2014) Evaluation of cauliflower genebank accessions under organic and conventional cultivation in Southern Germany. Euphytica. Journal Data{:.btn .btn-success .btn-xs}

• K. J. Schmid and P. Thorwarth. Genomic Selection. In: Biotechnological Approaches to Barley Improvement. N. Stein and J. Kumlehn (Eds.). Journal

• F. Freund and A. Siri-Jégousse (2014) Minimal clade size in the Bolthausen-Sznitman coalescent. J. Appl. Probab. 51(3), 657-668. Journal

• M Siqueira, ML Bonatelli, T Günther, I Gawenda, KJ Schmid, VA Pavinato, EA Veasey (2014) Water yam (Dioscorea alata L.) diversity pattern in Brazil: an analysis with SSR and morphological markers. Genetic Resources and Crop Evolution 61:611-624 Journal

• G Bedada, A Westerbergh, E Nevo, A Korol and K J Schmid (2014) DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel. Heredity 112, 646–655. Journal

• Gossmann TI, Schmid MW, Grossniklaus U, Schmid KJ (2014) Selection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana. Mol Biol Evol. 2014 31:574-83. Journal

2013

• T. Günther, G. Coop (2013) Robust identification of local adaptation from allele frequencies. Genetics. 195:205-220. Journal

• J.S. Dhersin, F. Freund, A. Siri-Jégousse and L. Yuan (2013) On the length of an external branch in the Beta-coalescent. Stoch. Proc. Appl. 123, 1691–1715. Journal

• S Hübner, E Bdolach, S Ein-Gedi, K J Schmid, Abraham Korol, E Fridman (2013) Phenotypic Landscapes: Phenological Patterns in Wild and Cultivated Barley. J. Evol. Biol. 26: 163-74. Journal

2012

• T. Günther, C. Lampei and K. J. Schmid (2012) Mutational bias and gene conversion affect the intraspecific nitrogen stoichiometry of the Arabidopsis thaliana transcriptome. Mol. Biol. Evol. 30:561-8. Journal

• T. Müller, I. Ensminger, K. J. Schmid. A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings (2012) BMC Genomics 13:673. Journal

• Hübner S, Günther T., Flavell A, Fridman E, Graner A., Korol A. and Schmid K. J. (2012) Islands and Streams: Clusters and gene flow in wild barley populations from the Levant. Molecular Ecology 21:1115-1129. Journal

• F. Freund (2012) Almost sure asymptotics for the number of types for simple Ξ-coalescents. ECP 17, article 3. Journal

2011

• Gossmann T. I. and Schmid K. J. (2011) Selection-driven divergence after gene duplication in Arabidopsis thaliana. J. Mol. Evol. 73: 153-165. Journal

• Cao J., Schneeberger K., Ossowski S., Günther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Wang X., Ott F., Müller J., Alonso-Blanco C., Borgwardt K., Schmid K.J., and Weigel D. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics 43:956-963. Journal

• Günther T. and Schmid K.J. (2011) Improved haplotype-based detection of ongoing selective sweeps towards an application in Arabidopsis thaliana. BMC Research Notes 4:232. Journal PDF

• Günther T., Gawenda I. and Schmid K.J. (2011) phenosim - A software to simulate phenotypes for testing in genome-wide association studies. BMC Bioinformatics 12:265. Journal PDF

2010

• O’Connell MJ, Loughran NB, Walsh TA, Donoghue MT, Schmid KJ, Spillane C (2010) A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals. Mamm. Genome DOI 10.1007/s00335-010-9283-5. Journal

• Günther T. and K. J. Schmid (2010) Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice. Theor. Appl. Genetics 121:157-168. Journal

• Childs L, H. Witucka-Wall H., T. Günther, R Sulpice , M v. Korff-Schmising, M Stitt, D Walther, K J Schmid, T Altmann (2010) Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11:188. Journal PDF

2009

• Hübner S., Höffken M., Oren E., Haseneyer G., Stein N., Graner A., Schmid K.J. and E. Fridman (2009) Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation. Molecular Ecology 18, 1523–1536. Journal

• Song B.-H., Windsor A. J., Schmid, K. J., Ramos-Onsins S., Schranz M. E., Heidel A. J., and T. Mitchell-Olds (2009) Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis. Genetics 181: 1021–1033. Journal

2008

• Oyama, R., Formanova N., Clauss, M. J., Kroymann, J., Schmid, K. J., Vogel H., Weniger K., Windsor A., and T. Mitchell-Olds (2008) The shrunken genome of Arabidopsis thaliana. Plant Systematics 273: 257-271. Journal

• Schmid K. J. and Z. Yang (2008) The trouble with sliding windows and the selective pressure in BRCA1. PLoS ONE 3(11): e3746. Journal