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1. Structural variation in the pangenome of wild and domesticated barley

Author

Jayakodi, Murukarthick, Lu, Qiongxian, Pidon, Hélène, Rabanus-Wallace, M. Timothy, Bayer, Micha, Lux, Thomas, Guo, Yu, Jaegle, Benjamin, Badea, Ana, Bekele, Wubishet, Brar, Gurcharn S., Braune, Katarzyna, Bunk, Boyke, Chalmers, Kenneth J., Chapman, Brett, Jørgensen, Morten Egevang, Feng, Jia-Wu, Feser, Manuel, Fiebig, Anne, Gundlach, Heidrun, Guo, Wenbin, Haberer, Georg, Hansson, Mats, Himmelbach, Axel, Hoffie, Iris, Hoffie, Robert E., Hu, Haifei, Isobe, Sachiko, König, Patrick, Kale, Sandip M., Kamal, Nadia, Keeble-Gagnère, Gabriel, Keller, Beat, Knauft, Manuela, Koppolu, Ravi, Krattinger, Simon G., Kumlehn, Jochen, Langridge, Peter, Li, Chengdao, Marone, Marina P., Maurer, Andreas, Mayer, Klaus F. X., Melzer, Michael, Muehlbauer, Gary J., Murozuka, Emiko, Padmarasu, Sudharsan, Perovic, Dragan, Pillen, Klaus, Pin, Pierre A., Pozniak, Curtis J., Ramsay, Luke, Pedas, Pai Rosager, Rutten, Twan, Sakuma, Shun, Sato, Kazuhiro, Schüler, Danuta, Schmutzer, Thomas, Scholz, Uwe, Schreiber, Miriam, Shirasawa, Kenta, Simpson, Craig, Skadhauge, Birgitte, Spannagl, Manuel, Steffenson, Brian J., Thomsen, Hanne C., Tibbits, Josquin F., Nielsen, Martin Toft Simmelsgaard, Trautewig, Corinna, Vequaud, Dominique, Voss, Cynthia, Wang, Penghao, Waugh, Robbie, Westcott, Sharon, Rasmussen, Magnus Wohlfahrt, Zhang, Runxuan, Zhang, Xiao-Qi, Wicker, Thomas, Dockter, Christoph, Mascher, Martin, and Stein, Nils

Published
2024
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6. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

Author

Gaurav, Kumar, Arora, Sanu, Silva, Paula, Sánchez-Martín, Javier, Horsnell, Richard, Gao, Liangliang, Brar, Gurcharn S, Widrig, Victoria, John Raupp, W, Singh, Narinder, Wu, Shuangye, Kale, Sandip M, Chinoy, Catherine, Nicholson, Paul, Quiroz-Chávez, Jesús, Simmonds, James, Hayta, Sadiye, Smedley, Mark A, Harwood, Wendy, Pearce, Suzannah, Gilbert, David, Kangara, Ngonidzashe, Gardener, Catherine, Forner-Martínez, Macarena, Liu, Jiaqian, Yu, Guotai, Boden, Scott A, Pascucci, Attilio, Ghosh, Sreya, Hafeez, Amber N, O’Hara, Tom, Waites, Joshua, Cheema, Jitender, Steuernagel, Burkhard, Patpour, Mehran, Justesen, Annemarie Fejer, Liu, Shuyu, Rudd, Jackie C, Avni, Raz, Sharon, Amir, Steiner, Barbara, Kirana, Rizky Pasthika, Buerstmayr, Hermann, Mehrabi, Ali A, Nasyrova, Firuza Y, Chayut, Noam, Matny, Oadi, Steffenson, Brian J, Sandhu, Nitika, Chhuneja, Parveen, Lagudah, Evans, Elkot, Ahmed F, Tyrrell, Simon, Bian, Xingdong, Davey, Robert P, Simonsen, Martin, Schauser, Leif, Tiwari, Vijay K, Randy Kutcher, H, Hucl, Pierre, Li, Aili, Liu, Deng-Cai, Mao, Long, Xu, Steven, Brown-Guedira, Gina, Faris, Justin, Dvorak, Jan, Luo, Ming-Cheng, Krasileva, Ksenia, Lux, Thomas, Artmeier, Susanne, Mayer, Klaus FX, Uauy, Cristobal, Mascher, Martin, Bentley, Alison R, Keller, Beat, Poland, Jesse, and Wulff, Brande BH

Subjects
Genetics, Biotechnology, Human Genome, Aegilops, Bread, Genomics, Metagenomics, Plant Breeding, Triticum
Abstract

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Published
2022

8. Multiple wheat genomes reveal global variation in modern breeding

Author

Walkowiak, Sean, Gao, Liangliang, Monat, Cecile, Haberer, Georg, Kassa, Mulualem T, Brinton, Jemima, Ramirez-Gonzalez, Ricardo H, Kolodziej, Markus C, Delorean, Emily, Thambugala, Dinushika, Klymiuk, Valentyna, Byrns, Brook, Gundlach, Heidrun, Bandi, Venkat, Siri, Jorge Nunez, Nilsen, Kirby, Aquino, Catharine, Himmelbach, Axel, Copetti, Dario, Ban, Tomohiro, Venturini, Luca, Bevan, Michael, Clavijo, Bernardo, Koo, Dal-Hoe, Ens, Jennifer, Wiebe, Krystalee, N’Diaye, Amidou, Fritz, Allen K, Gutwin, Carl, Fiebig, Anne, Fosker, Christine, Fu, Bin Xiao, Accinelli, Gonzalo Garcia, Gardner, Keith A, Fradgley, Nick, Gutierrez-Gonzalez, Juan, Halstead-Nussloch, Gwyneth, Hatakeyama, Masaomi, Koh, Chu Shin, Deek, Jasline, Costamagna, Alejandro C, Fobert, Pierre, Heavens, Darren, Kanamori, Hiroyuki, Kawaura, Kanako, Kobayashi, Fuminori, Krasileva, Ksenia, Kuo, Tony, McKenzie, Neil, Murata, Kazuki, Nabeka, Yusuke, Paape, Timothy, Padmarasu, Sudharsan, Percival-Alwyn, Lawrence, Kagale, Sateesh, Scholz, Uwe, Sese, Jun, Juliana, Philomin, Singh, Ravi, Shimizu-Inatsugi, Rie, Swarbreck, David, Cockram, James, Budak, Hikmet, Tameshige, Toshiaki, Tanaka, Tsuyoshi, Tsuji, Hiroyuki, Wright, Jonathan, Wu, Jianzhong, Steuernagel, Burkhard, Small, Ian, Cloutier, Sylvie, Keeble-Gagnère, Gabriel, Muehlbauer, Gary, Tibbets, Josquin, Nasuda, Shuhei, Melonek, Joanna, Hucl, Pierre J, Sharpe, Andrew G, Clark, Matthew, Legg, Erik, Bharti, Arvind, Langridge, Peter, Hall, Anthony, Uauy, Cristobal, Mascher, Martin, Krattinger, Simon G, Handa, Hirokazu, Shimizu, Kentaro K, Distelfeld, Assaf, Chalmers, Ken, Keller, Beat, Mayer, Klaus FX, Poland, Jesse, Stein, Nils, McCartney, Curt A, Spannagl, Manuel, Wicker, Thomas, and Pozniak, Curtis J

Subjects
Genetics, Biotechnology, Human Genome, Acclimatization, Animals, Centromere, Chromosome Mapping, Cloning, Molecular, DNA Copy Number Variations, DNA Transposable Elements, Edible Grain, Genes, Plant, Genetic Introgression, Genetic Variation, Genome, Plant, Genomics, Haplotypes, Insecta, Internationality, NLR Proteins, Plant Breeding, Plant Diseases, Plant Proteins, Polymorphism, Single Nucleotide, Polyploidy, Triticum, General Science & Technology
Abstract

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Published
2020

10. Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade

Author

Sotiropoulos, Alexandros G., Arango-Isaza, Epifanía, Ban, Tomohiro, Barbieri, Chiara, Bourras, Salim, Cowger, Christina, Czembor, Paweł C., Ben-David, Roi, Dinoor, Amos, Ellwood, Simon R., Graf, Johannes, Hatta, Koichi, Helguera, Marcelo, Sánchez-Martín, Javier, McDonald, Bruce A., Morgounov, Alexey I., Müller, Marion C., Shamanin, Vladimir, Shimizu, Kentaro K., Yoshihira, Taiki, Zbinden, Helen, Keller, Beat, and Wicker, Thomas

Published
2022
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14. Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing.

Author

Feehan, Joanna M, Scheibel, Katherine E, Bourras, Salim, Underwood, William, Keller, Beat, and Somerville, Shauna C

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Biotechnology, Ascomycota, DNA, Fungal, Genome, Fungal, Molecular Weight, Plant Diseases, Sequence Analysis, DNA, Spores, Fungal, Issue 121, fungus, genomic DNA, high molecular weight DNA, obligate pathogen, powdery mildew, sequencing, Biochemistry and Cell Biology, Psychology, Cognitive Sciences, Biochemistry and cell biology
Abstract

The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.

Published
2017

15. Pyramiding of transgenic immune receptors from primary and tertiary wheat gene pools improves powdery mildew resistance in the field

Author

Koller, Teresa; https://orcid.org/0000-0002-3443-8858, Camenzind, Marcela; https://orcid.org/0009-0005-4773-7231, Jung, Esther, Brunner, Susanne; https://orcid.org/0000-0002-4473-3199, Herren, Gerhard; https://orcid.org/0000-0002-3963-4815, Armbruster, Cygni, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Koller, Teresa; https://orcid.org/0000-0002-3443-8858, Camenzind, Marcela; https://orcid.org/0009-0005-4773-7231, Jung, Esther, Brunner, Susanne; https://orcid.org/0000-0002-4473-3199, Herren, Gerhard; https://orcid.org/0000-0002-3963-4815, Armbruster, Cygni, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

Introgression of resistance genes from wild or related species is a common strategy to improve disease resistance of wheat cultivars. Pm17 is a gene that confers powdery mildew resistance in wheat. It encodes an NLR type of immune receptor and was introgressed from rye to wheat as part of the 1RS chromosome arm translocation several decades ago. So far it was not possible to separate Pm17 from its co-introgressed rye genes due to suppressed recombination. Here we tested transgenic Bobwhite wheat, overexpressing Pm17 without any other rye genes, in the field. Four transgenic events showed high levels of PM17 protein accumulation, strong powdery mildew resistance and no pleiotropic effects during three field seasons. We used a combined approach of transgene insertion and crossbreeding to generate lines co-expressing Pm17 and Pm3, or Pm17 and Pm8, respectively. Blumeria graminis f.sp. tritici infection tests confirmed additive, race-specific resistance of the two pyramided transgenes in lines Pm17+Pm3b and Pm17+Pm8. Furthermore, pyramided lines showed strong powdery mildew resistance during three field seasons. We conclude that the combination of overexpressed NLR genes from the extended gene pool broadens and diversifies wheat disease resistance.

Published
2024

16. Breeding for durable resistance against biotrophic fungal pathogens using transgenes from wheat

Author

Camenzind, Marcela; https://orcid.org/0009-0005-4773-7231, Koller, Teresa; https://orcid.org/0000-0002-3443-8858, Armbruster, Cygni, Jung, Esther, Brunner, Susanne; https://orcid.org/0000-0002-4473-3199, Herren, Gerhard; https://orcid.org/0000-0002-3963-4815, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Camenzind, Marcela; https://orcid.org/0009-0005-4773-7231, Koller, Teresa; https://orcid.org/0000-0002-3443-8858, Armbruster, Cygni, Jung, Esther, Brunner, Susanne; https://orcid.org/0000-0002-4473-3199, Herren, Gerhard; https://orcid.org/0000-0002-3963-4815, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

Breeding for resistant crops is a sustainable way to control disease and relies on the introduction of novel resistance genes. Here, we tested three strategies on how to use transgenes from wheat to achieve durable resistance against fungal pathogens in the field. First, we tested the highly effective, overexpressed single transgene Pm3e in the background of spring wheat cultivar Bobwhite in a long-term field trial over many years. Together with previous results, this revealed that transgenic wheat line Pm3e#2 conferred complete powdery mildew resistance during a total of nine field seasons without a negative impact on yield. Furthermore, overexpressed Pm3e provided resistance to powdery mildew isolates from our worldwide collection when crossed into the elite wheat cultivar Fiorina. Second, we pyramided the four overexpressed transgenes Pm3a, Pm3b, Pm3d, and Pm3f in the background of cultivar Bobwhite and showed that the pyramided line Pm3a,b,d,f was completely resistant to powdery mildew in five field seasons. Third, we performed field trials with three barley lines expressing adult plant resistance gene Lr34 from wheat during three field seasons. Line GLP8 expressed Lr34 under control of the pathogen-inducible Hv-Ger4c promoter and provided partial barley powdery mildew and leaf rust resistance in the field with small, negative effects on yield components which might need compensatory breeding. Overall, our study demonstrates and discusses three successful strategies for achieving fungal disease resistance of wheat and barley in the field using transgenes from wheat. These strategies might confer long-term resistance if applied in a sustainable way. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11032-024-01451-2.

Published
2024

18. Corrigendum

Author

Keller, Beat and Yu, Dazhao

Published
2019

24. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Author

Consortium, The International Wheat Genome Sequencing, Mayer, Klaus FX, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J, Sourdille, Pierre, Endo, Takashi R, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, McLay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Sandve, Simen Rød, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Pfeifer, Matthias, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikaël, Keller, Beat, and Praud, Sebastien

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Human Genome, Bread, Chromosomes, Plant, Evolution, Molecular, Gene Order, Genetic Variation, Genome, Plant, Molecular Sequence Annotation, Phylogeny, Plant Proteins, Polyploidy, Sequence Analysis, DNA, Transcriptome, Triticum, International Wheat Genome Sequencing Consortium, General Science & Technology
Abstract

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Published
2014

28. Structural polymorphisms within a common powdery mildew effector scaffold as a driver of coevolution with cereal immune receptors

Author

Cao, Yu, primary, Kümmel, Florian, additional, Logemann, Elke, additional, Gebauer, Jan M., additional, Lawson, Aaron W., additional, Yu, Dongli, additional, Uthoff, Matthias, additional, Keller, Beat, additional, Jirschitzka, Jan, additional, Baumann, Ulrich, additional, Tsuda, Kenichi, additional, Chai, Jijie, additional, and Schulze-Lefert, Paul, additional

Published
2023
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29. The Sorghum bicolor genome and the diversification of grasses

Author

Paterson, Andrew H., Bowers, John E., Bruggmann, Remy, dubchak, Inna, Grimwood, Jane, Gundlach, Heidrun, Haberer, Georg, Hellsten, Uffe, Mitros, Therese, Poliakov, Alexander, Schmutz, Jeremy, Spannagl, Manuel, Tang, Haibo, Wang, Xiyin, Wicker, Thomas, Bharti, Arvind K., Chapman, Jarrod, Feltus, F. Alex, Gowik, Udo, Grigoriev, Igor V., Lyons, Eric, Maher, Christopher A., Martis, Mihaela, Marechania, Apurva, Otillar, Robert P., Penning, Bryan W., Salamov, Asaf. A., Wang, Yu, Zhang, Lifang, Carpita, Nicholas C., Freeling, Michael, Gingle, Alan R., hash, C. Thomas, Keller, Beat, Klein, Patricia, Kresovich, Stephen, McCann, Maureen C., Ming, Ray, Peterson, Daniel G., ur-Rahman, Mehboob-, Ware, Doreen, Westhoff, Peter, Mayer, Klaus F. X., Messing, Joachim, and Rokhsar, Daniel S.

Abstract

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approx730-megabase Sorghum bicolor (L.) Moench genome, placing approx98percent of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approx75percent larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approx70 million years ago, most duplicated gene sets lost one member before the sorghum rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24percent of genes are grass-specific and 7percent are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Published
2009

36. The apple REFPOP—a reference population for genomics-assisted breeding in apple

Author

Jung, Michaela, Roth, Morgane, Aranzana, Maria José, Auwerkerken, Annemarie, Bink, Marco, Denancé, Caroline, Dujak, Christian, Durel, Charles-Eric, Font i Forcada, Carolina, Cantin, Celia M., Guerra, Walter, Howard, Nicholas P., Keller, Beat, Lewandowski, Mariusz, Ordidge, Matthew, Rymenants, Marijn, Sanin, Nadia, Studer, Bruno, Zurawicz, Edward, Laurens, François, Patocchi, Andrea, and Muranty, Hélène

Published
2020
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40. 454 sequencing put to the test using the complex genome of barley

Author

Wicker, Thomas, Schlagenhauf, Edith, Graner, Andreas, Close, Timothy J, Keller, Beat, and Stein, Nils

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Base Pairing, Base Sequence, Chromosomes, Artificial, Bacterial, Genes, Plant, Genome, Plant, Hordeum, Molecular Sequence Data, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundDuring the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing"), promising an approximately 100-fold increase in throughput over Sanger technology--an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley.ResultsTo study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC) clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences.ConclusionOur data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing and targeted sequence analysis can result in large regions of high-quality finished genomic sequences.

Published
2006

44. Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat

Author

Wicker, Thomas, Yahiaoui, Nabila, Guyot, Romain, Schlagenhauf, Edith, Liu, Zhong-Da, Dubcovsky, Jorge, and Keller, Beat

Subjects
Genetics, Human Genome, Biotechnology, Base Sequence, Chromosomes, Plant, Conserved Sequence, Contig Mapping, DNA, Intergenic, Evolution, Molecular, Genes, Plant, Genetic Variation, Genome, Plant, Glutens, Molecular Sequence Data, Molecular Weight, Physical Chromosome Mapping, Pseudogenes, Species Specificity, Triticum, Biochemistry and Cell Biology, Plant Biology, Plant Biology & Botany
Abstract

To study genome evolution in wheat, we have sequenced and compared two large physical contigs of 285 and 142 kb covering orthologous low molecular weight (LMW) glutenin loci on chromosome 1AS of a diploid wheat species (Triticum monococcum subsp monococcum) and a tetraploid wheat species (Triticum turgidum subsp durum). Sequence conservation between the two species was restricted to small regions containing the orthologous LMW glutenin genes, whereas >90% of the compared sequences were not conserved. Dramatic sequence rearrangements occurred in the regions rich in repetitive elements. Dating of long terminal repeat retrotransposon insertions revealed different insertion events occurring during the last 5.5 million years in both species. These insertions are partially responsible for the lack of homology between the intergenic regions. In addition, the gene space was conserved only partially, because different predicted genes were identified on both contigs. Duplications and deletions of large fragments that might be attributable to illegitimate recombination also have contributed to the differentiation of this region in both species. The striking differences in the intergenic landscape between the A and A(m) genomes that diverged 1 to 3 million years ago provide evidence for a dynamic and rapid genome evolution in wheat species.

Published
2003

45. Wheat zinc finger protein TaZF interacts with both the powdery mildew AvrPm2 protein and the corresponding wheat Pm2a immune receptor

Author

Manser, Beatrice; https://orcid.org/0000-0002-7592-5089, Zbinden, Helen; https://orcid.org/0000-0001-9812-923X, Herren, Gerhard; https://orcid.org/0000-0002-3963-4815, Steger, Joel, Isaksson, Jonatan; https://orcid.org/0000-0003-3934-4241, Bräunlich, Stephanie, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Manser, Beatrice; https://orcid.org/0000-0002-7592-5089, Zbinden, Helen; https://orcid.org/0000-0001-9812-923X, Herren, Gerhard; https://orcid.org/0000-0002-3963-4815, Steger, Joel, Isaksson, Jonatan; https://orcid.org/0000-0003-3934-4241, Bräunlich, Stephanie, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

Plant defense responses to pathogens are induced after direct or indirect perception of effector proteins or their activity on host proteins. In fungal-plant interactions, relatively little is known about whether, in addition to avirulence effectors and immune receptors, other proteins contribute to specific recognition. The nucleotide-binding leucine-rich repeat (NLR) immune receptor Pm2a in wheat recognizes the fungal powdery mildew effector AvrPm2. We found that the predicted wheat zinc finger TaZF interacts with both the fungal avirulence protein AvrPm2 and the wheat NLR Pm2a. We further demonstrated that the virulent AvrPm2-H2 variant does not interact with TaZF. TaZF silencing in wheat resulted in a reduction but not a loss of Pm2a-mediated powdery mildew resistance. Interaction studies showed that the leucine-rich repeat domain of Pm2a is the mediator of the interaction with TaZF. TaZF recruits both Pm2a and AvrPm2 from the cytosol to the nucleus, resulting in nuclear localization of Pm2a, TaZF, and AvrPm2 in wheat. We propose that TaZF acts as a facilitator of Pm2a-dependent AvrPm2 effector recognition. Our findings highlight the importance of identifying effector host targets for characterization of NLR-mediated effector recognition.

Published
2023

46. Structural polymorphisms within a common powdery mildew effector scaffold as a driver of coevolution with cereal immune receptors

Author

Cao, Yu; https://orcid.org/0000-0003-2263-4234, Kümmel, Florian; https://orcid.org/0009-0006-2169-0890, Logemann, Elke; https://orcid.org/0000-0002-0478-8072, Gebauer, Jan M; https://orcid.org/0000-0002-3989-4748, Lawson, Aaron W; https://orcid.org/0000-0001-8164-2555, Yu, Dongli, Uthoff, Matthias; https://orcid.org/0000-0002-6477-5505, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Jirschitzka, Jan; https://orcid.org/0000-0003-1007-4700, Baumann, Ulrich; https://orcid.org/0000-0003-0383-0168, Tsuda, Kenichi; https://orcid.org/0000-0001-7074-0731, Chai, Jijie, Schulze-Lefert, Paul; https://orcid.org/0000-0002-8978-1717, Cao, Yu; https://orcid.org/0000-0003-2263-4234, Kümmel, Florian; https://orcid.org/0009-0006-2169-0890, Logemann, Elke; https://orcid.org/0000-0002-0478-8072, Gebauer, Jan M; https://orcid.org/0000-0002-3989-4748, Lawson, Aaron W; https://orcid.org/0000-0001-8164-2555, Yu, Dongli, Uthoff, Matthias; https://orcid.org/0000-0002-6477-5505, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Jirschitzka, Jan; https://orcid.org/0000-0003-1007-4700, Baumann, Ulrich; https://orcid.org/0000-0003-0383-0168, Tsuda, Kenichi; https://orcid.org/0000-0001-7074-0731, Chai, Jijie, and Schulze-Lefert, Paul; https://orcid.org/0000-0002-8978-1717

Abstract

In plants, host-pathogen coevolution often manifests in reciprocal, adaptive genetic changes through variations in host nucleotide-binding leucine-rich repeat immune receptors (NLRs) and virulence-promoting pathogen effectors. In grass powdery mildew (PM) fungi, an extreme expansion of a RNase-like effector family, termed RALPH, dominates the effector repertoire, with some members recognized as avirulence (AVR) effectors by cereal NLR receptors. We report the structures of the sequence-unrelated barley PM effectors AVR$_{A6}$, AVR$_{A7}$, and allelic AVR$_{A10}$/AVR$_{A22}$ variants, which are detected by highly sequence-related barley NLRs MLA6, MLA7, MLA10, and MLA22 and of wheat PM AVR$_{PM2}$ detected by the unrelated wheat NLR PM2. The AVR effectors adopt a common scaffold, which is shared with the RNase T1/F1 family. We found striking variations in the number, position, and length of individual structural elements between RALPH AVRs, which is associated with a differentiation of RALPH effector subfamilies. We show that all RALPH AVRs tested have lost nuclease and synthetase activities of the RNase T1/F1 family and lack significant binding to RNA, implying that their virulence activities are associated with neo-functionalization events. Structure-guided mutagenesis identified six AVR$_{A6}$ residues that are sufficient to turn a sequence-diverged member of the same RALPH subfamily into an effector specifically detected by MLA6. Similar structure-guided information for AVR$_{A10}$ and AVR$_{A22}$ indicates that MLA receptors detect largely distinct effector surface patches. Thus, coupling of sequence and structural polymorphisms within the RALPH scaffold of PMs facilitated escape from NLR recognition and potential acquisition of diverse virulence functions.

Published
2023

47. The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen

Author

Kunz, Lukas; https://orcid.org/0000-0002-8155-5408, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Graf, Johannes; https://orcid.org/0000-0001-5419-9842, Razavi, Mohammad; https://orcid.org/0000-0002-6434-1838, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Müller, Marion C; https://orcid.org/0000-0001-5594-2319, Kunz, Lukas; https://orcid.org/0000-0002-8155-5408, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Graf, Johannes; https://orcid.org/0000-0001-5419-9842, Razavi, Mohammad; https://orcid.org/0000-0002-6434-1838, Keller, Beat; https://orcid.org/0000-0003-2379-9225, and Müller, Marion C; https://orcid.org/0000-0001-5594-2319

Abstract

Background: Worldwide wheat production is under constant threat by fast-evolving fungal pathogens. In the last decades, wheat breeding for disease resistance heavily relied on the introgression of chromosomal segments from related species as genetic sources of new resistance. The Pm8 resistance gene against the powdery mildew disease has been introgressed from rye into wheat as part of a large 1BL.1RS chromosomal translocation encompassing multiple disease resistance genes and yield components. Due to its high agronomic value, this translocation has seen continuous global use since the 1960s on large growth areas, even after Pm8 resistance was overcome by the powdery mildew pathogen. The long-term use of Pm8 at a global scale provided the unique opportunity to study the consequences of such extensive resistance gene application on pathogen evolution. Results: Using genome-wide association studies in a population of wheat mildew isolates, we identified the avirulence effector AvrPm8 specifically recognized by Pm8. Haplovariant mining in a global mildew population covering all major wheat growing areas of the world revealed 17 virulent haplotypes of the AvrPm8 gene that grouped into two functional categories. The first one comprised amino acid polymorphisms at a single position along the AvrPm8 protein, which we confirmed to be crucial for the recognition by Pm8. The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame such as disruptions of the start codon, gene truncations, gene deletions, and interference with mRNA splicing. With the exception of a single, likely ancient, gain-of-virulence mutation found in mildew isolates around the world, all AvrPm8 virulence haplotypes were found in geographically restricted regions, indicating that they occurred recently as a consequence of the frequent Pm8 use. Conclusions: In this study, we show that the broad and prolonged use of the Pm8 gene in wheat production worldwide resulted in a

Published
2023

48. The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat

Author

Bourras, Salim, Kunz, Lukas, Xue, Minfeng, Praz, Coraline Rosalie, Müller, Marion Claudia, Kälin, Carol, Schläfli, Michael, Ackermann, Patrick, Flückiger, Simon, Parlange, Francis, Menardo, Fabrizio, Schaefer, Luisa Katharina, Ben-David, Roi, Roffler, Stefan, Oberhaensli, Simone, Widrig, Victoria, Lindner, Stefan, Isaksson, Jonatan, Wicker, Thomas, Yu, Dazhao, and Keller, Beat

Published
2019
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