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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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2. Origin and evolution of the bread wheat D genome

Author

Cavalet-Giorsa, Emile, González-Muñoz, Andrea, Athiyannan, Naveenkumar, Holden, Samuel, Salhi, Adil, Gardener, Catherine, Quiroz-Chávez, Jesús, Rustamova, Samira M., Elkot, Ahmed Fawzy, Patpour, Mehran, Rasheed, Awais, Mao, Long, Lagudah, Evans S., Periyannan, Sambasivam K., Sharon, Amir, Himmelbach, Axel, Reif, Jochen C., Knauft, Manuela, Mascher, Martin, Stein, Nils, Chayut, Noam, Ghosh, Sreya, Perovic, Dragan, Putra, Alexander, Perera, Ana B., Hu, Chia-Yi, Yu, Guotai, Ahmed, Hanin Ibrahim, Laquai, Konstanze D., Rivera, Luis F., Chen, Renjie, Wang, Yajun, Gao, Xin, Liu, Sanzhen, Raupp, W. John, Olson, Eric L., Lee, Jong-Yeol, Chhuneja, Parveen, Kaur, Satinder, Zhang, Peng, Park, Robert F., Ding, Yi, Liu, Deng-Cai, Li, Wanlong, Nasyrova, Firuza Y., Dvorak, Jan, Abbasi, Mehrdad, Li, Meng, Kumar, Naveen, Meyer, Wilku B., Boshoff, Willem H. P., Steffenson, Brian J., Matny, Oadi, Sharma, Parva K., Tiwari, Vijay K., Grewal, Surbhi, Pozniak, Curtis J., Chawla, Harmeet Singh, Ens, Jennifer, Dunning, Luke T., Kolmer, James A., Lazo, Gerard R., Xu, Steven S., Gu, Yong Q., Xu, Xianyang, Uauy, Cristobal, Abrouk, Michael, Bougouffa, Salim, Brar, Gurcharn S., Wulff, Brande B. H., and Krattinger, Simon G.

Published
2024
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4. Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility

Author

Kuijer, Hendrik N. J., Wang, Jian You, Bougouffa, Salim, Abrouk, Michael, Jamil, Muhammad, Incitti, Roberto, Alam, Intikhab, Balakrishna, Aparna, Alvarez, Derry, Votta, Cristina, Chen, Guan-Ting Erica, Martínez, Claudio, Zuccolo, Andrea, Berqdar, Lamis, Sioud, Salim, Fiorilli, Valentina, de Lera, Angel R., Lanfranco, Luisa, Gojobori, Takashi, Wing, Rod A., Krattinger, Simon G., Gao, Xin, and Al-Babili, Salim

Published
2024
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11. Einkorn genomics sheds light on history of the oldest domesticated wheat

Author

Ahmed, Hanin Ibrahim, Heuberger, Matthias, Schoen, Adam, Koo, Dal-Hoe, Quiroz-Chavez, Jesus, Adhikari, Laxman, Raupp, John, Cauet, Stéphane, Rodde, Nathalie, Cravero, Charlotte, Callot, Caroline, Lazo, Gerard R., Kathiresan, Nagarajan, Sharma, Parva K., Moot, Ian, Yadav, Inderjit Singh, Singh, Lovepreet, Saripalli, Gautam, Rawat, Nidhi, Datla, Raju, Athiyannan, Naveenkumar, Ramirez-Gonzalez, Ricardo H., Uauy, Cristobal, Wicker, Thomas, Tiwari, Vijay K., Abrouk, Michael, Poland, Jesse, and Krattinger, Simon G.

Published
2023
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12. 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

19. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author

Abrouk, Michael, Ahmed, Hanin Ibrahim, Cubry, Philippe, Šimoníková, Denisa, Cauet, Stéphane, Pailles, Yveline, Bettgenhaeuser, Jan, Gapa, Liubov, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leila, Kathiresan, Nagarajan, Čížková, Jana, Hřibová, Eva, Doležel, Jaroslav, Arribat, Sandrine, Bergès, Hélène, Wieringa, Jan J., Gueye, Mathieu, Kane, Ndjido A., Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas, Vigouroux, Yves, Barnaud, Adeline, and Krattinger, Simon G.

Published
2020
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20. An online database for einkorn wheat to aid in gene discovery and functional genomics studies

Author

Sharma, Parva Kumar, Ahmed, Hanin Ibrahim, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus, Adhikari, Laxman, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte, Callot, Caroline, Yadav, Inderjit Singh, Kathiresan, Nagarajan, Athiyannan, Naveenkumar, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Abrouk, Michael, Gu, Yong Q, Poland, Jesse, Krattinger, Simon G, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, Tiwari, Vijay K, Sharma, Parva Kumar, Ahmed, Hanin Ibrahim, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus, Adhikari, Laxman, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte, Callot, Caroline, Yadav, Inderjit Singh, Kathiresan, Nagarajan, Athiyannan, Naveenkumar, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Abrouk, Michael, Gu, Yong Q, Poland, Jesse, Krattinger, Simon G, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, and Tiwari, Vijay K

Abstract

Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.

Published
2023

21. Einkorn genomics sheds light on history of the oldest domesticated wheat

Author

Ahmed, Hanin Ibrahim; https://orcid.org/0000-0001-9078-183X, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Schoen, Adam, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus; https://orcid.org/0000-0001-5935-2578, Adhikari, Laxman; https://orcid.org/0000-0001-9507-5117, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte; https://orcid.org/0009-0005-1461-1894, Callot, Caroline, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, Kathiresan, Nagarajan; https://orcid.org/0000-0002-5558-6331, Sharma, Parva K; https://orcid.org/0000-0002-0393-6432, Moot, Ian, Yadav, Inderjit Singh, Singh, Lovepreet, Saripalli, Gautam, Rawat, Nidhi, Datla, Raju; https://orcid.org/0000-0003-0790-5569, Athiyannan, Naveenkumar; https://orcid.org/0000-0002-9232-4680, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Tiwari, Vijay K; https://orcid.org/0000-0001-7297-4048, Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Poland, Jesse; https://orcid.org/0000-0002-7856-1399, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Ahmed, Hanin Ibrahim; https://orcid.org/0000-0001-9078-183X, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Schoen, Adam, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus; https://orcid.org/0000-0001-5935-2578, Adhikari, Laxman; https://orcid.org/0000-0001-9507-5117, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte; https://orcid.org/0009-0005-1461-1894, Callot, Caroline, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, Kathiresan, Nagarajan; https://orcid.org/0000-0002-5558-6331, Sharma, Parva K; https://orcid.org/0000-0002-0393-6432, Moot, Ian, Yadav, Inderjit Singh, Singh, Lovepreet, Saripalli, Gautam, Rawat, Nidhi, Datla, Raju; https://orcid.org/0000-0003-0790-5569, Athiyannan, Naveenkumar; https://orcid.org/0000-0002-9232-4680, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Tiwari, Vijay K; https://orcid.org/0000-0001-7297-4048, Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Poland, Jesse; https://orcid.org/0000-0002-7856-1399, and Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411

Abstract

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago$^{1,2}$. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

Published
2023

22. An online database for einkorn wheat to aid in gene discovery and functional genomics studies

Author

Sharma, Parva Kumar, primary, Ahmed, Hanin Ibrahim, additional, Heuberger, Matthias, additional, Koo, Dal-Hoe, additional, Quiroz-Chavez, Jesus, additional, Adhikari, Laxman, additional, Raupp, John, additional, Cauet, Stéphane, additional, Rodde, Nathalie, additional, Cravero, Charlotte, additional, Callot, Caroline, additional, Yadav, Inderjit Singh, additional, Kathiresan, Nagarajan, additional, Athiyannan, Naveenkumar, additional, Ramirez-Gonzalez, Ricardo H, additional, Uauy, Cristobal, additional, Wicker, Thomas, additional, Abrouk, Michael, additional, Gu, Yong Q, additional, Poland, Jesse, additional, Krattinger, Simon G, additional, Lazo, Gerard R, additional, and Tiwari, Vijay K, additional

Published
2023
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25. From shade to light: Fonio, an African orphan crop, towards renewed challenges

Author

Barnaud, Adeline, Billot, Claire, Abrouk, Michael, Adjebeng-Danquah, Joseph, Akanvou, Louise, Ibrahim Ahmed, Hanin, Adje, Charlotte O.A., Bakasso, Yacoubou, Barry, Mamadou Billo, Achigan-Dako, Enoch G., Yerima, Abdou R. Ibrahim Bio, Kane, Ndjido Ardo, Krattinger, Simon G., Oselebe, Happiness, Saidou, Sani, Sêkloka, Emmanuel, Uyoh, Edak A., Vigouroux, Yves, Gueye, Mame Codou, Barnaud, Adeline, Billot, Claire, Abrouk, Michael, Adjebeng-Danquah, Joseph, Akanvou, Louise, Ibrahim Ahmed, Hanin, Adje, Charlotte O.A., Bakasso, Yacoubou, Barry, Mamadou Billo, Achigan-Dako, Enoch G., Yerima, Abdou R. Ibrahim Bio, Kane, Ndjido Ardo, Krattinger, Simon G., Oselebe, Happiness, Saidou, Sani, Sêkloka, Emmanuel, Uyoh, Edak A., Vigouroux, Yves, and Gueye, Mame Codou

Abstract

The FAO recently estimated that demand for food will increase by 70% by 2050. The challenge will not only be on increasing the food supply but also on improving its nutritional value under an accelerating rate of environmental and social changes. One solution would be the wider use of underutilized crops to diversify alimentation and develop sustainable and low-input agriculture. Are orphan crops commodities for the future, and how can they be promoted? In this regard, fonio (Digitaria exilis Stapf) appears to be a promising crop. It is an indigenous staple cereal from Western Africa playing a crucial role in food security. Additionally, it is a model crop in important up-to-date concepts such as resilience, agroecology, population health, climatic changes, poverty reduction, and women's empowerment. Nevertheless, fonio has received limited attention from mainstream research compared to other dryland cereals, such as pearl millet and sorghum. Increasingly available genomic resources promise to promote advanced breeding strategies in fonio. This paper presents the past, present, and future of fonio research. We argue the need for interdisciplinarity and multistakeholder research approaches for increasing fonio production, conservation, and sustainable uses.

Published
2022

29. Comparative Transcriptome Analysis of Wheat Lines in the Field Reveals Multiple Essential Biochemical Pathways Suppressed by Obligate Pathogens

Author

Poretti, Manuel, Sotiropoulos, Alexandros G, Graf, Johannes, Jung, Esther, Bourras, Salim, Krattinger, Simon G, Wicker, Thomas, University of Zurich, and Wicker, Thomas

Subjects
field trial, 10126 Department of Plant and Microbial Biology, wheat, 1110 Plant Science, food and beverages, compatible interaction, RNA-Seq, Plant Science, 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center, Agricultural Science, Original Research, obligate pathogens
Abstract

Mildew and rust are the most devastating cereal pathogens, and in wheat they can cause up to 50% yield loss every year. Wheat lines containing resistance genes are used to effectively control fungal diseases, but the molecular mechanisms underlying the interaction between wheat and its fungal pathogens are poorly understood. Here, we used RNA sequencing (RNA-Seq) to compare the transcriptomic landscape of susceptible and resistant wheat lines to identify genes and pathways that are targeted by obligate biotrophic fungal pathogens. The five lines differed in the expression of thousands of genes under infection as well as control conditions. Generally, mixed infection with powdery mildew and leaf rust resulted in downregulation of numerous genes in susceptible lines. Interestingly, transcriptomic comparison between the nearly isogenic lines Thatcher and Thatcher-Lr34 identified 753 genes that are uniquely downregulated in the susceptible line upon infection. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, revealed the suppression of six major biochemical pathways, namely nuclear transport, alternative splicing, DNA damage response, ubiquitin-mediated proteolysis, phosphoinositol signaling, and photosynthesis. We conclude that powdery mildew and leaf rust evade the wheat defense system by suppression of programmed cell death (PCD) and responses to cellular damage. Considering the broad range of the induced changes, we propose that the pathogen targets “master regulators” at critical steps in the respective pathways. Identification of these wheat genes targeted by the pathogen could inspire new directions for future wheat breeding.

Published
2021

31. Expression of the wheat disease resistance gene Lr34 in transgenic barley leads to accumulation of abscisic acid at the leaf tip

Author

Bräunlich, Stephanie, Koller, Teresa; https://orcid.org/0000-0002-3443-8858, Glauser, Gaétan, Krattinger, Simon G, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Bräunlich, Stephanie, Koller, Teresa; https://orcid.org/0000-0002-3443-8858, Glauser, Gaétan, Krattinger, Simon G, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

Durable disease resistance genes such as the wheat gene Lr34 are valuable sources of resistance for agricultural breeding programs. Lr34 encodes an ATP-binding cassette transporter protein involved in the transport of the phytohormone abscisic acid. Lr34 from wheat is functionally transferable to barley, maize, rice and sorghum. A pleiotropic effect of Lr34 induces the development of a senescence-like phenotype, referred to as leaf tip necrosis. We used Lr34-expressing wheat and transgenic barley plants to elucidate the role of abscisic acid in the development of leaf tip necrosis. Leaf tips in Lr34-expressing wheat and barley showed an accumulation of abscisic acid. No increase of Lr34 expression was detected in the leaf tip. Instead, the development of ectopic, Lr34-induced leaf tip necrosis after removing the leaf tip suggests an increased flux of abscisic acid towards the tip, where it accumulates and mediates the development of leaf tip necrosis. This redistribution of abscisic acid was also observed in adult transgenic barley plants with a high Lr34 expression level growing in the field and coincided with leaf tip necrosis as well as complete field resistance against Puccinia hordei and Blumeria graminis f. sp. hordei. In a barley transgenic line with a lower Lr34 expression level, a quantitative resistance against Puccinia hordei was still observed, but without a significant redistribution of abscisic acid or apparent leaf tip necrosis. Thus, our results imply that fine-tuning the Lr34 expression level is essential to balance disease resistance versus leaf tip necrosis to deploy transgenic Lr34 in breeding programs.

Published
2021

32. Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

Author

Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Athiyannan, Naveenkumar; https://orcid.org/0000-0002-9232-4680, Müller, Thomas, Pailles, Yveline, Stritt, Christoph, Roulin, Anne C; https://orcid.org/0000-0002-6668-3321, Chu, Chenggen, Liu, Shuyu, Morita, Takumi, Handa, Hirokazu, Poland, Jesse; https://orcid.org/0000-0002-7856-1399, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Athiyannan, Naveenkumar; https://orcid.org/0000-0002-9232-4680, Müller, Thomas, Pailles, Yveline, Stritt, Christoph, Roulin, Anne C; https://orcid.org/0000-0002-6668-3321, Chu, Chenggen, Liu, Shuyu, Morita, Takumi, Handa, Hirokazu, Poland, Jesse; https://orcid.org/0000-0002-7856-1399, Keller, Beat; https://orcid.org/0000-0003-2379-9225, and Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411

Abstract

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

Published
2021

33. A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat

Author

Kolodziej, Markus C; https://orcid.org/0000-0003-3155-2935, Singla, Jyoti, Sánchez-Martín, Javier; https://orcid.org/0000-0002-0284-7219, Zbinden, Helen, Šimková, Hana; https://orcid.org/0000-0003-4159-7619, Karafiátová, Miroslava; https://orcid.org/0000-0003-1177-6472, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Gronnier, Julien; https://orcid.org/0000-0002-1429-0542, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Glauser, Gaétan, Zhu, Wangsheng; https://orcid.org/0000-0001-7773-3438, Köster, Philipp; https://orcid.org/0000-0002-1359-822X, Zipfel, Cyril; https://orcid.org/0000-0003-4935-8583, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Kolodziej, Markus C; https://orcid.org/0000-0003-3155-2935, Singla, Jyoti, Sánchez-Martín, Javier; https://orcid.org/0000-0002-0284-7219, Zbinden, Helen, Šimková, Hana; https://orcid.org/0000-0003-4159-7619, Karafiátová, Miroslava; https://orcid.org/0000-0003-1177-6472, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Gronnier, Julien; https://orcid.org/0000-0002-1429-0542, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Glauser, Gaétan, Zhu, Wangsheng; https://orcid.org/0000-0001-7773-3438, Köster, Philipp; https://orcid.org/0000-0002-1359-822X, Zipfel, Cyril; https://orcid.org/0000-0003-4935-8583, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

Plasma membrane-associated and intracellular proteins and protein complexes play a pivotal role in pathogen recognition and disease resistance signaling in plants and animals. The two predominant protein families perceiving plant pathogens are receptor-like kinases and nucleotide binding-leucine-rich repeat receptors (NLR), which often confer race-specific resistance. Leaf rust is one of the most prevalent and most devastating wheat diseases. Here, we clone the race-specific leaf rust resistance gene Lr14a from hexaploid wheat. The cloning of Lr14a is aided by the recently published genome assembly of ArinaLrFor, an Lr14a-containing wheat line. Lr14a encodes a membrane-localized protein containing twelve ankyrin (ANK) repeats and structural similarities to Ca2+-permeable non-selective cation channels. Transcriptome analyses reveal an induction of genes associated with calcium ion binding in the presence of Lr14a. Haplotype analyses indicate that Lr14a-containing chromosome segments were introgressed multiple times into the bread wheat gene pool, but we find no variation in the Lr14a coding sequence itself. Our work demonstrates the involvement of an ANK-transmembrane (TM)-like type of gene family in race-specific disease resistance in wheat. This forms the basis to explore ANK-TM-like genes in disease resistance breeding.

Published
2021

34. Comparative Transcriptome Analysis of Wheat Lines in the Field Reveals Multiple Essential Biochemical Pathways Suppressed by Obligate Pathogens

Author

Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Graf, Johannes, Jung, Esther, Bourras, Salim, Krattinger, Simon G, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Graf, Johannes, Jung, Esther, Bourras, Salim, Krattinger, Simon G, and Wicker, Thomas; https://orcid.org/0000-0002-6777-7135

Abstract

Mildew and rust are the most devastating cereal pathogens, and in wheat they can cause up to 50% yield loss every year. Wheat lines containing resistance genes are used to effectively control fungal diseases, but the molecular mechanisms underlying the interaction between wheat and its fungal pathogens are poorly understood. Here, we used RNA sequencing (RNA-Seq) to compare the transcriptomic landscape of susceptible and resistant wheat lines to identify genes and pathways that are targeted by obligate biotrophic fungal pathogens. The five lines differed in the expression of thousands of genes under infection as well as control conditions. Generally, mixed infection with powdery mildew and leaf rust resulted in downregulation of numerous genes in susceptible lines. Interestingly, transcriptomic comparison between the nearly isogenic lines Thatcher and Thatcher-Lr34 identified 753 genes that are uniquely downregulated in the susceptible line upon infection. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, revealed the suppression of six major biochemical pathways, namely nuclear transport, alternative splicing, DNA damage response, ubiquitin-mediated proteolysis, phosphoinositol signaling, and photosynthesis. We conclude that powdery mildew and leaf rust evade the wheat defense system by suppression of programmed cell death (PCD) and responses to cellular damage. Considering the broad range of the induced changes, we propose that the pathogen targets “master regulators” at critical steps in the respective pathways. Identification of these wheat genes targeted by the pathogen could inspire new directions for future wheat breeding.

Published
2021

35. Alleles of a wall‐associated kinase gene account for three of the major northern corn leaf blight resistance loci in maize

Author

Yang, Ping, primary, Scheuermann, Daniela, additional, Kessel, Bettina, additional, Koller, Teresa, additional, Greenwood, Julian R., additional, Hurni, Severine, additional, Herren, Gerhard, additional, Zhou, Shenghui, additional, Marande, William, additional, Wicker, Thomas, additional, Krattinger, Simon G., additional, Ouzunova, Milena, additional, and Keller, Beat, additional

Published
2021
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36. The NLR-annotator tool enables annotation of the intracellular immune receptor repertoire

Author

Steuernagel, Burkhard, Witek, Kamil, Krattinger, Simon G, Ramirez-Gonzalez, Ricardo H, Schoonbeek, Henk-jan, Yu, Guotai, Baggs, Erin, Witek, Agnieszka I, Yadav, Inderjit, Krasileva, Ksenia V, Jones, Jonathan D G, Uauy, Cristobal, Keller, Beat, Ridout, Christopher J, Wulff, Brande B H, University of Zurich, and Wulff, Brande B H

Subjects
10126 Department of Plant and Microbial Biology, 1311 Genetics, Physiology, 1110 Plant Science, Genetics, 1314 Physiology, Plant Science, 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center
Published
2020

37. Multiple wheat genomes reveal global variation in modern breeding

Author

70983196, 10273492, 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 F. X., Poland, Jesse, Stein, Nils, McCartney, Curt A., Spannagl, Manuel, Wicker, Thomas, Pozniak, Curtis J., 70983196, 10273492, 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 F. X., Poland, Jesse, Stein, Nils, McCartney, Curt A., Spannagl, Manuel, Wicker, Thomas, and Pozniak, Curtis J.

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 genome, and the lack of genome-assembly data for multiple wheat lines. 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 stresses. 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 Sm1, 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

38. The NLR-annotator tool enables annotation of the intracellular immune receptor repertoire

Author

Steuernagel, Burkhard; https://orcid.org/0000-0002-8284-7728, Witek, Kamil; https://orcid.org/0000-0003-0659-5562, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Ramirez-Gonzalez, Ricardo H; https://orcid.org/0000-0001-5745-7085, Schoonbeek, Henk-jan; https://orcid.org/0000-0002-1087-2553, Yu, Guotai, Baggs, Erin; https://orcid.org/0000-0003-3076-9489, Witek, Agnieszka I; https://orcid.org/0000-0001-7395-687X, Yadav, Inderjit, Krasileva, Ksenia V; https://orcid.org/0000-0002-1679-0700, Jones, Jonathan D G; https://orcid.org/0000-0002-4953-261X, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Ridout, Christopher J; https://orcid.org/0000-0001-9287-938X, Wulff, Brande B H; https://orcid.org/0000-0003-4044-4346, Steuernagel, Burkhard; https://orcid.org/0000-0002-8284-7728, Witek, Kamil; https://orcid.org/0000-0003-0659-5562, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Ramirez-Gonzalez, Ricardo H; https://orcid.org/0000-0001-5745-7085, Schoonbeek, Henk-jan; https://orcid.org/0000-0002-1087-2553, Yu, Guotai, Baggs, Erin; https://orcid.org/0000-0003-3076-9489, Witek, Agnieszka I; https://orcid.org/0000-0001-7395-687X, Yadav, Inderjit, Krasileva, Ksenia V; https://orcid.org/0000-0002-1679-0700, Jones, Jonathan D G; https://orcid.org/0000-0002-4953-261X, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Ridout, Christopher J; https://orcid.org/0000-0001-9287-938X, and Wulff, Brande B H; https://orcid.org/0000-0003-4044-4346

Abstract

Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny, and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress, we found up-regulation of 266 of the NLRs To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.

Published
2020

39. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author

Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Ahmed, Hanin Ibrahim, Cubry, Philippe; https://orcid.org/0000-0003-1561-8949, Šimoníková, Denisa, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Pailles, Yveline, Bettgenhaeuser, Jan; https://orcid.org/0000-0002-6901-1774, Gapa, Liubov; https://orcid.org/0000-0002-2744-9858, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leila, Kathiresan, Nagarajan, Čížková, Jana, Hřibová, Eva, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Arribat, Sandrine, Bergès, Hélène, Wieringa, Jan J; https://orcid.org/0000-0003-0566-372X, Gueye, Mathieu, Kane, Ndjido A; https://orcid.org/0000-0002-1879-019X, Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Vigouroux, Yves; https://orcid.org/0000-0002-8361-6040, Barnaud, Adeline; https://orcid.org/0000-0001-9896-1210, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Ahmed, Hanin Ibrahim, Cubry, Philippe; https://orcid.org/0000-0003-1561-8949, Šimoníková, Denisa, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Pailles, Yveline, Bettgenhaeuser, Jan; https://orcid.org/0000-0002-6901-1774, Gapa, Liubov; https://orcid.org/0000-0002-2744-9858, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leila, Kathiresan, Nagarajan, Čížková, Jana, Hřibová, Eva, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Arribat, Sandrine, Bergès, Hélène, Wieringa, Jan J; https://orcid.org/0000-0003-0566-372X, Gueye, Mathieu, Kane, Ndjido A; https://orcid.org/0000-0002-1879-019X, Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Vigouroux, Yves; https://orcid.org/0000-0002-8361-6040, Barnaud, Adeline; https://orcid.org/0000-0001-9896-1210, and Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411

Abstract

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

Published
2020

41. The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire

Author

Steuernagel, Burkhard, primary, Witek, Kamil, additional, Krattinger, Simon G., additional, Ramirez-Gonzalez, Ricardo H., additional, Schoonbeek, Henk-jan, additional, Yu, Guotai, additional, Baggs, Erin, additional, Witek, Agnieszka I., additional, Yadav, Inderjit, additional, Krasileva, Ksenia V., additional, Jones, Jonathan D.G., additional, Uauy, Cristobal, additional, Keller, Beat, additional, Ridout, Christopher J., additional, and Wulff, Brande B.H., additional

Published
2020
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42. Pathogen-inducible Ta-Lr34res expression in heterologous barley confers disease resistance without negative pleiotropic effects

Author

Boni, Rainer, Chauhan, Harsh, Hensel, Goetz, Roulin, Anne, Sucher, Justine, Kumlehn, Jochen, Brunner, Susanne, Krattinger, Simon G, Keller, Beat, University of Zurich, and Krattinger, Simon G

Subjects
10126 Department of Plant and Microbial Biology, 1110 Plant Science, 1305 Biotechnology, food and beverages, 1102 Agronomy and Crop Science, 580 Plants (Botany)
Published
2018

44. Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34

Author

Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Kang, Joohyun; https://orcid.org/0000-0002-3394-7087, Bräunlich, Stephanie, Boni, Rainer, Chauhan, Harsh; https://orcid.org/0000-0002-1396-5464, Selter, Liselotte L, Robinson, Mark D; https://orcid.org/0000-0002-3048-5518, Schmid, Marc W, Wiederhold, Elena, Hensel, Goetz; https://orcid.org/0000-0002-5539-3097, Kumlehn, Jochen; https://orcid.org/0000-0001-7080-7983, Sucher, Justine, Martinoia, Enrico, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Kang, Joohyun; https://orcid.org/0000-0002-3394-7087, Bräunlich, Stephanie, Boni, Rainer, Chauhan, Harsh; https://orcid.org/0000-0002-1396-5464, Selter, Liselotte L, Robinson, Mark D; https://orcid.org/0000-0002-3048-5518, Schmid, Marc W, Wiederhold, Elena, Hensel, Goetz; https://orcid.org/0000-0002-5539-3097, Kumlehn, Jochen; https://orcid.org/0000-0001-7080-7983, Sucher, Justine, Martinoia, Enrico, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

The wheat Lr34res allele, coding for an ATP-binding cassette transporter, confers durable resistance against multiple fungal pathogens. The Lr34sus allele, differing from Lr34res by two critical nucleotide polymorphisms, is found in susceptible wheat cultivars. Lr34res is functionally transferrable as a transgene into all major cereals, including rice, barley, maize, and sorghum. Here, we used transcriptomics, physiology, genetics, and in vitro and in vivo transport assays to study the molecular function of Lr34. We report that Lr34res results in a constitutive induction of transcripts reminiscent of an abscisic acid (ABA)-regulated response in transgenic rice. Lr34-expressing rice was altered in biological processes that are controlled by this phytohormone, including dehydration tolerance, transpiration and seedling growth. In planta seedling and in vitro yeast accumulation assays revealed that both LR34res and LR34sus act as ABA transporters. However, whereas the LR34res protein was detected in planta the LR34sus version was not, suggesting a post-transcriptional regulatory mechanism. Our results identify ABA as a substrate of the LR34 ABC transporter. We conclude that LR34res-mediated ABA redistribution has a major effect on the transcriptional response and physiology of Lr34res-expressing plants and that ABA is a candidate molecule that contributes to Lr34res-mediated disease resistance.

Published
2019

45. Genebank genomics highlights the diversity of a global barley collection

Author

Milner, Sara G; https://orcid.org/0000-0002-1600-5979, Jost, Matthias; https://orcid.org/0000-0001-8796-1768, Taketa, Shin, et al, Herren, Gerhard, Müller, Thomas; https://orcid.org/0000-0002-8723-5173, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Milner, Sara G; https://orcid.org/0000-0002-1600-5979, Jost, Matthias; https://orcid.org/0000-0001-8796-1768, Taketa, Shin, et al, Herren, Gerhard, Müller, Thomas; https://orcid.org/0000-0002-8723-5173, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world’s major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.

Published
2019

46. Fungal resistance mediated by maize wall‐associated kinase Zm WAK‐RLK1 correlates with reduced benzoxazinoid content

Author

Yang, Ping, Praz, Coraline, Li, Beibei, Singla, Jyoti, Robert, Christelle A M, Kessel, Bettina, Scheuermann, Daniela, Lüthi, Linda, Ouzunova, Milena, Erb, Matthias, Krattinger, Simon G, Keller, Beat, University of Zurich, and Erb, Matthias

Subjects
10126 Department of Plant and Microbial Biology, 1110 Plant Science, 1314 Physiology, 580 Plants (Botany)
Published
2018

50. Fungal resistance mediated by maize wall‐associated kinase Zm WAK‐RLK1 correlates with reduced benzoxazinoid content

Author

Yang, Ping; https://orcid.org/0000-0002-6977-8449, Praz, Coraline, Li, Beibei, Singla, Jyoti, Robert, Christelle A M, Kessel, Bettina, Scheuermann, Daniela, Lüthi, Linda, Ouzunova, Milena, Erb, Matthias, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Yang, Ping; https://orcid.org/0000-0002-6977-8449, Praz, Coraline, Li, Beibei, Singla, Jyoti, Robert, Christelle A M, Kessel, Bettina, Scheuermann, Daniela, Lüthi, Linda, Ouzunova, Milena, Erb, Matthias, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, and Keller, Beat; https://orcid.org/0000-0003-2379-9225

Abstract

Wall‐associated kinases (WAKs) have recently been identified as major components of fungal and bacterial disease resistance in several cereal crop species. However, the molecular mechanisms of WAK‐mediated resistance remain largely unknown. Here, we investigated the function of the maize gene ZmWAK‐RLK1 (Htn1) that confers quantitative resistance to northern corn leaf blight (NCLB) caused by the hemibiotrophic fungal pathogen Exserohilum turcicum. ZmWAK‐RLK1 was found to localize to the plasma membrane and its presence resulted in a modification of the infection process by reducing pathogen penetration into host tissues. A large‐scale transcriptome analysis of near‐isogenic lines (NILs) differing for ZmWAK‐RLK1 revealed that several differentially expressed genes are involved in the biosynthesis of the secondary metabolites benzoxazinoids (BXs). The contents of several BXs including DIM2BOA‐Glc were significantly lower when ZmWAK‐RLK1 is present. DIM2BOA‐Glc concentration was significantly elevated in ZmWAK‐RLK1 mutants with compromised NCLB resistance. Maize mutants that were affected in overall BXs biosynthesis or content of DIM2BOA‐Glc showed increased NCLB resistance. We conclude that Htn1‐mediated NCLB resistance is associated with a reduction of BX secondary metabolites. These findings suggest a link between WAK‐mediated quantitative disease resistance and changes in biochemical fluxes starting with indole‐3‐glycerol phosphate.

Published
2018

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