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2. A wheat kinase and immune receptor form host-specificity barriers against the blast fungus

Author

Arora, Sanu, Steed, Andrew, Goddard, Rachel, Gaurav, Kumar, O’Hara, Tom, Schoen, Adam, Rawat, Nidhi, Elkot, Ahmed F, Korolev, Andrey V, Chinoy, Catherine, Nicholson, Martha H, Asuke, Soichiro, Antoniou-Kourounioti, Rea, Steuernagel, Burkhard, Yu, Guotai, Awal, Rajani, Forner-Martínez, Macarena, Wingen, Luzie, Baggs, Erin, Clarke, Jonathan, Saunders, Diane GO, Krasileva, Ksenia V, Tosa, Yukio, Jones, Jonathan DG, Tiwari, Vijay K, Wulff, Brande BH, and Nicholson, Paul

Subjects
Genetics, Infection, Triticum, Plant Diseases, Brazil, Magnaporthe, Bangladesh, Plant Biology, Crop and Pasture Production
Abstract

Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. Here we show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes will enable study of the molecular interaction between pathogen effector and host resistance genes.

Published
2023

3. 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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5. 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

6. Structural network alterations in focal and generalized epilepsy assessed in a worldwide ENIGMA study follow axes of epilepsy risk gene expression

Author

Larivière, Sara, Royer, Jessica, Rodríguez-Cruces, Raúl, Paquola, Casey, Caligiuri, Maria Eugenia, Gambardella, Antonio, Concha, Luis, Keller, Simon S, Cendes, Fernando, Yasuda, Clarissa L, Bonilha, Leonardo, Gleichgerrcht, Ezequiel, Focke, Niels K, Domin, Martin, von Podewills, Felix, Langner, Soenke, Rummel, Christian, Wiest, Roland, Martin, Pascal, Kotikalapudi, Raviteja, O’Brien, Terence J, Sinclair, Benjamin, Vivash, Lucy, Desmond, Patricia M, Lui, Elaine, Vaudano, Anna Elisabetta, Meletti, Stefano, Tondelli, Manuela, Alhusaini, Saud, Doherty, Colin P, Cavalleri, Gianpiero L, Delanty, Norman, Kälviäinen, Reetta, Jackson, Graeme D, Kowalczyk, Magdalena, Mascalchi, Mario, Semmelroch, Mira, Thomas, Rhys H, Soltanian-Zadeh, Hamid, Davoodi-Bojd, Esmaeil, Zhang, Junsong, Winston, Gavin P, Griffin, Aoife, Singh, Aditi, Tiwari, Vijay K, Kreilkamp, Barbara AK, Lenge, Matteo, Guerrini, Renzo, Hamandi, Khalid, Foley, Sonya, Rüber, Theodor, Weber, Bernd, Depondt, Chantal, Absil, Julie, Carr, Sarah JA, Abela, Eugenio, Richardson, Mark P, Devinsky, Orrin, Severino, Mariasavina, Striano, Pasquale, Tortora, Domenico, Kaestner, Erik, Hatton, Sean N, Vos, Sjoerd B, Caciagli, Lorenzo, Duncan, John S, Whelan, Christopher D, Thompson, Paul M, Sisodiya, Sanjay M, Bernasconi, Andrea, Labate, Angelo, McDonald, Carrie R, Bernasconi, Neda, and Bernhardt, Boris C

Subjects
Neurodegenerative, Genetics, Neurosciences, Brain Disorders, Epilepsy, Aetiology, 2.1 Biological and endogenous factors, Neurological, Adult, Connectome, Epilepsy, Generalized, Epilepsy, Temporal Lobe, Gene Expression, Humans, Immunoglobulin E, Magnetic Resonance Imaging, Nerve Net
Abstract

Epilepsy is associated with genetic risk factors and cortico-subcortical network alterations, but associations between neurobiological mechanisms and macroscale connectomics remain unclear. This multisite ENIGMA-Epilepsy study examined whole-brain structural covariance networks in patients with epilepsy and related findings to postmortem epilepsy risk gene expression patterns. Brain network analysis included 578 adults with temporal lobe epilepsy (TLE), 288 adults with idiopathic generalized epilepsy (IGE), and 1328 healthy controls from 18 centres worldwide. Graph theoretical analysis of structural covariance networks revealed increased clustering and path length in orbitofrontal and temporal regions in TLE, suggesting a shift towards network regularization. Conversely, people with IGE showed decreased clustering and path length in fronto-temporo-parietal cortices, indicating a random network configuration. Syndrome-specific topological alterations reflected expression patterns of risk genes for hippocampal sclerosis in TLE and for generalized epilepsy in IGE. These imaging-transcriptomic signatures could potentially guide diagnosis or tailor therapeutic approaches to specific epilepsy syndromes.

Published
2022

8. Gene regulatory landscape of cerebral cortex folding

Author

Singh, Aditi, primary, Del-Valle-Anton, Lucia, additional, de Juan Romero, Camino, additional, Zhang, Ziyi, additional, Ortuño, Eduardo Fernández, additional, Mahesh, Arun, additional, Espinós, Alexandre, additional, Soler, Rafael, additional, Cárdenas, Adrián, additional, Fernández, Virginia, additional, Lusby, Ryan, additional, Tiwari, Vijay K., additional, and Borrell, Víctor, additional

Published
2024
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13. Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii

Author

Lin, Guifang, Chen, Hui, Tian, Bin, Sehgal, Sunish K., Singh, Lovepreet, Xie, Jingzhong, Rawat, Nidhi, Juliana, Philomin, Singh, Narinder, Shrestha, Sandesh, Wilson, Duane L., Shult, Hannah, Lee, Hyeonju, Schoen, Adam William, Tiwari, Vijay K., Singh, Ravi P., Guttieri, Mary J., Trick, Harold N., Poland, Jesse, Bowden, Robert L., Bai, Guihua, Gill, Bikram, and Liu, Sanzhen

Published
2022
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14. Evolution of Einkorn wheat centromeres is driven by the mutualistic interplay of two LTR retrotransposons.

Author

Heuberger, Matthias, Koo, Dal-Hoe, Ahmed, Hanin Ibrahim, Tiwari, Vijay K., Abrouk, Michael, Poland, Jesse, Krattinger, Simon G., and Wicker, Thomas

Subjects
TRANSPOSONS, GAG proteins, OATS, CENTROMERE, HOST plants, TANDEM repeats
Abstract

Background: Centromere function is highly conserved across eukaryotes, but the underlying centromeric DNA sequences vary dramatically between species. Centromeres often contain a high proportion of repetitive DNA, such as tandem repeats and/or transposable elements (TEs). Einkorn wheat centromeres lack tandem repeat arrays and are instead composed mostly of the two long terminal repeat (LTR) retrotransposon families RLG_Cereba and RLG_Quinta which specifically insert in centromeres. However, it is poorly understood how these two TE families relate to each other and if and how they contribute to centromere function and evolution. Results: Based on conservation of diagnostic motifs (LTRs, integrase and primer binding site and polypurine-tract), we propose that RLG_Cereba and RLG_Quinta are a pair of autonomous and non-autonomous partners, in which the autonomous RLG_Cereba contributes all the proteins required for transposition, while the non-autonomous RLG_Quinta contributes GAG protein. Phylogenetic analysis of predicted GAG proteins showed that the RLG_Cereba lineage was present for at least 100 million years in monocotyledon plants. In contrast, RLG_Quinta evolved from RLG_Cereba between 28 and 35 million years ago in the common ancestor of oat and wheat. Interestingly, the integrase of RLG_Cereba is fused to a so-called CR-domain, which is hypothesized to guide the integrase to the functional centromere. Indeed, ChIP-seq data and TE population analysis show only the youngest subfamilies of RLG_Cereba and RLG_Quinta are found in the active centromeres. Importantly, the LTRs of RLG_Quinta and RLG_Cereba are strongly associated with the presence of the centromere-specific CENH3 histone variant. We hypothesize that the LTRs of RLG_Cereba and RLG_Quinta contribute to wheat centromere integrity by phasing and/or placing CENH3 nucleosomes, thus favoring their persistence in the competitive centromere-niche. Conclusion: Our data show that RLG_Cereba cross-mobilizes the non-autonomous RLG_Quinta retrotransposons. New copies of both families are specifically integrated into functional centromeres presumably through direct binding of the integrase CR domain to CENH3 histone variants. The LTRs of newly inserted RLG_Cereba and RLG_Quinta elements, in turn, recruit and/or phase new CENH3 deposition. This mutualistic interplay between the two TE families and the plant host dynamically maintains wheat centromeres. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Comparative immune profiling of acute respiratory distress syndrome patients with or without SARS-CoV-2 infection

Author

Roussel, Mikael, Ferrant, Juliette, Reizine, Florian, Le Gallou, Simon, Dulong, Joelle, Carl, Sarah, Lesouhaitier, Matheiu, Gregoire, Murielle, Bescher, Nadège, Verdy, Clotilde, Latour, Maelle, Bézier, Isabelle, Cornic, Marie, Vinit, Angélique, Monvoisin, Céline, Sawitzki, Birgit, Leonard, Simon, Paul, Stéphane, Feuillard, Jean, Jeannet, Robin, Daix, Thomas, Tiwari, Vijay K., Tadié, Jean Marc, Cogné, Michel, and Tarte, Karin

Published
2021
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17. Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Author

Rabanus-Wallace, M. Timothy, Hackauf, Bernd, Mascher, Martin, Lux, Thomas, Wicker, Thomas, Gundlach, Heidrun, Baez, Mariana, Houben, Andreas, Mayer, Klaus F. X., Guo, Liangliang, Poland, Jesse, Pozniak, Curtis J., Walkowiak, Sean, Melonek, Joanna, Praz, Coraline R., Schreiber, Mona, Budak, Hikmet, Heuberger, Matthias, Steuernagel, Burkhard, Wulff, Brande, Börner, Andreas, Byrns, Brook, Čížková, Jana, Fowler, D. Brian, Fritz, Allan, Himmelbach, Axel, Kaithakottil, Gemy, Keilwagen, Jens, Keller, Beat, Konkin, David, Larsen, Jamie, Li, Qiang, Myśków, Beata, Padmarasu, Sudharsan, Rawat, Nidhi, Sesiz, Uğur, Biyiklioglu-Kaya, Sezgi, Sharpe, Andy, Šimková, Hana, Small, Ian, Swarbreck, David, Toegelová, Helena, Tsvetkova, Natalia, Voylokov, Anatoly V., Vrána, Jan, Bauer, Eva, Bolibok-Bragoszewska, Hanna, Doležel, Jaroslav, Hall, Anthony, Jia, Jizeng, Korzun, Viktor, Laroche, André, Ma, Xue-Feng, Ordon, Frank, Özkan, Hakan, Rakoczy-Trojanowska, Monika, Scholz, Uwe, Schulman, Alan H., Siekmann, Dörthe, Stojałowski, Stefan, Tiwari, Vijay K., Spannagl, Manuel, and Stein, Nils

Published
2021
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18. Ageing impairs the regenerative capacity of regulatory T cells in mouse central nervous system remyelination.

Author

de la Fuente, Alerie Guzman, Dittmer, Marie, Heesbeen, Elise J., de la Vega Gallardo, Nira, White, Jessica A., Young, Andrew, McColgan, Tiree, Dashwood, Amy, Mayne, Katie, Cabeza-Fernández, Sonia, Falconer, John, Rodriguez-Baena, Francisco Javier, McMurran, Christopher E., Inayatullah, Mohammed, Rawji, Khalil S., Franklin, Robin J. M., Dooley, James, Liston, Adrian, Ingram, Rebecca J., and Tiwari, Vijay K.

Abstract

Myelin regeneration (remyelination) is essential to prevent neurodegeneration in demyelinating diseases such as Multiple Sclerosis, however, its efficiency declines with age. Regulatory T cells (Treg) recently emerged as critical players in tissue regeneration, including remyelination. However, the effect of ageing on Treg-mediated regenerative processes is poorly understood. Here, we show that expansion of aged Treg does not rescue age-associated remyelination impairment due to an intrinsically diminished capacity of aged Treg to promote oligodendrocyte differentiation and myelination in male and female mice. This decline in regenerative Treg functions can be rescued by a young environment. We identified Melanoma Cell Adhesion Molecule 1 (MCAM1) and Integrin alpha 2 (ITGA2) as candidates of Treg-mediated oligodendrocyte differentiation that decrease with age. Our findings demonstrate that ageing limits the neuroregenerative capacity of Treg, likely limiting their remyelinating therapeutic potential in aged patients, and describe two mechanisms implicated in Treg-driven remyelination that may be targetable to overcome this limitation.Factors limiting CNS remyelination with age are poorly understood. Here the authors show that aged Treg lose capacity to support CNS remyelination in mice, which can be restored in a young environment. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Origin and evolution of the bread wheat D genome

Author

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

Published
2023
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25. MicroRNA-335-5p suppresses voltage-gated sodium channel expression and may be a target for seizure control

Author

Heiland, Mona, primary, Connolly, Niamh M. C., additional, Mamad, Omar, additional, Nguyen, Ngoc T., additional, Kesavan, Jaideep C., additional, Langa, Elena, additional, Fanning, Kevin, additional, Sanfeliu, Albert, additional, Yan, Yan, additional, Su, Junyi, additional, Venø, Morten T., additional, Costard, Lara S., additional, Neubert, Valentin, additional, Engel, Tobias, additional, Hill, Thomas D. M., additional, Freiman, Thomas M., additional, Mahesh, Arun, additional, Tiwari, Vijay K., additional, Rosenow, Felix, additional, Bauer, Sebastian, additional, Kjems, Jørgen, additional, Morris, Gareth, additional, and Henshall, David C., additional

Published
2023
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26. The centrosome protein AKNA regulates neurogenesis via microtubule organization

Author

Camargo Ortega, Germán, Falk, Sven, Johansson, Pia A., Peyre, Elise, Broix, Loïc, Sahu, Sanjeeb Kumar, Hirst, William, Schlichthaerle, Thomas, De Juan Romero, Camino, Draganova, Kalina, Vinopal, Stanislav, Chinnappa, Kaviya, Gavranovic, Anna, Karakaya, Tugay, Steininger, Thomas, Merl-Pham, Juliane, Feederle, Regina, Shao, Wei, Shi, Song-Hai, Hauck, Stefanie M., Jungmann, Ralf, Bradke, Frank, Borrell, Victor, Geerlof, Arie, Reber, Simone, Tiwari, Vijay K., Huttner, Wieland B., Wilsch-Bräuninger, Michaela, Nguyen, Laurent, and Götz, Magdalena

Published
2019
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30. 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.

Abstract

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch’s goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschiigenomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschiisubpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.

Published
2024
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32. 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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34. Comparative genomic analysis of 5Mg chromosome of Aegilops geniculata and 5Uu chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool.

Author

Yadav, Inderjit S., Rawat, Nidhi, Chhuneja, Parveen, Kaur, Satinder, Uauy, Christobal, Lazo, Gerard, Gu, Yong Q., Doležel, Jaroslav, and Tiwari, Vijay K.

Subjects
CHROMOSOME analysis, GENOMICS, CHROMOSOMES, AEGILOPS, GENE families, WHEAT, COMPARATIVE genomics
Abstract

Wheat is one of the most important cereal crops for the global food security. Due to its narrow genetic base, modern bread wheat cultivars face challenges from increasing abiotic and biotic stresses. Since genetic improvement is the most sustainable approach, finding novel genes and alleles is critical for enhancing the genetic diversity of wheat. The tertiary gene pool of wheat is considered a gold mine for genetic diversity as novel genes and alleles can be identified and transferred to wheat cultivars. Aegilops geniculata and Ae. umbellulata are the key members of the tertiary gene pool of wheat and harbor important genes against abiotic and biotic stresses. Homoeologous-group five chromosomes (5Uu and 5Mg) have been extensively studied from Ae. geniculata and Ae. umbellulata as they harbor several important genes including Lr57, Lr76, Yr40, Yr70, Sr53 and chromosomal pairing loci. In the present study, using chromosome DNA sequencing and RNAseq datasets, we performed comparative analysis to study homoeologous gene evolution in 5Mg, 5Uu, and group 5 wheat chromosomes. Our findings highlight the diversity of transcription factors and resistance genes, resulting from the differential expansion of the gene families. Both the chromosomes were found to be enriched with the "response to stimulus" category of genes providing resistance against biotic and abiotic stress. Phylogenetic study positioned the M genome closer to the D genome, with higher proximity to the A genome than the B genome. Over 4000 genes were impacted by SNPs on 5D, with 4-5% of those genes displaying nondisruptive variations that affect gene function. [ABSTRACT FROM AUTHOR]

Published
2023
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40. A wheat kinase and immune receptor form the host-specificity barrier against the blast fungus

Author

Arora, Sanu, primary, Steed, Andrew, additional, Goddard, Rachel, additional, Gaurav, Kumar, additional, O'Hara, Tom, additional, Schoen, Adam, additional, Rawat, Nidhi, additional, Elkot, Ahmed F., additional, Chinoy, Catherine, additional, Nicholson, Martha H., additional, Asuke, Soichiro, additional, Steuernagel, Burkhard, additional, Yu, Guotai, additional, Awal, Rajani, additional, Forner-Martinez, Macarena, additional, Wingen, Luzie, additional, Baggs, Erin, additional, Clarke, Jonathan, additional, Krasileva, Ksenia V., additional, Tosa, Yukio, additional, Jones, Jonathan D. G., additional, Tiwari, Vijay K., additional, Wulff, Brande B. H., additional, and Nicholson, Paul, additional

Published
2022
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42. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

Author

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

Published
2021
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44. A whole-genome, radiation hybrid mapping resource of hexaploid wheat

Author

Tiwari, Vijay K., Heesacker, Adam, Riera-Lizarazu, Oscar, Gunn, Hilary, Wang, Shichen, Wang, Yi, Gu, Young Q., Paux, Etienne, Koo, Dal-Hoe, Kumar, Ajay, Luo, Ming-Cheng, Lazo, Gerard, Zemetra, Robert, Akhunov, Eduard, Friebe, Bernd, Poland, Jesse, Gill, Bikram S., Kianian, Shahryar, and Leonard, Jeffrey M.

Published
2016
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47. Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii

Author

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

Published
2021
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48. Genomic resources in plant breeding for sustainable agriculture

Author

Thudi, Mahendar, primary, Palakurthi, Ramesh, additional, Schnable, James C., additional, Chitikineni, Annapurna, additional, Dreisigacker, Susanne, additional, Mace, Emma, additional, Srivastava, Rakesh K., additional, Satyavathi, C. Tara, additional, Odeny, Damaris, additional, Tiwari, Vijay K., additional, Lam, Hon-Ming, additional, Hong, Yan Bin, additional, Singh, Vikas K., additional, Li, Guowei, additional, Xu, Yunbi, additional, Chen, Xiaoping, additional, Kaila, Sanjay, additional, Nguyen, Henry, additional, Sivasankar, Sobhana, additional, Jackson, Scott A., additional, Close, Timothy J., additional, Shubo, Wan, additional, and Varshney, Rajeev K., additional

Published
2021
Full Text
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