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1. Nitrogen deficiency tolerance conferred by introgression of a QTL derived from wild emmer into bread wheat.

Author

Govta, Nikolai, Fatiukha, Andrii, Govta, Liubov, Pozniak, Curtis, Distelfeld, Assaf, Fahima, Tzion, Beckles, Diane, and Krugman, Tamar

Subjects
Triticum, Quantitative Trait Loci, Nitrogen, Phenotype, Genetic Introgression, Chromosome Mapping, Stress, Physiological, Droughts, Chromosomes, Plant
Abstract

Genetic dissection of a QTL from wild emmer wheat, QGpc.huj.uh-5B.2, introgressed into bread wheat, identified candidate genes associated with tolerance to nitrogen deficiency, and potentially useful for improving nitrogen-use efficiency. Nitrogen (N) is an important macronutrient critical to wheat growth and development; its deficiency is one of the main factors causing reductions in grain yield and quality. N availability is significantly affected by drought or flooding, that are dependent on additional factors including soil type or duration and severity of stress. In a previous study, we identified a high grain protein content QTL (QGpc.huj.uh-5B.2) derived from the 5B chromosome of wild emmer wheat, that showed a higher proportion of explained variation under water-stress conditions. We hypothesized that this QTL is associated with tolerance to N deficiency as a possible mechanism underlying the higher effect under stress. To validate this hypothesis, we introgressed the QTL into the elite bread wheat var. Ruta, and showed that under N-deficient field conditions the introgression IL99 had a 33% increase in GPC (p

Published
2024

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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3. Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Author

Li, Yinghui, Wei, Zhen-Zhen, Sela, Hanan, Govta, Liubov, Klymiuk, Valentyna, Roychowdhury, Rajib, Chawla, Harmeet Singh, Ens, Jennifer, Wiebe, Krystalee, Bocharova, Valeria, Ben-David, Roi, Pawar, Prerna B, Zhang, Yuqi, Jaiwar, Samidha, Molnár, István, Doležel, Jaroslav, Coaker, Gitta, Pozniak, Curtis J, and Fahima, Tzion

Subjects
Plant Biology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Triticum, Genes, Plant, Chromosome Mapping, Cloning, Molecular, Multigene Family, Plant biology
Abstract

Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

Published
2024

4. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression.

Author

Xiong, Hongchun, Burguener, Germán, Vasquez-Gross, Hans, Liu, Qiujie, Debernardi, Juan, Akhunova, Alina, Garland-Campbell, Kimberly, Kianian, Shahryar, Brown-Guedira, Gina, Pozniak, Curtis, Faris, Justin, Akhunov, Eduard, Dubcovsky, Jorge, and Zhang, Junli

Subjects
VRN1, exome capture, functional genomics, promoter capture, wheat, Biological Assay, Gene Expression, Mutation, Triticum, Promoter Regions, Genetic
Abstract

Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.

Published
2023

8. Tandem Protein Kinases Emerge as New Regulators of Plant Immunity

Author

Klymiuk, Valentyna, Coaker, Gitta, Fahima, Tzion, and Pozniak, Curtis J

Subjects
Plant Biology, Biological Sciences, Infectious Diseases, Inflammatory and immune system, Disease Resistance, Hordeum, Plant Diseases, Plant Immunity, Protein Kinases, Triticum, fungus-plant interactions, intracellular perception proteins, plant defense response system, plant-pathogen interactions, plant responses to pathogens, Pm24, resistance gene, Rpg1, Sr60, wheat tandem kinase, WTK4, Yr15, fungus–plant interactions, plant–pathogen interactions, Genetics, Microbiology, Plant Biology & Botany, Plant biology
Abstract

Plant-pathogen interactions result in disease development in a susceptible host. Plants actively resist pathogens via a complex immune system comprising both surface-localized receptors that sense the extracellular space as well as intracellular receptors recognizing pathogen effectors. To date, the majority of cloned resistance genes encode intracellular nucleotide-binding leucine-rich repeat receptor proteins. Recent discoveries have revealed tandem kinase proteins (TKPs) as another important family of intracellular proteins involved in plant immune responses. Five TKP genes-barley Rpg1 and wheat WTK1 (Yr15), WTK2 (Sr60), WTK3 (Pm24), and WTK4-protect against devastating fungal diseases. Moreover, a large diversity and numerous putative TKPs exist across the plant kingdom. This review explores our current knowledge of TKPs and serves as a basis for future studies that aim to develop and exploit a deeper understanding of innate plant immunity receptor proteins.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Published
2021

9. 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. Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1

Author

Klymiuk, Valentyna, Fatiukha, Andrii, Raats, Dina, Bocharova, Valeria, Huang, Lin, Feng, Lihua, Jaiwar, Samidha, Pozniak, Curtis, Coaker, Gitta, Dubcovsky, Jorge, and Fahima, Tzion

Subjects
Biological Sciences, Genetics, Human Genome, Generic health relevance, Basidiomycota, Chromosome Mapping, Disease Resistance, Genes, Plant, Genetic Markers, Plant Diseases, Poaceae, EMS mutants, phenotypic response, positional cloning, tandem kinase domains, wild emmer wheat, Wtk1, yellow rust, Yr15, YrH52, YrG303, Plant Biology, Crop and Pasture Production, Plant Biology & Botany, Crop and pasture production, Biochemistry and cell biology, Plant biology
Abstract

The wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303, and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and show here that these three resistance loci co-segregate in fine-mapping populations and share an identical full-length genomic sequence of functional Wtk1. Independent ethyl methanesulfonate (EMS)-mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303, and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303-, and YrH52-mediated resistances to yellow rust are encoded by a single locus, Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks.

Published
2020

17. Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

Author

Yu, Guotai, Matny, Oadi, Champouret, Nicolas, Steuernagel, Burkhard, Moscou, Matthew J., Hernández-Pinzón, Inmaculada, Green, Phon, Hayta, Sadiye, Smedley, Mark, Harwood, Wendy, Kangara, Ngonidzashe, Yue, Yajuan, Gardener, Catherine, Banfield, Mark J., Olivera, Pablo D., Welchin, Cole, Simmons, Jamie, Millet, Eitan, Minz-Dub, Anna, Ronen, Moshe, Avni, Raz, Sharon, Amir, Patpour, Mehran, Justesen, Annemarie F., Jayakodi, Murukarthick, Himmelbach, Axel, Stein, Nils, Wu, Shuangye, Poland, Jesse, Ens, Jennifer, Pozniak, Curtis, Karafiátová, Miroslava, Molnár, István, Doležel, Jaroslav, Ward, Eric R., Reuber, T. Lynne, Jones, Jonathan D. G., Mascher, Martin, Steffenson, Brian J., and Wulff, Brande B. H.

Published
2022
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20. Copy number variation of TdDof controls solid-stemmed architecture in wheat

Author

Nilsen, Kirby T., Walkowiak, Sean, Xiang, Daoquan, Gao, Peng, Quilichini, Teagen D., Willick, Ian R., Byrns, Brook, N’Diaye, Amidou, Ens, Jennifer, Wiebe, Krystalee, Ruan, Yuefeng, Cuthbert, Richard D., Craze, Melanie, Wallington, Emma J., Simmonds, James, Uauy, Cristobal, Datla, Raju, and Pozniak, Curtis J.

Published
2020

22. Genome‐wide Association Study of Agronomic Traits in a Spring‐Planted North American Elite Hard Red Spring Wheat Panel

Author

Godoy, Jayfred, Gizaw, Shiferaw, Chao, Shiaoman, Blake, Nancy, Carter, Arron, Cuthbert, Richard, Dubcovsky, Jorge, Hucl, Pierre, Kephart, Ken, Pozniak, Curtis, Prasad, PV Vara, Pumphrey, Michael, and Talbert, Luther

Subjects
Agriculture, Land and Farm Management, Agricultural, Veterinary and Food Sciences, Crop and Pasture Production, Human Genome, Biotechnology, Genetics, Plant Biology & Botany, Crop and pasture production
Abstract

Inbred cultivars and advanced breeding lines have been subjected to numerous recombination cycles, have strong allelic selection for desired traits, and share important attributes for adaptation and agronomic performance. Genetic variation in elite gene pools captured using molecular markers is immediately useful for cultivar development. The primary goal of this study was to implement a genome‐wide association study for 17 agronomic traits using elite inbred lines. A panel consisting of 237 elite hard red spring wheat (Triticum aestivum L.) lines from different wheat breeding institutions in North America were evaluated in 11 locations over 2 yr. A total of 19,192 polymorphic single‐nucleotide polymorphism (SNP) markers from the Illumina 90K SNP array and markers linked to major genes controlling plant height, photoperiod sensitivity, and vernalization were used to assay the population. Linkage disequilibrium was observed to decay within a map distance of ∼3 cM in the A and B genomes and 7 cM in the D genome. A total of 226 marker‐trait associations were identified. Potentially novel associations were detected for grain yield on chromosome 2B and kernels per spike on 1B and 7D, whereas others colocalized with well‐known adaptation loci for photoperiod response, vernalization, and plant height. The frequency of positive alleles for specific marker‐trait associations differed among the programs, suggesting targets for introgression by the respective breeding programs.

Published
2018

23. 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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24. The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding

Author

Gao, Liangliang, Koo, Dal-Hoe, Juliana, Philomin, Rife, Trevor, Singh, Daljit, Lemes da Silva, Cristiano, Lux, Thomas, Dorn, Kevin M., Clinesmith, Marshall, Silva, Paula, Wang, Xu, Spannagl, Manuel, Monat, Cecile, Friebe, Bernd, Steuernagel, Burkhard, Muehlbauer, Gary J., Walkowiak, Sean, Pozniak, Curtis, Singh, Ravi, Stein, Nils, Mascher, Martin, Fritz, Allan, and Poland, Jesse

Published
2021
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27. The barley pan-genome reveals the hidden legacy of mutation breeding

Author

Jayakodi, Murukarthick, Padmarasu, Sudharsan, Haberer, Georg, Bonthala, Venkata Suresh, Gundlach, Heidrun, Monat, Cécile, Lux, Thomas, Kamal, Nadia, Lang, Daniel, Himmelbach, Axel, Ens, Jennifer, Zhang, Xiao-Qi, Angessa, Tefera T., Zhou, Gaofeng, Tan, Cong, Hill, Camilla, Wang, Penghao, Schreiber, Miriam, Boston, Lori B., Plott, Christopher, Jenkins, Jerry, Guo, Yu, Fiebig, Anne, Budak, Hikmet, Xu, Dongdong, Zhang, Jing, Wang, Chunchao, Grimwood, Jane, Schmutz, Jeremy, Guo, Ganggang, Zhang, Guoping, Mochida, Keiichi, Hirayama, Takashi, Sato, Kazuhiro, Chalmers, Kenneth J., Langridge, Peter, Waugh, Robbie, Pozniak, Curtis J., Scholz, Uwe, Mayer, Klaus F. X., Spannagl, Manuel, Li, Chengdao, Mascher, Martin, and Stein, Nils

Published
2020
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28. Genetic analyses of native Fusarium head blight resistance in two spring wheat populations identifies QTL near the B1, Ppd-D1, Rht-1, Vrn-1, Fhb1, Fhb2, and Fhb5 loci

Author

Thambugala, Dinushika, Brûlé-Babel, Anita L., Blackwell, Barbara A., Fedak, George, Foster, Adam J., MacEachern, Dan, Gilbert, Jeannie, Henriquez, Maria Antonia, Martin, Richard A., McCallum, Brent D., Spaner, Dean, Iqbal, Muhammad, Pozniak, Curtis J., N’Diaye, Amidou, and McCartney, Curt A.

Published
2020
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29. Reduced response diversity does not negatively impact wheat climate resilience

Author

Snowdon, Rod J., Stahl, Andreas, Wittkop, Benjamin, Friedt, Wolfgang, Voss-Fels, Kai, Ordon, Frank, Frisch, Matthias, Dreisigacker, Susanne, Hearne, Sarah J., Bett, Kirstin E., Cuthbert, Richard D., Bentley, Alison R., Melchinger, Albrecht E., Tuberosa, Roberto, Langridge, Peter, Uauy, Cristobal, Sorrells, Mark E., Poland, Jesse, and Pozniak, Curtis J.

Published
2019

30. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

Author

Jordan, Katherine W, Wang, Shichen, Lun, Yanni, Gardiner, Laura-Jayne, MacLachlan, Ron, Hucl, Pierre, Wiebe, Krysta, Wong, Debbie, Forrest, Kerrie L, IWGS Consortium, Sharpe, Andrew G, Sidebottom, Christine HD, Hall, Neil, Toomajian, Christopher, Close, Timothy, Dubcovsky, Jorge, Akhunova, Alina, Talbert, Luther, Bansal, Urmil K, Bariana, Harbans S, Hayden, Matthew J, Pozniak, Curtis, Jeddeloh, Jeffrey A, Hall, Anthony, and Akhunov, Eduard

Subjects
Biological Sciences, Genetics, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Chromosome Mapping, Chromosomes, Plant, Exome, Gene Frequency, Genome, Plant, Genotype, Haplotypes, Polymorphism, Single Nucleotide, Polyploidy, Selection, Genetic, Triticum, IWGS Consortium, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundBread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.ResultsA sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.ConclusionsEvidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.

Published
2015

33. A high‐density, SNP‐based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding

Author

Maccaferri, Marco, Ricci, Andrea, Salvi, Silvio, Milner, Sara Giulia, Noli, Enrico, Martelli, Pier Luigi, Casadio, Rita, Akhunov, Eduard, Scalabrin, Simone, Vendramin, Vera, Ammar, Karim, Blanco, Antonio, Desiderio, Francesca, Distelfeld, Assaf, Dubcovsky, Jorge, Fahima, Tzion, Faris, Justin, Korol, Abraham, Massi, Andrea, Mastrangelo, Anna Maria, Morgante, Michele, Pozniak, Curtis, N'Diaye, Amidou, Xu, Steven, and Tuberosa, Roberto

Subjects
Human Genome, Genetics, Biotechnology, Breeding, Chromosome Mapping, Chromosomes, Plant, Genetic Linkage, Genome, Plant, Genomics, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Tetraploidy, Triticum, durum wheat, single nucleotide polymorphism, consensus map, genomics-assisted breeding, homeologous loci, chromosome translocation events, anchor markers, Biological Sciences, Technology, Medical and Health Sciences
Abstract

Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.

Published
2015

35. A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping.

Author

Maccaferri, Marco, Cane', Maria Angela, Sanguineti, Maria C, Salvi, Silvio, Colalongo, Maria C, Massi, Andrea, Clarke, Fran, Knox, Ron, Pozniak, Curtis J, Clarke, John M, Fahima, Tzion, Dubcovsky, Jorge, Xu, Steven, Ammar, Karim, Karsai, Ildikó, Vida, Gyula, and Tuberosa, Roberto

Subjects
Triticum, Chromosome Mapping, Linkage Disequilibrium, Genome, Plant, Quantitative Trait Loci, Triticum durum Desf, Consensus map, Linkage disequilibrium, Genome-wide association mapping, Heading date, QTL, Genome, Plant, Bioinformatics, Biological Sciences, Medical and Health Sciences, Information and Computing Sciences
Abstract

BackgroundDurum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.ResultsHigh quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.ConclusionsThe consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

Published
2014

36. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

Author

Wang, Shichen, Wong, Debbie, Forrest, Kerrie, Allen, Alexandra, Chao, Shiaoman, Huang, Bevan E, Maccaferri, Marco, Salvi, Silvio, Milner, Sara G, Cattivelli, Luigi, Mastrangelo, Anna M, Whan, Alex, Stephen, Stuart, Barker, Gary, Wieseke, Ralf, Plieske, Joerg, Consortium, International Wheat Genome Sequencing, Lillemo, Morten, Mather, Diane, Appels, Rudi, Dolferus, Rudy, Brown‐Guedira, Gina, Korol, Abraham, Akhunova, Alina R, Feuillet, Catherine, Salse, Jerome, Morgante, Michele, Pozniak, Curtis, Luo, Ming‐Cheng, Dvorak, Jan, Morell, Matthew, Dubcovsky, Jorge, Ganal, Martin, Tuberosa, Roberto, Lawley, Cindy, Mikoulitch, Ivan, Cavanagh, Colin, Edwards, Keith J, Hayden, Matthew, and Akhunov, Eduard

Subjects
Biological Sciences, Ecology, Genetics, Human Genome, Biotechnology, Alleles, Chromosome Mapping, Cluster Analysis, Gene Frequency, Genetic Loci, Genetic Markers, Genetic Variation, Genome, Plant, Genotype, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Polyploidy, Triticum, single nucleotide polymorphism, polyploid wheat, wheat iSelect array, genotyping, high-density map, genetic diversity, International Wheat Genome Sequencing Consortium, Genetic diversity, Genotyping, High-density map, Polyploid wheat, Single nucleotide polymorphism, Wheat iSelect array, Technology, Medical and Health Sciences, Agricultural biotechnology, Plant biology
Abstract

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Published
2014

37. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

Author

Wang, Shichen, Wong, Debbie, Forrest, Kerrie, Allen, Alexandra, Chao, Shiaoman, Huang, Bevan E, Maccaferri, Marco, Salvi, Silvio, Milner, Sara G, Cattivelli, Luigi, Mastrangelo, Anna M, Whan, Alex, Stephen, Stuart, Barker, Gary, Wieseke, Ralf, Plieske, Joerg, International Wheat Genome Sequencing Consortium, Lillemo, Morten, Mather, Diane, Appels, Rudi, Dolferus, Rudy, Brown-Guedira, Gina, Korol, Abraham, Akhunova, Alina R, Feuillet, Catherine, Salse, Jerome, Morgante, Michele, Pozniak, Curtis, Luo, Ming-Cheng, Dvorak, Jan, Morell, Matthew, Dubcovsky, Jorge, Ganal, Martin, Tuberosa, Roberto, Lawley, Cindy, Mikoulitch, Ivan, Cavanagh, Colin, Edwards, Keith J, Hayden, Matthew, and Akhunov, Eduard

Subjects
International Wheat Genome Sequencing Consortium, Triticum, Genetic Markers, Oligonucleotide Array Sequence Analysis, Cluster Analysis, Chromosome Mapping, Gene Frequency, Genotype, Polyploidy, Polymorphism, Single Nucleotide, Alleles, Genome, Plant, Genetic Variation, Genetic Loci, genetic diversity, genotyping, high-density map, polyploid wheat, single nucleotide polymorphism, wheat iSelect array, Genetic diversity, Genotyping, High-density map, Polyploid wheat, Single nucleotide polymorphism, Wheat iSelect array, Biotechnology, Technology, Biological Sciences, Medical and Health Sciences
Abstract

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Published
2014

38. 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

40. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

Author

He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, Keeble-Gagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L., Davies, John P., Webb, Steve R., Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew, and Akhunov, Eduard

Published
2019
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41. Durum wheat genome highlights past domestication signatures and future improvement targets

Author

Maccaferri, Marco, Harris, Neil S., Twardziok, Sven O., Pasam, Raj K., Gundlach, Heidrun, Spannagl, Manuel, Ormanbekova, Danara, Lux, Thomas, Prade, Verena M., Milner, Sara G., Himmelbach, Axel, Mascher, Martin, Bagnaresi, Paolo, Faccioli, Primetta, Cozzi, Paolo, Lauria, Massimiliano, Lazzari, Barbara, Stella, Alessandra, Manconi, Andrea, Gnocchi, Matteo, Moscatelli, Marco, Avni, Raz, Deek, Jasline, Biyiklioglu, Sezgi, Frascaroli, Elisabetta, Corneti, Simona, Salvi, Silvio, Sonnante, Gabriella, Desiderio, Francesca, Marè, Caterina, Crosatti, Cristina, Mica, Erica, Özkan, Hakan, Kilian, Benjamin, De Vita, Pasquale, Marone, Daniela, Joukhadar, Reem, Mazzucotelli, Elisabetta, Nigro, Domenica, Gadaleta, Agata, Chao, Shiaoman, Faris, Justin D., Melo, Arthur T. O., Pumphrey, Mike, Pecchioni, Nicola, Milanesi, Luciano, Wiebe, Krystalee, Ens, Jennifer, MacLachlan, Ron P., Clarke, John M., Sharpe, Andrew G., Koh, Chu Shin, Liang, Kevin Y. H., Taylor, Gregory J., Knox, Ron, Budak, Hikmet, Mastrangelo, Anna M., Xu, Steven S., Stein, Nils, Hale, Iago, Distelfeld, Assaf, Hayden, Matthew J., Tuberosa, Roberto, Walkowiak, Sean, Mayer, Klaus F. X., Ceriotti, Aldo, Pozniak, Curtis J., and Cattivelli, Luigi

Published
2019
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42. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

Author

Avni, Raz, Nave, Moran, Barad, Omer, Baruch, Kobi, Twardziok, Sven O., Gundlach, Heidrun, Hale, Iago, Mascher, Martin, Spannagl, Manuel, Wiebe, Krystalee, Jordan, Katherine W., Golan, Guy, Deek, Jasline, Ben-Zvi, Batsheva, Ben-Zvi, Gil, Himmelbach, Axel, MacLachlan, Ron P., Sharpe, Andrew G., Fritz, Allan, Ben-David, Roi, Budak, Hikmet, Fahima, Tzion, Korol, Abraham, Faris, Justin D., Hernandez, Alvaro, Mikel, Mark A., Levy, Avraham A., Steffenson, Brian, Maccaferri, Marco, Tuberosa, Roberto, Cattivelli, Luigi, Faccioli, Primetta, Ceriotti, Aldo, Kashkush, Khalil, Pourkheirandish, Mohammad, Komatsuda, Takao, Eilam, Tamar, Sela, Hanan, Sharon, Amir, Ohad, Nir, Chamovitz, Daniel A., Mayer, Klaus F.X., Stein, Nils, Ronen, Gil, Peleg, Zvi, Pozniak, Curtis J., Akhunov, Eduard D., and Distelfeld, Assaf

Published
2017

43. 4th Conference of Cereal Biotechnology and Breeding jointly organized by EUCARPIA Cereal Section November 6–9, 2017 • Budapest, Hungary : BOOK OF ABSTRACTS

Author

Consortium INEW, PPP Barley Consortium, Börner, Andreas, Nagel, Manuela, Tarawneh, Rasha, Arif, Mian Abdur Rehman, Agacka-Mołdoch, Monika, Börner, Mariann, Lohwasser, Ulrike, Rieweach, David, Wieb, Janine, Altmann, Thomas, Góralska, Magdalena, Lenarczyk-Puri, Natalia, Podgórska, Katarzyna, Berdzik, Marcin, Stojałowski, Stefan, Myśków, Beata, Kiss, Tibor, Veisz, Ottó, Karsai, Ildikó, Martín, Antonio, Rasmussen, Søren K., Legzdina, Linda, Fan, Weiyao, Tikhenko, Natalia, Rutten, Twan, Senula, Angelika, Rubtsova, Myroslava, Keller, E. R. Joachim, Vitányi, Beáta, Nagy, Katalin, Fekete, Anna Katalin, Dudás, Brigitta, Lantos, Csaba, Pauk, János, Jenes, Barnabás, Yu, Bianyun, Zhang, Wentao, Gao, Peng, Sidebottom, Christine, Lokuruge, Prabhath, Polley, Brittany, Clarke, Carling, Sharpe, Andrew, Knox, Ron, Cuthbert, Richard, Ruan, Yuefeng, Pozniak, Curtis J., Fobert, Pierre, Dziurka, Kinga, Noga, Angelika, Marcińska, Izabela, Czyczyło-Mysza, Ilona, Warchoł, Marzena, Kapłoniak, Kamila, Warzecha, Tomasz, Sutkowska, Agnieszka, Werwińska, Krystyna, Nita, Zygmunt, Skrzypek, Edyta, Fradgley, Nick, Bentley, Alison, Gardner, Keith, Howell, Phil, Mackay, Ian, Scott, Mike, Mott, Richard, Cockram, James, Galani, Saddia, Sahar, Shagufta, Musharraf, Syed Ghulam, Azhar, Abid, Ferjaoui, Sahbi, Bouslimi, Chadha, Udupa, Sripada M., Hamza, Sonia, Mariana, Ittu, Ciuca, Matilda, Marinciu, Cristina, Cristina, Daniel, Turcu, Alina, Mandea, Vasile, Ittu, Gheorghe, Jabłoński, Bartosz, Onyśk, Agnieszka, Wyszyńska, Renata, Boczkowska, Maja, Przyborowski, Mateusz, Gasparis, Sebastian, Orczyk, Wacław, Nadolska-Orczyk, Anna, Bińkowski, Jan, Kubiś, Jakub, Pogorzelska, Katarzyna, Pellny, Till K, Bolibok-Brągoszewska, Hanna, Idziak-Helmcke, Dominika, Rojek, Magdalena, Hosiawa-Barańska, Marta, Tsai, Hsin-Yuan, Cericola, Fabio, Edriss, Vahid, Andersen, Jeppe, Orabi, Jihad, Jensen, Jens, Jahoor, Ahmed, Janss, Luc, Jensen, Just, Lawrenson, Tom, Hayta, Sadiye, Smedley, Mark, Hinchliffe, Alison, Harwood, Wendy, Gimenez, Guillermo G., Barakate, Abdellah, Russell, Joanne, Stephens, Jennifer, Lampugnani, Edwin R., Doblin, Monika S., Fincher, Geoffrey B., Burton, Rachel A., Waugh, Robbie, Tucker, Matthew, Houston, Kelly, Jouanin, Aurelie, Leigh, Fiona, Wallington, Emma, Schaart, Jan, Smulders, Marinus J.M., Kała, Maciej, Kim, Sung-Yong, Brueggeman, Robert, Åhman, Inger, Zhu, Li-Hua, Bouchet, Sophie, Lemarié, Stéphane, Fugeray-Scarbel, Aline, Auzanneau, Jérôme, Charmet, Gilles, Ali, Ahmad, Mastrangelo, Anna Maria, De Vita, Pasquale, Laido, Giovanni, Marone, Daniale, Arshad, Muhammad, Naqvi, S.M. Sawlan, Sher, Hassan, Rasheed, Awais, Kazi, Abdul Mujeeb, Oakey, Helena, Bayer, Micha, Macaulay, Malcolm, Byrt, Caitlin, Gilliham, Matthew, Salt, David E, István, Monostori, Fruzsina, Szira, Alessandro, Tondelli, Tamás, Árendás, Krisztián, Gierczik, Luigi, Cattivelli, Gábor, Galiba, Attila, Vágújfalvi, Bakuma, Alla, Chebotar, Galyna, Filimonov, Vadim, Kyrylyuk, Tetyana, Chebotar, Sabina, Kristensen, Peter Skov, Andersen, Jeppe Reitan, Guzmán, Carlos, Schurr, Ulrich, Pieruschka, Roland, Neumann, Kerstin, Zhao, Yusheng, Dhanagond, Sidram, Reif, Jochen C., Graner, Andreas, Raymaekers, Dries, Taylor, Mike, Åhman, Inger M., Crespo-Herrera, Leonardo A., Kobiljski, Borislav, Mladenović, Gojko, Jestrović, Zorica, Jancsó, Mihály, Ács, Katalin, Bóna, Lajos, Purgel, Szandra, Békés, Ferenc, Schwember, A.R., Matus, I., Sharma, Dew Kumari, Rosenqvist, Eva, Carl-Otto-Ottosen, Torp, Anna Maria, Andersen, Sven Bode, El-Haddoury, Jamal, Henkrar, Fatima, Grana, Zahra, Nyiraguhirwa, Solange, Gyawali, Sanjaya, Verma, Ramesh, Ouabbou, Hassan, Ibriz, Mohammed, Iraqi, Driss, Forgeois, Paul, Grausgruber, Heinrich, Cuendet, Catherine, Dell’Avo, Franca, Koppel, Reine, Weyermann, Verena, Mikó, Péter, Vida, Gyula, Rakszegi, Marianna, Lafferty, Julia, Lorentz, Bruno, Longin, Carl Friedrich Horst, Megyeri, Mária, Kaskarbayev, Zheksenbay, Zhloba, Ludmila, Kiyas, Aldabergen, Kunanbayev, Kairat, Churkina, Galina, Zueva, Nataliya, Cattivelli, Luigi, Guerra, Davide, Tondelli, Alessandro, Bustos-Korts, D., Rizza, Fulvia, Bretani, Gianluca, Ferrandi, Chiara, Lazzari, Barbara, Rossini, Laura, Ozkan, Hakan, Molnar-Lang, Marta, van Eeuwijk, Fred, Dawson, Ian K, Fricano, Agostino, Azad, Md. Abul Kalam, Kamruzzaman, Md., Yasmine, Fahmina, Islam, Mirza Mofazzal, Jankuloski, Ljupcho, Christopher, John (Jack), Anzooman, Monia, Menzies, Neal, Dalal, Ram, Dang, Yash, Novák, Aliz, Boldizsár, Ákos, Gierczik, Krisztián, Mohamed, Ahres, Ádám, Éva, Bognár, László Kozma, Vágújfalvi, Attila, Båga, Monica, Chibbar, Ravindra, Galiba, Gábor, Gottwald, Sven, Bhandari, Dhaka Ram, Wang, Qing, Li, Bin, Römpp, Andreas, Friedt, Wolfgang, Spengler, Bernhard, Jäger, Katalin, Sáfrán, Eszter, Fábián, Attila, Deák, Csilla, Papp, István, Barnabás, Beáta, Mesterhazy, Akos, Varga, Mónika, Bartók, Tibor, Lehoczki-Krjak, Szabolcs, Toth, Beata, Miloud, Hafsi, Pál, Magda, Szalai, Gabriella, Janda, Tibor, Molnár, István, Lovegrove, Alison, Darkó, Éva, Farkas, András, Láng, László, Bedő, Zoltán, Doležel, Jaroslav, Molnár-Láng, Márta, Shewry, Peter, Tiryakioğlu, Murat, Sakallı, Abdulla, Alloudane, Rajae, El Mourabit, Nourdin, Barrijal, Said, Bengtsson, Therése, Manninen, Outi, Bulatova, Kulpash, Mazkirat, Shynar, Babissekova, Dilyara, Aytimbetova, Klara, Goncharova, Anastasiya, Lavrinenko, Yuriy, Bazaliy, Galyna, Cope, Jonathan, Norton, Gareth, George, Timothy, Newton, Adrian, Császár, Orsolya, Lajos, Károly, Szalai, Márk, Dziurka, Michał, Dashkevich, Svetlana, Utebayev, Maral, Chilimova, Irina, Babkenov, Adilchan, Akhmetova, Galiya, Chaimae, Senhaji, Khadija, Ahansal, Rabha, Abdelwahd, Allal, Douira, Driss, Iraqi, Gracz, Joanna, Karłowski, Wojciech, Kuczyński, Jakub, Tyczewska, Agata, Haberle, Jan, Svoboda, Pavel, Neumannová, Adéla, Kurešová, Gabriela, Raimanová, Ivana, Holková, Ludmila, Solařová, Eva, Bradáčová, Marta, Smutná, Pavlína, Horčička, P., Pospíšilová, V., Veškrna, O., Bížova, I., Chrpova, J., Sumíková, T., Ittu, Mariana, Marinciu, Cristina Mihaela, Voica, Maria, Banateanu, Cecilia, Mayer, Marianna, Karsai, Idikó, Mirosavljević, Milan, Momčilović, Vojislava, Mikić, Sanja, Trkulja, Dragana, Denčić, Srbislav, Jocković, Bojan, Aćin, Vladimir, Pržulj, Novo, Nakhoda, Babak, Mohammadi-Nejad, Ghasem, Mardi, Mohsen, Amini, Ashkboos, Tabatabaei, Mohammad-Taghi, Parsayev, Evgeniy, Filippova, Nadezhda, Permana, Hadian, Ishii, Kazuo, Murata, Kazumasa, Yamada, Tetsuya, Kanekatsu, Motoki, Prokesova, Lenka, Smutna, Pavlina, Holkova, Ludmila, Rukavitsina, Irina, Suleimenov, Mechlis, Yerpasheva, Dana, Shtefan, Galina, Ivanova, Galina, Ferderer, Ella, Kalapos, Balázs, Ahres, Mohamed, Székely, András, Gulyás, Zsolt, Kovács, Kristóf, Jones, Huw D, Dalmay, Tamás, Soltész, Alexandra, Trávníčková, Martina, Chrpová, Jana, Martinek, Petr, Hnilička, František, Żywicki, Marek, Twardowski, Tomasz, Végh, Balázs, Marček, Tihana, Wiśniewska, Halina, Kwiatek, Michał, Majka, Maciej, Gawłowska, Magdalena, Korbas, Marek, Danielewicz, Jakub, Belter, Jolanta, Bilgrami, Sayedeh Saba, Sichani, Jalal Sabouri, Zandi, Peiman, Zhunusbayeva, Zhazira, Omirbekova, Nargul, Zhussupova, Aizhan, Mursalieva, Valentina, Nam, Svetlana, Żur, Iwona, Surówka, Ewa, Dubas, Ewa, Nowicka, Anna, Krzewska, Monika, Hura, Tomasz, Rapacz, Marcin, Wójcik-Jagła, Magdalena, Ostrowska, Agnieszka, Malaga, Sabina, Janowiak, Franciszek, Pellny, Till, Patil, Archana, Freeman, Jackie, Plummer, Amy, Hess, Linde, Phillips, Andy, Berry, Simon, Mitchell, Rowan, Larkin, Philip, Tanner, Gregory, Colgrave, Michelle, Blundell, Malcolm, Howitt, Crispin, Morita, Naofumi, Van Hung, Pham, Cegiełko, Małgorzata, Kiecana, Irena, Mielniczuk, Elżbieta, Pastucha, Alina, Perkowski, Juliusz, Áy, Zoltán, Czirle, Csaba, Palágyi, András, Mihály, Róbert, Vermeulen, Philippe, Suman, Michele, Pierna, Juan Antonio Fernández, and Baeten, Vincent

Published
2017

45. Historic recombination in a durum wheat breeding panel enables high-resolution mapping of Fusarium head blight resistance quantitative trait loci

Author

Sari, Ehsan, Knox, Ron E., Ruan, Yuefeng, Henriquez, Maria Antonia, Kumar, Santosh, Burt, Andrew J., Cuthbert, Richard D., Konkin, David J., Walkowiak, Sean, Campbell, Heather L., Singh, Asheesh K., Ross, Jay, Lokuruge, Prabhath, Hsueh, Emma, Boyle, Kerry, Sidebottom, Christine, Condie, Janet, Yates, Shawn, Pozniak, Curtis J., and Fobert, Pierre R.

Published
2020
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48. Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat.

Author

Haile, Jemanesh K., Sertse, Demissew, N'Diaye, Amidou, Klymiuk, Valentyna, Wiebe, Krystalee, Yuefeng Ruan, Chawla, Harmeet S., Henriquez, Maria-Antonia, Lipu Wang, Kutcher, Hadley R., Steiner, Barbara, Buerstmayr, Hermann, and Pozniak, Curtis J.

Subjects
DURUM wheat, GENOME-wide association studies, FUSARIUM, GERMPLASM
Abstract

Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019-2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium-damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2, associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking. [ABSTRACT FROM AUTHOR]

Published
2023
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49. Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes

Author

Bokore, Firdissa E., Cuthbert, Richard D., Knox, Ron E., Randhawa, Harpinder S., Hiebert, Colin W., DePauw, Ron M., Singh, Asheesh K., Singh, Arti, Sharpe, Andrew G., N’Diaye, Amidou, Pozniak, Curtis J., McCartney, Curt, Ruan, Yuefeng, Berraies, Samia, Meyer, Brad, Munro, Catherine, Hay, Andy, Ammar, Karim, Huerta-Espino, Julio, and Bhavani, Sridhar

Published
2017
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