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1. Updated guidelines for gene nomenclature in wheat

Author

Boden, SA, McIntosh, RA, Uauy, C, Krattinger, SG, Dubcovsky, J, Rogers, WJ, Xia, XC, Badaeva, ED, Bentley, AR, Brown-Guedira, G, Caccamo, M, Cattivelli, L, Chhuneja, P, Cockram, J, Contreras-Moreira, B, Dreisigacker, S, Edwards, D, González, FG, Guzmán, C, Ikeda, TM, Karsai, I, Nasuda, S, Pozniak, C, Prins, R, Sen, TZ, Silva, P, Simkova, H, and Zhang, Y

Subjects
Genetics, Triticum, Plant Breeding, Phenotype, Genes, Plant, Edible Grain, Wheat Initiative, Biological Sciences, Agricultural and Veterinary Sciences, Technology, Plant Biology & Botany
Abstract

Key messageHere, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

Published
2023

2. Global Wheat Head Detection (GWHD) dataset: a large and diverse dataset of high resolution RGB labelled images to develop and benchmark wheat head detection methods

Author

David, E., Madec, S., Sadeghi-Tehran, P., Aasen, H., Zheng, B., Liu, S., Kirchgessner, N., Ishikawa, G., Nagasawa, K., Badhon, M. A., Pozniak, C., de Solan, B., Hund, A., Chapman, S. C., Baret, F., Stavness, I., and Guo, W.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Detection of wheat heads is an important task allowing to estimate pertinent traits including head population density and head characteristics such as sanitary state, size, maturity stage and the presence of awns. Several studies developed methods for wheat head detection from high-resolution RGB imagery. They are based on computer vision and machine learning and are generally calibrated and validated on limited datasets. However, variability in observational conditions, genotypic differences, development stages, head orientation represents a challenge in computer vision. Further, possible blurring due to motion or wind and overlap between heads for dense populations make this task even more complex. Through a joint international collaborative effort, we have built a large, diverse and well-labelled dataset, the Global Wheat Head detection (GWHD) dataset. It contains 4,700 high-resolution RGB images and 190,000 labelled wheat heads collected from several countries around the world at different growth stages with a wide range of genotypes. Guidelines for image acquisition, associating minimum metadata to respect FAIR principles and consistent head labelling methods are proposed when developing new head detection datasets. The GWHD is publicly available at http://www.global-wheat.com/ and aimed at developing and benchmarking methods for wheat head detection., Comment: 16 pages, 7 figures, Dataset paper

Published
2020

3. Genome-wide association study of agronomic traits in a spring-planted north american elite hard red spring wheat panel

Author

Godoy, J, Gizaw, S, Chao, S, Blake, N, Carter, A, Cuthbert, R, Dubcovsky, J, Hucl, P, Kephart, K, Pozniak, C, Prasad, PVV, Pumphrey, M, and Talbert, L

Subjects
Human Genome, Genetics, Biotechnology, 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

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

Author

Wang, S, Wong, D, Forrest, K, Allen, A, Chao, S, Huang, BE, Maccaferri, M, Salvi, S, Milner, SG, Cattivelli, L, Mastrangelo, AM, Whan, A, Stephen, S, Barker, G, Wieseke, R, Plieske, J, Lillemo, M, Mather, D, Appels, R, Dolferus, R, Brown-Guedira, G, Korol, A, Akhunova, AR, Feuillet, C, Salse, J, Morgante, M, Pozniak, C, Luo, MC, Dvorak, J, Morell, M, Dubcovsky, J, Ganal, M, Tuberosa, R, Lawley, C, Mikoulitch, I, Cavanagh, C, Edwards, KJ, Hayden, M, and Akhunov, E

Subjects
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. © 2014 The Authors Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Published
2014

5. The transcriptional landscape of polyploid wheat

Author

International Wheat Genome Sequencing Consortium, Ramírez-González, R. H., Borrill, P., Lang, D., Harrington, S. A., Brinton, J., Venturini, L., Davey, M., Jacobs, J., van Ex, F., Pasha, A., Khedikar, Y., Robinson, S. J., Cory, A. T., Florio, T., Concia, L., Juery, C., Schoonbeek, H., Steuernagel, B., Xiang, D., Ridout, C. J., Chalhoub, B., Mayer, K. F. X., Benhamed, M., Latrasse, D., Bendahmane, A., Wulff, B. B. H., Appels, R., Tiwari, V., Datla, R., Choulet, F., Pozniak, C. J., Provart, N. J., Sharpe, A. G., Paux, E., Spannagl, M., Bräutigam, A., and Uauy, C.

Published
2018

6. Updated guidelines for gene nomenclature in wheat

Author

0000-0001-5297-4067, Boden, S. A., McIntosh, R. A., Uauy, C., Krattinger, S. G., Dubcovsky, J., Rogers, W. J., Xia, X. C., Badaeva, E. D., Bentley, A. R., Brown-Guedira, G., Caccamo, M., Cattivelli, L., Chhuneja, P., Cockram, J., Contreras-Moreira, Bruno, Dreisigacker, S., Edwards, D., González, F. G., Guzmán, C., Ikeda, T. M., Karsai, I., Nasuda, S., Pozniak, C., Prins, R., Sen, T. Z., Silva, P., Simkova, H., Zhang, Y., 0000-0001-5297-4067, Boden, S. A., McIntosh, R. A., Uauy, C., Krattinger, S. G., Dubcovsky, J., Rogers, W. J., Xia, X. C., Badaeva, E. D., Bentley, A. R., Brown-Guedira, G., Caccamo, M., Cattivelli, L., Chhuneja, P., Cockram, J., Contreras-Moreira, Bruno, Dreisigacker, S., Edwards, D., González, F. G., Guzmán, C., Ikeda, T. M., Karsai, I., Nasuda, S., Pozniak, C., Prins, R., Sen, T. Z., Silva, P., Simkova, H., and Zhang, Y.

Abstract

Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

Published
2023

15. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Author

Monat, C., Padmarasu, S., Lux, T., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G.J., Schulman, A.H., Waugh, R., Braumann, I., Pozniak, C., Scholz, U., Mayer, K.F.X., Spannagl, M., Stein, N., Mascher, M., Monat, C., Padmarasu, S., Lux, T., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G.J., Schulman, A.H., Waugh, R., Braumann, I., Pozniak, C., Scholz, U., Mayer, K.F.X., Spannagl, M., Stein, N., and Mascher, M.

Abstract

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

Published
2019

16. Ancient hybridizations among the ancestral genomes of bread wheat

Author

Marcussen, T., Sandve, S., Heier, L., Spannagl, M., Pfeifer, M., Jakobsen, K., Wulff, B., Steuernagel, B., Mayer, K., Olsen, O.-A., Rogers, J., Dole el, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A., Sourdille, Pierre, Endo, T., Kubalakova, M., ihalikova, J., Dubska, Z., Vrana, J., perkova, R., imkova, H., Febrer, M., Clissold, L., McLay, K., Singh, K., Chhuneja, P., Singh, N., Khurana, J., Akhunov, E., Choulet, F., Alberti, A., Barbe, Valérie, Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J., Ogihara, Y., Handa, H., Maclachlan, P., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Lien, S., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R., Clavijo, B., Wright, J., Martis, M., Mascher, M., Chapman, J., Poland, J., Scholz, U., Barry, K., Waugh, R., Rokhsar, D., Muehlbauer, G., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Faccioli, P., Colaiacovo, M., Stanca, A., Budak, H., Cattivelli, L., Glover, N., Pingault, L., Paux, E., Sharma, S., Appels, R., Bellgard, M., Chapman, B., Nussbaumer, T., Bader, K., Rimbert, H., Wang, S., Knox, R., Kilian, A., Alaux, M., Alfama, F., Couderc, L., Guilhot, N., Viseux, C., Loaec, M., Keller, B., Praud, S., Norwegian University of Life Sciences (NMBU), Helmholtz-Zentrum München (HZM), Helmholtz Centre Munich, Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health - Helmholtz Center München (GmbH), John Innes Centre [Norwich], Eversole Associates, Bayer Corporation, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Laboratoire d'hydrodynamique (LadHyX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), Consiglio Nazionale delle Ricerche (CNR), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Seismological Laboratory, California Institute of Technology (CALTECH), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Physics, University of Tokyo, The University of Tokyo (UTokyo), National Institute for Environmental Studies (NIES), Université de Lille, Sciences et Technologies, The University of Western Australia (UWA), Leibniz Institute of Plant Genetics and Crop Plant Research, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), Consiglio per la Ricerca e Sperimentazione in Agricoltura, Climate Research Division [Toronto], Environment and Climate Change Canada, School of Biosciences, University of Birmingham [Birmingham], Centre for Comparative Genomics, Murdoch University, Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, BIOGEMMA, Centre de Recherche de Chappes, Diversity Arrays Technology Pty Ltd (DArT P/L), Institute of plant biology, Universität Zürich [Zürich] = University of Zurich (UZH), Research Council of Norway 199387Biotechnology and Biological Sciences Research Council (BBSRC) BB/J003166/1,BBS/E/T/000PR6193National Science Foundation (NSF) - Directorate for Computer & Information Science & Engineering (CISE) 1126709, Helmholtz Zentrum München = German Research Center for Environmental Health, Biotechnology and Biological Sciences Research Council (BBSRC), Laboratoire Chrono-environnement (UMR 6249) (LCE), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Oslo (UiO), The Sainsbury Laboratory (TSL), and Norwegian Research Council 199387

Subjects
0106 biological sciences, TRITICUM, GENES, [SDV]Life Sciences [q-bio], Biology, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Polyploid, Phylogenetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, DRAFT GENOME, Phylogeny, AEGILOPS-TAUSCHII, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Phylogenetic tree, A-GENOME, myr, food and beverages, Bread, EVOLUTION, ALIGNMENT, DOMESTICATION, Hybridization, Genetic, Hybrid speciation, Ploidy, Genome, Plant, 010606 plant biology & botany, PACKAGE
Abstract

International audience; The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor similar to 7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.

Published
2014

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

Author

Mayer, K.F.X., Rogers, J., Dole el, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A.J., Sourdille, P., Endo, T.R., Kubalakova, M., Ihalikova, J., Dubska, Z., Vrana, J., Perkova, R., Imkova, H., Febrer, M., Clissold, L., McLay, K., Singh, K., Chuneja, P., Singh, N.K., Khurana, J., Akhunov, E., Choulet, F., Alberti, A., Barbe, V., Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J., Ogihara, Y., Handa, H., Maclachlan, P.R., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Olsen, O-A, Sandve, S.R., Lien, S., Steuernagel, B., Wulff, B., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R.H., Clavijo, B.J., Wright, J., Pfeifer, M., Spannagl, M., Martis, M.M., Mascher, M., Chapman, J., Poland, J.A., Scholz, U., Barry, K., Waugh, R., Rokhsar, D.S., Muehlbauer, G.J., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Faccioli, P., Colaiacovo, M., Stanca, A.M., Budak, H., Cattivelli, L., Glover, N., Pingault, L., Paux, E., Sharma, S., Appels, R., Bellgard, M., Chapman, B., Nussbaumer, T., Bader, K.C., Rimbert, H., Wang, S., Knox, R., Kilian, A., Alaux, M., Alfama, F., Couderc, L., Guilhot, N., Viseux, C., Loaec, M., Keller, B., Praud, S., Mayer, K.F.X., Rogers, J., Dole el, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A.J., Sourdille, P., Endo, T.R., Kubalakova, M., Ihalikova, J., Dubska, Z., Vrana, J., Perkova, R., Imkova, H., Febrer, M., Clissold, L., McLay, K., Singh, K., Chuneja, P., Singh, N.K., Khurana, J., Akhunov, E., Choulet, F., Alberti, A., Barbe, V., Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J., Ogihara, Y., Handa, H., Maclachlan, P.R., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Olsen, O-A, Sandve, S.R., Lien, S., Steuernagel, B., Wulff, B., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R.H., Clavijo, B.J., Wright, J., Pfeifer, M., Spannagl, M., Martis, M.M., Mascher, M., Chapman, J., Poland, J.A., Scholz, U., Barry, K., Waugh, R., Rokhsar, D.S., Muehlbauer, G.J., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Faccioli, P., Colaiacovo, M., Stanca, A.M., Budak, H., Cattivelli, L., Glover, N., Pingault, L., Paux, E., Sharma, S., Appels, R., Bellgard, M., Chapman, B., Nussbaumer, T., Bader, K.C., Rimbert, H., Wang, S., Knox, R., Kilian, A., Alaux, M., Alfama, F., Couderc, L., Guilhot, N., Viseux, C., Loaec, M., Keller, B., and Praud, S.

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

22. Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array

Author

Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B.E., Maccaferri, M., Salvi, S., Milner, S.G., Cattivelli, L., Mastrangelo, A.M., Whan, A., Stephen, S., Barker, G., Wieseke, R., Plieske, J., Lillemo, M., Mather, D., Appels, R., Dolferus, R., Brown-Guedira, G., Korol, A., Akhunova, A.R., Feuillet, C., Salse, J., Morgante, M., Pozniak, C., Luo, M-C, Dvorak, J., Morell, M., Dubcovsky, J., Ganal, M., Tuberosa, R., Lawley, C., Mikoulitch, I., Cavanagh, C., Edwards, K.J., Hayden, M., Akhunov, E., Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B.E., Maccaferri, M., Salvi, S., Milner, S.G., Cattivelli, L., Mastrangelo, A.M., Whan, A., Stephen, S., Barker, G., Wieseke, R., Plieske, J., Lillemo, M., Mather, D., Appels, R., Dolferus, R., Brown-Guedira, G., Korol, A., Akhunova, A.R., Feuillet, C., Salse, J., Morgante, M., Pozniak, C., Luo, M-C, Dvorak, J., Morell, M., Dubcovsky, J., Ganal, M., Tuberosa, R., Lawley, C., Mikoulitch, I., Cavanagh, C., Edwards, K.J., Hayden, M., and Akhunov, E.

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

23. CDC Dynamic durum wheat.

Author

Pozniak, C. J. and Clarke, J. M.

Subjects
DURUM wheat, GRAIN yields, WHEAT proteins, WHEAT varieties
Abstract

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2017
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24. CDC Alloy durum wheat.

Author

Pozniak, C. J. and Clarke, J. M.

Subjects
DURUM wheat, WHEAT quality, WHEAT varieties, WHEAT proteins
Abstract

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2017
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25. CDC Precision durum wheat.

Author

Pozniak, C. J. and Clarke, J. M.

Subjects
DURUM wheat, WHEAT varieties, WHEAT yields, EFFECT of cadmium on plants
Abstract

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2017
Full Text
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26. The p75 Neurotrophin Receptor Mediates Neuronal Apoptosis and Is Essential for Naturally Occurring Sympathetic Neuron Death

Author

Bamji, S. X., Majdan, M., Pozniak, C. D., Belliveau, Daniel, Aloyz, R., Kohn, J., Causing, C. G., and Miller, F. D.

Subjects
Curriculum and Instruction, nervous system, Neoplasms, sense organs, Nervous System Diseases, Nervous System, Nervous System Disease, Educational Assessment, Evaluation, and Research
Abstract

To determine whether the p75 neurotrophin receptor (p75NTR) plays a role in naturally occurring neuronal death, we examined neonatal sympathetic neurons that express both the TrkA tyrosine kinase receptor and p75NTR. When sympathetic neuron sur- vival is maintained with low quantities of NGF or KC1, the neurotrophin brain-derived neurotrophic factor (BDNF), which does not activate Trk receptors on sympathetic neurons, causes neuronal apoptosis and increased phosphorylation of c-jun. Function-blocking antibody studies indicate that this apoptosis is due to BDNF-mediated activation of p75NTR. To determine the physiological relevance of these culture findings, we examined sympathetic neurons in BDNF-/- and p75NTR-/- mice. In BDNF-/- mice, sympathetic neuron number is increased relative to BDNF+/+ littermates, and in p75NTR-/- mice, the normal period of sympathetic neuron death does not occur, with neuronal attrition occurring later in life. This deficit in apoptosis is intrinsic to sympathetic neurons, since cultured p75NTR-/- neurons die more slowly than do their wild-type counterparts. Together, these data indicate that p75NTR can signal to mediate apoptosis, and that this mechanism is essential for naturally occurring sympathetic neuron death.

Published
1998

31. Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat

Author

Singh, A., primary, Pandey, M. P., additional, Singh, A. K., additional, Knox, R. E., additional, Ammar, K., additional, Clarke, J. M., additional, Clarke, F. R., additional, Singh, R. P., additional, Pozniak, C. J., additional, DePauw, R. M., additional, McCallum, B. D., additional, Cuthbert, R. D., additional, Randhawa, H. S., additional, and Fetch, T. G., additional

Published
2012
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32. New breeding tools impact Canadian commercial farmer fields

Author

DePAUW, R.M., primary, KNOX, R.E., additional, HUMPHREYS, D.G., additional, THOMAS, J.B., additional, FOX, S.L., additional, BROWN, P.D., additional, SINGH, A.K., additional, POZNIAK, C., additional, RANDHAWA, H.S., additional, FOWLER, D.B., additional, GRAF, R.J., additional, and HUCL, P., additional

Published
2011
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42. Mapping QTL, Selection Differentials, and the Effect of Rht-B1 under Organic and Conventionally Managed Systems in the Attila × CDC Go Spring Wheat Mapping Population.

Author

Asif, M., Yang, R.-C., Navabi, A., Iqbal, M., Kamran, A., Lara, E. P., Randhawa, H., Pozniak, C., and Spaner, D.

Subjects
WHEAT hybridization, PLANT gene mapping, PLANT selection, WHEAT genetics, GENETIC engineering of crops, INBREEDING, AGRONOMY, PLANTS
Abstract

A randomly derived recombinant inbred line (RIL) population (n = 163) from a cross between CIMMYT spring wheat 'Attila' and the Canadian 'CDC Go' was used to map quantitative trait loci (QTL) affecting various agronomic and quality traits. The experiment was also designed to investigate the feasibility of organic wheat breeding by determining selection differentials and the effect of Rht-B1 in paired organic and conventional management systems. Heritability estimates differed between systems for five of nine traits measured; including grain yield, number of tillers, plant height, kernel weight, and grain protein content. Direct selection in each management system resulted in 50% or fewer selected individuals in common between the two systems, for eight of the nine (except for flowering time) studied traits. Most QTL were specific to either the organic or the conventional management system. However, consistent QTL for grain yield, grain volume weight, kernel weight, and days to flowering were mapped in both systems on chromosomes 6A, 1B, 3A, and 5B, respectively. The effect of Rht-B1 was more pronounced in organic systems, where RILs carrying the wild-type allele were taller, produced more grain yield with higher grain protein content, and suppressed weed biomass to a greater extent than those carrying dwarfing alleles. Results of the present study suggest that differences exist between the two management systems for QTL effects. Indirect selection of superior genotypes from one system to another will not result in the advancement of the best possible genotypes. Therefore, selection of spring wheat cultivars for organic systems should be conducted on organically managed lands. [ABSTRACT FROM AUTHOR]

Published
2015
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48. 100 Years of Excellence in Grain Research.

Author

Burnett, Peter A., Clarke, J., Pozniak, C., Rossnagel, B., and Fetch, T.

Subjects
GOVERNMENT laboratories, GRAIN research, GRAIN trade, ANNIVERSARIES
Abstract

The article discusses the history, achievements and future plans of the Canadian Grain Commission's Grain Research Laboratory which is celebrating its 100th anniversary this 2014. Topics discussed include the image of the Canadian Grain Commission as the country's scientific organization on grain quality, function of the Harvest Sample Program, and research programs of the Grain Research Laboratory. Also highlighted is the contribution of the laboratory to the Canadian grain industry.

Published
2014
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49. Mapping QTL, Selection Differentials, and the Effect of Rht‐B1under Organic and Conventionally Managed Systems in the Attila × CDC Go Spring Wheat Mapping Population

Author

Asif, M., Yang, R.‐C., Navabi, A., Iqbal, M., Kamran, A., Lara, E. P., Randhawa, H., Pozniak, C., and Spaner, D.

Abstract

A randomly derived recombinant inbred line (RIL) population (n= 163) from a cross between CIMMYT spring wheat ‘Attila’ and the Canadian ‘CDC Go’ was used to map quantitative trait loci (QTL) affecting various agronomic and quality traits. The experiment was also designed to investigate the feasibility of organic wheat breeding by determining selection differentials and the effect of Rht‐B1in paired organic and conventional management systems. Heritability estimates differed between systems for five of nine traits measured; including grain yield, number of tillers, plant height, kernel weight, and grain protein content. Direct selection in each management system resulted in 50% or fewer selected individuals in common between the two systems, for eight of the nine (except for flowering time) studied traits. Most QTL were specific to either the organic or the conventional management system. However, consistent QTL for grain yield, grain volume weight, kernel weight, and days to flowering were mapped in both systems on chromosomes 6A, 1B, 3A, and 5B, respectively. The effect of Rht‐B1was more pronounced in organic systems, where RILs carrying the wild‐type allele were taller, produced more grain yield with higher grain protein content, and suppressed weed biomass to a greater extent than those carrying dwarfing alleles. Results of the present study suggest that differences exist between the two management systems for QTL effects. Indirect selection of superior genotypes from one system to another will not result in the advancement of the best possible genotypes. Therefore, selection of spring wheat cultivars for organic systems should be conducted on organically managed lands.

Published
2015
Full Text
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