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2. A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes

Author

Püpke Marone, Marina, Singh, Harmeet Chawla, Pozniak, Curtis, Mascher, Martin, and University of Manitoba

Subjects
Genetics, Plant Science, Pangenome, Genetic map, Long-read sequence assembly, Genome sequence assembly, Chromosome conformation capture sequencing, Biotechnology
Abstract

Background As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects. Results We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive. Conclusion Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/. The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly.

Published
2022

3. Global Wheat Head Dataset 2021: more diversity to improve the benchmarking of wheat head localization methods

Author

David, Etienne, Serouart, Mario, Smith, Daniel, Madec, Simon, Velumani, Kaaviya, Liu, Shouyang, Wang, Xu, Espinosa, Francisco Pinto, Shafiee, Shahameh, Tahir, Izzat S. A., Tsujimoto, Hisashi, Nasuda, Shuhei, Zheng, Bangyou, Kichgessner, Norbert, Aasen, Helge, Hund, Andreas, Sadhegi-Tehran, Pouria, Nagasawa, Koichi, Ishikawa, Goro, Dandrifosse, Sébastien, Carlier, Alexis, Mercatoris, Benoit, Kuroki, Ken, Wang, Haozhou, Ishii, Masanori, Badhon, Minhajul A., Pozniak, Curtis, LeBauer, David Shaner, Lilimo, Morten, Poland, Jesse, Chapman, Scott, de Solan, Benoit, Baret, Frédéric, Stavness, Ian, and Guo, Wei

Subjects
FOS: Computer and information sciences, Computer Vision and Pattern Recognition (cs.CV), Computer Science - Computer Vision and Pattern Recognition
Abstract

The Global Wheat Head Detection (GWHD) dataset was created in 2020 and has assembled 193,634 labelled wheat heads from 4,700 RGB images acquired from various acquisition platforms and 7 countries/institutions. With an associated competition hosted in Kaggle, GWHD has successfully attracted attention from both the computer vision and agricultural science communities. From this first experience in 2020, a few avenues for improvements have been identified, especially from the perspective of data size, head diversity and label reliability. To address these issues, the 2020 dataset has been reexamined, relabeled, and augmented by adding 1,722 images from 5 additional countries, allowing for 81,553 additional wheat heads to be added. We now release a new version of the Global Wheat Head Detection (GWHD) dataset in 2021, which is bigger, more diverse, and less noisy than the 2020 version. The GWHD 2021 is now publicly available at http://www.global-wheat.com/ and a new data challenge has been organized on AIcrowd to make use of this updated dataset., Comment: 8 pages, 2 figures, 1 table

Published
2021
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4. 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
Internationality, Insecta, DNA Copy Number Variations, General Science & Technology, Acclimatization, Centromere, NLR Proteins, Genetic Introgression, Polyploidy, Genetics, Animals, Polymorphism, Triticum, Plant Proteins, Plant Diseases, Genome, Human Genome, Chromosome Mapping, Molecular, Genetic Variation, Genomics, Single Nucleotide, Plant, Plant Breeding, Haplotypes, Genes, DNA Transposable Elements, Edible Grain, Cloning, Biotechnology
Abstract

Advances in genomics have expeditedthe 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

5. Additional file 1 of Evaluation of variant calling tools for large plant genome re-sequencing

Author

Yao, Zhen, You, Frank M., Amidou N’Diaye, Knox, Ron E., McCartney, Curt, Hiebert, Colin W., Pozniak, Curtis, and Xu, Wayne

Abstract

Additional file: Supplementary material file: detailed information. Supplementary Fig. S1. Venn diagrams for SNP calls on different preprocessed read sets. Supplementary Fig. S2. Venn diagram for SNP calls on differently mapped reads. Supplementary Fig. S3. Receiver operating characteristic curve (ROC) comparison of variant calling tools. Supplementary Fig. S4. Performance comparison of read mapping tools in terms of variant calling. Supplementary Fig. S5. Performance comparison of data preprocesses in terms of variant calling. Supplementary Table S1. Statistics of short read mapping by different mapping tools. Supplementary Table S2. Numbers of SNP calls of seven variant calling tools with default and post-filtering criteria. Supplementary Data 1. Data_1_FreeBayes.6.f.vcf.gz. Six VCF files generated by FreeBayes calling tool from alignment data of three sets (raw, trim, and rep1) and two mapping tools (BWA-mem and Bowtie2). Supplementary Data 2. Data_2_GATK.6.f.vcf.gz. Six VCF files generated by GATK calling tool from alignment data of three sets (raw, trim, and rep1) and two mapping tools (BWA-mem and Bowtie2). Supplementary Data 3. Data_3_Platypus.6.f.vcf.gz. Six VCF files generated by Platypus calling tool from alignment data of three sets (raw, trim, and rep1) and two mapping tools (BWA-mem and Bowtie2). Supplementary Data 4. Data_4_Samtools.6.f.vcf.gz. Six VCF files generated by Samtools/mpileup calling tool from alignment data of three sets (raw, trim, and rep1) and two mapping tools (BWA-mem and Bowtie2). Supplementary Data 5. Data_5_SNVer.6.f.vcf.gz. Six VCF files generated by SNVer calling tool from alignment data of three sets (raw, trim, and rep1) and two mapping tools (BWA-mem and Bowtie2). The VCF file has been filtered by criteria described in text. Supplementary Data 6. Data_6_VarDict.6.f.vcf.gz. Six VCF files generated by VarDict calling tool from alignment data of three sets (raw, trim, and rep1) and two mapping tools (BWA-mem and Bowtie2). Supplementary Data 7. Data_7_VarScan.6.f.vcf.gz. Six VCF files generated by VarScan calling tool from alignment data of three sets (raw, trim, and rep1) and two mapping tools (BWA-mem and Bowtie2).

Published
2020
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6. Additional file 1: of Genetic factors affecting Fusarium head blight resistance improvement from introgression of exotic Sumai 3 alleles (including Fhb1, Fhb2, and Fhb5) in hard red spring wheat

Author

Gurcharn Brar, Brûlé-Babel, Anita, Yuefeng Ruan, Henriquez, Maria, Pozniak, Curtis, Kutcher, Hadley, and Hucl, Pierre

Subjects
food and beverages, health care economics and organizations
Abstract

Protocol #1.Procedure for Neogen enzyme linked immune-sorbent aasay (ELISA) for deoxynivalenol (DON) quantification in Fusarium head blight infected grains. Table S1. Proportions of the recurrent parent (RP) and donor parent (DP) genomes in the near-isogenic lines for CDC Go and CDC Alsask streams based on 81,587 SNP markers from 90 K iSelect assay. Here: A, B, H, U represent recurrent parent, donor parent, heterozygous, and unknown alleles, respectively. Figure S1. Polymorphism in CDC Go and CDC Alsask near-isogenic lines (NILs). Figure S2. Polymorphism in CDC Alsask near-isogenic lines on Chromosomes other than 3B, 5A, 6B. Figure S3. Polymorphism in CDC Go near-isogenic lines on Chromosomes other than 3B, 5A, 6B. Figure S4. GGE Biplots for CDC Go and CDC Alsask near-isogenic lines (NILs). (DOCX 1474 kb)

Published
2019
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8. MOESM1 of TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Author

CéCile Monat, Sudharsan Padmarasu, Lux, Thomas, Wicker, Thomas, Gundlach, Heidrun, Himmelbach, Axel, Ens, Jennifer, Chengdao Li, Muehlbauer, Gary, Schulman, Alan, Waugh, Robbie, Braumann, Ilka, Pozniak, Curtis, Scholz, Uwe, Mayer, Klaus, Spannagl, Manuel, Stein, Nils, and Mascher, Martin

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, ComputingMilieux_COMPUTERSANDEDUCATION, Data_FILES, ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract

Additional file 1. Supplementary Tables and Figures.

Published
2019
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9. Additional file 1: of MeioCapture: an efficient method for staging and isolation of meiocytes in the prophase I sub-stages of meiosis in wheat

Author

Shunmugam, Arun, Bollina, Venkatesh, Dukowic-Schulze, Stefanie, Bhowmik, Pankaj, Ambrose, Chris, Higgins, James, Pozniak, Curtis, Sharpe, Andrew, Rozwadowski, Kevin, and Sateesh Kagale

Abstract

Figure S1. Transmission electron microscopy images of ultra-thin sections of Chinese Spring wheat anthers varying in length from 0.5 to 1.4 mm. Scale bar = 50 μm. (PDF 570 kb)

Published
2018
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10. Additional file 2: Figure S1. of Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16

Author

Mulualem Kassa, You, Frank, Hiebert, Colin, Pozniak, Curtis, Fobert, Pierre, Sharpe, Andrew, Menzies, James, D. Humphreys, Harrison, Nicole Rezac, Fellers, John, McCallum, Brent, and McCartney, Curt

Abstract

Genotyping profile of the KASP markers (A) 2BS-5194460_kwm747, (B) 2BS-5192454_kwm677, (C) 2BS-5175914_kwm847, (D) 2BS-5175914_kwm849, (E) 2BS-5203447_kwm742, and (F) BS00108724_kwm461 tested on homozygous Lr16 carriers, homozygous susceptible wheats, and heterozygous plants to show the diagnostic potential of the KASP assays to distinguish between heterozygous and homozygous samples. (PPTX 826 kb)

Published
2017
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11. 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
Genome, Genotype, Bioinformatics, Human Genome, Chromosome Mapping, Plant, Single Nucleotide, Biological Sciences, Chromosomes, Polyploidy, Gene Frequency, Haplotypes, Genetic, Information and Computing Sciences, Genetics, 2.1 Biological and endogenous factors, Exome, Generic health relevance, Polymorphism, Aetiology, Selection, IWGS Consortium, Triticum, Environmental Sciences
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

12. 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
Genetic Markers, Genotyping, Technology, Genotype, Polyploid wheat, Medical and Health Sciences, Genetic diversity, Polyploidy, Gene Frequency, single nucleotide polymorphism, Genetics, Cluster Analysis, Polymorphism, Triticum, Alleles, Oligonucleotide Array Sequence Analysis, International Wheat Genome Sequencing Consortium, Genome, Human Genome, High-density map, food and beverages, Chromosome Mapping, Genetic Variation, Wheat iSelect array, Single Nucleotide, Plant, Biological Sciences, Genetic Loci, Biotechnology
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

13. Genome interplay in the grain transcriptome of hexaploid bread wheat

Author

Pfeifer, Matthias, Kugler, Karl, Sandve, Simen, Zhan, Bujie, Rudi, Heidi, Hvidsten, Torgeir, Mayer, Klaus, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam, Sourdille, Pierre, Endo, Takashi, 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, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, 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, Mikael, Keller, Beat, Praud, Sébastien, Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Norwegian University of Life Sciences (NMBU), University of Norway, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Norwegian Research Council 199387, Deutsche Forschungsgemeinschaft (DFG) SFB924, German Federal Ministry of Education and Research (BMBF), European Commission's 7th Framework Program, Plant Genome and Systems Biology (PGSB), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre for Integrative Genetics, Department of Chemistry, Biotechnology and Food Science, Eversole Associates, Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Bayer Crop Science, Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA, Partenaires INRAE, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Centre of the Region Haná for Biotechnological and Agricultural Research, Fraunhofer Institute for Intelligent Analysis and Information Systems (Fraunhofer IAIS), Fraunhofer (Fraunhofer-Gesellschaft), National Research Centre Plant Biotechnology, Dept Plant Pathol, Kansas State University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Bayer Cropscience, Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Chinese Academy of Agricultural Sciences (CAAS), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Natl Inst Agrobiol Sci, JST-CREST, Japan Science and Technology Agency, Global Institute of Food Security, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, The Sainsbury Laboratory [Norwich] (TSL), Genome Analysis Centre, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), European Synchrotron Radiation Facility (ESRF), German Research Center for Environmental Health - Helmholtz Center München (GmbH), MIPS/IBIS, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), DOE Joint Genome Institute [Walnut Creek], United States Department of Energy, The James Hutton Institute, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Fac Engn & Nat Sci, Sabanci University [Istanbul], Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, York University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for Comparative Genomics, Murdoch University, CUBE Division of Computational Systems Biology, University of Vienna [Vienna], Department of Plant Pathology, Shizuoka University, Diversity Arrays Technology Pty Ltd (DArT P/L), Centre de Recherche de Chappes, BIOGEMMA, Research Council of Norway [199387], German Research Foundation (DFG) [SFB924], German Federal Ministry of Education and Research (BMBF), European Project: 283496,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-2,TRANSPLANT(2011), Helmholtz-Zentrum München (HZM), Univ Saskatchewan, Dept Plant Sci, Saskatoon, SK, Canada, University of California [Riverside] (UCR), University of California-University of California, 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, University of Saskatchewan, John Innes Centre, and University of Zurich

Subjects
MESH: Genome, Plant, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, [SDV]Life Sciences [q-bio], Gene Dosage, 01 natural sciences, Genome, MESH: Gene Dosage, Endosperm, Transcriptome, Gene Expression Regulation, Plant, Triticum, Cancer, Plant Proteins, International Wheat Genome Sequencing Consortium, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, MESH: Plant Proteins, food and beverages, alignment, Bread, MESH: Edible Grain, starchy endosperm, reveals, Genome, Plant, Biotechnology, profiles, General Science & Technology, Cereals, MESH: Triticum, Biology, Gene dosage, MESH: Endosperm, Polyploidy, MESH: Bread, 03 medical and health sciences, Polyploid, MESH: Polyploidy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Gene Expression Regulation, Plant, Gene, Metabolic and endocrine, 030304 developmental biology, Whole genome sequencing, triticum, MESH: Transcriptome, Human Genome, Plant, Gene Expression Regulation, germination, gene expression, RNA, identification, Edible Grain, protein, 010606 plant biology & botany
Abstract

Allohexaploid bread wheat ( Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

Published
2014

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

Author

Mayer, Klaus F. X., Rogers, Jane, Jaroslav Dolezel, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J., Sourdille, Pierre, Endo, Takashi R., Kubalakova, Marie, Cihalikova, Jarmila, Dubska, Zdenka, Vrana, Jan, Sperkova, Romana, Simkova, Hana, Febrer, Melanie, Clissold, Leah, Mclay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K., Khurana, Jitendra, Akhunov, Eduard, Choulet, Frederic, Alberti, Adriana, Barbe, Valerie, 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 Rod, Lien, Sigbjorn, 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, Veronique, 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, Helene, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Francoise, Couderc, Loic, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikael, Keller, Beat, Praud, Sebastien, and IWGSC

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