The transcriptional landscape of polyploid wheat

Autor: Christopher J. Ridout, Henk-jan Schoonbeek, F. van Ex, Caroline Juery, Jemima Brinton, Yogendra Khedikar, Brande B. H. Wulff, Mark W. Davey, Andrew G. Sharpe, Aron T. Cory, Nicholas J. Provart, Burkhard Steuernagel, Daniel Lang, Asher Pasha, Cristobal Uauy, David Latrasse, Daoquan Xiang, Luca Venturini, Andrea Bräutigam, Ricardo H. Ramirez-Gonzalez, Manuel Spannagl, Sophie A. Harrington, Raju Datla, Lorenzo Concia, Abdelhafid Bendahmane, Moussa Benhamed, Rudi Appels, Vijay K. Tiwari, Curtis J. Pozniak, Tobin Florio, Klaus F. X. Mayer, Stephen J. Robinson, Boulos Chalhoub, Etienne Paux, John Jacobs, Frédéric Choulet, Philippa Borrill
Přispěvatelé: John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Earlham Institute, Norwich Research Park, Innovation Center®, Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Saskatoon Research and Development Centre, Agriculture and Agri-Food (AAFC), University of Saskatchewan [Saskatoon] (U of S), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Aquatic and Crop Resource Development, National Research Council of Canada (NRC), Institut National de la Recherche Agronomique (INRA), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), School of Biosciences, University of Birmingham [Birmingham], AgriBio, School of Veterinary and Life Sciences, Murdoch University, University of Maryland [College Park], University of Maryland System, Global Institute for Food Security, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Agriculture and Agri-Food [Ottawa] (AAFC), University of Saskatchewan
Jazyk: angličtina
Rok vydání: 2018
Předmět:
Zdroj: Science
Science, 2018, 361 (6403), pp.eaar6089. ⟨10.1126/science.aar6089⟩
Science, American Association for the Advancement of Science, 2018, 361 (6403), pp.eaar6089. ⟨10.1126/science.aar6089⟩
ISSN: 0036-8075
1095-9203
Popis: Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.; International audience; The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.nonbalanced expression patterns, with higher or lower expression from a single homoeolog with respect to the other two. These differences between homoeologs were associated with epigenetic changes affecting DNA methylation and histone modifications. Although nonbalanced homoeolog expression could be partially predicted by expression in diploid ancestors, large changes in relative homoeolog expression were observed owing to polyploidization. Our results suggest that the transposable elements in promoters relate more closely to the variation in the relative expression of homoeologs across tissues than to a ubiquitous effect across all tissues. We found that homoeologs with the highest inter-tissue variation had promoters with more frequent transposable element insertions and more varied cis-regulatory elements than homoeologs that were stable across tissues. We also identified expression asymmetry along wheat chromosomes. Homoeologs with the largest inter-tissue, inter-cultivar, and coding sequence variation were most often located in the highly recombinogenic distal ends of chromosomes. These transcriptionally dynamic homoeologs are under more relaxed selection pressure, potentially representing the first steps toward functional innovation through neo- or subfunctionalization. We generated tissue- and stress-specific coexpression networks that reveal extensive coordination of homoeolog expression throughout development. These networks, alongside detailed gene expression atlases (www.wheat-expression.com and http://bar.utoronto.ca), lay the groundwork to identify candidate genes influencing agronomic traits in wheat. CONCLUSION This study provides detailed insights into the transcriptional landscape of bread wheat, an evolutionarily young polyploid. Our work shows that homoeolog expression patterns in bread wheat have been shaped by polyploidy and are associated with both epigenetic modifications and variation in transposable elements within promoters of homoeologous genes. The extensive datasets and analyses presented here provide a framework that can help researchers and breeders develop strategies to improve crops by manipulating individual or multiple homoeologs to modulate trait responses.
Databáze: OpenAIRE
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