February 20, 2024  |  Agrigenomics

De novo annotation of the wheat pan-genome reveals complexity and diversity within the hexaploid wheat pan-transcriptome

Authors: Benjamen White1, Thomas Lux2, Rachel L Rusholme-Pilcher1†, Angéla Juhász6†, Gemy Kaithakottil1, Susan Duncan13, James Simmonds3, Hannah Rees1, Jonathan Wright1, Joshua Colmer1, Sabrina Ward1, Ryan Joynson14, Benedict Coombes1, Naomi Irish1, Suzanne Henderson1, Tom Barker1, Helen Chapman1, Leah Catchpole1, Karim Gharbi1, Moeko Okada51617, Hirokazu Handa18, Shuhei Nasuda19, Kentaro K. Shimizu516, Heidrun Gundlach2, Daniel Lang2, Guy Naamati7, Erik J. Legg8, Arvind K. Bharti8, Michelle L. Colgrave69, Wilfried Haerty1, Cristobal Uauy3, David Swarbreck1, Philippa Borrill3, Jesse A. Poland10, Simon Krattinger10, Nils Stein1115, Klaus F.X. Mayer212, Curtis Pozniak13, 10+ Wheat Genome Project, Manuel Spannagl2* and Anthony Hall114* 1) Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK 2) PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Researc h Center for Environmental Health, Neuherberg, Germany 3) John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK 4) Limagrain Europe, Clermont-Ferrand, Auvergne-Rhône-Alpes, France 5) Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland 6) Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, 6027, Australia 7) EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK 8) Syngenta Crop Protection, Research Triangle Park, NC, USA 9) CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia 10) Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia 11) Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany 12) School of Life Sciences, Technical University Munich, Freising, Germany 13) Crop Development Centre, The University of Saskatchewan, Saskatoon, Canada 14) School of Biological Sciences, University of East Anglia, Norwich, UK 15) Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany 16) Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan 17) Graduate School of Science and Technology, Niigata University, Niigata, Japan 18) Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan 19) Graduate School of Agriculture, Kyoto University, Kyoto, Japan

Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled the genomes of 15 wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for nine of these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of these de novo annotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homoeologous genes, but also widespread changes in sub-genome homoeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homoeolog expression and identified tissue-associated cultivar-specific expression profiles. In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.

Journal: Biorxiv
DOI: 10.1101/2024.01.09.574802
Year: 2024

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