Durum wheat genome highlights past domestication signatures and future improvement targets

Marco Maccaferri(Cereal Research Centre), Neil S. Harris(University of Alberta), Sven Twardziok(Helmholtz Zentrum München), Raj Pasam(Agriculture Victoria), Heidrun Gundlach(Helmholtz Zentrum München), M. Spannagl(Helmholtz Zentrum München), Danara Ormanbekova(Helmholtz Zentrum München), Thomas Lux(Helmholtz Zentrum München), Verena M. Prade(Helmholtz Zentrum München), Sara G. Milner(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Axel Himmelbach(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Martin Mascher(German Centre for Integrative Biodiversity Research), Paolo Bagnaresi(Institut thématique Génétique, génomique et bioinformatique), Primetta Faccioli(Institut thématique Génétique, génomique et bioinformatique), Paolo Cozzi(Institute of Agricultural Biology and Biotechnology), Massimiliano Lauria(Institute of Agricultural Biology and Biotechnology), Barbara Lazzari(Institute of Agricultural Biology and Biotechnology), Alessandra Stella(Institute of Agricultural Biology and Biotechnology), Andrea Manconi(Institute of Biomedical Technologies), Matteo Gnocchi(Institute of Biomedical Technologies), Marco Moscatelli(Institute of Biomedical Technologies), Raz Avni(Tel Aviv University), Jasline Deek(Tel Aviv University), Sezgi Biyiklioglu(Montana State University), Elisabetta Frascaroli(University of Bologna), Simona Corneti(University of Bologna), Silvio Salvi(University of Bologna), Gabriella Sonnante(Institute of Biosciences and Bioresources), Francesca Desiderio(Institut thématique Génétique, génomique et bioinformatique), Caterina Marè(Institut thématique Génétique, génomique et bioinformatique), Cristina Crosatti(Institut thématique Génétique, génomique et bioinformatique), Erica Mica(Institut thématique Génétique, génomique et bioinformatique), Hakan Özkan(Cukurova University), Benjamin Kilian(Global Crop Diversity Trust), Pasquale De Vita(Cereal Research Centre), Daniela Marone(Cereal Research Centre), Reem Joukhadar(La Trobe University), Elisabetta Mazzucotelli(Institut thématique Génétique, génomique et bioinformatique), Domenica Nigro(University of Bari Aldo Moro), Ágata Gadaleta(University of Bari Aldo Moro), Shiaoman Chao(Agricultural Research Service), Justin D. Faris(Agricultural Research Service), Arthur Melo(University of New Hampshire), Mike Pumphrey(Washington State University), Nicola Pecchioni(Cereal Research Centre), Luciano Milanesi(Institute of Biomedical Technologies), Krystalee Wiebe(University of Saskatchewan), Jennifer Ens(University of Saskatchewan), Ron MacLachlan(University of Saskatchewan), J. M. Clarke(University of Saskatchewan), Andrew Sharpe(University of Saskatchewan), ChuShin Koh(University of Saskatchewan), Kevin Y. H. Liang(University of Alberta), Gregory J. Taylor(University of Alberta), R. E. Knox(Agriculture and Agri-Food Canada), Hikmet Budak(Montana State University), Anna Maria Mastrangelo(Cereal Research Centre), Steven S. Xu(Agricultural Research Service), Nils Stein(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Iago Hale(University of New Hampshire), Assaf Distelfeld(Tel Aviv University), Matthew Hayden(La Trobe University), Roberto Tuberosa(University of Bologna), Sean Walkowiak(University of Saskatchewan), Klaus Mayer(Helmholtz Zentrum München), Aldo Ceriotti(Institute of Agricultural Biology and Biotechnology), Curtis Pozniak(University of Saskatchewan), Luigi Cattivelli(Forestry Research Centre)
Nature Genetics
April 8, 2019
10.1038/s41588-019-0381-3
Cited by 820Open Access
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Abstract

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.

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