Durum wheat genome highlights past domestication signatures and future improvement targets

Marco Maccaferri, Neil S. Harris, Sven O. Twardziok, Raj K. Pasam, Heidrun Gundlach, Manuel Spannagl, Danara Ormanbekova, Thomas Lux, Verena M. Prade, Sara G. Milner, Axel Himmelbach, Martin Mascher, Paolo Bagnaresi, Primetta Faccioli, Paolo Cozzi, Massimiliano Lauria, Barbara Lazzari, Alessandra Stella, Andrea Manconi, Matteo GnocchiMarco Moscatelli, Raz Avni, Jasline Deek, Sezgi Biyiklioglu, Elisabetta Frascaroli, Simona Corneti, Silvio Salvi, Gabriella Sonnante, Francesca Desiderio, Caterina Marè, Cristina Crosatti, Erica Mica, Hakan Özkan, Benjamin Kilian, Pasquale De Vita, Daniela Marone, Reem Joukhadar, Elisabetta Mazzucotelli, Domenica Nigro, Agata Gadaleta, Shiaoman Chao, Justin D. Faris, Arthur T.O. Melo, Mike Pumphrey, Nicola Pecchioni, Luciano Milanesi, Krystalee Wiebe, Jennifer Ens, Ron P. MacLachlan, John M. Clarke, Andrew G. Sharpe, Chu Shin Koh, Kevin Y.H. Liang, Gregory J. Taylor, Ron Knox, Hikmet Budak, Anna M. Mastrangelo, Steven S. Xu, Nils Stein, Iago Hale, Assaf Distelfeld, Matthew J. Hayden, Roberto Tuberosa, Sean Walkowiak, Klaus F.X. Mayer, Aldo Ceriotti, Curtis J. Pozniak, Luigi Cattivelli

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)885-895
Number of pages11
JournalNature Genetics
Volume51
Issue number5
DOIs
StatePublished - 1 May 2019
Externally publishedYes

Bibliographical note

Funding Information:
We acknowledge the funding support of: the Italian Ministry of Education and Research with projects CNR Flagship InterOmics PB05 (L.M., A.C., G.S.), PON ELIXIR CNR-BiOmics PIR01_00017 (L.M., M.G., M.Mo.) and PON ISCOCEM (P.D.); CREA project Interomics (L.C.); Fondazione in rete per la ricerca agroalimentare AGER project From Seed to Pasta (R.T.); FP7-KBBE Project DROPS ID244347 (R.T.); Genome Canada (A.G.S., C.P.); the Western Grain Research Foundation (A.G.S., C.P.); the Manitoba Wheat and Barley Commission (A.G.S., C.P.); the Saskatchewan Wheat Development Commission (A.G.S., C.P.); the Alberta Wheat Development Commission (A.G.S., C.P.); the Saskatchewan Ministry of Agriculture (A.G.S., C.P.); the administrative support of Genome Prairie (A.G.S., C.P.); Canadian Triticum Applied Genomics -CTAG2-(A.G.S., C.P.); Binational Science Foundation grant no. 2015409 (I.H., A.D.); Israel Science Foundation grant no. 1137/17 (A.D.); USDA-Agricultural Research Service Current Research Information System project 3060-21000-038-00-D (J.D.F., S.S.X.); German Federal Ministry of Food and Agriculture grant no. 2819103915 (N.S., K.F.X.M.); German Ministry of Education and Research grant no. 031A536 (K.F.X.M.); and Natural Sciences and Engineering Council of Canada grant nos. SPG 336119-06 and RGPIN 92787 (G.J.T., C.P.). The authors are grateful to E. Elias (North Dakota State University) for providing nine DW cultivars, included in the Global Tetraploid Wheat Collection and E. Scarpella (University of Alberta, Edmonton, Canada) for assistance with confocal microscopy.

Publisher Copyright:
© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.

ASJC Scopus subject areas

  • Genetics

Fingerprint

Dive into the research topics of 'Durum wheat genome highlights past domestication signatures and future improvement targets'. Together they form a unique fingerprint.

Cite this