Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Carolina Sansaloni (), Jorge Franco, Bruno Santos, Lawrence Percival-Alwyn, Sukhwinder Singh, Cesar Petroli, Jaime Campos, Kate Dreher, Thomas Payne, David Marshall, Benjamin Kilian, Iain Milne, Sebastian Raubach, Paul Shaw, Gordon Stephen, Jason Carling, Carolina Saint Pierre, Juan Burgueño, José Crosa, HuiHui Li, Carlos Guzman, Zakaria Kehel, Ahmed Amri, Andrzej Kilian, Peter Wenzl, Cristobal Uauy, Marianne Banziger, Mario Caccamo and Kevin Pixley
Additional contact information
Carolina Sansaloni: International Maize and Wheat Improvement Center (CIMMYT)
Jorge Franco: Facultad de agronomía, Universidad de la República
Bruno Santos: NIAB
Lawrence Percival-Alwyn: NIAB
Sukhwinder Singh: International Maize and Wheat Improvement Center (CIMMYT)
Cesar Petroli: International Maize and Wheat Improvement Center (CIMMYT)
Jaime Campos: International Maize and Wheat Improvement Center (CIMMYT)
Kate Dreher: International Maize and Wheat Improvement Center (CIMMYT)
Thomas Payne: International Maize and Wheat Improvement Center (CIMMYT)
David Marshall: The James Hutton Institute
Benjamin Kilian: Global Crop Diversity Trust
Iain Milne: The James Hutton Institute
Sebastian Raubach: The James Hutton Institute
Paul Shaw: The James Hutton Institute
Gordon Stephen: The James Hutton Institute
Jason Carling: Diversity Arrays Technology, Building 3, Level D, University of Canberra
Carolina Saint Pierre: International Maize and Wheat Improvement Center (CIMMYT)
Juan Burgueño: International Maize and Wheat Improvement Center (CIMMYT)
José Crosa: International Maize and Wheat Improvement Center (CIMMYT)
HuiHui Li: International Maize and Wheat Improvement Center (CIMMYT)
Carlos Guzman: Departamento de Genética Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba
Zakaria Kehel: International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat
Ahmed Amri: International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat
Andrzej Kilian: Diversity Arrays Technology, Building 3, Level D, University of Canberra
Peter Wenzl: International Center for Tropical Agriculture (CIAT)
Cristobal Uauy: John Innes Centre, Norwich Research Park
Marianne Banziger: International Maize and Wheat Improvement Center (CIMMYT)
Mario Caccamo: NIAB
Kevin Pixley: International Maize and Wheat Improvement Center (CIMMYT)

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.

Date: 2020
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DOI: 10.1038/s41467-020-18404-w

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