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; Hui Hui Li; Carlos Guzman; Zakaria Kehel; Ahmed Amri; Andrzej Kilian; Peter Wenzl; Cristobal Uauy; Marianne Banziger; Mario Caccamo; Kevin Pixley

doi:10.1038/s41467-020-18404-w

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

Carolina Sansaloni (Lead / Corresponding author), 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, Hui Hui LiCarlos Guzman, Zakaria Kehel, Ahmed Amri, Andrzej Kilian, Peter Wenzl, Cristobal Uauy, Marianne Banziger, Mario Caccamo, Kevin Pixley

DArcy Thompson Unit

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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 DArTseq^TM 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.

Original language	English
Article number	4572
Number of pages	12
Journal	Nature Communications
Volume	11
DOIs	https://doi.org/10.1038/s41467-020-18404-w
Publication status	Published - 11 Sept 2020

Keywords

Agricultural genetics
Genetic markers
Genetic variations
Plant breeding

ASJC Scopus subject areas

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General Physics and Astronomy

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41467-020-18404-wLicence: CC BY

Final Published VersionFinal published version, 2.66 MBLicence: CC BY

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Sansaloni, C., Franco, J., Santos, B., Percival-Alwyn, L., Singh, S., Petroli, C., Campos, J., Dreher, K., Payne, T., Marshall, D., Kilian, B., Milne, I., Raubach, S., Shaw, P., Stephen, G., Carling, J., Pierre, C. S., Burgueño, J., Crosa, J., ... Pixley, K. (2020). Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nature Communications, 11, Article 4572. https://doi.org/10.1038/s41467-020-18404-w

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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.",

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Sansaloni, C, Franco, J, Santos, B, Percival-Alwyn, L, Singh, S, Petroli, C, Campos, J, Dreher, K, Payne, T, Marshall, D, Kilian, B, Milne, I, Raubach, S, Shaw, P, Stephen, G, Carling, J, Pierre, CS, Burgueño, J, Crosa, J, Li, HH, Guzman, C, Kehel, Z, Amri, A, Kilian, A, Wenzl, P, Uauy, C, Banziger, M, Caccamo, M & Pixley, K 2020, 'Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints', Nature Communications, vol. 11, 4572. https://doi.org/10.1038/s41467-020-18404-w

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T1 - Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

AU - Sansaloni, Carolina

AU - Franco, Jorge

AU - Santos, Bruno

AU - Percival-Alwyn, Lawrence

AU - Singh, Sukhwinder

AU - Petroli, Cesar

AU - Campos, Jaime

AU - Dreher, Kate

AU - Payne, Thomas

AU - Marshall, David

AU - Kilian, Benjamin

AU - Milne, Iain

AU - Raubach, Sebastian

AU - Shaw, Paul

AU - Stephen, Gordon

AU - Carling, Jason

AU - Pierre, Carolina Saint

AU - Burgueño, Juan

AU - Crosa, José

AU - Li, Hui Hui

AU - Guzman, Carlos

AU - Kehel, Zakaria

AU - Amri, Ahmed

AU - Kilian, Andrzej

AU - Wenzl, Peter

AU - Uauy, Cristobal

AU - Banziger, Marianne

AU - Caccamo, Mario

AU - Pixley, Kevin

PY - 2020/9/11

Y1 - 2020/9/11

N2 - 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.

AB - 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.

KW - Agricultural genetics

KW - Genetic markers

KW - Genetic variations

KW - Plant breeding

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U2 - 10.1038/s41467-020-18404-w

DO - 10.1038/s41467-020-18404-w

M3 - Article

C2 - 32917907

AN - SCOPUS:85090762773

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

M1 - 4572

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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