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

Carolina Sansaloni; Bruno Santos; Lawrence Percival-Alwyn; Sukhwinder Singh; Cesar Petroli; Kate  Dreher; Thomas Payne; David Marshall; Benjamin Kilian; Iain Milne; Sebastian Raubach; Paul D Shaw; Gordon Stephen; Jason Carling; Carolina  Saint Pierre; Juan Burgueno; Jose Crosa; HuiHui Li; Carlos Guzman; Zacharia 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^*, Bruno Santos, Lawrence Percival-Alwyn, Sukhwinder Singh, Cesar Petroli, Kate Dreher, Thomas Payne, David Marshall, Benjamin Kilian, Iain Milne, Sebastian Raubach, Paul D Shaw, Gordon Stephen, Jason Carling, Carolina Saint Pierre, Juan Burgueno, Jose Crosa, HuiHui Li, Carlos Guzman, Zacharia KehelAhmed Amri, Andrzej Kilian, Peter Wenzl, Cristobal Uauy, Marianne Banziger, Mario Caccamo, Kevin Pixley

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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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.

Original language	English
Article number	4572
Journal	Nature Communications
Volume	11
Early online date	11 Sept 2020
DOIs	https://doi.org/10.1038/s41467-020-18404-w
Publication status	First published - 11 Sept 2020
Externally published	Yes

Keywords

Alleles
Domestication
Genetic Variation
Genome, Plant
Genotype
Models, Genetic
Polymorphism, Single Nucleotide
Sequence Alignment
Tetraploidy
Triticum/genetics

UN SDGs

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

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s41467-020-18404-wFinal published version, 2.66 MBLicence: CC BY

Cite this

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

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

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.",

keywords = "Alleles, Domestication, Genetic Variation, Genome, Plant, Genotype, Models, Genetic, Polymorphism, Single Nucleotide, Sequence Alignment, Tetraploidy, Triticum/genetics",

author = "Carolina Sansaloni and Bruno Santos and Lawrence Percival-Alwyn and Sukhwinder Singh and Cesar Petroli and Kate Dreher and Thomas Payne and David Marshall and Benjamin Kilian and Iain Milne and Sebastian Raubach and Shaw, {Paul D} and Gordon Stephen and Jason Carling and {Saint Pierre}, Carolina and Juan Burgueno and Jose Crosa and HuiHui Li and Carlos Guzman and Zacharia Kehel and Ahmed Amri and Andrzej Kilian and Peter Wenzl and Cristobal Uauy and Marianne Banziger and Mario Caccamo and Kevin Pixley",

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doi = "10.1038/s41467-020-18404-w",

language = "English",

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Sansaloni, C, Santos, B, Percival-Alwyn, L, Singh, S, Petroli, C, Dreher, K, Payne, T, Marshall, D, Kilian, B, Milne, I, Raubach, S, Shaw, PD, Stephen, G, Carling, J, Saint Pierre, C, Burgueno, J, Crosa, J, Li, H, 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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AU - Sansaloni, Carolina

AU - Santos, Bruno

AU - Percival-Alwyn, Lawrence

AU - Singh, Sukhwinder

AU - Petroli, Cesar

AU - Dreher, Kate

AU - Payne, Thomas

AU - Marshall, David

AU - Kilian, Benjamin

AU - Milne, Iain

AU - Raubach, Sebastian

AU - Shaw, Paul D

AU - Stephen, Gordon

AU - Carling, Jason

AU - Saint Pierre, Carolina

AU - Burgueno, Juan

AU - Crosa, Jose

AU - Li, HuiHui

AU - Guzman, Carlos

AU - Kehel, Zacharia

AU - Amri, Ahmed

AU - Kilian, Andrzej

AU - Wenzl, Peter

AU - Uauy, Cristobal

AU - Banziger, Marianne

AU - Caccamo, Mario

AU - Pixley, Kevin

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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 - Alleles

KW - Domestication

KW - Genetic Variation

KW - Genome, Plant

KW - Genotype

KW - Models, Genetic

KW - Polymorphism, Single Nucleotide

KW - Sequence Alignment

KW - Tetraploidy

KW - Triticum/genetics

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U2 - 10.1038/s41467-020-18404-w

DO - 10.1038/s41467-020-18404-w

M3 - Article

C2 - 32917907

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

UN SDGs

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