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Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization

Array-based single nucleotide polymorphism (SNP) genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical...

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Autores principales: Keeble-Gagnère, Gabriel, Pasam, Raj, Forrest, Kerrie L., Wong, Debbie, Robinson, Hannah, Godoy, Jayfred, Rattey, Allan, Moody, David, Mullan, Daniel, Walmsley, Tresslyn, Daetwyler, Hans D., Tibbits, Josquin, Hayden, Matthew J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728019/
https://www.ncbi.nlm.nih.gov/pubmed/35003156
http://dx.doi.org/10.3389/fpls.2021.756877
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author Keeble-Gagnère, Gabriel
Pasam, Raj
Forrest, Kerrie L.
Wong, Debbie
Robinson, Hannah
Godoy, Jayfred
Rattey, Allan
Moody, David
Mullan, Daniel
Walmsley, Tresslyn
Daetwyler, Hans D.
Tibbits, Josquin
Hayden, Matthew J.
author_facet Keeble-Gagnère, Gabriel
Pasam, Raj
Forrest, Kerrie L.
Wong, Debbie
Robinson, Hannah
Godoy, Jayfred
Rattey, Allan
Moody, David
Mullan, Daniel
Walmsley, Tresslyn
Daetwyler, Hans D.
Tibbits, Josquin
Hayden, Matthew J.
author_sort Keeble-Gagnère, Gabriel
collection PubMed
description Array-based single nucleotide polymorphism (SNP) genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Illumina Infinium Wheat Barley 40K SNP array Version 1.0. We show that the approach delivers high quality and high resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimizing ascertainment bias. Comprising mostly biallelic markers that were designed to be species-specific and single-copy, the array permits highly accurate imputation in diverse germplasm to improve the statistical power of genome-wide association studies (GWAS) and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Aegilops tauschii Coss. (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheat, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley, as well as direct connections to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool, Pretzel (https://plantinformatics.io/) which enables the content of the array to be visualized and interrogated interactively in the context of numerous genetic and genomic resources to be connected more seamlessly to research and breeding. The array is available for use by the international wheat and barley community.
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spelling pubmed-87280192022-01-06 Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization Keeble-Gagnère, Gabriel Pasam, Raj Forrest, Kerrie L. Wong, Debbie Robinson, Hannah Godoy, Jayfred Rattey, Allan Moody, David Mullan, Daniel Walmsley, Tresslyn Daetwyler, Hans D. Tibbits, Josquin Hayden, Matthew J. Front Plant Sci Plant Science Array-based single nucleotide polymorphism (SNP) genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Illumina Infinium Wheat Barley 40K SNP array Version 1.0. We show that the approach delivers high quality and high resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimizing ascertainment bias. Comprising mostly biallelic markers that were designed to be species-specific and single-copy, the array permits highly accurate imputation in diverse germplasm to improve the statistical power of genome-wide association studies (GWAS) and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Aegilops tauschii Coss. (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheat, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley, as well as direct connections to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool, Pretzel (https://plantinformatics.io/) which enables the content of the array to be visualized and interrogated interactively in the context of numerous genetic and genomic resources to be connected more seamlessly to research and breeding. The array is available for use by the international wheat and barley community. Frontiers Media S.A. 2021-12-22 /pmc/articles/PMC8728019/ /pubmed/35003156 http://dx.doi.org/10.3389/fpls.2021.756877 Text en Copyright © 2021 Keeble-Gagnère, Pasam, Forrest, Wong, Robinson, Godoy, Rattey, Moody, Mullan, Walmsley, Daetwyler, Tibbits and Hayden. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Keeble-Gagnère, Gabriel
Pasam, Raj
Forrest, Kerrie L.
Wong, Debbie
Robinson, Hannah
Godoy, Jayfred
Rattey, Allan
Moody, David
Mullan, Daniel
Walmsley, Tresslyn
Daetwyler, Hans D.
Tibbits, Josquin
Hayden, Matthew J.
Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization
title Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization
title_full Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization
title_fullStr Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization
title_full_unstemmed Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization
title_short Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization
title_sort novel design of imputation-enabled snp arrays for breeding and research applications supporting multi-species hybridization
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728019/
https://www.ncbi.nlm.nih.gov/pubmed/35003156
http://dx.doi.org/10.3389/fpls.2021.756877
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