Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization.
GWAS
SNP genotyping
barley
dual sample hybridization
genomic selection
imputation
molecular breeding
wheat
Journal
Frontiers in plant science
ISSN: 1664-462X
Titre abrégé: Front Plant Sci
Pays: Switzerland
ID NLM: 101568200
Informations de publication
Date de publication:
2021
2021
Historique:
received:
11
08
2021
accepted:
27
10
2021
entrez:
10
1
2022
pubmed:
11
1
2022
medline:
11
1
2022
Statut:
epublish
Résumé
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
Identifiants
pubmed: 35003156
doi: 10.3389/fpls.2021.756877
pmc: PMC8728019
doi:
Types de publication
Journal Article
Langues
eng
Pagination
756877Informations de copyright
Copyright © 2021 Keeble-Gagnère, Pasam, Forrest, Wong, Robinson, Godoy, Rattey, Moody, Mullan, Walmsley, Daetwyler, Tibbits and Hayden.
Déclaration de conflit d'intérêts
HR, JG, AR, DMo, DMu, and TW were employed by InterGrain. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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