RT Journal Article
SR Electronic
T1 Novel design of imputation-enabled SNP arrays for breeding and research applications supporting multi-species hybridisation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.03.454059
DO 10.1101/2021.08.03.454059
A1 G Keeble-Gagnère
A1 R Pasam
A1 KL Forrest
A1 D Wong
A1 H Robinson
A1 J Godoy
A1 A Rattey
A1 D Moody
A1 D Mullan
A1 T Walmsley
A1 HD Daetwyler
A1 J Tibbits
A1 MJ Hayden
YR 2021
UL http://biorxiv.org/content/early/2021/08/05/2021.08.03.454059.abstract
AB Array-based 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 Infinium Wheat Barley 40K SNP array. We show 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 minimising ascertainment bias. Comprising mostly biallelic markers designed to be species-specific and single-copy, it permits highly accurate imputation in diverse germplasm to improve statistical power for GWAS and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Ae. tauschii (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheats, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley and that directly connect 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 array’s content to be visualised and interrogated interactively in the context of numerous genetic and genomic resources to more seamlessly connect research and breeding. The array is available for use by the international wheat and barley community.Short summary Designing SNP genotyping arrays for closely related species with broad applicability in both research and breeding is challenging. Here we describe a novel generic approach to select SNP content for such arrays and demonstrate its utility in wheat and barley to: capture haplotypic diversity while minimising ascertainment bias;accurately impute to high SNP density in diverse germplasm;generate high-quality high-resolution genotypic data; andjointly hybridise samples to the same bead chip array.Competing Interest StatementThe authors have declared no competing interest.