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

Gabriel Keeble-Gagnère,Debbie Wong,Jayfred Godoy,Daniel Mullan,Josquin Tibbits,Hannah Robinson,Tresslyn Walmsley,Hans D Daetwyler,Allan Rattey,Matthew J Hayden,Kerrie L Forrest,Raj Pasam,David Moody

doi:10.3389/fpls.2021.756877

Gabriel Keeble-Gagnère, Debbie Wong + Show 11 more

Open Access

https://doi.org/10.3389/fpls.2021.756877

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Abstract

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.

Highlights

High-density genotyping arrays that simultaneously interrogate thousands of single nucleotide polymorphisms (SNPs) have proven to be a powerful tool in genetic studies
We assume that the relationship is symmetrical; i.e., if SNP A is in the tagging SNPs (tSNPs) set of SNP B, SNP B should be in the tSNP set of SNP A
To design a genotyping array that has broader applicability in research and breeding, the SNPs should be discovered in diverse germplasm to avoid ascertainment bias and with sufficient density to produce large tSNP sets

Summary

Introduction

High-density genotyping arrays that simultaneously interrogate thousands of single nucleotide polymorphisms (SNPs) have proven to be a powerful tool in genetic studies. High quality assemblies are already available in cereal crop species, such as barley (Mascher et al, 2017; Monat et al, 2019), emmer wheat (Avni et al, 2017), durum wheat (Maccaferri et al, 2019), and bread wheat (The International Wheat Genome Sequencing Consortium [IWGSC], 2018), as well as for the diploid ancestors of wheat (Luo et al, 2017; Ling et al, 2018) These assemblies have accelerated SNP discovery and our understanding of the breeding history of wheat and patterns of genome-wide linkage disequilibrium (LD) in different germplasm pools. Mascher et al (2019) discovered almost 15M varietal SNPs from exome sequence generated for 96 two-row spring and winter barley accessions, a subset of which was used to investigate the extent and partitioning of molecular variation within and between the two groups

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