Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum)

Abstract

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom^® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'.

Keywords: genotyping array; single nucleotide polymorphism (SNP); wheat.

Figure 1

Manhattan plots showing the level of segregation distortion of SNP loci distributed across the wheat genome in four mapping populations: (a) Avalon × Cadenza; (b) Savannah × Rialto; (c) Opata × Synthetic; (d) Apogee × Paragon; (e) Chinese Spring × Paragon. The guideline indicates the significance threshold of the chi‐square test at P = 0.05.

Figure 2

(a) Distribution of minor allele frequencies (MAFs) of SNP loci within germplasm collections. (b) Average MAF of A, B and D genome mapped SNPs in the different germplasm collections.

Figure 3

Principal coordinate analysis (PCoA) plots coloured by (a) collection, (b) country of origin (c) date of line release. Coordinate 1 is plotted along the x‐axis, coordinate 2 is plotted along the y‐axis.

Figure 4

Signal intensity (Log₂R ratio) plots of copy number variation (CNV) across the genome for different hexaploid wheat accessions. The accessions displayed are as follows: (a) Chinese Spring nullisomic 3A deletion; (b) Chinese Spring monosomic 3A deletion; (c) Chinese Spring ditelosomic 5DS deletion; (d) Paragon gamma‐irradiated 5B deletion; (e) Paragon gamma‐irradiated line exhibiting CNV loss and gain; (f) cv. Savannah, carrying the 1RS translocation from rye. Blue circles highlight copy number‐gained CNV regions, red circles highlight copy number‐loss CNV regions.