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

. 2017 Mar;15(3):390-401.

doi: 10.1111/pbi.12635. Epub 2016 Nov 23.

Mark O Winfield 1, Amanda J Burridge 1, Rowena C Downie 1 2, Harriet R Benbow 1, Gary L A Barker 1, Paul A Wilkinson 1, Jane Coghill 1, Christy Waterfall 1, Alessandro Davassi 3, Geoff Scopes 3, Ali Pirani 3, Teresa Webster 3, Fiona Brew 3, Claire Bloor 3, Simon Griffiths 4, Alison R Bentley 2, Mark Alda 5, Peter Jack 5, Andrew L Phillips 6, Keith J Edwards 1

Affiliations

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

Alexandra M Allen et al. Plant Biotechnol J. 2017 Mar.

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.

© 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

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Conflict of interest statement

The authors declare no conflict of interests.

Figures

Figure 1

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

Figure 2

(a) Distribution of minor allele frequencies (

MAF

s) of

SNP

loci within germplasm collections. (b) Average

MAF

of A, B and D genome mapped

SNP

s in the different germplasm collections.

Figure 3

Figure 3

Principal coordinate analysis (

PC

oA) 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

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 5

DS

deletion; (d) Paragon gamma‐irradiated 5B deletion; (e) Paragon gamma‐irradiated line exhibiting

CNV

loss and gain; (f) cv. Savannah, carrying the 1

RS

translocation from rye. Blue circles highlight copy number‐gained

CNV

regions, red circles highlight copy number‐loss

CNV

regions.

References

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