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

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

doi:10.1111/pbi.12635

Abstract

SummaryTargeted 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’.

Highlights

Increasing wheat yields is a major global priority for feeding the world’s growing population
Hybridization, domestication and strong selection pressure has reduced the level of genetic diversity available to wheat breeders, and this lack of diversity is widely recognized as a limiting factor in the breeding of high yielding varieties, in response to changing biotic and abiotic stresses (Haudry et al, 2007; Tanksley and McCouch, 1997)
We recently reported the generation of an ultra-high-density Affymetrix Axiomâ array, containing 820 000 single nucleotide polymorphism (SNP) markers (Winfield et al, 2015)

Summary

Introduction

Increasing wheat yields is a major global priority for feeding the world’s growing population. Hybridization, domestication and strong selection pressure has reduced the level of genetic diversity available to wheat breeders, and this lack of diversity is widely recognized as a limiting factor in the breeding of high yielding varieties, in response to changing biotic and abiotic stresses (Haudry et al, 2007; Tanksley and McCouch, 1997). The ability to assess and fully utilize the genetic diversity present in germplasm collections will inform breeding efforts, enabling potential yield increases to be attained, and it has been recognized in recent years that national efforts should be co-ordinated to maximize progress in wheat breeding (Wheat Initiative, 2011). The ability to assess germplasm on a common genotyping platform will assist exchanges of material between countries for the introduction and mobilization of novel genetic diversity

Results

Discussion

Conclusion