High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

Mark Winfield ,Fiona Brew,Harriet R Benbow,Claire West,Simon Griffiths,Julie King,Keith J Edwards,Geoff Scopes,Ali Pirani,Alessandro Davassi,Christy Waterfall,Claire Bloor,Alexandra M Allen,Alison R Bentley,Jane A Coghill ,Teresa A Webster ,Amanda Burridge ,Gary Barker ,Paul Wilkinson ,Ian P King

doi:10.1111/pbi.12485

Abstract

SummaryIn wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.

Highlights

Bread wheat (Triticum aestivum) is an allohexaploid crop derived from the hybridization of diploid Aegilops tauschii with tetraploid wild emmer, Triticum turgidum ssp. dicoccoides (Dubcovsky and Dvorak, 2007; Matsuoka, 2011; Shewry, 2009)
We recently reported the use of a sequence capture targeted re-sequencing approach to characterize a significant proportion of the wheat exome (Winfield et al, 2012), which was used to identify large numbers of exome-specific single nucleotide polymorphisms (SNPs) (Allen et al, 2013)
Putative SNPs, together with their flanking sequences, were processed using the Affymetrix design protocol for the Axiomâ platform to generate 819 571 putative SNP probes (Axiomâ HD Wheat Genotyping Array; this data set may be downloaded from the CerealsDB web site: http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/Excel/axiom820Data.txt.zip)

Summary

Introduction

Bread wheat (Triticum aestivum) is an allohexaploid crop derived from the hybridization of diploid Aegilops tauschii with tetraploid wild emmer, Triticum turgidum ssp. dicoccoides (Dubcovsky and Dvorak, 2007; Matsuoka, 2011; Shewry, 2009). Dicoccoides (Dubcovsky and Dvorak, 2007; Matsuoka, 2011; Shewry, 2009) This hybridization, subsequent domestication and inbreeding have reduced genetic diversity in cultivated wheat compared with its wild ancestors (Haudry et al, 2007; Tanksley and McCouch, 1997). The negative impact of linkage drag can be minimized by reducing the size of the introgressed fragment to the minimum necessary to retain the desired phenotype (Wulff and Moscou, 2014). This can be achieved through repeated backcrossing to the elite parent but is often a lengthy process (Qi et al, 2007). On the other hand, which can be adapted for high sample throughput, enable the rapid and costeffective characterization of introgressions (Thomson, 2014)

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