Development and validation of an exome-based SNP marker set for identification of the St, Jr and Jvs genomes of Thinopyrym intermedium in a wheat background

Andras Cseh,Amanda J Burridge,Ian P King,Stephen S Ashling,Duncan Scholefield,Julie King,Surbhi Grewal,Paul A Wilkinson,Stella Hubbart-Edwards,Caiyun Yang

doi:10.1007/s00122-019-03300-9

Abstract

Key messageCytogenetic analysis and array-based SNP genotyping of wheat–Th. intermediumintrogression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes ofTh. intermedium(StJrJvs, 2n = 6x = 42).Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat–Th. intermedium introgression lines and the Axiom® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1Jvs, 2Jvs, 3Jvs and 7Jvs. The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat.

Highlights

The domestication of wheat (Triticum aestivum L., BBAADD, 2n = 6x = 42) and 10,000 years of wheat breeding practices have led to a genetic bottleneck
We present a new single-nucleotide polymorphism (SNP) marker set for identification of Th. intermedium chromosomes in a wheat background, while the new wheat/Th. intermedium introgression lines can be used as a valuable genetic tool in future wheat improvement programmes
The results suggest that Th. intermedium had 42 chromosomes originating from three different genomes (Fig. 1a–b)

Summary

Introduction

Dewey, StJrJvs, 2n = 6x = 42) is one of the most promising gene reservoirs within the Triticeae family It is frequently used in modern pre-breeding programmes as a donor of drought tolerance, high-temperature tolerance and salinity tolerance genes and is considered as a useful genetic material providing resistance against a Theoretical and Applied Genetics (2019) 132:1555–1570 wide spectrum of fungal pathogens (wheat leaf rust, stripe rust, stem rust, powdery mildew and eyespot; immunity to smut, leaf blight, root rot) and barley yellow dwarf virus and stripe mosaic viruses (Friebe et al 1996; Li et al 2005, 2012; Li and Wang 2009; Zeng et al 2013; Danilova et al 2017). Th. intermedium may have the potential to improve wheat end-product quality and to provide perennial growth habit (Li et al 2013)

Methods

Results

Conclusion