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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

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


Andras Cseh

Caiyun Yang

Duncan Scholefield

Stephen S. Ashling

Amanda J. Burridge

Paul A. Wilkinson


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.


Cseh, A., Yang, C., Hubbart-Edwards, S., Scholefield, D., Ashling, S. S., Burridge, A. J., …Grewal, S. (2019). 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. TAG Theoretical and Applied Genetics, 132(5), 1555–1570.

Journal Article Type Article
Acceptance Date Feb 2, 2019
Online Publication Date Feb 14, 2019
Publication Date 2019-05
Deposit Date Feb 12, 2019
Publicly Available Date Mar 1, 2019
Journal Theoretical and Applied Genetics
Print ISSN 0040-5752
Electronic ISSN 1432-2242
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 132
Issue 5
Pages 1555–1570
Keywords Biotechnology; Agronomy and Crop Science; Genetics; General Medicine
Public URL
Publisher URL
Additional Information Received: 30 October 2018; Accepted: 2 February 2019; First Online: 14 February 2019; : ; : On behalf of all authors, the corresponding author states that there is no conflict of interest.


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