Theoretical and Applied Genetics

, Volume 132, Issue 1, pp 125–135 | Cite as

A strategy for identifying markers linked with stem rust resistance in wheat harbouring an alien chromosome introgression from a non-sequenced genome

  • Jianping Zhang
  • Peng Zhang
  • Timothy Hewitt
  • Jianbo Li
  • Ian Dundas
  • Wendelin Schnippenkoetter
  • Sami Hoxha
  • Chunhong Chen
  • Robert Park
  • Evans Lagudah
Original Article


Key message

A set of molecular markers was developed for Sr26 from comparative genomic analysis. The comparative genomic approach also enabled the identification of a previously uncharacterised wheat chromosome that carried Sr26.


Stem rust of wheat, a biotic stress caused by a fungal pathogen, continues to pose significant threats to wheat production. Considerable effort has been directed at surveillance and breeding approaches to minimize the impact of the widely virulent race of the stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) commonly known as Ug99 (TTKSK) and other races in its lineage. The stem rust resistance gene Sr26, derived from Thinopyrum ponticum, is an excellent example of the successful utilization of a gene from a wild relative of a crop plant and remains one of the few durable sources of resistance currently effective against all known field isolates of Pgt. We explored comparative genomic analysis of the nucleotide binding leucine rich repeat (NLR) genes of the diploid D genome and bread wheat genomes to target the Sr26 region from the non-sequenced Th. ponticum genome. A chromosomal interval harboring NLR genes in the distal end of homoeologous group 6 chromosomes was used to demarcate the Sr26 locus. A set of closely linked PCR-based molecular markers was developed for Sr26. Furthermore, the comparative analysis approach enabled the unambiguous identification of a previously uncharacterised wheat chromosome that carried Sr26 in an introgressed Th. ponticum segment and was validated by fluorescent and genomic in situ hybridisation (FISH/GISH) experiments. The genetic information generated from the target interval based on this study will benefit future related studies on group 6 chromosomes of wheat, including 6Dt from Aegilops tauschii, and chromosome 6Ae#1 from Th. ponticum.



This work was financially supported by the Grains Research and Development Corporation (GRDC), Australia. The first author was supported by the National Science Foundation (NSF), the Monsanto Beachell–Borlaug International Scholars Programs (MBBISP), USA, and the Research Training Program (RTP) of the Australian Department of Education and Training. We thank Dr. Xiuying Kong from CAAS for kindly providing the 6Dt NLR annotation information and Prof. Robert A. McIntosh from the University of Sydney for comment on the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.University of Sydney, Plant Breeding Institute CobbittyCobbittyAustralia
  2. 2.CSIRO Agriculture & FoodCanberraAustralia
  3. 3.Henan Tianmin Seed Company Ltd.South Industrial District, LankaoPeople’s Republic of China
  4. 4.School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengduPeople’s Republic of China
  5. 5.School of Agriculture, Food and WineThe University of AdelaideUrrbraeAustralia

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