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A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes


Stripe rust and leaf rust are among the most devastating diseases of wheat, limiting its production globally. Wheat wild relatives harbour genetic diversity for new genes and alleles for all major wheat diseases. However, the use of this genetic variation from wild progenitor and non-progenitor species has been limited in the breeding programs. Reasons include limited recombination of donor and recipient genomes and the lack of tertiary gene pool markers. Here, we describe the development of a SNP based marker from the flow-sorted and sequenced Aegilops umbellulata chromosome 5U which can be used for marker assisted selection of four pair of alien leaf rust and stripe rust resistance genes. Lr57-Yr40_CAPS16 marker was reported earlier to be linked with alien leaf and stripe rust resistance genes introgressed on wheat chromosome 5DS. Due to its dominant nature and laborious to work with, a new SNP-based KASP marker, XTa5DS-2754099_kasp23, was developed from the same CAPS marker contig. XTa5DS-2754099_kasp23 was tested in Aegilops umbellulata, Ae. geniculata, Ae. peregrina and Ae. caudata derived alien introgression lines, which harbour four pairs of linked leaf and stripe rust genes; Lr76-Yr70, Lr57-Yr40, LrP- YrP, LrAc-YrAc, respectively. This KASP marker was found to be effective for the selection of the aforesaid four pairs of leaf rust and stripe rust resistance genes. Further, we tested and validated XTa5DS-2754099_kasp23 on commercial varieties and advanced breeding lines from four countries (India, Egypt, Australia and UK) including hexaploid and durum wheat. Our results provide evidence that KASP marker, XTa5DS-2754099_kasp23 can be used in marker-assisted selection of the four pairs of rust resistance alien genes in wheat breeding programmes.

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Data availability

All the data generated or analysed during this study are included in the published article and its supplementary information file. The material is available from the corresponding author on reasonable request.


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We thank Dr Ahmed Fawzy Elkot for providing the Egyptian breeding lines/varieties for genotyping. We also gratefully acknowledge Dr Oluwaseyi Shorinola for facilitating the genotyping at John Inns Centre, Norwich, UK.


This work was carried out under the Sustainable Crop Production Research for International Development (SCPRID). The financial support provided by the Department of Biotechnology, Ministry of Science and Technology, Government of India (grant No. BT/IN/UK/08/PC/2012) and the UK Biotechnology and Biological Sciences Research Council (grants No. BB/JO12017/1 and BB/P016855/1) is gratefully acknowledged. MB, PC and CU gratefully acknowledge the support provided by Monsanto Beachell Borlaug International Scholars Programme (MBBISP).

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MB analysed both genotype and phenotype data and wrote the draft of the manuscript; NMA helped in the assembly of flow sorted chromosome sequence and SNP detection; PIT helped in genotyping the Ae. caudata population; SK maintains the germplasm at PAU, Ludhiana; AS and PS provided the Indian advanced breeding lines and varieties; UB carried out genotyping of the marker on Australian varieties; CU helped in analysis of 5U chromosome data, marker generation and supervised the study; PC conceived the idea, designed and supervised the study, prepared the draft of the manuscript and submitted it. All the authors have read the manuscript and approved it.

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Correspondence to Parveen Chhuneja.

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Supplementary file1 List of commercial varieties/breeding lines from India, Egypt, Australia, and UK along with the score of allele that amplified with XTa5DS-2754099_kasp23 marker (XLSX 19 kb)

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Bansal, M., Adamski, N.M., Toor, P.I. et al. A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes. Mol Biol Rep 48, 5209–5216 (2021).

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  • KASP marker
  • Leaf rust
  • Stripe rust
  • Alien genes
  • Tertiary gene pool
  • Flow sorting