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Genetic mapping of the wheat leaf rust resistance gene Lr2a and its importance in Canadian wheat cultivars

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Abstract

Key message

Leaf rust resistance gene Lr2a was located to chromosome arm 2DS in three mapping populations, which will facilitate map-based cloning and marker-assisted selection of Lr2a in wheat breeding programs.

Abstract

Incorporating effective leaf rust resistance (Lr) genes into high-yielding wheat cultivars has been an efficient method of disease control. One of the most widely used genes in Canada is the multi-allelic resistance gene Lr2, with alleles Lr2a, Lr2b, Lr2c, and Lr2d. The Lr2a allele confers complete resistance to a large portion of the Puccinia triticina (Pt) population in Canada. In this study, Lr2a was genetically mapped in two doubled haploid populations developed from the crosses Superb/BW278 and Superb/86ISMN 2137, and an F2 population developed from the cross Chinese Spring/RL6016. Seedlings were tested with the Lr2a avirulent Pt races 74-2 MGBJ (Superb/BW278) and 12-3 MBDS (Superb/86ISMN 2137 and Chinese Spring/RL6016) in greenhouse assays and were genotyped with 90K wheat Infinium SNP and kompetitive allele-specific PCR (KASP) markers. Lr2a was mapped to a collinear position on chromosome arm 2DS in all three populations, within a 1.00 cM genetic interval between KASP markers kwm1620 and kwm1623. This corresponded to a 305 kb genomic region of chromosome 2D in Chinese Spring RefSeq v2.1. The KASP marker kwh740 was predictive of Lr2a in all mapping populations. A panel of 260 wheats were tested with three Pt isolates, which revealed that Lr2a is common in Canadian wheats. The KASP markers kwh740 and kwm1584 were highly associated with resistance at the Lr2 locus, while kwm1622 was slightly less correlated. Genetic mapping of the leaf rust resistance gene Lr2a and DNA markers developed here will facilitate its use in wheat breeding programs.

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Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors thank Mira Popovic, Ghassan Mardli, Leslie Bezte, Alain Ngantcha, and Elsa Reimer at the Morden Research and Development Centre for their contributions to this research. Funding was provided by Western Grains Research Foundation, CAP Ag Action Manitoba, Manitoba Crop Alliance, and Alberta Wheat Commission as part of the Genome Canada projects CTAG2 and 4DWheat.

Funding

Funding was provided by Agriculture and Agri-Food Canada, Western Grains Research Foundation, CAP Ag Action Manitoba, Manitoba Crop Alliance, and Alberta Wheat Commission as part of the Genome Canada projects CTAG2 and 4DWheat.

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Authors and Affiliations

  1. Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada

    Dinushika Thambugala, Brent D. McCallum, Andriy Bilichak & Colin W. Hiebert

  2. Manitoba Crop Alliance, 38 4th Avenue NE, Box 188, Carman, MB, R0G 0J0, Canada

    Mallorie K. Lewarne

  3. Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada

    Curt A. McCartney

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  1. Dinushika Thambugala
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Contributions

DT phenotyped the Chinese Spring/RL6016 population, developed and tested kwm KASP markers, and co-wrote the first draft of the manuscript. ML phenotyped the Superb/BW278 and Superb/86ISMN 2137 DH populations, developed and tested the kwh KASP markers, and co-wrote the first draft of the manuscript. BDM phenotyped all wheat populations. CWH designed many of the kwh KASP markers. CAM designed the kwm KASP markers. BDM, AB, CWH, and CAM conceived, implemented, and supervised various aspects of the study. All authors read, edited, and approved the final manuscript.

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Correspondence to Colin W. Hiebert or Curt A. McCartney.

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Communicated by Albrecht E. Melchinger.

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Supplementary Table S1

Kompetitive allele-specific PCR (KASP) markers developed from the Lr2a region of chromosome 2D, SNP name, its location in Chinese Spring RefSeq v1.0 and v2.1, and primer information. Supplementary Table S2 Seedling response to Puccinia triticina Eriks. (Pt) races and validation analysis of Lr2a linked kompetitive allele-specific PCR (KASP) markers Excalibur_c1944_1017_kwh740, kwm1584, kwm1618, kwm1620, kwm1621, kwm1622, and kwm1623 on a wheat panel consisting of 260 wheat lines. Supplementary Table S3 The chromosome 2D genetic map developed for the Superb/BW278 DH population. Summary of data for 71 SNP markers with chromosome assignment and map position and newly developed kompetitive allele-specific PCR (KASP) markers. Supplementary Table S4 The chromosome 2D genetic map developed for the Superb/86ISMN 2137 DH population. Summary of data for 165 SNP markers with chromosome assignment and map position and newly developed kompetitive allele-specific PCR (KASP) markers. Supplementary Table S5 The chromosome 2D genetic map developed for the Chinese Spring/RL6016 F2 population. Summary of data for 45 SNP markers with chromosome assignment and map position and newly developed kompetitive allele-specific PCR (KASP) markers. Supplementary Fig. S1 Pedigree diagram indicating the presence or absence of Lr2a in older Canada Western Red Spring (CWRS) wheat cultivars. Cultivars in red carry Lr2a, cultivars in blue have the susceptible allele at the Lr2 locus, and cultivars in black have not been tested (XLSX 285 KB)

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Thambugala, D., Lewarne, M.K., McCallum, B.D. et al. Genetic mapping of the wheat leaf rust resistance gene Lr2a and its importance in Canadian wheat cultivars. Theor Appl Genet 136, 198 (2023). https://doi.org/10.1007/s00122-023-04440-9

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