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Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69
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Abstract
Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.
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Metadata
- Authors
- Li, Y., Wei, Z.-Z., Sela, H., Govta, L., Klymiuk, V., Roychowdhury, R., Chawla, H. S., Ens, J., Wiebe, K., Bocharova, V., Ben-David, R., Pawar, P. B., Zhang, Y., Jaiwar, S., Molnár, I., Doležel, J., Coaker, G., Pozniak, C. J., & Fahima, T.
- Affiliations
- University of Haifa (IL)
- Sichuan Academy of Agricultural Sciences (CN)
- University of Saskatchewan (CA)
- China Agricultural University (CN)
- Czech Academy of Sciences, Institute of Experimental Botany (CZ)
- University of California, Davis (US)
- Corresponding author
- Fahima, Tzion
- ORCID
- Venue
- Plant Communications
- Publisher
- Elsevier BV
- Published
- 2024-01
- Volume
- 5
- Issue
- 1
- Pages
- 100646
- ISSN
- 2590-3462 (ISSN-L)
- PMC
- PMC10811346
- OpenAlex
- W4383197277
- Cited by
- 103
- References
- 102
- Citations by year
- 2026: 25 · 2025: 26 · 2024: 42
- FWCI
- 16.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Plant Communications (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
- Funders
- Genome Canada
- United States-Israel Binational Science Foundation (2019654)
- Israel Science Foundation (1366/18, 2289/16, 2342/18)
- National Science Foundation (1937855)
- Council for Higher Education
- European Regional Development Fund (CZ.02.1.01/0.0/0.0/16_019/0000827)
- United States - Israel Binational Science Foundation
- U.S. Department of Agriculture (2020-67013-32577)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Wheat and Barley Genetics and Pathology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Powdery Mildew Fungal Diseases
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Disease Resistance and Genetics
- Keywords
- powdery mildew resistance, disease resistance genes, NLR, nucleotide-binding leucine-rich repeat, wild emmer wheat, tetraploid wheat, long-read genome sequencing, Oxford Nanopore, physical map, suppressed recombination, structural variants, virus-induced gene silencing, candidate gene identification
- MeSH terms
- Chromosome Mapping, Cloning, Molecular, Multigene Family, Triticum, Genes, Plant
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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