Cited by 103Wheat and Barley Genetics and PathologyPowdery Mildew Fungal DiseasesPlant Disease Resistance and Genetics

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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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
Venue
Plant Communications
Publisher
Elsevier BV
Published
2024-01
Volume
5
Issue
1
Pages
100646
ISSN
2590-3462 (ISSN-L)
OpenAlex
W4383197277
Cited by
103
References
102
Citations by year
2026: 25 · 2025: 26 · 2024: 42 · 2023: 10
FWCI
16.23
Type
journal article
Language
en
Open access
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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