Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks in the cloning of the powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional cloning approach was not e...

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Published in:Plant communications 2024-01, Vol.5 (1), p.100646-100646, Article 100646
Main Authors: Li, Yinghui, Wei, Zhen-Zhen, Sela, Hanan, Govta, Liubov, Klymiuk, Valentyna, Roychowdhury, Rajib, Chawla, Harmeet Singh, Ens, Jennifer, Wiebe, Krystalee, Bocharova, Valeria, Ben-David, Roi, Pawar, Prerna B., Zhang, Yuqi, Jaiwar, Samidha, Molnár, István, Doležel, Jaroslav, Coaker, Gitta, Pozniak, Curtis J., Fahima, Tzion
Format: Article
Language:English
Subjects:
Chromosome Mapping
Cloning, Molecular
Genes, Plant - genetics
Multigene Family
Triticum - genetics
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Summary:Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks in the cloning of the powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional cloning approach was not effective due 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 RNASeq reads of susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR, which was discovered only in one location across the WEW 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.
ISSN:2590-3462
2590-3462
DOI:10.1016/j.xplc.2023.100646