The November 2020 Editor’s Pick for MPMI is “Extensive Genetic Variation at the Sr22 Wheat Stem Rust Resistance Gene Locus in the Grasses Revealed through Evolutionary Genomics and Functional Analyses.” The first author is Muhammad Asyraf Md Hatta, a former graduate student in the lab of Brande Wulff at the John Innes Centre. To read more about Asyraf, you can find his bio here​. Asyraf is now a senior lecturer at the Faculty of Agriculture, Universiti Putra Malaysia. Below is some background on Asyraf’s project that led to the publication in MPMI.

Extensive Genetic Variation at the Sr22 Wheat Stem Rust Resistance Gene Locus in the Grasses Revealed Through Evolutionary Genomics and Functional Analyses

Submitted by Muhammad Asyraf Md Hatta

Wheat stem rust caused by the fungus Puccinia graminis f. sp. tritici is a major disease of wheat. The disease epidemics in major wheat-growing areas around the world pose a major threat to global food security. Fungicide application can only partly control this disease. Therefore, the deployment of resistance genes remains the preferred control method.

This has been one of the research focus areas of Wulff’s group at the John Innes Centre, UK, with which I worked during my Ph.D. studies. In our previous manuscript, we reported the cloning of the Sr22 gene, which confers broad spectrum resistance to multiple races of P. graminis f. sp. tritici, including the Ug99 race group. In a similar study, we also identified several Sr22 alleles from both Triticum boeoticum and the domesticated form of this species, T. monococcum.

Following the cloning of the gene, our industrial collaborator, the 2Blades Foundation, gathered information for their patenting and deployment strategy. The patenting process required information on the functional testing of the different Sr22 alleles driven by domesticated native and non-native 5′ and 3′ regulatory elements.

This patenting strategy motivated us to generate a suite of Sr22 chimeric constructs. Since one of my Ph.D. projects involved development of gene constructs using the Golden Gate cloning method, my supervisor had assigned me the task of collaborating with other colleagues from my group, as well as from the Commonwealth Scientific and Industrial Research Organization, Canberra, Australia.

From that point, I was given the opportunity to lead the project, and I studied the sequence relationship between the alleles, in which I found evidence of extensive historical recombination between alleles. The analysis also revealed the greatest sequence variation in the leucine-rich repeat (LRR) domain, in line with its proposed role in pathogen recognition specificity.

We also functionally characterized three of the alleles in transgenic wheat, in which two of them were found to confer resistance to the Ug99 isolate, thus advancing our previous work on cloning the gene.

We then expanded the work to include a large-scale comparison of the Sr22 locus across monocot species. This is when we discovered the surprising large-scale expansion of the Sr22 locus in the barley and oat lineages. Based on a comprehensive search of the genomes and transcriptomes of 80 plant species, it appears that the gene is conserved among grasses in the Triticeae and Poeae lineages. All Triticeae species examined in this study contain a single copy of the gene, except barley, which has undergone complex expansions and rearrangements.