Diverse epistatic effects in barley-powdery mildew interactions localize to host chromosome hotspots

Authors: VELASQUEZ-ZAPATA, VALERIA - Iowa State University; SMITH, SCHUYLER - Iowa State University; PRIYANKA, SURANA - Sanger Institute; CHAPMAN, ANTONY - Rothamsted Research; Jaiswal, Namrata; Helm, Matthew; Wise, Roger

Submitted to: iScience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2024
Publication Date: 9/21/2024
Citation: Velasquez-Zapata, V., Smith, S., Priyanka, S., Chapman, A.V., Jaiswal, N., Helm, M.D., Wise, R.P. 2024. Diverse epistatic effects in barley-powdery mildew interactions localize to host chromosome hotspots. iScience. https://doi.org/10.1016/j.isci.2024.111013.
DOI: https://doi.org/10.1016/j.isci.2024.111013

Interpretive Summary: Plant pathogens are among the greatest threats to crop production worldwide, resulting in yield losses of 10 to 20% (= $100 to 200 billion) each year. Obligate biotrophic fungi, for example, mildews and rusts, require a living host to survive and cause some of the most destructive epidemics. A general view of the regulatory programs that render a plant resistant to pathogens is beginning to emerge in model organisms, but is still in its infancy in large-genome temperate cereals that are vital to feeding the world's growing population. The interaction between barley, and the powdery mildew fungus, is central to address this challenge. The nucleotide-binding leucine-rich-repeat (NLR) immune receptor encoded by Mildew locus a (MLA) is an ancestral protein required for protection against destructive cereal diseases, including powdery mildew, Ug99 stem rust, stripe rust, and rice blast. This research reports the use of time-course gene expression of barley infected with the powdery mildew pathogen to infer diverse gene effects governed by the MLA immune receptor and two other host factors critical to disease defense, Blufensin1 (Bln1) and Required for Mla6 resistance3 (Rar3). Gene effect models revealed epistatic interactions between Mla6 and Bln1 (a situation where the expression of one gene is modified by the expression of other genes) and the impact of rar3 on the barley and powdery mildew transcriptomes. For the first time, we classified 115 novel NLRs under unique gene effect models, which clustered at chromosome hotspots, suggesting genome accessibility and recruitment of transcriptional machinery as a contributing factor to resistance activation. Impact: Most plant resistance genes deployed in agriculture encode NLRs. However, the mechanisms by which NLR receptors impart critical functions to plant cells are often targets of pathogen effectors, thus, these discoveries provide a foundation for further research into the complex molecular interactions that control disease resistance in crops. These results impact modern breeding approaches to expand resistance to new and emerging pathogens.

Technical Abstract: Barley Mildew locus a (Mla) encodes a multi-allelic series of nucleotide-binding leucine-rich repeat (NLR) receptors that specify recognition to diverse cereal diseases. We exploited time-course transcriptome dynamics of barley and derived immune mutants infected with the powdery mildew fungus, Blumeria hordei (Bh), to infer gene effects governed by Mla6 and two other loci significant to disease development, Blufensin1 (Bln1), and Required for Mla6 resistance3 (rar3 = Sgt1'KL308-309). Interactions of Mla6 and Bln1 resulted in diverse epistatic effects on the Bh-induced barley transcriptome, differential immunity to Pseudomonas syringae expressing the effector protease AvrPphB, and reaction to Bh. From a total of 468 barley NLRs, 115 grouped under different gene effect models; genes classified under these models localized to host chromosome hotspots. The corresponding Bh infection transcriptome was classified into nine co-expressed modules, linking differential expression with pathogen structures, signifying that disease is regulated by an inter-organismal network that diversifies the response.