Genetic elucidation of complex biochemical traits mediating maize innate immunity

Authors: DING, YEZHANG - University Of California, San Diego; WECKWERTH, PHILLIP - University Of California, San Diego; PORETSKY, ELLY - University Of California, San Diego; MURPHY, KATHERINE - University Of California, San Diego; SIMS, JAMES - Institute Of Agricultural Sciences; SALDIVAR, EVAN - University Of California, San Diego; Christensen, Shawn; CHAR, SI NIAN - University Of Missouri; YANG, BING - University Of Missouri; TONG, ANH-DAO - University Of California, San Diego; SHEN, ZHOUXIN - University Of California, San Diego; KREMLING, KARL - Cornell University; Buckler, Edward - Ed; KONO, TOM - University Of Minnesota; NELSON, DAVID - University Of Tennessee; BOHLMANN, JORG - University Of British Columbia; Bakker, Matthew; Vaughan, Martha; KHALIL, AHMED - University Of California, San Diego; BETSIASHVILI, MARIAM - University Of California, San Diego; BRIGGS, STEVEN - University Of California, San Diego; ZERBE, PHILIPP - University Of California, San Diego; SCHMELZ, ERIC - University Of California, San Diego; HUFFAKER, ALISA - University Of California, San Diego

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 3/5/2020
Publication Date: 3/5/2020
Citation: Ding, Y., Weckwerth, P., Poretsky, E., Murphy, K., Sims, J., Saldivar, E., Christensen, S.A., Char, S., Yang, B., Tong, A., Shen, Z., Kremling, K., Buckler IV, E.S., Kono, T., Nelson, D., Bohlmann, J., Bakker, M.G., Vaughan, M.M., Khalil, A., Betsiashvili, M., Briggs, S., Zerbe, P., Schmelz, E., Huffaker, A. 2020. Genetic elucidation of complex biochemical traits mediating maize innate immunity. bioRxiv. https://doi.org/10.1101/2020.03.04.977355.
DOI: https://doi.org/10.1101/2020.03.04.977355

Interpretive Summary: It’s known that crops produce specialized molecules to defend against diseases and pathogens; however, due to difficulty in piecing together the pathways that result in the production and utilization of the molecules, we are unable to properly discern their function. Obtaining a detailed and accurate blueprint of the pathways is crucial for any effort to synthetically improve the effectiveness and efficiency of the pathways. Terpenoids are a class of molecules that largely contribute to a plant's ability to fight off pathogens and zealexins are the largest class of defensive terpenoids in corn. Through the integration of methods from various fields of biology, ten genes existing in three clusters were identified to interact to produce a diverse set of defensive zealexins. Redundancy of zealexin pathway genes ensures the production of zealexins even if one copy of a gene is non-functional. The new understanding of the zealexin pathway interactions opens it up for consideration in breeding and synthetic pathway improvements through genetic engineering. This research is important because it advances the development of a methodology for identifying molecular pathway elements and it also increases the understanding of the zealexin pathway and its interactions. The multiomic approach developed during this study provides an example experiment structure that can be followed by the scientific community to elucidate other complex pathways, improving our basic knowledge of metabolic pathways.

Technical Abstract: Specialized metabolites constitute key layers of immunity underlying crop resistance; however, challenges in resolving complex pathways limit our understanding of their functions and applications. In maize (Zea mays) the inducible accumulation of acidic terpenoids is increasingly considered as a defense regulating disease resistance. To understand maize antibiotic biosynthesis, we integrated association mapping, pan-genome multi-omic correlations, enzyme structure-function studies, and targeted mutagenesis. We now define ten genes in three zealexin (Zx) gene clusters comprised of four sesquiterpene synthases and six cytochrome P450s that collectively drive the production of diverse antibiotic cocktails. Quadruple mutants blocked in the production of B-macrocarpene exhibit a broad-spectrum loss of disease resistance. Genetic redundancies ensuring pathway resiliency to single null mutations are combined with enzyme substrate-promiscuity creating a biosynthetic hourglass pathway utilizing diverse substrates and in vivo combinatorial chemistry to yield complex antibiotic blends. The elucidated genetic basis of biochemical phenotypes underlying disease resistance demonstrates a predominant maize defense pathway and informs innovative strategies for transferring chemical immunity between crops.