Location: Corn Insects and Crop Genetics Research
2019 Annual Report
Objectives
Objective 1. Discover diverse fungal disease resistance mechanisms in cereal (barley and maize) crops.
Sub-Objective 1A. Use expression quantitative trait locus (eQTL) analysis in combination with genome-wide promoter-motif enrichment strategies to discover master regulators of immunity.
Sub-Objective 1B: Identify host targets of pathogen effectors by next generation yeast-two-hybrid interaction screens.
Sub-Objective 1C: Identify and characterize the genetic and molecular pathological modes of action for isolate-specific and non-specific Quantitative Disease Resistance (QDR) mechanisms that protect corn plants against northern leaf blight.
Objective 2: Generate novel sets of disease defense alleles for mechanistic dissection and application to crop protection.
Sub-Objective 2A: Functional confirmation via integrated reverse genetic analysis.
Sub-Objective 2B: Evaluate yield and northern leaf blight resistance properties of QDR alleles in hybrid genetic contexts.
Approach
Large-scale sequencing of plant and pathogen genomes has provided unprecedented access to the genes and gene networks that underlie diverse outcomes in host-pathogen interactions. Determination of regulatory focal points critical to these interactions will provide the molecular foundation necessary to dissect important disease resistance pathways. This knowledge can be used to guide modern plant breeding efforts in response to pathogens that present diverse challenges to the host.
Progress Report
Fungal pathogens are the greatest threats to cereal grain production worldwide. Effector proteins secreted by these pathogens manipulate host processes in order to create an ideal environment for colonization. To defend themselves, plants have evolved a battery of receptors that activate immune responses. Using plant-pathogen interaction systems of barley and corn, this project aims to identify both host disease defense components and pathogen signaling molecules that suppress them. By understanding how plants and pathogens manipulate each other during complex interactions, geneticists and breeders can tip the scales in favor of the crop plants to promote more stable and more efficient production.
Plant disease resistance is often mediated by intracellular innate immune receptors known as nucleotide-binding leucine-rich repeat proteins (NLRs). The primary function of NLRs is to detect the presence of pathogen-secreted effector proteins, sometimes indirectly through effector-induced modification of other host proteins. Our ongoing research in barley leverages a well-studied NLR in Arabidopsis, named RPS5, which indirectly detects its cognate bacterial effector, named AvrPphB, from the pathogen Pseudomonas syringae pv. Phaseolicola. RPS5 detects AvrPphB by monitoring the conformational status of an Arabidopsis substrate of AvrPphB, the serine/threonine protein kinase PBS1. PBS1 is one of the most well conserved defense-related genes in flowering plants, and the products of PBS1 orthologs in wheat and Arabidopsis can be cleaved by AvrPphB. Determining whether PBS1 orthologs are guarded by a second resistance protein in diverse plant species is of particular interest, because it will provide insight into the evolution of disease resistance gene specificity and could enable engineering of new disease resistance specificities in crop plants. Thus, in plant species in which a PBS1 ortholog is guarded, engineering these orthologs to serve as substrates of other pathogen proteases offers an attractive approach for generating resistance tailored to pathogens of those species. Given that plant pathogenic viruses, bacteria, fungi, oomycetes, and nematodes express proteases during infection, engineering the RPS5/PBS1 surveillance system is an effective strategy for developing resistance to many important plant diseases.
ARS scientists in Ames, Iowa collaborated with colleagues at Cornell University in Ithaca, New York and Indiana University in Bloomington, Indiana to show that barley varieties recognize and respond to AvrPphB protease activity. The AvrPphB response was mapped to a single segregating locus on chromosome 3HS, and identified an NLR gene that was designated AvrPphB Resistance1 (Pbr1). Furthermore, it was shown that wheat varieties also recognize AvrPphB protease activity and harbor two copies of Pbr1. Phylogenetic analyses indicate that the ability to recognize AvrPphB evolved independently in monocots and dicots, and imply that selection to guard PBS1-like proteins occurs across species. Also, these results suggest that PBS1-based decoys may be used to engineer protease effector recognition-based resistance in barley and wheat.
In contrast to barley, whose disease defense relies heavily on NLR genes that often provide qualitative resistance, maize relies more on quantitative disease resistance (QDR) mechanisms. This has a consequence to breeding insofar as the types of approaches that should be used to prevent disease outbreaks as well as recovery from them after they occur. Significant progress was made by this project in proposing and supporting this idea as part of a peer-reviewed chapter in the new Maize Genome book (Log No. 358008). We suggest that incorporating disease pressure into trial and testing environments will permit genomic selection techniques to be fruitfully applied in corn crop protection.
While breeding is quite effective for crop protection, it is also vital to understand the mechanisms of disease defense and the magnitude and stability of their effects using genetic-based research approaches. To this end, we previously characterized the genetics of the quantitative disease resistance against Setosphaerica turcica, the causal agent of northern corn leaf blight. In the past year, we performed a myriad of breeding tasks to set up future genetic experiments that will allow yield and northern corn leaf blight resistance effects of transgenic and natural QDR alleles at varying dosages to be assessed in replicated multi-environment iso-hybrid trials. For the introgression breeding to enable implementation of these tests, we utilize both field and greenhouse nurseries, both of which have risks.
During this period of several years that elapse while the introgression breeding efforts occur, we are implementing the experimental framework for the testing using materials that we have developed previously. In the past year, we completed our first full-scale, replicated, multi-environment trials of iso-hybrids with varying resistance allele dosages under disease and non-disease conditions. We found that the resistance alleles did not offer economically valuable levels of supplemental protection, but that they incurred no yield penalties either. The successful execution of this work is foundational to our future success in testing the new sets of materials under development
Accomplishments
1. Convergent evolution of a novel plant disease resistance locus. Plant disease resistance is often mediated by intracellular immune receptors known as nucleotide-binding leucine-rich repeat proteins (NLRs). The primary function of the many NLR-type resistance genes deployed in crop protection is to detect the presence of pathogen-secreted effector proteins. ARS scientists in Ames, Iowa collaborated with colleagues at Cornell University in Ithaca, New York and Indiana University in Bloomington, Indiana to discover that multiple barley varieties recognize and respond to a conserved protease activity mediated by the pathogen effector, designated AvrPphB. Barley reaction to the AvrPphB effector is controlled by a novel NLR disease resistance gene, designated AvrPphB Response 1 (Pbr1). Wheat varieties also possess copies of Pbr1, suggesting that this new disease resistance system can be deployed in cereal grain crops. These results provide the first evidence that host targets of AvrPphB have essential immune functions in both monocot and dicot crops. This knowledge will be used to expand protease effector recognition, creating disease resistant crops.
2. Evaluation of maize silk resistance to corn earworm. Caterpillar pests like corn earworm are among the most damaging to corn because they reduce grain quantity by herbivory and grain quality by vectoring diseases. While present chemical and biochemical technologies are protective, corn with its own genetic resistance mechanisms is important for both organic and future conventional growers. ARS scientists in Ames, Iowa developed a quantitative corn earworm bioassay and applied it to the discovery of new genetic resistance mechanisms found in tropical corn. Because genetic solutions can reduce or eliminate pesticide use, this research offers opportunities to simultaneously lower farm input costs, protect crop health, and prevent damage to the environment.
Review Publications
Carter, M., Helm, M., Chapman, A., Wan, E., Restrepo Sierra, A., Innes, R., Bogdanove, A., Wise, R.P. 2019. Convergent evolution of effector protease recognition by Arabidopsis and barley. Molecular Plant-Microbe Interactions. 32(5):550-565. https://doi.org/10.1094/MPMI-07-18-0202-FI.
Wisser, R.J., Lauter, N.C. 2018. Genomics of fungal disease resistance. In: Bennetzen J., Flint-Garcia S., Hirsch C., Tuberosa R., editors. The Maize Genome. Compendium of Plant Genomes. Cham, Switzerland: Springer International. p. 201-211. https://doi.org/10.1007/978-3-319-97427-9_13.
Lopez, M.D., Dennison, T., Ward, T.M., Yandeau-Nelson, M.D., Abel, C.A., Lauter, N.C. 2019. Development and application of a quantitative bioassay to evaluate maize silk resistance to corn earworm herbivory among progenies derived from Peruvian landrace Piura. PLoS One. 14(4):e0215414. https://doi.org/10.1371/journal.pone.0215414.
Elmore, J.M., Perovic, D., Ordon, F., Schweizer, P., Wise, R.P. 2018. A genomic view of biotic stress resistance. In: Stein, N., Muehlbauer, G., editors. The Barley Genome. Cham, Switzerland: Springer International. p. 233-257. https://doi.org/10.1007/978-3-319-92528-8_14.
Carter, M., Bogdanove, A., Innes, R., Wise, R.P. 2018. A confounding effect of bacterial titer in a type III delivery-based assay of eukaryotic effector function. Molecular Plant-Microbe Interactions. 31(11):1115-1116. https://doi.org/10.1094/MPMI-05-18-0128-LE.
