Location: Corn Insects and Crop Genetics Research
2016 Annual Report
Objectives
Objective 1: Discover and functionally characterize host genes and pathways that respond to pathogen infection in barley and maize.
Sub-Objective 1A: Identification of barley Blufensin1 (Bln1)-mediated response pathways.
Sub-Objective 1B: Functional confirmation via integrated reverse genetic analysis.
Sub-Objective 1C: Identify and functionally characterize mechanisms of defense against leaf blights with hemi-biotrophic and necrotrophic lifestyles in maize.
Objective 2: Identify and analyze the role of pathogen effectors that influence host response in barley and maize.
Sub-Objective 2A: Isolation of Blumeria graminis f. sp. hordei (Bgh) effectors to identify plant targets that promote or suppress defense in host and nonhost interactions.
Sub-Objective 2B: Identification of candidate effectors produced by S. turcica and C. heterostrophus during interactions with maize.
Approach
Large scale sequencing of pathogen genomes, as well as their plant hosts, has provided unprecedented access to the genes and gene networks that underlie host-pathogen interactions. Regulatory focal points critical to these interactions will be investigated. Determination of these focal points will enable the molecular dissection of important disease resistance pathways, as well as the creation of a molecular toolbox from which to apply modern plant breeding methodologies.
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. While many aspects of plant defense have been studied using a reductionist approach, a comprehensive view of the cellular changes that actually render a plant resistant to pathogens has been a major challenge for plant-microbe research.
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.
Significant new insights into disease resistance signaling were obtained in FY2016; ARS scientists used the cereal grain crop, barley, and its powdery mildew pathogen to perform a genome-wide analysis of plant disease resistance, and as part of Objective 1, discovered a novel disease resistance mechanism. Two independent resistance genes act as master regulators and control the expression of “worker” genes, respectively. Moreover, of the 961 genes regulated by one of the resistant genes during the early stages of attack, control of >30% of these are repurposed by this gene as infection progresses. This finding shows that 1) these genes are part of an immune regulatory complex activated by disparate resistance genes, and 2) a major portion of the encoded proteins function together to achieve immunity in response to different pathogen isolates or infection stages. This means that there is a conserved core of genes that can be activated by master resistance genes to respond to diverse pathogen attack scenarios.
Similarly complex results were obtained from experiments conducted using corn and two of its pathogens that attack leaves and thereby reduce crop yields. In gene expression experiments involving corn and Cochliobolus heterostrophus, the causal agent of Southern Leaf Blight, it was observed that 242 fungal genes are expressed differently according to the genotype of the corn plant that serves as the host. This indicates that the pathogen is carefully responding to the unique sets of defense mechanisms that are engaged by the host. In a multi-location genetic mapping experiment involving Setosphaeria turcica, the causal agent of Northern Leaf Blight (NLB), fungal isolates collected in Ithaca, NY and Ames, IA were used to challenge 220 corn genotypes belonging to a high resolution mapping population. While a core of common genetic factors were deployed in disease defense against these two NLB isolates, several genetic factors engaged in defense only against one of the two isolates, demonstrating on the host defense side that at least in some circumstances, isolate specificity does play a role in triggering quantitative disease defense mechanisms.
The molecular mechanisms by which pathogen effectors manipulate the host are poorly understood and disease epidemics are accelerated during shifting climate conditions. Identification of barley and corn proteins targeted by multiple pathogen effectors would indicate that these proteins are critical to conserved defense responses and would be priority targets for resistance breeding, enabling advanced cultivar development. Knowledge gained from this project will promote broadly applicable disease control strategies.
Accomplishments
ARS scientist established and led National Science Foundation funded K-12 research experience for teachers program on inheritance of traits and genes in barley (iTAG Barley) for high school biology curricula, including Advanced Placement courses. The Digital iBook for iPAD (v6; Student & Teacher editions) sixth edition is published on iTunes, and has been used successfully in over fifty high school biology classes -- more than 2,400 students, of whom 50% were from underrepresented and/or underserved groups from urban to rural communities. Participants discuss how to relate iTAG to broader real-world applications in agriculture and medicine. Based on these successes, we have extended this training to workshops at Tuskegee University, a 1890 land-grant institution, and Des Moines Area Community College, providing hands-on training in genetics as it applies to agriculture and human health.
Review Publications
Zuo, T., Zhang, J., Lithio, A., Dash, S., Weber, D., Wise, R.P., Nettleton, D., Peterson, T. 2016. Genes and small RNA transcripts exhibit dosage-dependent expression pattern in maize copy-number alterations. Genetics. 203(1):1177-1190. doi: 10.1534/genetics.116.188235.
Munoz-Amatriain, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J., Moscou, M., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G., Wise, R.P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bartos, J., Bhat, P., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J., Dolezel, J., Grimwood, J., Schmutz, J., Duma, D., Altschmied, L., Blake, T., Bregitzer, P.P., Cooper, L., Dilbirligi, M., Falk, A., Feiz, L., Graner, A., Gustafson, P., Hayes, P., Lemaux, P., Mammadov, J., Close, T. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal. 84(1):216-227. doi: 10.1111/tpj.12959.
McGhee, L., Hayes, N., Schuck, R., Maffin, L., Hall, G., Hubband, T., Whigham, E., Fuerst, G.S., Wise, R.P. 2016. iTAG Barley: A grade 7-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe Barley. iTunes. Available: https://itunes.apple.com/us/book/itag-barley-grade-7-12-curriculum/id1110510488?mt=11 & https://itunes.apple.com/us/book/itag-barley-grade-7-12-curriculum/id1108586855?mt=11.
Jansen, C., Zhang, Y., Liu, H., Gonzalez-Portilla, P.J., Lauter, N.C., Kumar, B., Trucillo-Silva, I., Martin, J., Lee, M., Simcox, K., Schussler, J., Dhugga, K., Lubberstedt, T. 2015. Genetic and agronomic assessment of cob traits in corn under low and normal nitrogen management conditions. Theoretical and Applied Genetics. 128:1231-1242. doi: 10.1007/s00122-015-2486-0.
Yandeau-Nelson, M.D., Lauter, N.C., Zabotina, O. 2016. Advances in metabolomic applications in plant genetics and breeding. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 10(040):1-15. doi: 10.1079/PAVSNNR201510040.
