Performing Department
(N/A)
Non Technical Summary
An organism's ability to respond to its environment is fundamental to its survival. When the organism of interest is involved in a host-pathogen interaction, "the environment" becomes complex: it includes not only external forces, but also the conditions imposed by the interacting partner. There are also two genomes at play; each of which affects the behavior of both organisms. Of course, external environmental forces impose additional pressures, and each genome can affect how both partners respond. This project examines the role the host genome plays in altering behavior of both host and pathogen under environmental stress. It leverages an agriculturally relevant system: nematode infection of tomato. Parasitic nematodes are responsible for around $125 billion in annual crop loss worldwide, and in tomato, yield loss can be upwards of 80%. Limited control options are available. The situation is exacerbated by an emerging concern in agriculture: the effect of warming nighttime temperatures (WNT). This unprecedented trend is causing critical challenges to crops. This project develops novel approaches to examine host-pathogen interactions and how they are affected by external conditions. Broader, future impacts of this work include the ability to identify plant lines that are more resilient, but importantly, also to elucidate the molecular biology behind the parasite response to those plants under WNT. This goes beyond merely identifying relevant host genes, it allows us to understand the mechanisms by which those genes alter the nematode biology. Understanding the nematode in addition to the plant paves the way towards targeting the parasite directly.
Animal Health Component
0%
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Goals / Objectives
The circadian clock is fundamental to many life functions. The ability to coordinate daily biochemical and metabolic activities based on environmental cues, like temperature, is important to all life. A less recognized role for the circadian clock is that of regulating responses to pathogen attack. With the observed and expected changes in global climate, there is a critical need to understand the importance of thermocycles in terms of plant growth and development, and their effects on plants response to pathogens. The major goals of this project are to identify and quantify differential plant responses to pathogen attack under normal night temperature (NNT) and warmer night temperature (WNT) and to dissect the genetic architecture in plants underpinning both these different responses and the signaling that occurs between plant host and pathogen. We will use the powerful genetic tools available in tomato and Root-Knot Nematode (RKN: Meloidogyne hapla). Our approach will enable us to identify genetic variants in plants that display more robust responses to infection during WNT and will also enable us to explore the biological basis of the interactions between a host plant, an important and agriculturally damaging plant pathogen, and environmental changes. This project is focused on understanding the intersection of abiotic and biotic stress responses of plants.Ultimately, our innovative findings will enable further translational work to help improve plant disease management, identify genetic components regulating the interactions between environment and pathogenicity, enhance breeding efforts to improve plant health and resilience in the face of the compounding challenges of a changing climate, and provide targets for combatting plant parasites.Specific Aims1. To identify DNA variants in the tomato genome that underlie phenotype responses to the interspecies-WNT meta-environment.2. To identify DNA variants in the tomato genome that underlie plant gene expression responses (eQTL) and nematode expression responses (cross-species eQTL) to the interspecies-WNT meta-environment.3. To infer pathways connecting DNA variants, plant and nematode gene expression responses, and phenotype responses to the interspecies-WNT meta-environment.4. To select and validate candidate genes experimentally.5. To integrate the project's basic and widely applicable research into our broad outreach programs including (a) UF DNA Day, which brings graduate students and postdocs to rural high schools to talk about genetics and careers in science; and (b) NCSU outreach to underrepresented students with St. Augustine's University that includes a summer internship program for undergraduates.
Project Methods
Summary of work to be completed for the remainder of the project:Specific Aim 1: We will measure traits from the plant (e.g., root and total biomass, leaf number, chlorosis, and photosynthetic capacity) and the nematode (e.g., infection efficiency, gall size, and gall ratings). These traits provide information on plant health/stress (total biomass, leaf number, chlorosis, and photosynthetic capacity) or on infection intensity (gall traits and root biomass). This will be performed under two temperatures regimens, representing NNT and WNT.We will use the tomato RIL population created by Ashrafi, et. al. (Dr. Ashrafi is an Assistant Professor at NCSU in the Dept. of Horticulture and is a member of the Bioinformatics Research Center, as are co-PIs Nielsen & Doherty). These RILs were developed through a cross between the cultivated tomato, Solanum lycopersicum (accession NCEBR-1), and the red-fruited wild tomato species, Solanum pimpinellifolium (accession LA2093). Using this population, Ashrafi, et. al. were able to generate a high-resolution linkage map, and to identify QTL for a number of agriculturally important traits, including disease resistance, defense-related response, and fruit quality. Seeds from 148 RILs are available through the tomato germplasm resource center at UC Davis.Specific Aim 2: eQTL mapping identifies DNA polymorphisms that are involved with changes in patterns of gene expression. In other words, individuals that have different genotypes at these loci will also have different expression patterns at the affected genes. eQTL mapping is performed much the same way standard QTL mapping is: genetic markers across the genome are examined to see if they are correlated with phenotypes. In eQTL mapping, the phenotype is the expression level of a given gene. Just as QTL mapping runs through the entire genetic map searching for connections between markers and a trait, eQTL mapping runs through the genetic map searching for connections with expression levels of a given gene. If expression has been assayed for 20,000 genes in the genome, 20,000 eQTL mapping runs are performed.Cross-species eQTL mapping occurs when genotypes in one species are correlated with gene expression in another, interacting species. For each nematode gene that is measured, the expression value for that gene is compared to the plant genotypes at each plant locus. Here we will map nematode expression onto the plant genome. A positive result connects the plant locus with the target nematode gene expression.Cross-species genotype-by-environment (GxE) interactions: Our cross-species approach will also be updated to identify DNA variants in the plant that interact with broader environmental conditions to affect gene expression responses in the nematode. This will allow us to pinpoint candidate genes in both species concurrently that are key to the meta-environment interaction.Specific Aim 3: Specific Aim 1 will identify DNA variants in the tomato genome that underlie phenotype responses to the interspecies-WNT meta-environment, and Specific Aim 2 will identify DNA variants that underlie both plant and parasite gene expression responses to the meta-environment. In Specific Aim 3, we integrate these components. Using a network approach, we will infer pathways connecting DNA markers, gene expression responses, and phenotype responses, and identify how environmental factors affect these connections. This type of network is illustrated in Fig. 5, from the previous Medicago-RKN experiment. Connections between genes and/or loci are indicated by lines in the figure. In this network, there are DNA variants at the HEM1 locus in the nematode genome that influence both plant and parasite gene expression changes. As a specific example, parasite HEM1 variants affect expression of plant gene 22: this is a direct connection. Plant gene 22 expression is connected to plant gene 23 expression: this is also a direct connection. HEM1 is indirectly connected to plant gene 23 through the inferred pathway. Identifying direct and indirect connections such as this allows us to prioritize target candidate genes for functional tests (Aim 4). In Fig. 5, priorities would be nematode genes within the HEM1 locus and the plant genes that have direct connections to HEM1. In the previous experiment, only expression data collected under common controlled environmental conditions were measured. No further phenotype information was available for this analysis, and thus no traits were included in the network. This will not be a limitation in the current project.Specific Aim 4: Aims 1-3 will provide candidate genes based on their connections within the inferred networks. For the current project, candidates are genes that function at the interface between the host-pathogen interaction and responses to WNT. To evaluate the success of our approach and to examine potential candidate loci for their practical applications, we will experimentally evaluate the interactions by altering the loci through genetic modification in tomato. Candidate gene selection will be based on the networks generated in Aim 3 (or directly from the results of Aim 1 or 2 if necessary). We expect to target 5-10 plant genes for initial validation in the time frame of this proposal. More detailed evaluation and molecular characterization will be pursued beyond the time frame of this proposal.Specific Aim 5: To integrate the project's basic and widely applicable research into our broad outreach programs including (a) UF DNA Day, which brings graduate students and postdocs to rural high schools to talk about genetics and careers in science; and (b) NCSU summer internship program for underrepresented undergraduate students with St. Augustine's University.