RESEARCH-PGR: QTL Analyses Identify Genetic Components Regulating the Interactions between Plants, Pathogens and the Environment in the Face of Climate Change

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, including 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. In addition, 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 with yield loss upwards of 80% for tomato. Limited control options are available, and 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. Broader, future impacts of this work include the development of novel approaches to examine host-pathogen interactions and how they are affected by external conditions. This then will lead to the identification of plant lines that are more resilient to both abiotic and biotic stresses. Importantly, by elucidating the molecular biology behind the parasite response to those plants under WNT, this study will go beyond merely identifying relevant host genes to contribute new insight into 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 for crop improvement. The goals of this project align with an overarching concern in genetics: to identify DNA variants that influence how individuals respond to their environment. Here, the concept of “individuals” and “environment” are complex. DNA variants in one species will be identified that, in tandem with external environmental conditions, affect how another, interacting species responds. The environmental context considered is warming nighttime temperatures (WNT), a critical, highly relevant, and current environmental concern. Genetically variable tomato plants derived from a cross between a cultivated line and a wild line will be infected with a genetically homogeneous strain of parasitic nematodes. A control experiment will also be performed with uninfected plants. These early, late, and control experiments will be carried out under two temperature regimes: normal nighttime temperatures and WNT. For each treatment combination, phenotypes related to infection and plant health will be collected, along with gene expression data for both plant and nematode. With this design, connections between DNA variants in the tomato genome and molecular responses of the nematode as well as the plant will be made, and the effect of WNT on these connections will be uncovered through via a series of genetic mapping experiments. Leveraging the connections identified in this way, more complex genotype-expression-phenotype pathways can subsequently be inferred, providing a detailed view of the molecular biology of the plant-parasite interaction response to WNT. It will also pinpoint promising candidate genes, which will be functionally validated. All project outcomes will be made publicly accessible through publications and deposition of data and resources in long-term repositories. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.