Ecological Genomics and Epidemiology

Abstract

The huge amount of genomic data now becoming available offers both opportunities and challenges for epidemiologists. In this ''preview'' of likely developments as the field of ecological genomics evolves and merges with epidemiology, we discuss how epidemiology can use new information about genetic sequences and gene expression to form predictions about epidemic features and outcomes and for understanding host resistance and pathogen evolution. DNA sequencing is now complete for some hosts and several pathogens. Microarrays make it possible to measure gene expression simultaneously for thousands of genes. These tools will contribute to plant disease epidemiology by providing information about which resistance or pathogenicity genes are present in individuals and populations, what genes other than those directly involved in resistance and virulence are important in epidemics, the role of the phenotypic status of hosts and pathogens, and the role of the status of the environmental metagenome. Conversely, models of group dynamics supplied by population biology and ecology may be used to interpret gene expression within individual organisms and in populations of organisms. Genomic tools have great potential for improving understanding of resistance gene evolution and the durability of resistance. For example, DNA sequence analysis can be used to evaluate whether an arms race model of co-evolution is supported. Finally, new genomic tools will make it possible to consider the landscape ecology of epidemics in terms of host resistance both as determined by genotype and as expressed in host phenotypes in response to the biotic and abiotic environment. Host phenotype mixtures can be modeled and evaluated, with epidemiological predictions based on phenotypic characteristics such as physiological age and status in terms of induced systemic resistance or systemic acquired resistance.

Meta-Analysis and Other Approaches for Synthesizing Structured and Unstructured Data in Plant Pathology

“…In return, this will allow for novel ecological perspectives on the role of particular genes and mechanistic understanding of ecological processes (136). In plant pathology, such an approach would open the potential for analysis of landscapes of host phenotypic resistance and their effects on epidemics (48). Similarly, there is potential to reconstruct aspects of long-term historical epidemiology by understanding plant and pathogen genomes as well as by studying the geographic distributions of genome components important to epidemics.…”

Functional agrobiodiversity and agroecosystem services in sustainable wheat production. A review

“…This suggests that no cultivar, be it homogeneous or heterogeneous, can provide a fully durable resistance. Hence, the approach of resistance deployment on a landscape scale is gaining interest (Fabre et al 2012;Garret et al 2006;Papaix et al 2011).…”

“…The yield advantage of cultivar mixtures over pure stands of their components has been proven especially in the presence of diseases (Akanda and Mundt 1997;Kiaer et al 2009). This is due to a host diversity effect (Garret et al 2006;Garret et al 2009) whose efficacy is strictly linked to the epidemiological conditions of the disease and to life histories of the pathogens. As an example, Cox et al (2004) hypothesised that host diversity would be more effective in reducing leaf rust (Puccinia triticina f. sp.…”

Climate change and plant health: designing research spillover from plant genomics for understanding the role of microbial communities

“…The host population or community can be characterized in terms of induced and acquired resistance levels (e.g. Garrett et al, 2006b). The environment can be characterized with more detail about abiotic features, or with information about abundance of other organisms, such as the abundance of mycorrhizal fungi, though integration across such datasets can be challenging (Jumpponen et al 2010).…”