Biology subjects

Eshbaugh, R.

Publications and source records attributed to Eshbaugh, R..

3 recordsLinked to original sources

bioRxiv2018

Resequencing and association mapping of the generalist pathogen Botrytis cinerea

We performed whole genome resequencing of 84 field isolates of Botrytis cinerea, largely collected from a local set of plant species. Combined with 13 previously resequenced isolates sampled from diverse locations, this gave a collection of 97 isolates for studies of natural variation. Alignment to the reference sequence T4 and SNP detection provided further data for population genetics analysis including a mapping population for association studies. Although much of the genomic diversity was captured in the original 13 isolates, the additional genomes increased total diversity in the population by a third. Surprisingly, the same additional genomes increase mitochondrial diversity 2-fold. Across the population, LD was limited and decayed rapidly, reflecting frequent outcrossings. Effectively, this sampling strategy increased the level of genetic diversity available, whilst limiting the problem of population stratification and enabling GWAS of several phenotypes on common Arabidopsis plants affected in disease pathways. Overlap of results using all GWAS methods revealed numerous candidate genes / pathways that potentially contribute to its broad host range and offer conceivable pathogen decrease targets.

genomics↗

bioRxiv2018

Plant-Necrotroph Co-transcriptome Networks Illuminate a Metabolic Battlefield

A central goal of studying host-pathogen interaction research is to understand how the host and pathogen manipulate each other to promote their own fitness in a pathosystem. Co-transcriptomic approaches can simultaneously analyze dual transcriptomes during infection and provide a systematic map of the cross-kingdom communication between two species. Here we used the Arabidopsis-B. cinerea pathosystem to test how plant host and fungal pathogen interaction at the transcriptomic level during infection. We assessed the impact of natural genetic diversity in the pathogen and plant host by utilization of a collection of 96 isolates of B. cinerea infection on Arabidopsis wild-type and two mutants with jasmonate or salicylic acid compromised immunities. We identified ten B. cinerea gene co-expression networks (GCNs) that encode known or novel virulence mechanisms. We constructed a dual interaction network by combining four host-and ten pathogen-GCNs into a single network, which revealed potential connections between the fungal and plant GCNs involving both novel and conserved mechanisms. These co-transcriptome data shed lights on the potential mechanisms underlying host-pathogen interaction and illustrate the continued need for advancements of in planta analysis of dual-species dynamics.

systems biology↗

bioRxiv2018

Combining Digital Imaging and Genome Wide Association Mapping to Dissect Uncharacterized Traits in Plant/Pathogen Interactions

Plant resistance to generalist pathogens with broad host ranges, such as Botrytis cinerea, is typically quantitative and highly polygenic. Recent studies have begun to elucidate the molecular genetic basis underpinning plant-pathogen interactions using commonly measured traits including lesion size and/or pathogen biomass. Yet with the advent of digital imaging and phenomics, there are a large number of additional resistance traits available to study quantitative resistance. In this study, we used high-throughput digital imaging analysis to investigate previously uncharacterized visual traits of plant-pathogen interactions related disease resistance using the Arabidopsis thaliana/Botrytis cinerea pathosystem. Using a large collection of 75 visual traits collected from every lesion, we focused on lesion color, lesion shape, and lesion size, to test how these aspects of the interaction are genetically related. Using genome wide association (GWA) mapping in A. thaliana, we show that lesion color and shape are genetically separable traits associated with plant-disease resistance. Using defined mutants in 23 candidate genes from the GWA mapping, we could identify and show that novel loci associated with each different plant-pathogen interaction trait, which expands our understanding of the functional mechanisms driving plant disease resistance.\n\nSummaryDigital imaging allows the identification of genes controlling novel lesion traits.

plant biology↗