Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

Genome Biology
Amelia HubbardDiane G O Saunders

Abstract

Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, reveali...Continue Reading

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Datasets Mentioned

BETA
PRJNA256347
PRJNA257181

Methods Mentioned

BETA
RNA-seq
genotyping
chips
PCR

Software Mentioned

DnaSP
edgeR
ggplot2
iTOL
StrAuto
STRUCTURE
- Toolkit
SAMtools
TopHat package
HTSeq

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