A pathogenomic approach towards characterising the South African population of puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust
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Date
2018-01
Authors
Van Schalkwyk, Hester Josina
Journal Title
Journal ISSN
Volume Title
Publisher
University of the Free State
Abstract
Stripe (yellow) rust caused by the fungus Puccinia striiformis Westend. f. sp. tritici
(Pst) is a major disease of wheat prevalent in most areas where wheat is cultivated
across the globe. It can completely destroy a crop if left untreated. The
Pst fungus develops feeding structures that form a close relationship with the
host tissue where it facilitates extraction of water and nutrients from the plant,
while manipulating the host for its own benefit using effector proteins. This
parasitic behaviour reduces yield and grain quality, leading to the propagation of
numerous Pst spores, spreading infection. In South Africa stripe rust was first
detected in 1996 with the initial pathotype being designated 6E16A-. Thereafter,
three more Pst pathotypes were detected in subsequent years (6E22A- in 1998,
7E22A- in 2001 and 6E22A+ in 2005), gaining virulence in a stepwise manner by
overcoming additional resistance genes one by one. However, the source of the
original pathotype and the current genetic diversity of the Pst population within
South Africa remain open questions.
To get a better understanding of the South African Pst pathotypes and how
they relate to Pst pathotypes globally, the historical population was described
using a recently developed “field pathogenomics” approach. High-resolution,
next-generation sequencing data utilised in this method aided in determining the
genomic relationships between the four historical pathotypes and investigating
their potential origin. Historic South African isolates representing the four identied
pathotypes were re-sequenced, and their comparison with isolates from the
United Kingdom, France, Pakistan, Ethiopia, Eritrea and Kenya revealed that the
closest relatives of the historical South African isolates were a group of isolates
from East Africa.
We further described polymorphisms in the South African Pst population
that supported the existing hypothesis of stepwise evolution. Through applying
pairwise comparisons between polymorphic sites across isolates, 27 potential
effector proteins that could be instrumental in the stepwise virulence gain, were
identified. To study the role these candidates may play during the infection
processes in different pathotypes, gene expression profiling was conducted using
RT-qPCR. Preliminary patterns of up- or down-regulation of these effectors between
time points, over a time course of compatible interactions, were described.
Furthermore, infected wheat tissues collected from locations across South Africa
during the 2013, 2014 and 2015 cropping seasons, were sequenced. The “field
pathogenomics” method, using RNA-Seq, was applied to compare the historic
Pst isolates with the recent population. This analysis indicated the possibility of a
novel introduction of Pst into South Africa in recent years, possibly between 2011
and 2013. Pathotyping of selected Pst isolates on supplementary wheat tester
genotypes revealed novel variation in infection types that has not been described
previously.
This study provides a high resolution, genomic view of the historical and
prevailing Pst populations and adds valuable information to the potential origin
and adaptation of stripe rust in South Africa. The research outcomes provide
a genomic base for further investigation of candidate effector genes and the
possible recent novel incursion of a pathotype group also seen in Europe, East
Africa and New Zealand into South Africa.
Description
Keywords
Effector, Origin, Plant pathology, Population genomics, Virulence, Thesis (Ph.D. (Plant Sciences (Plant Pathology and Plant Breeding))--University of the Free State, 2018