A pathogenomic approach towards characterising the South African population of puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust
Van Schalkwyk, Hester Josina
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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.