Genotype-based monitoring for fungicide resistance management of cereal pathogens

Cook, Nicola (2020) Genotype-based monitoring for fungicide resistance management of cereal pathogens. Doctoral thesis, University of East Anglia.

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Abstract

Cereal crops are a vital source of nutrients and are crucial to meet the increasing demands on food production. However, up to 40 % of total crop losses can be attributed to fungal pathogens such as the wheat rust Puccinia striiformis f. sp. tritici (Pst). There are three main methods of controlling fungal pathogens: cultivar resistance genes; cultural practices and the use of chemical control methods such as fungicides. Fungicides are a crucial method of controlling fungal pathogens however, the over application and reliance on fungicides has resulted in fungicide resistance within fungal pathogen populations and isolates have been identified that contain non-synonymous mutations which confer resistance to the three main classes of fungicide currently in use. Surveillance of fungal pathogens is an important tool to monitor for new pathogen races that could potentially be virulent on previously resistant cultivars and detect mutations within fungicide target genes that could confer resistance. In this thesis, I used next-generation sequencing technologies to develop novel monitoring methods to investigate both the race composition and state of fungicide resistance in a number of economically important fungal pathogens. Using transcriptomic data of Pst-infected leaf samples, I identified a potential fungicide resistance mutation within the Cyp51 gene in two genetically distant Pst populations. This mutation was heterokaryotic and analysis indicated that the mutation could have arisen twice independently which suggests that it is likely to become prevalent in the global Pst population. I assisted in the development of a mobile method for genotyping Pst-infected samples which used the targeted sequencing of 242 polymorphic genes to characterise Pst races. I used this method to characterise the Ethiopian Pst population and identified a potential population shift over a four-year period. I also developed a genotyping method that would allow the identification of fungicide resistance mutations within multiple fungicide target genes from six fungal pathogens simultaneously that can be used to process samples collected from large scale fungicide field trials. In summary, I used next-generation sequencing technologies to characterise fungal pathogen populations which enabled me to i) identify a potential fungicide resistance mutation within Pst populations, ii) develop a mobile method of genotyping Pst populations that can identify shifts in race and iii) develop a method of genotyping for fungicide resistance mutations within multiple fungicide target genes and fungal pathogens, simultaneously.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	24 Oct 2022 13:58
Last Modified:	31 Jan 2023 01:38
URI:	https://ueaeprints.uea.ac.uk/id/eprint/89306
DOI:

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