<i>Rhynchosporium commune</i> is one of the most destructive fungal pathogens of barley worldwide. It causes scald, responsible for reduced grain quality and yield losses of up to 40%. This project aimed to identify genetic resistance in barley using two different approaches: an effector approach through the identification of important pathogen virulence factors and their barley targets, and a genomics association approach. Numerous secreted effectors have been identified in many phytopathogens including <i>R. commune</i>. <i>Rrs1</i> resistance, recognising the <i>R. commune </i>avirulence protein - AvrRrs1 (NIP1) has been deployed in the field to prevent infection but has soon proven ineffective. <i>R. commune </i>has managed to overcome this resistance by alteration or deletion of the <i>NIP1</i> gene as it is not essential for pathogenicity. However, our field trial data suggests that <i>Rrs1</i> remains an important component of resistance to <i>R. commune</i> in the field. Resistance genes recognising more essential <i>Avr</i> genes are likely to be more durable and as a consequence, the discovery of novel <i>R. commune Avr</i> genes is fundamental for the implementation of an integrated pest management approach to prevent this disease. Recent sequencing of the<i> R. commune</i> genome allowed identification of putative effectors. Expression of 26 potential effectors with low sequence variability in 9 sequenced <i>R. commune</i> strains have been analysed during barley infection. The best genes were selected for gene disruption and individual expression in barley cultivars and landraces using the Barley Stripe Mosaic Virus (BSMV) – based expression system to see if they are recognised by the plant. The work also focused on candidate effectors with putative functions. A putative protease inhibitor was chosen for functional characterisation but its function and importance for pathogenicity could not be confirmed. In addition, high amount of the candidate protein appeared to be toxic for barley and <i>Nicotinana benthamiana</i>. Two SA (salicylic acid)-related putative effectors were also chosen for further characterisation and revealed a direct link between the SA pathway of barley and <i>R. commune</i>. The results of this project suggest that <i>R. commune</i> might be able to manipulate the SA pathway of the host confirming the existence of a biotrophic phase of the fungus. The genomics association approach to identify resistance genes against <i>R. commune</i> in barley used a Genome Wide Association Scan (GWAS) using a combination of three years of disease nursery field trial data for a collection of over 500 elite spring barley cultivars. This analysis identified a number of quantitative trait loci (QTL) in barley genome regions previously shown to contain major resistance genes such as <i>Rrs1</i> on chromosome 3H, <i>Rrs2</i> on chromosome 7H, <i>Rrs3</i> on chromosome 4H, <i>Rrs4</i> on chromosome 3H, <i>Rrs13</i> on chromosome 6H, <i>Rrs14</i> on chromosome 1H and<i> Rrs16</i> on chromosome 4H, as well as novel QTL. The work was focused on <i>Rrs1</i> resistance.<i> R. commune</i> strains producing a type of NIP1 effector, recognised by barley lines containing <i>Rrs1</i>, were used to confirm the resistance in predicted <i>Rrs1</i> barley cultivars. The <i>Rrs1</i> interval has been narrowed down to 3 Mbp, and high resolution mapping led to the identification of 3 SNP markers which perfectly discriminated <i>Rrs1Rh4</i> lines from susceptible lines. These diagnostic markers will provide a useful breeding tool for improving the design of new varieties allowing the incorporation of the<i> Rrs1</i> resistance. This research takes us a step closer towards cloning the first barley major resistance (R) gene against <i>R. commune</i>, which is likely to be present only in<i> Rrs1</i> lines and have a kinase domain very similar to the one in a putative wall associated kinase found within the <i>Rrs1 </i>interval in the genome assembly of susceptible cultivar Morex. It will also help us to better understand <i>R. commune</i>-barley pathosystem and to identify further R genes.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:743118 |
| Date | January 2017 |
| Creators | Griffe, Lucie L. |
| Contributors | Hein, Ingo ; Birch, Paul |
| Publisher | University of Dundee |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | https://discovery.dundee.ac.uk/en/studentTheses/72e2cc57-c7fd-4158-991e-03127df74984 |
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