{"id":{"repo_id":"dundee","oai_identifier":"oai:discovery.dundee.ac.uk:studenttheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a"},"canonical_url":"https://search.dev.ndltd.org/etd/dundee/oai:discovery.dundee.ac.uk:studenttheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a","repository":{"repo_id":"dundee","name":"University of Dundee","base_url":"https://discovery.dundee.ac.uk/ws/oai"},"display":{"title":"Engineering durable late blight resistance to protect solanaceous plants","abstract":"<i>Phytophthora infestans</i>, the oomycete pathogen responsible for late blight of potato and tomato, is regarded as the biggest threat to global potato production and is thought to cost the industry around £6 billion annually. Traditionally, fungicides have been used to control the disease, but this is both economically and environmentally costly, as multiple chemical applications may be required during a single growing season. <i>P. infestans</i> has rapidly overcome genetic resistances introduced into cultivated potato from wild species. This provides the rationale for developing artificial resistance genes to create durable resistance to late blight disease.<i>Phytophthora</i> species secrete essential effectors into plant cells that target critical host cellular mechanisms to promote disease. One such <i>P. infestans</i> effector is AVR3a<sup>KI</sup> which is recognised by the potato R3a protein, a member of the CC-NB-LRR type resistance gene family. However, the closely related virulent form, AVR3a<sup>EM</sup>, which is homozygous in more than 70% of wild <i>P. infestans</i> isolates, evades this recognition.Domain swapping experiments have revealed that the LRR domain of R3a is involved in recognition of AVR3a<sup>KI</sup>, as the CC-NB domain of an R3a-paralog which does not mediate recognition of AVR3a<sup>KI</sup>, is able to induce a HR when combined with the LRR of wild-type R3a. However, a chimeric protein consisting of the CC-NB domain of a more distantly-related homolog of R3a and the LRR of domain of R3a, is unable to recognise AVR3a<sup>KI</sup>, suggesting that function is achieved only when the different domains of an R protein are attuned to recognition and signalling.Gain-of-function variants of <i>R3a</i> (<i>R3a*</i>), engineered by an iterative process of error-prone PCR, DNA fragmentation, re-assembly of the leucine rich repeat (LRR)-encoding region of <i>R3a</i>, are able to recognise both forms of AVR3a. This gain-of-recognition is accompanied by a gain-of-mechanism, as shown by a cellular re-localisation from the cytoplasm to prevacuolar compartments upon perception of recognised effector forms. However, R3a* variants do not confer resistance to AVR3a<sup>EM</sup>-carrying isolates of <i>P. infestans</i>.Future efforts will target the NB-ARC domain of R3a, in a bid to fine-tune the intra-cellular signalling of gain-of-recognition R3a* variants. It is hoped that a shuffled <i>R3a*</i> gene, capable of conferring resistance to <i>P. infestans</i> isolates harbouring AVR3a<sup>EM</sup>, will provide durable late blight resistance when deployed in the field in combination with other mechanistically different R proteins.","abstract_html":"&lt;i&gt;Phytophthora infestans&lt;/i&gt;, the oomycete pathogen responsible for late blight of potato and tomato, is regarded as the biggest threat to global potato production and is thought to cost the industry around £6 billion annually. Traditionally, fungicides have been used to control the disease, but this is both economically and environmentally costly, as multiple chemical applications may be required during a single growing season. &lt;i&gt;P. infestans&lt;/i&gt; has rapidly overcome genetic resistances introduced into cultivated potato from wild species. This provides the rationale for developing artificial resistance genes to create durable resistance to late blight disease.&lt;i&gt;Phytophthora&lt;/i&gt; species secrete essential effectors into plant cells that target critical host cellular mechanisms to promote disease. One such &lt;i&gt;P. infestans&lt;/i&gt; effector is AVR3a&lt;sup&gt;KI&lt;/sup&gt; which is recognised by the potato R3a protein, a member of the CC-NB-LRR type resistance gene family. However, the closely related virulent form, AVR3a&lt;sup&gt;EM&lt;/sup&gt;, which is homozygous in more than 70% of wild &lt;i&gt;P. infestans&lt;/i&gt; isolates, evades this recognition.Domain swapping experiments have revealed that the LRR domain of R3a is involved in recognition of AVR3a&lt;sup&gt;KI&lt;/sup&gt;, as the CC-NB domain of an R3a-paralog which does not mediate recognition of AVR3a&lt;sup&gt;KI&lt;/sup&gt;, is able to induce a HR when combined with the LRR of wild-type R3a. However, a chimeric protein consisting of the CC-NB domain of a more distantly-related homolog of R3a and the LRR of domain of R3a, is unable to recognise AVR3a&lt;sup&gt;KI&lt;/sup&gt;, suggesting that function is achieved only when the different domains of an R protein are attuned to recognition and signalling.Gain-of-function variants of &lt;i&gt;R3a&lt;/i&gt; (&lt;i&gt;R3a*&lt;/i&gt;), engineered by an iterative process of error-prone PCR, DNA fragmentation, re-assembly of the leucine rich repeat (LRR)-encoding region of &lt;i&gt;R3a&lt;/i&gt;, are able to recognise both forms of AVR3a. This gain-of-recognition is accompanied by a gain-of-mechanism, as shown by a cellular re-localisation from the cytoplasm to prevacuolar compartments upon perception of recognised effector forms. However, R3a* variants do not confer resistance to AVR3a&lt;sup&gt;EM&lt;/sup&gt;-carrying isolates of &lt;i&gt;P. infestans&lt;/i&gt;.Future efforts will target the NB-ARC domain of R3a, in a bid to fine-tune the intra-cellular signalling of gain-of-recognition R3a* variants. It is hoped that a shuffled &lt;i&gt;R3a*&lt;/i&gt; gene, capable of conferring resistance to &lt;i&gt;P. infestans&lt;/i&gt; isolates harbouring AVR3a&lt;sup&gt;EM&lt;/sup&gt;, will provide durable late blight resistance when deployed in the field in combination with other mechanistically different R proteins.","abstract_has_math":false,"creators":["Stevens, Laura J."],"institution":"University of Dundee","degree_name":"Doctor of Philosophy","degree_level":"Doctoral Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Birch, Paul","Chapman, Sean","Hein, Ingo"],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016","date_published":"2016","updated_at":"2026-07-24T02:08:12Z","subjects":["Resistance gene","Artificial evolution","Effectors","Phytophthora infestans","Potato","Plant pathology","Oomycete","PCR shuffling"],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["oai:discovery.dundee.ac.uk:studenttheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a"],"render_values":[{"text":"oai:discovery.dundee.ac.uk:studenttheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a","href":null,"code":true}]}]},"links":{"outbound_url":"https://discovery.dundee.ac.uk/en/studentTheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Birch, Paul","Chapman, Sean","Hein, Ingo"]},{"key":"dc:contributor.sponsor","label":"Sponsor","values":["The James Hutton Institute"]},{"key":"dc:creator","label":"Author","values":["Stevens, Laura J."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2016"]},{"key":"dc:date.issued","label":"Date","values":["2016"]},{"key":"dc:publisher.department","label":"Dc Publisher Department","values":["Plant Sciences"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Dundee"]},{"key":"dc:relation.isreferencedby","label":"Dc Relation Isreferencedby","values":["https://discovery.dundee.ac.uk/en/studentTheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral Thesis"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Resistance gene","Artificial evolution","Effectors","Phytophthora infestans","Potato","Plant pathology","Oomycete","PCR shuffling"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["oai:discovery.dundee.ac.uk:studenttheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a","https://discovery.dundee.ac.uk/en/studentTheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://discovery.dundee.ac.uk/files/8345646/Engineering_durable_late_blight_resistance_to_protect_solanaceous_plants.pdf"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["<i>Phytophthora infestans</i>, the oomycete pathogen responsible for late blight of potato and tomato, is regarded as the biggest threat to global potato production and is thought to cost the industry around £6 billion annually. Traditionally, fungicides have been used to control the disease, but this is both economically and environmentally costly, as multiple chemical applications may be required during a single growing season. <i>P. infestans</i> has rapidly overcome genetic resistances introduced into cultivated potato from wild species. This provides the rationale for developing artificial resistance genes to create durable resistance to late blight disease.<i>Phytophthora</i> species secrete essential effectors into plant cells that target critical host cellular mechanisms to promote disease. One such <i>P. infestans</i> effector is AVR3a<sup>KI</sup> which is recognised by the potato R3a protein, a member of the CC-NB-LRR type resistance gene family. However, the closely related virulent form, AVR3a<sup>EM</sup>, which is homozygous in more than 70% of wild <i>P. infestans</i> isolates, evades this recognition.Domain swapping experiments have revealed that the LRR domain of R3a is involved in recognition of AVR3a<sup>KI</sup>, as the CC-NB domain of an R3a-paralog which does not mediate recognition of AVR3a<sup>KI</sup>, is able to induce a HR when combined with the LRR of wild-type R3a. However, a chimeric protein consisting of the CC-NB domain of a more distantly-related homolog of R3a and the LRR of domain of R3a, is unable to recognise AVR3a<sup>KI</sup>, suggesting that function is achieved only when the different domains of an R protein are attuned to recognition and signalling.Gain-of-function variants of <i>R3a</i> (<i>R3a*</i>), engineered by an iterative process of error-prone PCR, DNA fragmentation, re-assembly of the leucine rich repeat (LRR)-encoding region of <i>R3a</i>, are able to recognise both forms of AVR3a. This gain-of-recognition is accompanied by a gain-of-mechanism, as shown by a cellular re-localisation from the cytoplasm to prevacuolar compartments upon perception of recognised effector forms. However, R3a* variants do not confer resistance to AVR3a<sup>EM</sup>-carrying isolates of <i>P. infestans</i>.Future efforts will target the NB-ARC domain of R3a, in a bid to fine-tune the intra-cellular signalling of gain-of-recognition R3a* variants. It is hoped that a shuffled <i>R3a*</i> gene, capable of conferring resistance to <i>P. infestans</i> isolates harbouring AVR3a<sup>EM</sup>, will provide durable late blight resistance when deployed in the field in combination with other mechanistically different R proteins."]},{"key":"dc:title","label":"Title","values":["Engineering durable late blight resistance to protect solanaceous plants"]}]}],"canonical_facts":{"dc:contributor.advisor":["Birch, Paul","Chapman, Sean","Hein, Ingo"],"dc:contributor.sponsor":["The James Hutton Institute"],"dc:creator":["Stevens, Laura J."],"dc:date":["2016"],"dc:date.issued":["2016"],"dc:description.abstract":["<i>Phytophthora infestans</i>, the oomycete pathogen responsible for late blight of potato and tomato, is regarded as the biggest threat to global potato production and is thought to cost the industry around £6 billion annually. Traditionally, fungicides have been used to control the disease, but this is both economically and environmentally costly, as multiple chemical applications may be required during a single growing season. <i>P. infestans</i> has rapidly overcome genetic resistances introduced into cultivated potato from wild species. This provides the rationale for developing artificial resistance genes to create durable resistance to late blight disease.<i>Phytophthora</i> species secrete essential effectors into plant cells that target critical host cellular mechanisms to promote disease. One such <i>P. infestans</i> effector is AVR3a<sup>KI</sup> which is recognised by the potato R3a protein, a member of the CC-NB-LRR type resistance gene family. However, the closely related virulent form, AVR3a<sup>EM</sup>, which is homozygous in more than 70% of wild <i>P. infestans</i> isolates, evades this recognition.Domain swapping experiments have revealed that the LRR domain of R3a is involved in recognition of AVR3a<sup>KI</sup>, as the CC-NB domain of an R3a-paralog which does not mediate recognition of AVR3a<sup>KI</sup>, is able to induce a HR when combined with the LRR of wild-type R3a. However, a chimeric protein consisting of the CC-NB domain of a more distantly-related homolog of R3a and the LRR of domain of R3a, is unable to recognise AVR3a<sup>KI</sup>, suggesting that function is achieved only when the different domains of an R protein are attuned to recognition and signalling.Gain-of-function variants of <i>R3a</i> (<i>R3a*</i>), engineered by an iterative process of error-prone PCR, DNA fragmentation, re-assembly of the leucine rich repeat (LRR)-encoding region of <i>R3a</i>, are able to recognise both forms of AVR3a. This gain-of-recognition is accompanied by a gain-of-mechanism, as shown by a cellular re-localisation from the cytoplasm to prevacuolar compartments upon perception of recognised effector forms. However, R3a* variants do not confer resistance to AVR3a<sup>EM</sup>-carrying isolates of <i>P. infestans</i>.Future efforts will target the NB-ARC domain of R3a, in a bid to fine-tune the intra-cellular signalling of gain-of-recognition R3a* variants. It is hoped that a shuffled <i>R3a*</i> gene, capable of conferring resistance to <i>P. infestans</i> isolates harbouring AVR3a<sup>EM</sup>, will provide durable late blight resistance when deployed in the field in combination with other mechanistically different R proteins."],"dc:identifier":["oai:discovery.dundee.ac.uk:studenttheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a","https://discovery.dundee.ac.uk/en/studentTheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a"],"dc:identifier.uri":["https://discovery.dundee.ac.uk/files/8345646/Engineering_durable_late_blight_resistance_to_protect_solanaceous_plants.pdf"],"dc:language":["eng"],"dc:publisher.department":["Plant Sciences"],"dc:publisher.institution":["University of Dundee"],"dc:relation.isreferencedby":["https://discovery.dundee.ac.uk/en/studentTheses/27fe2bc9-ac18-4000-a3cf-9bb895cabe3a"],"dc:subject":["Resistance gene","Artificial evolution","Effectors","Phytophthora infestans","Potato","Plant pathology","Oomycete","PCR shuffling"],"dc:title":["Engineering durable late blight resistance to protect solanaceous plants"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["Doctoral Thesis"],"dc:type.qualificationname":["Doctor of Philosophy"]},"updated_at":"2026-07-24T02:08:12Z"}