{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/31918"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/31918","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Host and pathogen genomics: the molecular repertoire of soybean and Sclerotinia interactions","abstract":"Sclerotinia sclerotiorum (Lib.) de Bary is an economically important soybean pathogen in the U.S. and worldwide. Understanding the disease caused by this fungus can help in controlling it. In the present study, genome-wide screenings were carried out to identify soybean mRNAs and small RNAs that change in expression during early infection stages with S. sclerotiorum or its primary virulence factor, oxalic acid. Microarray expression data was obtained from a transgenic soybean line expressing oxalate oxidase (OxO), an enzyme that degrades oxalic acid, and from its parent, the soybean cultivar ‘AC-Colibri’. Treatments included direct inoculations with S. sclerotiorum and leaf infiltrations with oxalic acid. Taking advantage of novel technologies, the profiling of gene expression was later expanded by subjecting the RNA samples used in the microarrays to deep sequencing using the Illumina/Solexa SBS platform. These studies allowed for the identification of a set of genes that may play important roles during pathogenicity, including several known defense-related genes. The data also suggested the possible involvement of iron homeostasis during disease development. In a second study, the Illumina/Solexa platform was used to query the small RNA composition of control and inoculated soybean stems, and of S. sclerotiorum mycelia grown on liquid media. In addition to these global RNA expression studies, a gene-specific study was carried out on the role of a putative G protein-coupled receptor possibly implicated in the plant interactions with pathogens. The gene was identified, cloned and an RNAi vector was constructed and transformed into soybean with the objective of carrying future functional analyses.","abstract_html":"Sclerotinia sclerotiorum (Lib.) de Bary is an economically important soybean pathogen in the U.S. and worldwide. Understanding the disease caused by this fungus can help in controlling it. In the present study, genome-wide screenings were carried out to identify soybean mRNAs and small RNAs that change in expression during early infection stages with S. sclerotiorum or its primary virulence factor, oxalic acid. Microarray expression data was obtained from a transgenic soybean line expressing oxalate oxidase (OxO), an enzyme that degrades oxalic acid, and from its parent, the soybean cultivar ‘AC-Colibri’. Treatments included direct inoculations with S. sclerotiorum and leaf infiltrations with oxalic acid. Taking advantage of novel technologies, the profiling of gene expression was later expanded by subjecting the RNA samples used in the microarrays to deep sequencing using the Illumina/Solexa SBS platform. These studies allowed for the identification of a set of genes that may play important roles during pathogenicity, including several known defense-related genes. The data also suggested the possible involvement of iron homeostasis during disease development. In a second study, the Illumina/Solexa platform was used to query the small RNA composition of control and inoculated soybean stems, and of S. sclerotiorum mycelia grown on liquid media. In addition to these global RNA expression studies, a gene-specific study was carried out on the role of a putative G protein-coupled receptor possibly implicated in the plant interactions with pathogens. The gene was identified, cloned and an RNAi vector was constructed and transformed into soybean with the objective of carrying future functional analyses.","abstract_has_math":false,"creators":["Calla Zalles, Bernarda"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Crop Sciences","degree_department":null,"school":null,"contributors":["Clough, Steven J.","Vodkin, Lila O.","Domier, Leslie L.","Ming, Ray R."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-06-27T21:19:16Z","date_published":"2012-06-27T21:19:16Z","updated_at":"2026-07-22T22:25:30Z","subjects":["Sclerotinia","soybean","genomics"],"languages":["en"],"rights":["Copyright 2012 Bernarda Calla Zalles"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/31918","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Clough, Steven J.","Vodkin, Lila O.","Domier, Leslie L.","Ming, Ray R."]},{"key":"dc:creator","label":"Author","values":["Calla Zalles, Bernarda"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2012-06-27T21:19:16Z","2014-06-28T10:00:18Z","2012-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Crop Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Sclerotinia","soybean","genomics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2012 Bernarda Calla Zalles"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/31918"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Sclerotinia sclerotiorum (Lib.) de Bary is an economically important soybean pathogen in the U.S. and worldwide. Understanding the disease caused by this fungus can help in controlling it. In the present study, genome-wide screenings were carried out to identify soybean mRNAs and small RNAs that change in expression during early infection stages with S. sclerotiorum or its primary virulence factor, oxalic acid. Microarray expression data was obtained from a transgenic soybean line expressing oxalate oxidase (OxO), an enzyme that degrades oxalic acid, and from its parent, the soybean cultivar ‘AC-Colibri’. Treatments included direct inoculations with S. sclerotiorum and leaf infiltrations with oxalic acid. Taking advantage of novel technologies, the profiling of gene expression was later expanded by subjecting the RNA samples used in the microarrays to deep sequencing using the Illumina/Solexa SBS platform. These studies allowed for the identification of a set of genes that may play important roles during pathogenicity, including several known defense-related genes. The data also suggested the possible involvement of iron homeostasis during disease development. In a second study, the Illumina/Solexa platform was used to query the small RNA composition of control and inoculated soybean stems, and of S. sclerotiorum mycelia grown on liquid media. In addition to these global RNA expression studies, a gene-specific study was carried out on the role of a putative G protein-coupled receptor possibly implicated in the plant interactions with pathogens. 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In a second study, the Illumina/Solexa platform was used to query the small RNA composition of control and inoculated soybean stems, and of S. sclerotiorum mycelia grown on liquid media. In addition to these global RNA expression studies, a gene-specific study was carried out on the role of a putative G protein-coupled receptor possibly implicated in the plant interactions with pathogens. The gene was identified, cloned and an RNAi vector was constructed and transformed into soybean with the objective of carrying future functional analyses.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2012-03-23T13:48:49Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 6 Dissertation final version March 20 2012.pdf: 4107929 bytes, checksum: 83f0cb1b09ed9e2307af4f96858eb485 (MD5) CallaZalles_Bernarda.pdf: 4107929 bytes, checksum: 83f0cb1b09ed9e2307af4f96858eb485 (MD5) Appendix E. 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