{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/130129"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/130129","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Unraveling sorghum stem biology through organ-specific and cell-type-specific transcriptomic analyses across development","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-08-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-08-01","abstract_has_math":false,"creators":["Fu, Jie"],"institution":"University of Illinois Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Plant Biology","degree_department":null,"school":null,"contributors":["Marshall-Colón, Amy","Brooks, Matthew","Moose, Stephen Patrick","Studer, Anthony Joseph"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-06-25","date_published":"2025-06-25","updated_at":"2026-07-22T22:25:06Z","subjects":["Sorghum","Bioenergy","Organ","Stem Specific","Development","Cell Type Specific","Gene Expression","Gene Regulatory Network","Multi-omics"],"languages":["en","eng"],"rights":["Copyright 2025 Jie Fu"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/130129","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Marshall-Colón, Amy","Brooks, Matthew","Moose, Stephen Patrick","Studer, Anthony Joseph"]},{"key":"dc:creator","label":"Author","values":["Fu, Jie"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-06-25","2025-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Plant Biology"]},{"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 Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Sorghum","Bioenergy","Organ","Stem Specific","Development","Cell Type Specific","Gene Expression","Gene Regulatory Network","Multi-omics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Jie Fu"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/130129"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-08-01","The student, Jie Fu, accepted the attached license on 2025-06-24 at 09:46.","The student, Jie Fu, submitted this Dissertation for approval on 2025-06-24 at 10:06.","This Dissertation was approved for publication on 2025-06-25 at 15:52.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22359 on 2025-10-25 at 15:52:34","Sorghum bicolor is a promising bioenergy crop due to its high biomass yield, resilience to environmental stress, and low nutrient requirement. However, a comprehensive molecular understanding of sorghum stem development and cell-type specialization remains limited, hindering targeted improvement of biomass quality and carbon allocation. This dissertation presents a multi-scale, transcriptome-centered approach to investigate sorghum stem biology at both organ and cell-type resolution across key developmental stages. Chapter 1 provides a detailed introduction to sorghum as an important feedstock, its stem structure and development, and current knowledge gaps and obstacles for “ideotype” development, laying the foundation for targeted investigation. Chapter 2 leverages public transcriptomic datasets to identify organ-specific expression patterns and uncover a set of stem-preferred/specific genes and their dynamic expression pattern across developmental stages. Motif enrichment and functional analyses highlight candidate regulatory elements and gene functions associated with stem identity. In Chapter 3, laser capture microdissection (LCM) was used to isolate five anatomically distinct cell types from the sorghum stem, enabling high-resolution transcriptomic profiling. This analysis reveals spatially organized metabolic and regulatory programs, cell-type-specific gene networks, and elucidates distinct cellular mechanisms for secondary cell wall formation. Chapter 4 integrates transcriptomic and proteomic analyses of stem cell types before and after floral initiation to explore developmental reprogramming. The results uncover a tradeoff between secondary cell wall biosynthesis and non-structural sugar accumulation and highlight the dynamic regulation of key biosynthetic pathways during the transition to reproductive growth. Together, these studies offer a systems-level view of sorghum stem biology, providing new insight into stem cell-type function, developmental programming, and regulatory network. The findings lay the groundwork for precision engineering of stem traits to optimize sorghum as a bioenergy feedstock."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Unraveling sorghum stem biology through organ-specific and cell-type-specific transcriptomic analyses across development"]}]}],"canonical_facts":{"dc:contributor":["Marshall-Colón, Amy","Brooks, Matthew","Moose, Stephen Patrick","Studer, Anthony Joseph"],"dc:creator":["Fu, Jie"],"dc:date":["2025-06-25","2025-08"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-08-01","The student, Jie Fu, accepted the attached license on 2025-06-24 at 09:46.","The student, Jie Fu, submitted this Dissertation for approval on 2025-06-24 at 10:06.","This Dissertation was approved for publication on 2025-06-25 at 15:52.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22359 on 2025-10-25 at 15:52:34","Sorghum bicolor is a promising bioenergy crop due to its high biomass yield, resilience to environmental stress, and low nutrient requirement. However, a comprehensive molecular understanding of sorghum stem development and cell-type specialization remains limited, hindering targeted improvement of biomass quality and carbon allocation. This dissertation presents a multi-scale, transcriptome-centered approach to investigate sorghum stem biology at both organ and cell-type resolution across key developmental stages. Chapter 1 provides a detailed introduction to sorghum as an important feedstock, its stem structure and development, and current knowledge gaps and obstacles for “ideotype” development, laying the foundation for targeted investigation. Chapter 2 leverages public transcriptomic datasets to identify organ-specific expression patterns and uncover a set of stem-preferred/specific genes and their dynamic expression pattern across developmental stages. Motif enrichment and functional analyses highlight candidate regulatory elements and gene functions associated with stem identity. In Chapter 3, laser capture microdissection (LCM) was used to isolate five anatomically distinct cell types from the sorghum stem, enabling high-resolution transcriptomic profiling. This analysis reveals spatially organized metabolic and regulatory programs, cell-type-specific gene networks, and elucidates distinct cellular mechanisms for secondary cell wall formation. Chapter 4 integrates transcriptomic and proteomic analyses of stem cell types before and after floral initiation to explore developmental reprogramming. The results uncover a tradeoff between secondary cell wall biosynthesis and non-structural sugar accumulation and highlight the dynamic regulation of key biosynthetic pathways during the transition to reproductive growth. Together, these studies offer a systems-level view of sorghum stem biology, providing new insight into stem cell-type function, developmental programming, and regulatory network. The findings lay the groundwork for precision engineering of stem traits to optimize sorghum as a bioenergy feedstock."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/130129"],"dc:language":["en","eng"],"dc:rights":["Copyright 2025 Jie Fu"],"dc:subject":["Sorghum","Bioenergy","Organ","Stem Specific","Development","Cell Type Specific","Gene Expression","Gene Regulatory Network","Multi-omics"],"dc:title":["Unraveling sorghum stem biology through organ-specific and cell-type-specific transcriptomic analyses across development"],"dc:type":["text"],"thesis:degree_discipline":["Plant Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:06Z"}