{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/108200"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/108200","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Understanding the genetic basis of dioecy in waterhemp (Amaranthus tuberculatus) and palmer amaranth (Amaranthus palmeri)","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2022-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2022-05-01","abstract_has_math":false,"creators":["Montgomery, Jacob Samuel"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Crop Sciences","degree_department":null,"school":null,"contributors":["Tranel, Patrick","Hind, Sarah","Catchen, Julian"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2020,"date_issued":"2020-08-26T23:58:50Z","date_published":"2020-08-26T23:58:50Z","updated_at":"2026-07-22T22:24:48Z","subjects":["Amaranthus Sex-determination"],"languages":["en"],"rights":["Copyright 2020 Jacob Montgomery"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/108200","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Tranel, Patrick","Hind, Sarah","Catchen, Julian"]},{"key":"dc:creator","label":"Author","values":["Montgomery, Jacob Samuel"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2020-08-26T23:58:50Z","2022-08-26T23:58:55Z","2020-05-14","2020-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Crop Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"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":["Amaranthus Sex-determination"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2020 Jacob Montgomery"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/108200"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2022-05-01","Amaranthus tuberculatus and Amaranthus palmeri are two of the most agronomically important weeds in the American Midwest. The over-dependence upon chemical control of these weeds has led to the evolution of resistance to many commonly used herbicides across multiple modes of action, including herbicides that target protoporphyrinogen oxidase (PPO). The rapid evolution of these resistance mechanisms necessitates investigation of novel weed control strategies to supplement chemical control methods. One such method for dioecious weeds may include a genetic control strategy, where manipulation of sex-ratios artificially increases the proportion of males within a population to the point of collapse due to lack of seed producers. Chapter 1 includes a literature review of the biology of A. tuberculatus and A. palmeri, PPO-inhibitor resistance, dioecy in plants, and a brief summary of gene-drive technology which could be used to implement such a genetic control strategy. Chapter 2 focuses on the isolation of the recently discovered G399A PPO2 substitution, which confers resistance to PPO-inhibiting herbicides in A. palmeri. Our results allow future studies to examine G399A in planta without the influence of any secondary mechanisms of resistance. Chapter 3 begins our investigation of dioecy within A. tuberculatus and A. palmeri. Here, we identify genomic sequences associated with maleness through a genome-wide association study approach in both species. Results confirm males to be the heterogametic sex, allow for predictions of the size of the male-specific Y (MSY) region, and identify markers to be used in future mapping studies to identify this MSY region in each species. Chapter 4 reports whole-genome assemblies of A. tuberculatus, A. palmeri, and Amaranthus hybridus. Pac-Bio and chromatin conformation capture sequence allowed for the assembly and ordering of contigs to form a near-chromosomal-level of the A. palmeri genome. For the two remaining species, we adapted a trio binning technique, which entailed the sequencing of an interspecific cross and the subsequent separation of haplotypes. These haplotypes were assembled independently to produce two genomes for the price of one. Chapter 5 is aimed at using the previously developed markers for maleness and reference genomes to identify candidate MSY regions in A. tuberculatus and A. palmeri. We identify one contiguous region believed to be the A. palmeri MSY region and several contigs that are hypothesized to be contained within the A. tuberculatus MSY region. The sixth and final chapter includes concluding remarks and future research objectives. These findings lay the groundwork for future studies to understand the mechanism of sex-determination in these species and may allow for the development of a novel genetic weed control strategy.","The student, Jacob Montgomery, accepted the attached license on 2020-05-13 at 14:22.","The student, Jacob Montgomery, submitted this Thesis for approval on 2020-05-13 at 14:30.","This Thesis was approved for publication on 2020-05-14 at 16:45.","DSpace SAF Submission Ingestion Package generated from Vireo submission #15382 on 2020-08-25 at 17:31:25","Made available in DSpace on 2020-08-26T23:58:50Z (GMT). No. of bitstreams: 3 MONTGOMERY-THESIS-2020.pdf: 1307825 bytes, checksum: 1fa842b5d6c1f240229a0c0d5b36d9f9 (MD5) Montgomery_Thesis_5-11.docx: 9988814 bytes, checksum: 878c11ba65e441e05fc1c5c8e2b2b4eb (MD5) LICENSE.txt: 4213 bytes, checksum: c32f618873340f999504be2f24f5168e (MD5) Previous issue date: 2020-05-14","Embargo set by: Seth Robbins for item 115813 Lift date: 2022-08-26T23:58:55Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Understanding the genetic basis of dioecy in waterhemp (Amaranthus tuberculatus) and palmer amaranth (Amaranthus palmeri)"]}]}],"canonical_facts":{"dc:contributor":["Tranel, Patrick","Hind, Sarah","Catchen, Julian"],"dc:creator":["Montgomery, Jacob Samuel"],"dc:date":["2020-08-26T23:58:50Z","2022-08-26T23:58:55Z","2020-05-14","2020-05"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2022-05-01","Amaranthus tuberculatus and Amaranthus palmeri are two of the most agronomically important weeds in the American Midwest. The over-dependence upon chemical control of these weeds has led to the evolution of resistance to many commonly used herbicides across multiple modes of action, including herbicides that target protoporphyrinogen oxidase (PPO). The rapid evolution of these resistance mechanisms necessitates investigation of novel weed control strategies to supplement chemical control methods. One such method for dioecious weeds may include a genetic control strategy, where manipulation of sex-ratios artificially increases the proportion of males within a population to the point of collapse due to lack of seed producers. Chapter 1 includes a literature review of the biology of A. tuberculatus and A. palmeri, PPO-inhibitor resistance, dioecy in plants, and a brief summary of gene-drive technology which could be used to implement such a genetic control strategy. Chapter 2 focuses on the isolation of the recently discovered G399A PPO2 substitution, which confers resistance to PPO-inhibiting herbicides in A. palmeri. Our results allow future studies to examine G399A in planta without the influence of any secondary mechanisms of resistance. Chapter 3 begins our investigation of dioecy within A. tuberculatus and A. palmeri. Here, we identify genomic sequences associated with maleness through a genome-wide association study approach in both species. Results confirm males to be the heterogametic sex, allow for predictions of the size of the male-specific Y (MSY) region, and identify markers to be used in future mapping studies to identify this MSY region in each species. Chapter 4 reports whole-genome assemblies of A. tuberculatus, A. palmeri, and Amaranthus hybridus. Pac-Bio and chromatin conformation capture sequence allowed for the assembly and ordering of contigs to form a near-chromosomal-level of the A. palmeri genome. For the two remaining species, we adapted a trio binning technique, which entailed the sequencing of an interspecific cross and the subsequent separation of haplotypes. These haplotypes were assembled independently to produce two genomes for the price of one. Chapter 5 is aimed at using the previously developed markers for maleness and reference genomes to identify candidate MSY regions in A. tuberculatus and A. palmeri. We identify one contiguous region believed to be the A. palmeri MSY region and several contigs that are hypothesized to be contained within the A. tuberculatus MSY region. The sixth and final chapter includes concluding remarks and future research objectives. These findings lay the groundwork for future studies to understand the mechanism of sex-determination in these species and may allow for the development of a novel genetic weed control strategy.","The student, Jacob Montgomery, accepted the attached license on 2020-05-13 at 14:22.","The student, Jacob Montgomery, submitted this Thesis for approval on 2020-05-13 at 14:30.","This Thesis was approved for publication on 2020-05-14 at 16:45.","DSpace SAF Submission Ingestion Package generated from Vireo submission #15382 on 2020-08-25 at 17:31:25","Made available in DSpace on 2020-08-26T23:58:50Z (GMT). No. of bitstreams: 3 MONTGOMERY-THESIS-2020.pdf: 1307825 bytes, checksum: 1fa842b5d6c1f240229a0c0d5b36d9f9 (MD5) Montgomery_Thesis_5-11.docx: 9988814 bytes, checksum: 878c11ba65e441e05fc1c5c8e2b2b4eb (MD5) LICENSE.txt: 4213 bytes, checksum: c32f618873340f999504be2f24f5168e (MD5) Previous issue date: 2020-05-14","Embargo set by: Seth Robbins for item 115813 Lift date: 2022-08-26T23:58:55Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only"],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/108200"],"dc:language":["en"],"dc:rights":["Copyright 2020 Jacob Montgomery"],"dc:subject":["Amaranthus Sex-determination"],"dc:title":["Understanding the genetic basis of dioecy in waterhemp (Amaranthus tuberculatus) and palmer amaranth (Amaranthus palmeri)"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Crop Sciences"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:48Z"}