Understanding gender determination in dioecious Amaranthus weeds palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus)

Sadeque, Ahmed

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https://hdl.handle.net/2142/106318 Copy

Description

Title

Understanding gender determination in dioecious Amaranthus weeds palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus)

Author(s)

Sadeque, Ahmed

Issue Date

2019-09-27

Director of Research (if dissertation) or Advisor (if thesis)

Tranel, Patrick J

Doctoral Committee Chair(s)

Tranel, Patrick J

Committee Member(s)

• Brown, Patrick J
• Rayburn, A. Lane
• Lipka, Alexander E
• Jamann, Tiffany M

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

Amaranthus, Waterhemp, Palmer amaranth, Permutation, gender determination, dioecy, sex-determining chromosomal system, markers, RAD-seq, evolution, gene-drive

Abstract

Over the last few decades, numerous examples of multiple herbicide resistance in weeds have been reported. Many studies have documented various mechanisms through which weeds evade herbicidal action. This evolution of resistance in weed populations has been fueled by the intensive and extensive use of herbicides. Thus, the tactics that helped us in weed management turned out to be short term and have put at risk the future of weed management. Various factors, such as reduced farming system diversity, extensive use of herbicide-resistant crops, and the recent lack of herbicide discovery by industry, have all contributed towards undermining the foundations of weed management. As of today, 217 weed species have been reported to have established resistance to the herbicides. Furthermore, resistance was reported to all major known herbicide modes of action. This rapid rise in herbicide resistance among key weed species requires immediate attention. Development of novel weed management strategies is necessary, as the last mode of action developed to act against weeds was in 1990. However, this will require a far better understanding of weed biology and ecology than we currently have. It is, therefore, pivotal to understand the biology beneath the sex determination of dioecious weeds. Common waterhemp (Amaranthus tuberculatus (Moq.) Sauer var. rudis (Sauer) Costea and Tardif) and Palmer amaranth (Amaranthus palmeri S. Watson) are troublesome weeds of row-crop production in the United States. Their dioecious reproductive systems ensure outcrossing, facilitating rapid evolution and distribution of resistances to multiple herbicides. Little is known, however, about the genetic basis of dioecy in Amaranthus species. Understanding dioecy in these weeds can help us in establishing a probable control strategy for both weeds. Thus, the major aim of this study is to identify the mechanism of sex-determination in both these weedy species. In this work, we use restriction-site associated DNA sequencing (RAD- Seq) to investigate the genetic basis of sex determination in A. tuberculatus and A. palmeri. For each species, approximately 200 plants of each sex were sampled and used to create RAD-Seq libraries. The resulting libraries were separately barcoded and then pooled for sequencing with the Illumina platform, yielding millions of 64-base-pair reads. These reads were analyzed to identify sex-specific and sex-biased sequences. We identified 345 male-specific sequences from the A. palmeri data set and 2754 male-specific sequences in A. tuberculatus. An unexpected 723 female-specific sequences were identified in a subset of the A. tuberculatus females. Markers were developed for a few of these female-specific sequences to test for the presence of female-specific sequences in waterhemp female plants. However, these markers were unable to be used successfully. Male-specific markers were developed for both species, and these were used successfully to identify males. In the near term, sex-specific markers will be useful to the A. tuberculatus and A. palmeri research communities (e.g., to predict sex for crossing experiments). In the long-term, this research will provide the foundational tools for detailed investigations into the molecular biology and evolution of dioecy in weedy amaranths.

Graduation Semester

2019-12

Type of Resource

text

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http://hdl.handle.net/2142/106318

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