Theses and Dissertations

ORCID

https://orcid.org/0000-0002-1326-7703

Advisor

Li, Ling

Committee Member

Gordon, Donna M.

Committee Member

Klink, Vincent

Committee Member

Wang, Ying

Date of Degree

8-13-2024

Original embargo terms

Embargo 2 years

Document Type

Dissertation - Open Access

Major

Biological Sciences

Degree Name

Doctor of Philosophy (Ph.D.)

College

College of Arts and Sciences

Department

Department of Biological Sciences

Abstract

In recent years, understanding the emergence and integration of novel genes into genomes has garnered significant interest within the scientific community. Species-specific orphan genes have become particularly intriguing due to their recent appearance and distinct structural characteristics. Despite their prevalence and potential evolutionary significance, studying orphan genes poses challenges due to their lack of similarity to other genes, resulting in limited functional annotations. This study aims to delve into the mechanisms, functions, networks, and agricultural implications of orphan genes. QQS (Qua-Quine Starch), exclusively identified in Arabidopsis thaliana, stands as the first functionally characterized orphan gene in plants. It regulates carbon and nitrogen allocation, influencing traits such as protein levels, starch content, and resistance to pests and pathogens through its interaction with NF-YC4 (Nuclear Factor Y subunit C4). However, the precise mechanism underlying QQS's function, whether as a noncoding transcript, a coding protein, or both—and its network and functional partners remain elusive. Furthermore, it raises questions about the operation of such an orphan gene, lacking homologs in other species, within those species. This study manipulates the QQS gene's sequence to produce exclusive mRNA or protein, unveiling its dual functionality in influencing metabolic pathways. Additionally, the research extends to evaluating the agricultural impact of QQS beyond Arabidopsis, in tobacco and potato. Expressing QQS or overexpressing NF-YC4 in tobacco enhances protein content, reduces starch levels, and strengthens resistance to pests, while in potatoes, it elevates protein content in tubers without affecting yield. Furthermore, exploring QQS's interactions with other orphan or taxonomically-restricted genes like TRQA1 reveals their roles in regulating starch and protein levels, broadening our understanding of plant metabolic regulation through orphan and taxonomically restricted genes. This comprehensive investigation sheds light on orphan gene functionality, highlighting their dual coding and noncoding roles, function through conserved factors across plant species, functional partners and interactors, and potential for crop improvement. These findings hold significance for agricultural sustainability, offering insights into enhancing crop productivity, nutritional quality, and resilience to environmental stresses, thereby addressing global food security challenges.

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