Theses and Dissertations

Issuing Body

Mississippi State University


Ling Li

Committee Member

Ying Wang

Committee Member

Donna M. Gordon

Committee Member

Vincent Klink

Committee Member

Zhaohua Peng

Date of Degree


Original embargo terms

Complete embargo for 2 years

Document Type

Dissertation - Open Access


Biological Sciences

Degree Name

Doctor of Philosophy


College of Arts and Sciences


Department of Biological Sciences


As sequencing technology has taken off since the late 1990's, a unique phenomenon has been observed repeatedly: genes with little to no conservation across species. For a while, the predominant theory that arose to explain these genes was duplication and subsequent evolution of conserved genes. While this theory can explain some, still many genes have now been proven to arrive de novo - from previously non-coding DNA. This work further investigates the origins of these de novo evolved genes and their practical application relevance in crop biotechnology. This work demonstrates the dynamic nature of plant mitochondrial genomes between even closely related species, and the integral role of mitochondrial genomes in the origin of de novo orphan genes in plants. To better understand the functional potential of plant orphan genes, the network of the orphan gene Qua Quine Starch (QQS) is further elucidated. This analysis demonstrates the broad functionality of an orphan gene as a "fine-tuning knob" in many plant pathways. Further, QQS' role in protein and starch allocation and plant defense is tied to the Nuclear Factor Y subunit C4 (NF-YC4) transcription factor - this knowledge leads us to manipulate expression of native NF-YC4 transcription factors in important crop species to successfully increase seed protein, increase broad disease resistance, and expedite maturation in soybean. A key goal in biotechnology is creating non-transgenic plants with advantageous traits. To accomplish this, the CRISPR-CAS9 system was used to target and delete repressive cis-regulatory elements in the GmNF-YC4-1 promoter sequence. This has allowed us to modify the activity of GmNF-YC4-1 and thus increase soybean seed protein, making it possible to get a non-transgenic plant by segregating out the CRISPR-CAS9 T-DNA and keeping the regulatory deletion. Overall, this work uncovers a novel mechanism of orphan gene evolution and uses the study of the orphan gene QQS to develop important crop biotechnology.

Available for download on Tuesday, August 15, 2023