Author ORCID Identifier
https://orcid.org/0000-0002-1685-1614
Date of Award
8-31-2026
Document Type
Open Access Thesis
Degree Name
Doctor of Philosophy (PhD)
Department
Biology
First Advisor
Dr. Brook T. Moyers
Abstract
Adaptation often proceeds by gradual changes in allele frequencies across many genes. However, evidence shows that adaptation is more complex and can depend on gene networks, environmental contexts, developmental timing, or even transgenerational effects. In this dissertation, I study the genetic basis of adaptation in two plant species: a wild sunflower (Helianthus argophyllus), a model of adaptation under natural selection, and domesticated rice (Oryza sativa), a model of adaptation under artificial selection. Together, these systems help explain how adaptation might proceed when genetic diversity is low and how environmental context influences the expression of adaptive traits.
In H. argophyllus, I examine how pronounced ecotypic divergence persists despite low genome-wide genetic diversity and ongoing gene flow. I use common garden experiments, transcriptomic analysis, and gene co-expression network analysis to demonstrate that adaptation in this system is not explained solely by genes with additive effects; instead, selection can also act on groups of interacting genes within regulatory networks, enabling populations to diverge even when genetic diversity is low.
In rice, I study how environmental and parental conditions shape the genetic architecture of stress responses and phenotypic expression in direct-seeded rice under field conditions and in rice seedlings grown in controlled environments. Using computer vision phenotyping and temporal assessment, I identify genetic loci linked to iron‑deficiency tolerance that traditional endpoint measurements fail to detect. I find that the environment experienced by parent plants and the quality of their seeds shape how genetic variation is expressed in seedlings, revealing genotype‑by‑environment‑by‑parental‑environment interactions.
These results show that adaptation involves more than just additive genetic effects; it proceeds through interactions among genes, environments, and generations. These results are especially important for agriculture, where domestication bottlenecks have reduced genetic diversity in many crops and may limit traditional breeding approaches. By demonstrating the complex interplay among gene regulatory networks, environment, time, and parental effects on adaptation, my research also suggests possible avenues for crop breeding to enhance crop resilience, such as targeting regulatory networks, selecting for dynamic stress responses, and considering seed quality and parental environment in breeding. These insights may help guide the development of crop varieties better able to withstand environmental stress under a changing climate.
Recommended Citation
Okinedo, Uzezi E., "The Genetic Architecture of Adaptation: Insights from Wild Sunflower (Helianthus argophyllus) and Domesticated Rice (Oryza sativa)" (2026). Graduate Doctoral Dissertations. 1202.
https://scholarworks.umb.edu/doctoral_dissertations/1202
Included in
Agriculture Commons, Biology Commons, Ecology and Evolutionary Biology Commons, Genetics and Genomics Commons, Plant Sciences Commons
Comments
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