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Author ORCID Identifier



Open Access Dissertation

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Plant Biology

Year Degree Awarded


Month Degree Awarded


First Advisor

Ana Caicedo

Second Advisor

Sam Hazen

Third Advisor

Lynn Adler

Fourth Advisor

Adam Porter

Subject Categories

Evolution | Genetics | Plant Biology


As angiosperm seeds mature within their ovaries, ovary tissue tends to grow and transform itself into fruit, which aids the success of the seeds. Fruits that are fleshy provide numerous ways to aid in the protection and the dispersal of seeds. First, they keep seeds hidden, encased in hard walls, surrounded by poisons and unpalatable compounds, and second, they undergo developmental changes that facilitate seeds’ release. Tomatoes, a model fleshy fruit, have all these protective traits, and over the course of ripening they become the familiar fruit that is a staple crop around the world. The wild relatives of cultivated tomatoes, however, have substantial variation in ripening habits. I characterized several fruit traits and their change during ripening in wild tomato species to get a better understanding of the phenotypic variation that exists in fruits. Acquiring this background for the clade enables further investigation of genes behind these variable traits and inferences of how the traits have evolved. To associate fruit traits with genes and genomic regions for further analysis I grew introgression lines (ILs) stemming from introgressions of small portions of the genome of the tomato clade outgroup Solanum lycopersicoides, in the background of the cultivated tomato, S. lycopersicum. With these lines, I found regions of the genome that are associated with change of fruit firmness during ripening, providing data for further investigation of the genetics behind this trait. I also investigated the genetic basis of ripe fruit color variation by characterizing the gene CYC-B, which produces the enzyme responsible for turning red lycopene into the orange β-carotene, across the tomato clade. My results suggest that regulation of CYC-B has been key to the evolution of different fruit colors across the clade, and that the promoter region of the gene is involved in differentiating a β-carotene accumulating plant from a lycopene accumulating plant. The research performed here enhances our understanding of phenotypic and genotypic variation in an understudied angiosperm organ that can alter how plant species interact with animals around them, contributing to our knowledge of how fruit traits evolve and how they can enable plant success.


Table S1.xlsx (30 kB)
Introgression Map

Table S2.xlsx (12 kB)
Sample Count

Table S3.xlsx (13 kB)
Firmness data

Table S4.xlsx (17 kB)
Sugar data

Table S5.xlsx (11 kB)
Correlation Coefficients

Table S6.xlsx (15 kB)
Firmness Gene Map

Table S7.xlsx (15 kB)
Sugar Gene Map

Table S8.xlsx (896 kB)
Complete Microarray Expression Data

Table S9.xlsx (17 kB)
Most Differentially Expressed

Table S10.xlsx (13 kB)
CYC-B Polymorphisms