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Scholarly Works (5 results)

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UC Davis Electronic Theses and Dissertations (2023)

Fruit ripening is a complex developmental process in which fruit undergo physiological and biochemical changes, transforming fruit into nutritious and flavorful foods. Fruit quality traits, such as flavor and aroma, texture, and color, are essential for product marketability and increase during ripening. The characteristic changes in fruit physiology and biochemical composition during ripening result from extensive transcriptional reprogramming. While some regulatory mechanisms governing ripening have been identified, such as, transcription factors (TFs), plant hormones, and post-transcriptional and epigeneticfactors, the genetic factors regulating fruit quality are not fully understood.

The overarching goal of this Ph.D. dissertation was to explain the physiological and genetic events determining fruit quality traits during ripening. First, I assessed the current knowledge of ripening regulators of fruit quality traits across diverse fruit species(Chapter 1). Five main categories emerged—color, flavor, nutrition, texture, and shelf life. Transcription factor regulators can act in a pathway-specific manner or as “master” regulators of multiple pathways. Pathway-specific regulators are promising targets for improving fruit quality because they cause fewer unwanted effects on other traits (Chapter 1). In contrast, manipulations to master regulators impact multiple quality attributes causing pleiotropic effects (Chapter 1, Chapter 2). Plant hormones act with transcription factors and are often non-specific to quality traits (Chapter 1).

I employed multiple approaches to provide a system-wide understanding of ripening regulation and events associated with fruit quality in two economically important crops for California, tomato (Solanum lycopersicum) and pistachio (Pistacia vera). In both studies (Chapters 2 and 3), fruit physiological parameters were measured in field conditions to provide evidence of physical changes occurring in the fruit through ripening. Biochemical measurements provided further evidence of the specific compounds being altered in each crop. Then, the information was integrated with genome-wide expression analysis to identify underlying molecular mechanisms for each study.

In Chapter 2, I studied the impact of mutations in ripening-related transcription factors (NOR, RIN, and CNR) on tomato fruit quality through trait phenotyping, transcriptional profiling, and hormone measurements over multiple field seasons. I hypothesized each mutant had distinct defects in fruit quality attributes. I determined that ripening in two mutants (nor and rin) is not entirely inhibited; instead, some ripening processes are delayed. I also demonstrate that the Cnr mutation affects fruit development long before the onset of ripening. We also generated homozygous double mutants of these genotypes for the first time to study the combined effect of the mutations on development and ripening. This study contributed new knowledge regarding the tomato ripening mutants, which have been employed to understand fruit ripening for at least the past two decades.Also, given the importance of both rin and nor in breeding, quality trait data from these mutants are of high value.

In Chapter 3, I applied the knowledge gained in the model system of tomato to investigate a nut crop, pistachio, in which ripening had not been previously described. With collaborators, we generated critical genomic resources to study pistachio ripening:a complete genome assembly for P. vera (c.v. Kerman) and a large transcriptomic study expanding 15 weeks of pistachio growth and development and three different fruit tissues (hull, shell, kernel). I also performed a multiyear multi-location analysis of pistachio phenology, allowing me to model multiple fruit physiological measurements across the growing season. The molecular and physiological data allowed me to determine four distinct stages of pistachio development, with Stage IV corresponding to fruit ripening and kernel maturation. I then hypothesize that transcriptional changes at Stage IV are critical for gaining and establishing nut quality traits. I identified hormones associated with fruit ripening and downstream genetic pathways that can explain the physiological changes observed in the nut. I gave particular attention to genes and pathways related to key quality attributes in pistachio, hull softening, shell hardening, and kernel fat composition.Overall, this work ascertained a complete characterization of pistachio development for the first time, generated valuable genetic resources for future nut research, and providednovel insights into the genetic programs governing pistachio ripening.

The results of this dissertation improve the understanding of the molecular basis of fruit quality traits. My research provides new knowledge about transcriptional regulation required for tomato fruit quality and the implications for better utilizing ripening mutants in breeding for hybrids with extended shelf-life. The genetic resources created for pistachio development will be a basis for continued research in pistachio and other nut tree crops. Further, identifying the timing and mechanisms of ripening in pistachio involved in hull softening and color changes will help develop management strategies for harvest time.

  • 4 supplemental ZIPs
Cover page: Physiological and Molecular Processes Driving Fruit Quality during Tomato and Pistachio Fruit Ripening
  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2021)
Spontaneous mutations associated with the tomato transcription factors COLORLESS NON-RIPENING (SPL-CNR), NON-RIPENING (NAC-NOR), and RIPENING-INHIBITOR (MADS-RIN) result in fruit that do not undergo the normal hallmarks of ripening but are phenotypically distinguishable. Here, we expanded knowledge of the physiological, molecular, and genetic impacts of the ripening mutations on fruit development beyond ripening. We demonstrated through phenotypic and transcriptome analyses that Cnr fruit exhibit a broad range of developmental defects before the onset of fruit ripening, but fruit still undergo some ripening changes similar to wild type. Thus, Cnr should be considered as a fruit developmental mutant and not just a ripening mutant. Additionally, we showed that some ripening processes occur during senescence in the nor and rin mutant fruit, indicating that while some ripening processes are inhibited in these mutants, others are merely delayed. Through gene expression analysis and direct measurement of hormones, we found that Cnr, nor, and rin have alterations in the metabolism and signaling of plant hormones. Cnr mutants produce more than basal levels of ethylene, while nor and rin accumulate high concentrations of abscisic acid. To determine genetic interactions between the mutations, we created for the first time homozygous double mutants. Phenotypic analyses of the double ripening mutants revealed that Cnr has a strong influence on fruit traits and that combining nor and rin leads to an intermediate ripening mutant phenotype. However, we found that the genetic interactions between the mutations are more complex than anticipated, as the Cnr/nor double mutant fruit has a Cnr phenotype but displayed inhibition of ripening-related gene expression just like nor fruit. Our reevaluation of the Cnr, nor, and rin mutants provides new insights into the utilization of the mutants for studying fruit development and their implications in breeding for tomato fruit quality.
    Cover page: Single and Double Mutations in Tomato Ripening Transcription Factors Have Distinct Effects on Fruit Development and Quality Traits
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2023)
    Tree source-sink ratio has a predominant and complex impact on tree performance and can affect multiple physiological processes including vegetative and reproductive growth, water and nutrient use, photosynthesis, and productivity. In this study, we manipulated the branch level source-sink ratio by reduction of photosynthetic activity (partial branch defoliation) or thinning branch fruit load early in the growing season (after fruit set) in pistachio (Pistacia vera) trees. We then characterized the leaf photosynthetic light response curves through leaf aging. In addition, we determined changes in leaf non-structural carbohydrates (NSC) and nitrogen (N) concentrations. In leaves with high source-sink ratios, there was a gradual decrease in maximum net photosynthetic rate (ANmax) over the growing season, while in branches with low source-sink ratios, there was a sharp decline in ANmax in the first two weeks of August. Branches with high-sink showed an up-regulation (increase) in photosynthesis toward the end of July (at 1,500 growing degree days) during the period of rapid kernel growth rate and increased sink strength, with ANmax being about 7 μmol m-1 s-1 higher than in branches with low-sink. In August, low source-sink ratios precipitated leaf senescence, resulting in a drastic ANmax decline, from 25 to 8 μmol m-1 s-1 (70% drop in two weeks). This reduction was associated with the accumulation of NSC in the leaves from 20 to 30 mg g-1. The mechanisms of ANmax reduction differ between the two treatments. Lower photosynthetic rates of 8-10 μmol m-1 s-1 late in the season were associated with lower N levels in high-sink branches, suggesting N remobilization to the kernels. Lower photosynthesis late in the season was associated with lower respiration rates in low-source branches, indicating prioritization of assimilates to storage. These results can facilitate the adaptation of management practices to tree crop load changes in alternate bearing species.
      Cover page: Interactive effect of branch source-sink ratio and leaf aging on photosynthesis in pistachio.
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2021)
      The increased susceptibility of ripe fruit to fungal pathogens poses a substantial threat to crop production and marketability. Here, we coupled transcriptomic analyses with mutant studies to uncover critical processes associated with defense and susceptibility in tomato (Solanum lycopersicum) fruit. Using unripe and ripe fruit inoculated with three fungal pathogens, we identified common pathogen responses reliant on chitinases, WRKY transcription factors, and reactive oxygen species detoxification. We established that the magnitude and diversity of defense responses do not significantly impact the interaction outcome, as susceptible ripe fruit mounted a strong immune response to pathogen infection. Then, to distinguish features of ripening that may be responsible for susceptibility, we utilized non-ripening tomato mutants that displayed different susceptibility patterns to fungal infection. Based on transcriptional and hormone profiling, susceptible tomato genotypes had losses in the maintenance of cellular redox homeostasis, while jasmonic acid accumulation and signaling coincided with defense activation in resistant fruit. We identified and validated a susceptibility factor, pectate lyase (PL). CRISPR-based knockouts of PL, but not polygalacturonase (PG2a), reduced susceptibility of ripe fruit by >50%. This study suggests that targeting specific genes that promote susceptibility is a viable strategy to improve the resistance of tomato fruit against fungal disease.
        Cover page: Host susceptibility factors render ripe tomato fruit vulnerable to fungal disease despite active immune responses
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2023)
        Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes to facilitate infections and promote disease in tomato (Solanum lycopersicum). Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, an enzyme-linked immunosorbent assay (ELISA)-based glycomics technique used to assess fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectic polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening depends on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbc polygalacturonase1 Δbc polygalacturonase2 lacking two critical pectin degrading enzymes was incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.
          Cover page: Botrytis cinerea infection accelerates ripening and cell wall disassembly to promote disease in tomato fruit
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