Browsing by Author "Minas, Ioannis, advisor"
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Item Open Access Addressing the threat of frost damage on peach floral buds through large-scale cold hardiness phenotyping, dynamic weather modeling and non-targeted metabolomic and proteomic analysis(Colorado State University. Libraries, 2023) Sterle, David, author; Minas, Ioannis, advisor; Sharp, Julia, committee member; Prenni, Jessica, committee member; Caspari, Horst, committee memberCold damage to reproductive tissues is the greatest threat to the profitability of peach (Prunus persica) growers worldwide. Cold hardiness is the extent to which peach floral buds super-freeze without suffering lethal damage. Although no changes are visible externally to floral buds for much of the dormant season, cold hardiness fluctuates as they acclimate, deacclimate and respond to abiotic stressors such as temperature or drought. A greater understanding of the mechanisms involved in these fluctuations involves accurate and frequent measurement of the extent to which cold hardiness is changing, and the ambient weather factors influencing the changes, at different stages of the dormant season. Warmer or more erratic temperature changes during the dormant season threatens peach floral buds to more frequently receive frost damage if cold hardiness becomes misaligned with the timing of lethally cold weather events. Statistical analysis of the trends and forces impacting the cold hardiness of floral buds can help identify significant patterns. These patterns can be used to better understand the physiological mechanisms affecting cold hardiness changes, and they can be used to help predict the impact of weather conditions on cold hardiness. In addition to their use in a practical sense by growers to aid in frost management decisions, accurate cold hardiness prediction models can be used to estimate what effects foreseeable climate effects can have on the outlook of future peach production. Metabolic changes are known to occur in dormant plants, although the effects of the metabolome in peaches on cold hardiness are unknown. Changes associated with cold hardiness likely follow several trends. One such trend is the fluctuations of metabolic abundances across the season, which are more associated with the endodormancy, and ecodormancy phases and the prebloom phase. These trends likely take place every dormant season as buds undergo a steady process of acclimating and deacclimating. Another trend is the response floral buds exhibit in response to acute cold events, in order to rapidly increase cold hardiness. The study of this response necessitates the monitoring of cold hardiness as well as the metabolic shift to the weather event. The response can be further elucidated by comparing cold hardiness and metabolic changes between genotypes that have different cold hardiness phenotypes. By exploring changes a cold hardy genotype undergoes, geneticists may be able to target certain metabolic expressions that may increase the frost tolerance of future cultivars. Since frost damage can be so destructive to peach production, it is necessary to understand the risks to the peach industry moving forward surrounding climate change, and it is also necessary to understand the extent to which frost tolerance can be improved in future cultivars. This study uses a multifaceted approach to cold hardiness which involves improved and large-scale cold hardiness phenotyping using differential thermal analysis, dynamic weather prediction models and associated metabolic regulation understanding.Item Open Access Bacteriomes of peaches and cover crops(Colorado State University. Libraries, 2024) Newberger, Derek R., author; Vivanco, Jorge M., advisor; Minas, Ioannis, advisor; Paschke, Mark, committee member; Manter, Daniel, committee memberReplant syndrome (RS) of fruit and nut trees causes reduced tree vigor and crop productivity in orchard systems due to repeated plantings of closely related tree species. Although RS etiology has not been clearly defined, the causal agents are thought to be a complex of soil microorganisms combined with abiotic factors and susceptible tree genetics. Different soil disinfection techniques alleviate RS symptoms by reducing the loads of the deleterious microbiome; however, the positive effect on crop growth is temporary. Here, the current understanding of RS in orchards from a soil microbiome perspective is reviewed. The resolution to RS will require experts to outline explicit descriptions for its symptoms, determine its etiology, identify the primary phytopathogens, and fully explore sustainable treatments which alleviate RS. Two sustainable treatments of RS were selected to explore at a deeper level, soil disinfection and increasing crop diversity to observe what technique could help establish a healthy soil bacteriome. In a greenhouse study, soil disinfection via autoclave was then followed by cover cropping. It was found that soil disinfection increases plant biomass as compared to the control for only the first crop cycle while non-autoclaved soils with a history of cover cropping alleviated RS in RS-susceptible 'Lovell' peach seedlings. Although soil disinfection via autoclave was found to distinctly alter the peach soil bacteriome for the full duration of the study, this sustainable practice mimicking solarization failed to provide relief from RS for peach seedlings. Instead of long-term benefits, differential abundance comparisons displayed a loss of potentially beneficial bacteria due to soil disinfection. Paenibacillus castaneae and Bellilinea caldifistulae were beneficial bacterial species that uniquely colonized peach rhizosphere of non-autoclaved soils with a cover crop history. As a promising sustainable technique, a greater understanding of how inter-/intra-specific competition of cover crops can influence the bulk soil bacteriome was pursued. Alfalfa, brassica, and fescue were grown in 7 different plant combinations (1. alfalfa, 2. brassica, 3. fescue, 4. alfalfa-brassica, 5. alfalfa-fescue, 6. brassica-fescue, 7. alfalfa-brassica-fescue) across 3 density concentrations (low: 1–3 plants, medium: 24 plants, and high: 48 plants) for a greenhouse microcosm experiment. It was found that even in highly competitive conditions beneficial bacteria were enriched, however, there was an apparent trade-off where different plant combinations enriched distinct beneficial bacteria. As an example, even if a free-living nitrogen fixing bacteria such as an Azospirillum spp. was enriched in the bulk soil of alfalfa and brassica monocultures, it was not enriched in the bulk soil of an alfalfa-brassica plant mixture. Instead Pseudarthrobacter phenanthrenivorans, a phytohormone producer, was enriched in alfalfa-brassica plant mixtures. When zooming into the rhizosphere compartment of these microcosms, it was found that regardless of plant neighbor identity or density, a few rhizobacteria were highly correlated with a specific plant species. Meanwhile, certain plant species specific rhizobacteria were enriched only if specific conditions such as plant neighbor identity or density were met. Overall, our research found that growing diverse plant species plants prior to the re-establishment of a peach orchard could alleviate RS symptoms. Furthermore, cover crops can enrich different microbes when grown together as opposed to when grown separately. Lastly, although plants recruit a particular set of bacteria, this recruitment can shift depending on plant neighbor identity or density. Further study of cover crops may identify how they can alleviate RS in orchards worldwide.Item Open Access Chemical control of Cytospora leucostoma, a major limiting factor of peach production in western Colorado(Colorado State University. Libraries, 2017) Miller, Stephan, author; Stewart, Jane, advisor; Minas, Ioannis, advisor; Norton, Andrew, committee member; Uchanski, Mark, committee memberCytospora canker, Cytospora leucostoma, is a major limiting factor of peach production in Colorado, accounting for 15-20% of crop production loss annually. Given the unique environmental factors of the western slope region of Colorado, C. leucostoma has developed into a severe fungal disease, reducing yields annually. Chemical measures are important for Cytospora control as few options currently exist for preventing new infections. The specific objectives of the following thesis are to: (1) evaluate the efficacy of conventional and organic fungicides for C. leucostoma control, (2) test wound sealing fungicides, embedded in paint or kaolin clay, to develop preventive and containment approaches in existing orchards. Topsin, Topsin amended in 50% latex, Captan, Captan amended in 50% latex, 50% latex, lime sulfur, and lime sulfur amended in kaolin clay (Surround WP) showed evidence of efficacy from laboratory and field trials. Of these treatments, 50% latex, Topsin amended in 50% latex, and Captan amended in 50% latex, were shown to limit pathogen growth most effectively on pruning wounds during field trials in the summer season. In all field trials, however, NuCop showed absolutely no efficacy and should be avoided for C. leucostoma control in western Colorado. When various chemicals were tested on existing cankers to reduce spore inoculum loads, efficacy could not be statistically confirmed. The results of this study were compicated by variable field conditions and a large range of spore produced by each canker. Thus, larger sample sizes should be used in future studies to tease a part chemical efficacy and abiotic influences. Further, kaolin clay alone may shield fungal cankers from extreme temperatures, enhancing its growth in the field.Item Open Access Impact of various factors on partial least squares model robustness for nondestructive peach fruit quality assessment(Colorado State University. Libraries, 2023) Pott, Jakob, author; Minas, Ioannis, advisor; Eakes, Joe, committee member; Koslovsky, Matt, committee memberGiven declining fruit consumption due to poor fruit quality and large amounts of waste, peach growers have continuously suffered from financial loss and the industry has seen a sharp decline in recent decades. Due to the time consuming and destructive nature of conventional fruit quality assessment, many peach growers prioritize fruit characteristics conducive to shipping and storage over characteristics which correlate with consumer acceptance. This prioritization has resulted in the poor-quality fruit which consumers have grown to associate with fresh peaches and contributed to large annual waste. A potential solution is the use of near-infrared spectroscopy (Vis-NIRS) paired with partial least squares (PLS) modeling, as a field deployable method that can be used to measure preharvest internal fruit quality to produce information quickly and non-destructively. These qualities offer an answer to declining fruit quality and waste. Although promising, the technology is only as good as the data used to train the models. Quality data is hard to collect as it requires the consideration of many factors including the temperature of the sample and the inclusion of biological variability impacted by seasonal changes, cultivar differences, fruit maturity, and many management factors such as crop load, rootstocks, irrigation regimes, and training systems to capture the relationships needed for good model performance. In tree fruit research, handheld Vis-NIRS devices have been used to predict internal quality parameters such as sweetness (dry matter content, DMC; soluble solids concentration, SSC) and fruit physiological maturity related to chlorophyll content (index of absorbance difference, IAD). Although accurate, the statistical models used to make such predictions often struggle with robustness across cultivars and growing seasons and regions due to a lack of biological variability, or a lack of representative data from factors like temperature. These challenges have led to slow industry adoption. To address this issue, models for 13 distinct peach cultivars were constructed by combining data from two seasons (2016 and 2021) followed by external validation with data from a third season (2022). The data from 2016 was collected over a range of preharvest factors, fruit development stages and temperatures, and the inclusion of 2021 data added additional biological variability. External validation produced error rates of 0.36 - 0.42%, 0.59 - 0.63%, and 0.05 - 0.04 for DMC, SSC and IAD, respectively, across the 13 peach cultivars indicating the models trained in 2021 were robust and performing at an acceptable level to impact grower decision making. It was observed that the additional inclusion of data from different cultivars and growing environments, as well as a third growing season (2017) did not significantly impact model performance. The lack of improvement suggests that the data from each year contain enough covariate variability to cover a broad range of measurements (i.e. input values) that growers and researchers are likely to observe when collecting data to predict peach quality in different orchards or seasons. This insensitivity to various environmental and growing conditions, generally referred to as external factors, due to the variability captured in the data used to build model is characteristic of a robust model.Item Unknown Influence of preharvest factors on peach fruit quality and metabolism(Colorado State University. Libraries, 2021) Anthony, Brendon, author; Minas, Ioannis, advisor; Musacchi, Stefano, committee member; Prenni, Jessica, committee member; Bunning, Marisa, committee memberWorldwide peach consumption has been in steady decline throughout the past few decades due to poor fruit quality and consumer experiences. Fruit quality is developed in the orchard by optimizing preharvest factors and orchard practices. Several studies have been conducted to understand how these factors influence peach internal quality, but fail to control for confounding variables. One particular confounding variable that is influenced by preharvest factors and directly impacts fruit quality is maturation. Pomological experiments investigating the impact of preharvest factors on internal fruit quality must control for maturity. Historically, maturity control through destructive and subjective methods was not feasible nor efficient. The development of new technologies, such as visual radiation and near-infrared spectroscopy allowed the development of novel maturity indices (index of absorbance difference) that can be used for maturity control and quality assessment simultaneously in a single scan. The following literature review and experiments investigate three critical preharvest factors: training systems, canopy position and crop load (i.e., carbon supply), for their true impact on peach fruit quality development and metabolism, while controlling for maturity. The training system review demonstrates the progression of orchard design from three-dimensional, low-planting densities to planar, high-density plantings through the application of size-controlling rootstocks and vigor diffusion architecture. The canopy position trial revealed that the fruit's light environment is more influential in quality development and metabolic shifts than genotype or position alone. Canopies with uniform light distribution generate fruit of uniform quality and metabolite profiles across distinct positions. Fruit under sufficient carbon supply (i.e., thinned fruit) will exhibit superior quality and phenotype when compared to carbon-starved fruits at harvest, even when assessed at equal maturity. Primary metabolite profile differences between distinct carbon supply conditions are minimal at harvest due to experimental maturity control and metabolic processes being heavily regulated by development and maturation. While differences in secondary metabolite profiles are more distinct at harvest between carbon supply treatments. Although, both the primary and secondary metabolism demonstrate vast profile differences between carbon supply treatments early, and may prime the quality phenotype at harvest. Flavonoids are consistently elevated in carbon sufficient fruit throughout development. Phenylpropanoids, such as catechin, along with benzenoids, sucrose and sorbitol demonstrate strong relationships with high-quality fruit throughout experiments, while lipids, amino acids, monosaccharides and organic acids showcase relationships with inferior quality fruit. Overall, maturity control is necessary in pomological experiments assessing the true impact of preharvest factors on fruit quality and metabolism.Item Unknown The impact of rootstock on peach tree vigor, light environment, fruit quality, and metabolism(Colorado State University. Libraries, 2024) Pieper, Jeffrey Ross, author; Minas, Ioannis, advisor; Bunning, Marisa, committee member; Caspari, Horst, committee member; Prenni, Jessica, committee memberThe key to Colorado's successful peach industry is superb fruit quality. The fruit quality growers achieve allows for the highest premium 'farm-gate' price per pound in the nation. Fruit quality is created in the orchard via the interaction of several pre-harvest factors. One critical pre-harvest factor that has several knock-on effects for orchard management decisions is rootstock selection. Rootstock selection has the potential to impact the longevity, productivity, efficiency, and profitability of an orchard, and is dependent on climatic and edaphic environments as well as the soil microbiome. Rootstock selection may also allow growers to augment orchard design through vigor manipulation. In Colorado, growers are faced with relatively short growing seasons, sudden fall and spring frost events, and calcareous soils which limit the availability of certain nutrients. The unique growing environments coupled with the need for high quality fruit production makes rootstock selection limited. Identifying rootstocks suitable for production in Colorado and determining how they impact fruit quality is paramount. While previous studies have evaluated rootstocks for their performance and relationship to fruit quality, few have limited confounding factors such as crop load, canopy position, and or physiological maturity when assessing fruit. The following experiments evaluated twenty-one genetically diverse rootstocks for their phenotypic and agronomic performance and potential use in Colorado production systems. The nine-year performance review, in chapter one, details the productivity and suitability of seventeen genetically diverse peach rootstocks in Colorado growing conditions. The trial determined rootstock vigor strongly correlates with cumulative yield. However, vigor also showed an inverse relationship with internal fruit quality development measured as dry matter content (DMC) and soluble solids concentration (SSC). The trial showed interspecific peach and non-peach hybrids outperformed peach seedling rootstocks. One interspecific peach rootstock in particular, 'Krymsk® 86', performed exceptionally well and has since been widely adopted by industry. By controlling for several confounding factors, the rootstock vigor trial, chapter two, demonstrated the true impact of vigor and light availability on fruit quality enhancement and primary metabolite profiles. Fruit developing in reduced vigor canopy of the dwarfing rootstock 'Krymsk® 1' had increased light availability and enhanced internal fruit quality parameters (DMC and SSC) at harvest. Mesocarp metabolites relating to internal quality showed they are up and down accumulated by rootstock vigor and the light environment. Several metabolite classes including soluble sugars, cyclitols, flavanols, and chlorogenic acids were associated with 'Krymsk® 1', a low vigor rootstock that had high light availability and enhanced fruit quality profiles. 'Atlas™' and 'Bright's Hybrid® 5', both vigorous rootstocks, showed low light availability and reduced fruit quality. The vigorous rootstocks also showed an increase of amino and fatty acids compared to the standard and dwarfing rootstocks. The six-year physiological and agronomic performance of modern semi-dwarfing rootstocks trial, chapter three, reiterated the impact of vigor on yield, light availability, and fruit quality development. Furthermore, the trial showed increased vigor was related to an increase of gummosis incidence and severity. Also, intra-specific Prunus hybrids had increased rates of proleptic shoot formation, however, some showed they were susceptible to iron chlorosis. Overall, the rootstock trials identify key parameters of performance and suitability in Colorado production systems. The outcomes indicate that rootstocks with increased vigor resulted in higher yields per tree, however, lower light availability in the canopy decreased DMC and SSC. While rootstock genotype and vigor are influencing peach fruit development and quality, their effect on light availability may play a more significant role in achieving optimal yield and fruit quality and augmented metabolite profiles. Additionally, this work demonstrates the importance of controlling for confounding variables when evaluating preharvest factors for their impact on internal fruit quality and metabolite profiles.