Browsing by Author "Argueso, Cristiana, committee member"
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Item Open Access A new woody perspective on copper homeostasis: systemic copper transport and distribution, effect of copper on lignification, and water transport in hybrid poplar(Colorado State University. Libraries, 2022) Hunter, Cameron Ross, author; Pilon, Marinus, advisor; Gleason, Sean, advisor; Pilon-Smits, Elizabeth, committee member; Argueso, Cristiana, committee member; Bush, Daniel, committee memberCopper (Cu) is an essential micronutrient for plants. Chapter 1, as background for this dissertation, reviews the functions and homeostasis of Cu. We know at the cellular level how Cu is delivered to target proteins in the chloroplasts, thus explaining in a large part why Cu deficient plants have reduced photosynthetic capacity. However, Cu is also a cofactor of lignin polymerization enzymes that affect cell wall and xylem structures required for water and mineral transport. How Cu deficiency affects water transport, mineral nutrition, and photosynthesis at a whole plant level is underexplored. To address this knowledge gap, we used hybrid white poplar as a model. In chapter 2, a stable isotope method to trace Cu movement in poplar tissues was coupled with analysis of photosynthesis and stomatal conductance. Upon resupply of Cu, priority targets identified were stems and younger leaves which recovered quickly and was associated with higher stomatal conductance. In chapter 3, the effect of Cu deficiency on the elemental composition of leaves and stems of different age were analyzed. Interestingly, tissue type and age, as well as Cu deficiency, were found to all significantly affect within-plant nutrient partitioning patterns. In chapter 4, the effects of Cu deficiency on cell wall chemical composition and water transport traits were determined. Although Cu deficiency strongly affected cell wall chemistry, it did not significantly impact hydraulic capacity nor the density and size of xylem vessels in stems. However, Cu deficiency resulted in markedly stiffer mesophyll cell walls, possibly arising from changes to cell wall chemistry or structure. Together, these results, as discussed in chapter 5, indicate that although xylem lignification was adversely affected by Cu deficiency, the water transporting vessels remained largely unaffected, thus allowing efficient recovery. This work opens new avenues to explore the effects of plant nutrition on whole-plant physiology and function.Item Open Access Characterizing host genetic resistance to Wheat streak mosaic virus (WSMV) and Fusarium wilt disease(Colorado State University. Libraries, 2021) Xie, Yucong, author; Pearce, Stephen, advisor; Argueso, Cristiana, committee member; Muñoz-Amatriaín, María, committee member; Nachappa, Punya, committee memberCrop production is limited by a variety of biotic stresses caused by pathogens. This study focuses on wheat streak mosaic disease in wheat, caused by the viral pathogen Wheat streak mosaic virus (WSMV), and Fusarium wilt disease in banana, caused by the fungal pathogen Fusarium oxysporium f.sp. cubense (Foc). In this dissertation, I applied genomic and transcriptomic tools to study the Wsm2 locus that confers genetic resistance to WSMV. Analyzing exome and transcriptome reads from wheat lines carrying Wsm2, I characterized structural variations and identified unique transcripts specific to these Wsm2 carrying lines. Moreover, examination of candidate genes within the Wsm2 interval identified several tandemly duplicated candidate genes annotated as Bowman-Birk inhibitor (BBIs), which triggered my interests to perform a genome-wide characterization of this gene family in wheat. I studied the possible mechanisms behind its copy number and functional domain duplications and analyzed its diverse role in plant biotic and abiotic stress using wheat RNA-seq expression data. Finally, I analyzed a time course transcriptomic dataset from banana root infected with Foc subtropical race 4 strain (Foc-STR4). I used gene co-expression assembly network (WGCNA) to study host plant transcriptional response to Foc infection and analyzed the expression profiles of candidate genes underlying a novel locus conferring resistance to Foc-STR4 and prioritized candidates. In summary, this dissertation studied genetic variants underlying host genetic resistance to WSMV and Foc and shed light on plant defense mechanisms against these two important crop pathogens.Item Open Access Exploiting rice diversity to uncover durable and broad-spectrum resistance(Colorado State University. Libraries, 2018) Bossa-Castro, Ana María, author; Leach, Jan E., advisor; Verdier, Valerie, committee member; Mosquera, Gloria, committee member; Argueso, Cristiana, committee member; Byrne, Patrick, committee memberRice is the staple food for human consumption and feeds over half the world's population. Major constraints towards a sustainable productivity of this cereal are losses caused by bacterial diseases, such as bacterial blight (BB) and bacterial leaf streak (BLS). Therefore, strategies aimed at increasing the global production of rice are essential. BB and BLS are caused by Xanthomonas oryzae pvs. oryzae (Xoo) and oryzicola (Xoc), respectively. This study aims to identify novel, broad-spectrum and durable sources of resistance to BB and BLS, and to pinpoint potential candidate genes for further characterization. We screened an indica rice Multi-parent Advanced Generation Inter-Cross (MAGIC) population, a novel mapping resource that allows high resolution detection for quantitative trait loci (QTL). A total of 14 disease resistance QTL effective against multiple X. oryzae strains were mapped, 11 confer resistance to both pathovars, i.e. broad-spectrum resistance (BSR), and three are pathovar-specific. We also detected specific alleles conferring disease resistance and susceptibility to these bacterial pathogens. Then, we combined diverse approaches to identify promising candidate genes, putatively involved in PAMP-triggered immunity (PTI) and effector triggered immunity (ETI), by (1) evaluating the presence and polymorphisms in defense-responsive cis-regulatory modules (CRMs) in gene promoters, (2) predicting gene promoters targeted by multiple X. oryzae strains, and (3) assessing the presence of SNP markers associated with resistance to X. oryzae strains. We also analyzed a cluster of MATH-BTB genes in a rice BSR QTL on chromosome 4 for polymorphisms between resistant and susceptible MAGIC lines. As a parallel approach to identify sources of durable resistance, the indica MAGIC population was also screened with an Xoo strain containing Tal7b, a transcription activator-like (TAL) virulence effector that is common to many Xoo strains. We mapped disease resistance QTL unique to this specific virulence factor and hypothesize that the mechanism of resistance conferred by one QTL is through a loss of susceptibility. BSR QTL and QTL specifically effective against virulence enhancing TALs may offer increased durability in the field. Because MAGIC lines are derived from elite cultivars, the use of identified QTL will be facilitated for the development of improved varieties.Item Open Access Initiation and regulation of iron economy in Arabidopsis thaliana chloroplasts(Colorado State University. Libraries, 2020) Kroh, Gretchen Elizabeth, author; Pilon, Marinus, advisor; Reddy, Anireddy, committee member; Bush, Daniel, committee member; Bedinger, Patricia, committee member; Argueso, Cristiana, committee memberIron (Fe) is biologically important for all organisms because of its role as a protein cofactor which provides redox and catalytic functions. Fe cofactors come in 3 different forms (Fe-S clusters, heme, and non-heme Fe). Plants have a stronger requirement for Fe than non-photosynthetic organisms because the chloroplast has a high demand for Fe. Plants are commonly Fe deficient because soil Fe is typically found in the non-bioavailable, ferric (Fe3+) form, which limits plant growth in natural and agricultural settings. When grown on soils where Fe availability is low, plants can increase Fe uptake and use Fe more efficiently. The leaf response to Fe limitation in the model plant, Arabidopsis thaliana, is the topic of my dissertation. As a major contribution to a larger study, I first characterized the transcriptional response for specific leaf genes to Fe deficiency in the leaf and found that transcripts for abundant chloroplast Fe proteins were down-regulated, suggesting an Fe economy response. Specifically, photosynthetic electron transport and chloroplast Fe-S assembly were targeted for down-regulation. Fe deficiency affects photosynthesis and chloroplast Fe protein expression. I characterized a photosynthesis mutant and found that the regulation of Fe protein expression is maintained, suggesting that loss of electron transport does not trigger down-regulation of Fe protein expression. By using RNA-seq, I analyzed genome-wide transcriptomic changes to identify co-regulated transcripts early in the Fe economy response, including candidate transcription factors. The transcriptional responses in wild type Fe limited plants and a chloroplast Fe-S assembly mutant were independent of each other, suggesting that Fe-S assembly does not generate a signal to regulate chloroplast Fe proteins. The novel insights provided in this dissertation form a foundation for understanding how photosynthetic organisms cope with Fe limitation. From an applied perspective, the results of this dissertation open new avenues to minimize effects of Fe deficiency in agricultural settings.Item Open Access Investigating fluroxypyr resistance in Bassia scoparia(Colorado State University. Libraries, 2021) Todd, Olivia, author; Gaines, Todd, advisor; Bedinger, Patricia, committee member; Argueso, Cristiana, committee member; Jahn, Courtney, committee memberSynthetic auxin herbicides are designed to mimic indole-3-acetic acid (IAA), an integral plant hormone affecting cell growth, development, and tropism. Recent developments in synthetic auxin herbicide research have produced several new reports of synthetic auxin resistant weeds and novel resistance mechanisms, including resistance by cytochrome P450 metabolism to mutations in auxin co-receptors. In this document, we investigate specific genes in the auxin signaling pathway that may be involved in weed resistance to the synthetic auxin herbicide fluroxypyr, an economically important method of broadleaf weed control in wheat. The auxin signaling pathway is well characterized, but for many herbicides in the synthetic auxin group, the specific gene family members for receptors and co-receptors with which they interact in the auxin signaling pathway remain unknown. We characterized this Bassia scoparia line using greenhouse studies, dose responses, absorption/translocation and metabolism using 14C-fluroxypyr. To supplement these physiology studies, we conducted an RNA-sequencing experiment using the de novo transcriptome of Bassia scoparia to characterize gene expression in response to fluroxypyr using variant calling and differential expression in R. In addition to investigating this resistance case, this document also describes methodologies for creating crop resistance to pendimethalin via EMS mutagenesis. Through this experiment, many individuals have been found to reach full maturity in the northern Colorado region before the growing season ends. Backcrossing to the inbred parent Sorghum bicolor to begin genetic characterization is the next step following completion of the early maturing line characterization and genetic validation.Item Open Access Organic nitrogen fertilizers influence nutritional value, water use efficiency, and nitrogen dynamics of drip irrigated lettuce and sweet corn(Colorado State University. Libraries, 2016) Sukor, Arina, author; Davis, Jessica G., advisor; Schipanski, Meagan E., committee member; Qian, Yaling, committee member; Argueso, Cristiana, committee memberFarmers usually rely on off-farm sources (fish emulsion, feather meal, blood meal) for the additional N needed during the growing season, and they are willing to pay the extra shipping cost. However, there is another fertilizer option being developed that could allow farmers to produce N on-farm, which is cyanobacteria, formerly known as the blue green algae. The general objectives of this study were to assess effects of organic N fertilizer application and N rates on nutritional value, water use efficiency, N dynamics of sweet corn and lettuce. A two-year field study was conducted in the summers of 2013 and 2014 at the Colorado State University Horticulture Research Center, Fort Collins, CO. The fertilizers used in this study were blood meal, feather meal, fish emulsion, and cyano-fertilizer. Both fish emulsion and cyano-fertilizer were supplied in four split applications over the growing season through drip irrigation, while the blood meal and feather meal were subsurface banded prior to planting. Lettuce and sweet corn were used as an indicator to evaluate effects of organic nitrogen (N) fertilizers on nutritional value, water use efficiency, and N dynamics. The aims of this study were to evaluate the effect of different types of organic N fertilizer on nutritional value; β-carotene, iron (Fe), zinc (Zn), marketable yield, water use efficiency (WUE), residual soil nitrate-N, N content, and N use efficiency (NUE) of horticultural crops, particularly lettuce and sweet corn. All fertilizer treatments in 2013 increased β-carotene concentration in leaf tissue compared to control, while only fish emulsion had a higher β-carotene concentration compared to other treatments in 2014. The high indole-3-acetic acid (IAA) applied in the fish emulsion treatment could have increased β- carotene concentration in lettuce in both years. Amount of IAA applied in the fish emulsion treatment was positively correlated with β-carotene concentration in both years. A significant negative correlation was found between marketable yield and β-carotene concentration in leaf tissue in 2014. High salicylic acid (SA) applied in the cyano-fertilizer treatment had a higher total leaf area compared to other fertilizers in both years. In lettuce, the blood meal treatment had a lower leaf Fe and Zn concentrations than other fertilizer treatments at 112 kg N ha-1. The cyano-fertilizer treatment had a higher leaf Fe concentration at 56 kg N ha-1. Leaf N concentration was positively correlated with Leaf Fe and Zn concentrations. Amount of NO3- -N applied in organic N fertilizers was negatively correlated with leaf Fe concentration. The cyano-fertilizer, fish emulsion, and blood meal treatments increased Fe concentration in sweet corn compared to feather meal. Amount of NO3- -N, Fe, and Zn applied in organic N fertilizers were positively correlated with kernel Fe concentration, while amount of NH4+ -N applied was negatively correlated with kernel Fe concentration. There was no N rate or treatment effect on leaf and kernel N concentrations in sweet corn. The amount of phytohormone, Ca, and Fe applied in organic N fertilizers may have affected field water use efficiency (fWUE), instantaneous water use efficiency (iWUE), kernel number, and leaf gas exchange components of sweet corn. Cyano-fertilizer apparently had a higher WUE, likely due to the high amount of SA applied. A positive relationship was observed between the amount of SA applied with iWUE and fWUE. The amount of Fe applied in organic N fertilizers had a positive correlation with leaf VPD and transpiration rate. The amount of Ca applied in the feather meal treatment may have contributed to increasing leaf temperature and decreasing net photosynthetic rate. The amount of NH4+ -N and Ca applied in the feather meal treatments were negatively correlated with both iWUE and fWUE. N rate effect was only observed in lettuce marketable yield and NUE in both years. Blood meal and feather meal fertilizers with higher percentage of N applied as NO3- -N compared to other fertilizer treatments had a higher residual soil NO3- -N concentration in 2013. Greater residual soil NO3 - -N was observed in the 0-30 cm depth compared to the 30-60 cm depth in 2014. Organic growers could achieve higher marketable yield and NUE when applying fertilizers at rates between 28 kg N ha-1 and 56 kg N ha-1 compared with 112 kg N ha-1. In sweet corn, the feather meal and fish emulsion treatments had a higher residual soil NO3- -N compared with other treatments. The fish emulsion, cyano-fertilizer, and blood meal had a higher leaf and kernel N contents and NUE compared with feather meal at 56 kg N ha-1. The cyanofertilizer treatment had a higher marketable ear yield and NUE compared with other treatments at 112 kg N ha-1 in 2014. The amount of C inputs and crop species may have affected soil permanganate oxidizable carbon (POXC) concentration in a single season study. Soil POXC concentration was higher in the cyanofertilizer treatment compared to the control treatment in sweet corn, while the opposite trend was found in lettuce. Depth effect was observed in soil POXC concentration at 0-30 cm compared to 30-60 cm in lettuce. Soil POXC concentration was higher at 112 kg N ha-1 compared to 56 kg N ha-1 in sweet corn, but there was no N rate effect in lettuce. Greater soil POXC concentration and marketable ear yield of sweet corn were observed in the cyano-fertilizer treatment compared to others at 112 kg N ha-1. Overall, our results indicate that organic N fertilizer, particularly cyano-fertilizer influenced soil POXC concentration over a short-term growing season of horticultural crops.Item Open Access Phytoalexin deficient4 (PAD4): a plant defense regulatory gene with distinct alternative splicing patterns in tomato (Solanum lycopersicum) and soybean (Glycine max)(Colorado State University. Libraries, 2023) Schmidt, Rebecca, author; Nalam, Vamsi, advisor; Argueso, Cristiana, committee member; Reddy, Anireddy, committee memberAlternative splicing is an important post-transcriptional regulatory mechanism that contributes to a plant's ability to perceive and respond to a variety of biotic and abiotic stressors. Alternative splicing has a documented role in plant immunity, as many R genes, which are important for plant defense against specialized pathogens, undergo alternative splicing in response to pathogen perception. Despite this, the role of alternative splicing in other components of plant defense responses is not well documented. As transcriptome data diversify to include more species and conditions, the extent of alternative splicing in plants has become apparent. PHYTOALEXIN DEFICIENT4 (PAD4), plays an integral role in plant defense signaling to biotic stressors, and in regulating responses to abiotic stresses. PAD4 undergoes alternative splicing in Soybean (Glycine max). Additionally, the expression pattern of Glycine max PAD4, GmPAD4, and its splice variant GmPAD4-AS1 are further characterized in early growth stages. We hypothesize PAD4 produces full-length and alternatively spliced transcripts in multiple species, and that PAD4 gene structure may influence the occurrence of alternatively spliced transcripts. Here we characterize alternative splicing of PAD4 in tomato (Solanum lycopersicum), identifying two splice variants. We also investigate the conservation of PAD4 intron-exon structure conservation across diverse species. PAD4 expression patterns are characterized using available expression data.Item Open Access THE IMPACTS OF HIGH TEMPERATURE ON BACTERIAL BLIGHT RESISTANCE GENES IN RICE(Colorado State University. Libraries, 2024) Shipp, Jennifer, author; Leach, Jan E., advisor; Argueso, Cristiana, committee member; Reddy, Anireddy, committee memberRice is cultivated around the world and serves as a primary source of income and calories for many people. However, rice yield is threatened by the bacteria Xanthomonas oryzae pv. oryzae (Xoo), and outbreaks can be devastating to global communities. Xoo is the causal agent of bacterial blight (BB) in rice, and it proliferates in rice-growing climates. As climate change progresses, the trend of increasing BB severity may result in increased losses for growers. Disease severity, quantified through lesion lengths, increases at high temperature in rice. Previous studies indicated this pattern of increased disease phenotypes occurs even when a resistance (R) gene is present, except for one, Xa7. Our rationale for these experiments is to determine if the classification of an R gene can predict its performance against BB outbreaks. The classification of R genes in rice is a recent addition to the scope of our knowledge of plant pathology and has been the result of studies on nucleotide polymorphisms, genetic mapping, and fluorescent imaging of protein localization. Grouping the underlying mechanisms of action of individual R genes, such as the executor genes Xa7 and Xa10, allow for comparative studies to further elucidate details of their assigned classes. Not all R genes have been classified, but establishing a trend that some R genes maintain efficacy under higher temperatures would provide breeders with more tools to develop climate-friendly rice lines. This study indicates that R genes that remain effective at high temperature may be classified into the same category of executor R genes. More research is needed to determine if R gene classification predicts durability under heat stress. This study explores BB lesion lengths and Xoo colony counts at high and low temperatures. We find that at high temperature relative to low temperature, disease lesions were more severe in IR24, containing no active R gene, and in plants containing the R genes Xa21, xa5, and Xa3. Lesions were shorter in plants with Xa7 and Xa10. Additionally, under the same treatments, bacterial numbers increased to higher levels in IR24, Xa21, xa5, and Xa3. Numbers in Xa7 were reduced while numbers in Xa10 were low early in infection, but eventually increased beyond those measured at low temperature. Degree of lesion restriction did not always correspond to degree of restricted bacterial numbers, suggesting that severity of lesions may not always be a predictor of bacterial multiplication in the plant. Xa7 and Xa10 are classified as executor R genes. The mechanism of action in these genes may play a role in their durability at high temperatures. We hypothesize that the success of executor R genes may be a result of protein accumulation in the nucleus. This mechanism might be analogous to instances of temperature sensitive pathogen defense related protein accumulation, as seen in Arabidopsis. This mechanism may be induced or enhanced by the presence of reactive oxygen species (ROS) or other heat-stress related markers. More research is needed to explore the signaling between heat-stress pathways and R genes.Item Open Access Unlocking sorghum adaptive potential through investigations into pleiotropic control of chilling tolerance by Tannin1(Colorado State University. Libraries, 2023) Schuh, Anthony, author; Morris, Geoffrey, advisor; Argueso, Cristiana, committee member; Wrighton, Kelly, committee memberChilling tolerant crops can positively impact agricultural sustainability through lengthened growing seasons and improved water and nitrogen use efficiency. In sorghum (Sorghum bicolor [L.] Moench), the fourth most grown grain, coinheritance of qSbCT04.62, the largest effect chilling tolerance locus, with Tannin1, the major gene underlying undesirable grain proanthocyanidins, has stymied breeding for chilling tolerance. To investigate the genetic basis of qSbCT04.62, including its coinheritance with Tan1, we developed near isogenic lines (NILs) with chilling tolerant haplotypes around qCT04.62. In the first study we genotype the NILs and investigate the introgressions physiological control over the cold stress response. Genome sequencing revealed that the CT04.62+ NILs introgressions on chr04 include Tannin1, a homolog of Arabidopsis cold regulator CBF, peak SNPs for qCT04.62 from multi-family NAM, and 61.2-62 Mb of HKZ ✕ BTx623 NAM family qCT04.62 confidence interval. Grain tannins were correlated with Tan1 genotype, revealing heterogeneity in one NIL at Tannin1. Controlled environment chilling assays found no genotype by environment interaction on growth by chilling per se in parents or NILs. Cold germination was reduced at 15°C and superior at 20 and 25°C in the chilling tolerant parent compared to chilling sensitive, but unchanged between NILs. The introgression also did not regulate a chilling induced increase in non-photochemical quenching. In the second study we investigated Tan1 function with a transcriptome analysis of the NIL's response to chilling stress. Tannin1 was widely expressed in sorghum tissues but did not promote a transcriptional response in chilling tolerance related molecular pathways including lipid remodeling, phytohormone signaling, CBF upregulation, photoprotection, and ROS mitigation. GO analysis also found no significant term enrichments at the p < 0.1 threshold. Only 17 genes had expression patterns regulated by polymorphisms in the introgressions, seven cis, and ten trans, with little evidence of co-regulation. Further, Tannin1 was functionally divergent from its Arabidopsis ortholog TTG1 and other WD40 orthologs in regulating leaf anthocyanin biosynthesis. Overall, these findings suggest that linkage, not pleiotropy, underpins the coinheritance of Tan1 and CT04.62+, unlocking the use of CT04.62+ for sorghum improvement. Further, these results imply a lack of deleterious fitness effects of tan1 alleles in commercial grain sorghum varieties and suggest the possibility of an unknown cold tolerance regulator which, if identified, could have implications for crop improvement of chilling tolerance outside sorghum.