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Department of Agricultural Biology

Permanent URI for this communityhttps://hdl.handle.net/10217/100336

These digital collections include theses, dissertations, faculty publications, and datasets from the Department of Agricultural Biology. Also present is a video documentary titled Complete Harvest: The Future of Rice as Bioenergy. Due to departmental name changes, materials from the following historical departments are also included here: Bioagricultural Sciences and Pest Management; Botany; Botany and Plant Pathology; Entomology; Plant Pathology and Weed Science; Zoology; Zoology and Entomology.

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Browsing Department of Agricultural Biology by Author "Argueso, Cristiana, committee member"

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    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 member
    Rice 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.
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    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 member
    Synthetic 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.
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    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 member
    Alternative 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.
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    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 member
    Rice 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.