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Theses and Dissertations

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Browsing Theses and Dissertations by Author "Argueso, Cristiana, committee member"

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    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 member
    Crop 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.
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    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 member
    Farmers 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.
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    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 member
    Chilling 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.