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Browsing by Author "Nalam, Vamsi, committee member"

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    An NLR gene likely underlying RMES1 provides global sorghum resistance bolstered by RMES2
    (Colorado State University. Libraries, 2023) VanGessel, Carl, author; Morris, Geoffrey, advisor; Nalam, Vamsi, committee member; Roberts, Robyn, committee member; Mason, Esten, committee member
    Breeding for aphid host plant resistance in sorghum has been an area of interest since the emergence of Melanaphis sorghi in North America a decade ago. In order to develop durable sorghum aphid resistance, breeders must be equipped with tools (trait package) and knowledge (molecular mechanisms) of host plant resistance. In this dissertation, I characterize the current state of sorghum aphid breeding and propose a genotype to phenotype map for the major source of global resistance, Resistance to Melanaphis sorghi 1. Relying on near-isogenic lines, I demonstrate that RMES1 is applying selection pressure to sorghum aphid through reduction in fecundity that discriminates among aphid species. In global sorghum lines, RMES1 is rare whereas a second resistance source, RMES2, is common and present in historic breeding germplasm. I mapped RMES2 in Haitian breeding populations where it contributes fitness increases while lacking antagonistic pleiotropy and is selected for alongside RMES1. These results suggest breeding programs may unknowingly be deploying both sources of resistance which in combination are reducing the likelihood of M. sorghi biotype shifts to overcome RMES1. As aphid resistance may rely on phytochemical and/or induction with extended phenotypes regarding aphid populations, I used pan-genomic, transcriptomic, and metabolomic resources to describe the molecular mechanism of RMES1. Structural variation at the Chr06 locus underlies presence/absence variation of several nucleotide-binding leucine-rich repeat receptor (NLR) genes. Two of these candidate genes, SbPI276837.06G016400 and SbPI276837.06G016600, are representatives of two orthologous NLR groups which have genomic and transcriptomic evidence of underlying RMES1 resistance. The PAL branch of the salicylic acid pathway is the primary phytohormone pathway responsible for RMES1-induced resistance. Finally, metabolome reorganization mirroring transcriptome changes suggest RMES1 is inducing multiple downstream mechanisms responsible for reducing aphid fecundity. While the causal gene underlying RMES1 remains to be cloned and the eliciting aphid factor is unknown, this research suggests that gene-for-gene dynamics could lead to resistance-breaking biotype shifts and combining RMES1 with additional resistance genes e.g. RMES2, will help achieve durability.
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    Artificial intelligence powered personalized agriculture
    (Colorado State University. Libraries, 2023) Tetala, Satya Surya Dattatreya Reddy, author; Simske, Steven, advisor; Conrad, Steve, committee member; Gaines, Todd, committee member; Nalam, Vamsi, committee member
    The integration of Artificial Intelligence (AI) in agriculture has shown the potential to improve crop selection and enhance sustainability practices. In this study, we aim to investigate the benefits and feasibility of using AI-powered personalized recommendations for crop selection and sustainability practices in the context of agroecology. We propose to lay the foundation for an agricultural recommendation engine that considers several parameters that influence yield and presents the best crop(s) to sow based on the model's output. We aim to examine this recommendation engine's impact on agriculture's sustainability and to evaluate its effectiveness and accuracy. Our ultimate goal is to provide a comprehensive understanding of the potential benefits and challenges of using AI-powered recommendations in agriculture and to lay the foundation for the development of a practical, effective, and user-friendly recommendation engine that can help farmers make informed decisions about their crops and improve the long-term sustainability of agriculture.
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    Sweet surprise: the search for genes conferring beet curly top virus resistance
    (Colorado State University. Libraries, 2023) Withycombe, Jordan, author; Nachappa, Punya, advisor; Nalam, Vamsi, committee member; Nishimura, Marc, committee member; Dorn, Kevin, committee member
    Sugar beets (Beta vulgaris L.) are grown across the western United States and suffer economic loss annually to curly top disease. Curly top disease is caused by the beet curly top virus (BCTV) and is spread by the only known insect vector the beet leafhopper, Circulifer tenellus Baker (BLH). Current management strategies for BCTV include chemical control using neonicotinoid seed treatments and foliar insecticidal sprays, as well as the use of BCTV-resistant sugar beet varieties. However, the underlying genetic mechanism surrounding resistance in sugar beet is unknown. The overarching goal of this study was to identify the mechanism of resistance in sugar beet to BCTV and identify potential genes conferring resistance. The objectives for this study were: 1) classify the nature of BCTV resistance in a resistant (EL10) and susceptible (FC709-2) genotype of sugar beet using host suitability and host preference insect assays, as well as assess viral load within each genotype and 2) characterize the transcriptional response to BCTV infection using RNA-sequencing. To classify the nature of BCTV resistance in each genotype of sugar beet, host suitability and preference assays were conducted using virus infected and uninfected BLH. In host suitability assays, the percentage of surviving BLH adults and the number of nymphs produced when reared on a single plant of either genotype was determined over a 3-week period. There was no difference in adult survival, or the number of nymphs produced on either genotype for the virus infected or uninfected leafhoppers. Host preference assays were used to assess settling behavior of BLH over time when given a choice between the two genotypes. It was concluded that virus infected leafhoppers had a clear choice to settle on the susceptible genotype at all timepoints after 4 hours, while uninfected leafhoppers did not make as strong of a settling choice. Average viral load for each genotype across three timepoints was estimated using qPCR. The results showed that the average viral load increased in each genotype over time, yet there was no difference in the average viral load between the genotypes at any individual timepoint. The global transcriptional response to BCTV infection over time for a resistant and susceptible genotype of sugar beet was conducted using RNA-sequencing technology. Mock-inoculated and BCTV-inoculated plants from each genotype were sampled on day 1, 7 or 14 post inoculation resulting in the preparation of 36 mRNA sequencing libraries. Comparison between mock-inoculated and BCTV-inoculated plants of each genotype and timepoint were conducted separately to generate six list of differentially expressed transcripts (DETs). Each transcript was annotated with a description and further classified for its role in the plant biological, cellular or molecular processes. The results showed that both genotypes of sugar beet had a dynamic response to BCTV infection over time, although there was minimal overlap between the responses to one another. EL10, the resistant genotype, had DETs associated with phytohormone production including jasmonic acid and abscisic acid, along with proteins linked to stress reduction and the downregulation of plant primary metabolic processes. In contrast FC709-2, the susceptible genotype, was found to produce opposing phytohormones like salicylic acid and auxins, as well as the production of volatile organic compounds and an increase of primary plant metabolic processes. These opposing responses shed light on the differences in the transcriptional response of a resistant and susceptible genotype of sugar beet. Understanding and classifying the mechanisms of resistance or susceptibility to BCTV infection in sugar beet is beneficial to researchers and plant breeders as it provides a basis for further exploration of the host plant-virus-vector interactions.