Plant Health Research and Extension Experiences for Undergraduates
Permanent URI for this collection
The Plant Health Research and Extension Experiences for Undergraduates is part of the Research and Extension Experiences for Undergraduates (REEU) program and is organized through the Department of Plant Pathology at Kansas State University (K-State) and is a summer internship program in plant pathology and related subjects (e.g. crop genetics, horticulture, entomology, and agronomy). The student interns will work with faculty, postdoctoral scholars, or graduate students at K-State on research projects that will be either lab-, greenhouse-, field-based, or a combination of above components. To learn more please visit the Summer Internships in Plant Health at Kansas State University website.
Browse
Recent Submissions
Item Open Access Exploring fungal and viral pathogens associated with intermediate wheatgrass, a promising new small grain crop(2023-07-27) Webb, Griffin; Tidakbi, Lawrence; Bruce, Myron; Rupp, JessicaSmall grain production in Kansas and other states in the central United States is a crucial component of agricultural economies. One emerging small grain is Kernza®, the grain harvested from intermediate wheatgrass (IWG, Thinopyrum intermedium). This crop is a perennial grass in contrast to common annual wheat varieties grown worldwide. This aspect of IWG allows it to develop a large root structure which provides soil structure and prevents the need for yearly tillage. With its recent emergence, however, there is little data available about the susceptibility of Kernza® to common small grain diseases. We are collecting and analyzing samples of Kernza® from growers to identify pathogens, with a special focus on Fusarium head blight (FHB). We cultured 29 samples by surface disinfesting grains, then incubating them on Spezieller Nahrstoffarmer Agar (SNA). The nutrient composition of SNA encourages growth of Fusarium spp. The resulting cultures were then used for DNA analysis to determine the species of fungi present. Additionally, 22 leaf samples obtained from growers were subjected to DAS-ELISA to determine if intermediate wheatgrass can be infected with wheat streak mosaic virus, a common viral pathogen of wheat. Our results indicate that Kernza® is susceptible to both FHB and wheat streak mosaic virus. Growers looking to plant Kernza® should be aware of these potential pathogens and take appropriate action to mitigate potential yield loss. Further investigation regarding the potential of other pathogens that could infect IWG is necessary.Item Open Access Diagnostic Testing for Kansas Wheat Viruses(2023-07-27) Trout, Landon; Day, Chandler; Redila, Carla; Fellers, John; O'Mara, JudyThe wheat streak mosaic virus complex consists of three viruses that are visually indistinguishable and often present together. These viruses are Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), and High Plains wheat mosaic virus (HPWMoV). Together, these viruses cause millions of bushels of yield loss to farmers every year and are of great interest to plant breeders. To determine which pathogens are present in infected plant tissue, samples were taken and analyzed by enzyme-linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT-PCR). This research will investigate regional virus makeup and compare results of RT-PCR and ELISA based diagnostics. Sixty-three samples were collected from various cultivars and multiple locations in Kansas and tested with ELISA. Eighteen samples tested positive for WSMV, two samples tested positive for TriMV, and one sample tested positive for HPWMoV. To compare the results to a more sensitive diagnostic assay, RT-PCR was performed and compared to ELISA results. Of the positive ELISA samples, four samples were false positives, and two samples were false negatives. This shows that ELISA has an 80.6% accuracy rate at correctly identifying wheat viruses compared to RT-PCR. Additionally, increases in TriMV infection were detected in Joe, Hamilton, and Dallas; wheat varieties with resistance to WSMV.Item Open Access Screening for WSMV Tolerance in Wild Wheat Relatives(2023-07-27) Sawyer, Caleb; Nouri, Shahideh; Prakash, Ved; Zarzynska-Nowak, AlexandraWheat Streak Mosaic Virus (WSMV) is a serious viral pathogen causing significant crop yield loss in wheat growing regions across the globe. In the United States, Its impacts are most heavily felt in the Great Plains, causing significant economic repercussions. While WSMV is primarily vectored by the wheat curl mite, this vector is difficult to control due to its size, resistance to pesticides, rapid reproduction, and feeding effects on host plants. Alongside efforts made to control the vector, our research attempts to circumvent this challenge in a search for genetic resistance and tolerance in wild wheat to combat the disease. In this study, a large panel of Aegilops tauschii accessions were grown in controlled environment growth chambers, then mechanically sap inoculated with WSMV and symptom severity was measured at different points post-inoculation. Viral titers were measured from systemic leaves in inoculated plants via real-time quantitative PCR. Based on the viral concentration and symptom severity, several tolerant and susceptible lines have been identified and selected for the genome wide association study (GWAS). Further analysis will be performed comparing the miRNA profiles of selected tolerant and susceptible lines to better understand their genetic regulation differences. These results could lead to the development of WSMV tolerant commercially used varieties. This research can help prevent high yield loss, securing reliable production of the United State’s top cereal food grain production.Item Open Access Impact of Rye Cover Crop on Pigweed Seed Viability(2023-07-27) Holguin, Kimberly; Woitaszewski, Lily; Lancaster, Sarah; Dille, AnitaPalmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus) are the two pigweed species most prevalent in Kansas. They are difficult to manage because they are resistant to herbicide applications. Cereal rye (Secale cereale) is a grass notable for its ability to hold soil in place against erosion. This study was conducted to test a cereal rye cover crop’s ability to deplete the presence of Palmer amaranth and waterhemp in the seedbank when buried compared to those with no cover crops present. Fifty seeds in wire mesh packets were buried in soybean fields at seven different sites in the states of Indiana, Kansas, Missouri, North Dakota, and Wisconsin. Packets were removed at three intervals and seed viability was determined by cleaning the wire mesh packets with a water and bleach solution followed by germination in petri dishes. If samples showed zero germination for three days, seeds were then squished and observed under a microscope. This determined whether seeds were dormant or nonviable. Seed viability data will be discussed and results will provide insight into whether cereal rye cover crop may have an impact on depletion of pigweed seeds in the north central region of the United States.Item Open Access Impacts of plant tafazzin deficiency on differential gene expression(2023-07-27) Hayden, Cole; Welti, Ruth; Zoong Lwe, ZolianTafazzin is a mitochondrial protein characterized in mammals and yeast. Tafazzin remodels the fatty acids of cardiolipin, aiding in the proper function of the electron transport chain. Although the function of tafazzin is known, the mechanisms and pathways that lead to apoptosis under tafazzin deficiency are unknown. Here we use a homolog of tafazzin in the model plant organism Arabidopsis thaliana to test our null hypothesis that gene expression is not dependent on the presence of functional tafazzin. RNA-seq was performed on leaf samples of wild type plants and mutant plants with mutations of varying severity in the gene encoding tafazzin. The sequencing output was analyzed with a selection of bioinformatics tools that includes HISAT2 (aligner), StringTie (assembler), and DESeq2 (differential gene expression identifier). The results indicate genes that are upregulated or downregulated in response to functional tafazzin’s absence. One outcome of analysis reveals that the genes that demonstrate the most statistically significant differential expression are nearly all downregulated in the mutants with respect to wild type, and many of them are localized to the mitochondria. Of these, the gene at locus AT3G54730 presents one possible direction of further study as it codes a transcription repressor protein. The downregulation of a transcription repressor may be a contributing factor to the phenotype observed under the condition of tafazzin deficiency, as transcripts relating to apoptosis would be repressed under healthy, unmutated cell conditions. One goal of this analysis is to develop a framework for the metabolic engineering of plants to display stronger resilience against environmental stress.Item Open Access Modifying Camelina Seed Oil Production Using CRISPR-Cas9 Gene Editing(2023-07-27) Snider, Grant; White, Dexter; Durrett, TimothyCamelina sativa, a member of the mustard family, is an increasingly studied oil seed crop with valuable agronomic traits that make it a potential source of biofuels in the future. Seed oil is composed mostly of triacylglycerol (TAG) which is synthesized by two major enzymes: diacylglycerol acyltransferase (DGAT1) and phospholipid: diacylglycerol acyltransferase (PDAT1). Acetyl-triacylglycerols (acetyl-TAG), an alternate triacylglycerol produced by Camelina, has desirable biofuel properties including reduced-viscosity and a low freezing point. Production of acetyl-TAG is competed by production of TAG by DGAT1 and PDAT1. The objective of this project is to induce mutations using clustered regularly interspaced palindromic repeats-associated protein 9 (CRISPR-Cas9) into the genes encoding for DGAT1 and PDAT1, inhibiting enzyme function to increase yield of acetyl-TAG within viable seeds that maintain these mutations in their germline. Camelina sativa has a hexaploid genome with three homeologs for each gene. Induced mutations could occur on some, none, or all three gene loci. This study uses gel electrophoresis to identify deletions within CsDGAT1 and CsPDAT1 gene loci and observe continuation of mutations between first- and second-generation plants. Ninety-nine second-generation (T2) Camelina plants were grown including wild- type and DGAT1-CRISPR mutant lines. Only one line with a deletion mutation was identified. However, this plant possessed a diseased phenotype, having stunted growth with sickly, wrinkled and spotted leaves. One possibility is that off-target effects of Cas9 that caused unwanted mutations leading to the defective phenotype. Future work should aim to screen for deletions in additional Camelina plants and in plants of diploid genomes like Pennycress.Item Open Access Evaluation of Fusarium Head Blight and Barley Yellow Dwarf Virus Incidences and Severity Among Winter Wheat Association Mapping Population(2023-07-27) Zhu, Daniel; Tidakbi, Lawrence; Wang, Hong; Rupp, Jessica; Jordan, KatherineFusarium head blight (FHB) and Barley Yellow Dwarf Virus (BYD) are diseases in winter wheat (Triticum aestivum) that caused an estimated $2.7 billion in damage and 0.65 bushels/acre in yield loss in a three-year period, respectively. Disease-resistant lines are the most efficient way to combat disease pressure. Disease resistances are quantitative in nature and many genes have not been well characterized. In addition, several minor effect QTLs identified in wheat make it difficult to design effective markers for resistance to FHB and BYD. Thus, the aim of this study is to identify genetic markers in genomic regions associated with resistance phenotypes. To do this, a panel of 270 different winter wheat lines from across the wheat-growing regions in the United States were scored for disease incidence and severity in the Kansas State University FHB nursery. The causative agent for FHB was introduced via corn spawn and the BYD was presented via natural infection by aphids. These wheat lines were also sequenced using exome capture, providing 450,000 high-quality SNPs for genome-wide association study (GWAS). We observed phenotypic variation in the field, suggesting an association study can be done. There were 30 significant (p<0.00001) SNPs for BYD resistance/susceptibility and 9 significant (p<0.0001) SNPS for FHB resistance/susceptibility. We identified 26 lines representing 10.4% of the total lines carrying the major Fhb1 resistance gene with lower area under the disease progressive curve (AUDPC) compared to the lines with no Fhb1 gene. Our results suggest that high-quality markers for both diseases may be designed. In the future, we hope to test these SNPs by developing KASP assays for these QTLs and validate the SNPs as gene markers in our trial population.Item Open Access Cattle Grazing Does Not Alter Early Season Insect Community Composition in Tallgrass Prairies(2023-07-27) Barajas, Aster; Kim, TaniaPrairie ecosystems are known to have cattle that graze on the different grasses, plants, and flowers. This is known to negatively impact insect communities because of the defoliation, or the removal of plants, of the environment. As cattle graze and change the environment of prairie foliage, arthropods lose valuable resources that are essential to mating, predation, and development. The current hypothesis is that insect communities in ungrazed land have greater order-level richness and insect abundance than communities in grazed land. In order to find what communities were present, 10 sites throughout eastern Kansas were sampled using sweep net methods. The sites are divided evenly into 5 grazed and 5 ungrazed land, and sweeps are conducted by moving a sweep net in a serpentine pattern through foliage along 2 50 meter transects. The collected insects are counted and identified to the order level under a microscope, then processed using Microsoft Excel’s data analysis tools. The experiment resulted in a higher insect abundance in grazed sites than in ungrazed sites, and slightly higher order richness in not grazed sites than in grazed sites. However, these results are not significant. There were differences found in community composition with Coleoptera (beetles) numbers differing in grazed (10%) and ungrazed sites (16%), Neuroptera (lacewings) not being present in grazed sites, and Odonata (dragon/damselflies) not being present in ungrazed sites. Further investigation into these differences could give deeper insights to the effects of cattle grazing on these communities.Item Open Access Effects of Different Sterilization Rinses on Germination of Hemp, Cannabis Sativa, for Tissue Culture(2022-07-28) Terry, Ash; Park, Sunghun; Motolai, Gergely; Stuart, NathanHemp, Cannabis sativa, is a plant valued for its medicinal properties, fiber, and oil. While the hemp industry has grown significantly in the past years, a protocol for its tissue culture has not been publicly established. Tissue culture allows for regeneration of plants in a controlled, sterile environment while utilizing less space. Since creating a sterile environment is critical to a successful tissue culture, this study focused on the effects of different sterilization methods on contamination and germination of hemp seeds. The different sterilization rinses tested were water (control), 5% hydrogen peroxide, 70% ethanol, 20% bleach, 30% bleach, 40% bleach, and 50% bleach solutions. One of these solutions was applied to a group of hemp seeds. Within each group one third was rinsed in the solution for 5 minutes, another third for 10 minutes, and the last third for 15 minutes. The seeds were then placed onto germination media and left to germinate in a growth chamber for one week. The 20% bleach rinse for 10 minutes generated the lowest contamination rate, 4.5%, while maintaining the highest germination rate, 77.3%. Excluding the control, the 70% ethanol rinses for 5 and 10 minutes had two of the highest contamination rates and the two lowest germination rates. These results provide preliminary information about sterilization of hemp seeds for tissue culture. Once a reliable hemp tissue culture protocol is fully developed it will provide hemp growers with a dependable method to produce quality, disease free hemp.Item Open Access CRISPR-Cas9 ribonucleoprotein-mediated gene editing in the plant pathogenic fungus Magnaporthe oryzae(2022-07-28) McAnany, Tomas; Rowe, David; Huang, Jun; Cook, David EMagnaporthe oryzae, the cause of rice blast disease, is a model fungus for studying plant-pathogen interactions and a major threat to global agriculture. From changes made to their DNA, pathogens like M. oryzae have evolved characteristics like aggressiveness, host range, and fungicide resistance. Once source of DNA variation, arises from DNA repair. There are many sources of DNA damage, with the most severe being double-strand breaks (DSBs) which can lead to genome instability if left unrepaired. Hence, eukaryotes have evolved complex repair mechanisms like microhomology-mediated-end-joining (MMEJ), non-homologous-end-joining (NHEJ) and homologous-recombination (HR) to repair DNA DSBs. Interestingly, these repair pathways have different rates of fidelity, meaning some pathways create more mutations than others. In filamentous fungi, the mechanism by which MMEJ repairs DSBs is not well molecularly characterized, so the purpose of this project is to identify genes controlling MMEJ. To facilitate this, we created knockouts for homologs of DNA repair genes. Five genes were selected for deletion, including ligase 1 A & B, and polymerases θ, 3, and 4. Two CRISPR-Cas9 ribonucleoproteins were used to make DNA DSBs surrounding our target genes. Donor DNA encoding resistance to G418 antibiotic was supplied for insertion into the DSB site, where it served as a selectable marker when plated on complete media containing G418 antibiotics. DNA was extracted from individual colonies and used in PCR genotyping to test for the target gene and correct G418 integration. These knockouts will be characterized in future work to determine their individual roles in MMEJ DSB repair.Item Open Access Development of strategies to improve modern wheat cultivars by adopting genetic diversity from wild relatives(2022-07-28) Stellin, Nick; Wang, Wei; Akhunov, EduardBread wheat is a hexaploid plant that contains three subgenomes derived from a hybridization event between tetraploid Triticum dicoccoides and diploid Aegilops taushii. These wild ancestors of wheat offer more genetic diversity, but they lack the domesticated traits critical for cultivating wheat and adapted to modern agricultural practices. In this study, we are optimizing the process of wild relative diversity introgression while reducing the negative impact of non-adaptive alleles on wheat performance. In a population created by crossing a wild relative and bread wheat, we remove a non-domesticated allele of Btr1, affecting traits important for mechanical harvesting, by genetic engineering or by using molecular markers. The resulting population of wheat lines has the domesticated allele at the Btr1 locus as well as novel genetic diversity from a wild relative for further evaluation.Item Open Access A Convoluted Neural Network for Object Detection of Common Flower-Visiting Insects(2022-07-28) Foley, Connor; Spiesman, BrianAn important aspect of pollinator ecology is monitoring and identifying the kinds of animal visitors to flowers. Conventional methods often use video recording or camera traps to collect data and human analysts for manual review. However, because of the large volumes of data collected and partiality in human reviewers, these methods are costly in terms of time and resources, can be prone to human error, and require taxonomic expertise. Computer vision (CV) is a branch of deep learning that has demonstrated promise as a lower-cost and rapid alternative to conventional methods for pollinator monitoring. Object detectors are a kind of deep learning network which use CV to identify and localize multiple different objects within an image. An object detector may be placed on a camera in the field to process in real time video and record different visitors to flowers, thus cutting out time for manual review. For this project, an object detector will be trained on 10,000 images from the iNaturalist research-grade database sourced from GBIF. Images are distributed across eight classes (Bees, Lepidoptera, Flies, Beetles, Wasps, Bugs, Ants, & Spiders) representing different common taxa observed at flowers and weighted according to frequency of visit and importance. Bees and Lepidoptera are weighted heaviest and spiders least. Several different architectures of the YOLO object detector infrastructure will be tested. Preliminary results show that this architecture will be useful for monitoring of pollinators in the field.Item Open Access Variability of protease activity and growth rate in isolates of Macrophomina phaseolina from various hosts(2022-07-28) Hobson, Sam; Waite, Natalie; Little, Christopher RMacrophomina phaseolina is a necrotrophic fungal pathogen that causes charcoal rot, among other diseases, on over 500 plant hosts and economically important crops in Kansas such as soybean and sorghum. Because it thrives in hot, dry environments, global climate change threatens to make this pathogen increasingly difficult to manage. M. phaseolina has a relatively low number of genes encoding proteases, protein-lysing enzymes commonly employed by plant pathogens. Further, their effect on virulence has been understudied. Three-hundred thirteen isolates of M. phaseolina from a variety of hosts were cultured on potato dextrose agar (PDA) plates to measure growth rate over one week, then were cultured on casein agar (CNA) to assess proteolytic activity over one week. Clearing zones that formed around the colonies on CNA represent areas where protein had been lysed, thus distinguishing isolates by their proteolytic activity. We hypothesize that different isolates will demonstrate varying levels of protease activity. This would shed light on the role that proteases play as a virulence factor for M. phaseolina and how this role may shift depending on the host and genetic identity of the isolate. Better understanding of M. phaseolina virulence mechanisms is vital to manage this pathogen, especially as climate change exacerbates the environmental conditions that promote charcoal rot.Item Open Access Analyzing Isolates of Fusarium Head Blight in Wheat Across Kansas(2022-07-28) Davis, Danielle; Dahal, Anusha; Bruce, Myron; Rupp, JessicaOne of the big threats to wheat farmers in Kansas is Fusarium Head Blight (FHB). This disease infects wheat heads, reducing the yield of the plant and releasing deoxynivalenol, a toxin that causes vomit sickness in humans and animals. This toxin is heavily regulated by the FDA making the sale of wheat seed infected with FHB nearly impossible and reducing the profit of that season. Preventing FHB in the field is difficult because wheat is only susceptible at heading, which makes the timing of fungicide application critical.. Research and communication between producers, breeders, and researchers attempt to find better ways of managing FHB. This project has collected samples of infected wheat heads from across Kansas from several different counties with the help of Kansas wheat breeders, Extension specialists, agents, ag industry professionals, and producers. Infected wheat heads are sterilized and the fungus is isolated. Fungal cultures underwent single-sporing to confirm a pure isolate. Then DNA is extracted and sequenced. This confirms that the fungus associated with the wheat head is Fusarium and what species. This process is done in hopes of different strains and a pattern in those differences across KS counties to develop more targeted methods of dealing with Fusarium Head Blight. This includes using these isolates in screening nurseries. This collaborative effort aims to help farmers respond more effectively to infection in the field and protect their crop and profit.Item Open Access Increasing Oil Production in Camelina sativa Engineered to Synthesize Unusual Lipids(2022-07-28) Davis, Isabella; Alkotami, Linah; Durrett, Timothy PDifferent Euonymus species naturally produce acetyl-triacylglycerol (acTAG) in their seed oil. AcTAG are unusual structures of the triacylglycerols (TAG) typically found in vegetable oil, and have lower freezing points and viscosity compared to regular vegetable oil. Seed oil containing AcTAG can be used as biodiesel, plasticizers, and other alternatives to petroleum-based products. AcTAG can be synthesized in Camelina sativa by expressing key enzymes from Euonymus and by using RNA interference (RNAi) to suppress competing camelina biochemical pathways. Previous observations of high acetyl-TAG camelina lines have shown an increase in overall TAG molecules, but lower fatty acid levels compared to wild-type seeds. It is hypothesized the decrease in overall fatty acid content is due to a limited amount of glycerol-3-phosphate (G3P) backbone. To increase G3P, C. sativa seeds were transformed to overexpress the gene that encodes glycerol-3-phosphate dehydrogenase (GPD1), which converts dihydroxyacetone phosphate (DHAP) to G3P. By increasing G3P synthesis, the fatty acid content is expected to increase to wild-type content or higher. C. sativa seeds were collected from third-generation homozygous transgenic lines for lipid analysis. These lines were analyzed in three or more replicates to measure the amount of AcTAG, TAG, and overall fatty acid per seed. The resulting data is expected to show increased fatty acid content closer to wild-type seeds. Higher fatty acid content using acTAG and TAG molecules can be used to decrease the number of plants needed to produce C. sativa oils and save agricultural space for farmers.Item Open Access A greenhouse study on ground beetle movement and predation rate based on habitat type(2022-07-28) Cox, Elijah; Kim, TaniaGround beetles (Coleoptera: Carabidae) are important in agro-ecosystems as generalist predators of invertebrate pests and weed seeds. However, less is known about ground beetles’ cross-over and predation rates between crop fields and grass habitats. This project seeks to identify how ground beetles move between agricultural crops and perennial grass habitats and what ground beetle predation rates are like in these habitats. We created greenhouse environments that mimic these habitats using corn, soybean, and a grass-perennial plant mix. We made planted trays of monocultures and pairwise mixtures of each plant type (6 treatments in total). Ground beetles were collected in grass habitats, marked with paint markers for identification purposes, and released at the center of each plant tray. Pitfalls were placed in a grid pattern throughout the cages for ground beetle recapture data. Their locations were determined using a labeled coordinate system for each pitfall. Pitfall locations were recorded twice a day over a 2-week period. To assess predation rates, moth egg cards were placed at eight locations in each tray for a 48-hour period and the number of removed eggs was counted. We hypothesize that ground beetle movement and foraging will be higher in the grass monoculture when compared to the corn and soybean monoculture. For the mixed plant trays, we expect the ground beetles to have higher predation rates and cross over into the grass habitats. Results from this study will give information on ground beetle movement and predation activity between agricultural crops and perennial grass habitats and can be useful for cultural control practices, such as prairie strips and diversified plantings, for pest management in agricultural systems.Item Open Access The Effects of Phosphorus Application and Cover Cropping on Soil Aggregate Stability(2022-07-28) Wood-Smith, Griffin; Stahl, Kendra; Presley, DeAnn RSoil aggregation is the clumping of multiple particles, forming one individual piece of soil. The stability of these aggregates impacts many factors such as preventing erosion, maintaining nutrients, and holding water. This study is conducted in the field at the Kansas Agricultural Watershed (KAW) and is testing the effect of three phosphorus applications, either fall broadcast, spring injection, and none, as well as having cover crops or no cover crops, on the soil aggregate stability. Three samples from 18 plots total are taken of the topsoil (0-5cm) and subsoil (5-10cm.) Next, when samples are dried, the Slakes application is used on a phone or tablet with a camera. The phone is held by a stabilizing device with the camera facing down. Three aggregates of a sample are taken and placed on a petri dish, then placed in a well-lit area that the camera can focus on. After setting up, water is introduced to the petri dish, submerging the aggregates. A timer of 10 minutes is started on the application. When the timer ends, the application produces a number, giving you the Slakes Stability Index, measuring aggregate stability in water. This process is repeated for all 54 samples. Using an SAS analytics software, with a two-way analysis of variance, the data shows all three factors of individual cover crops, individual P application, and the combination of both, have no significant difference regarding aggregate stability. This means there is no need to add either input to maintain healthy soil aggregation.Item Open Access Genome assembly and visualization of aggressive wheat blast strain 16MoT01(2022-07-28) Burke, Eva; Bika, Ravi; Lin, Guifang; Liu, SanzhenWheat blast, a highly destructive fungal disease caused by pathotype Magnaporthe oryzae Triticum, can cause up to 100% yield loss in wheat fields under optimal pathogen conditions. Until 2016, the disease had been confined to South America, but recent outbreaks of the disease in Asia and Africa threaten the global wheat supply. This study aims to characterize the genome structure of strain 16MoT01, which has proven to be particularly aggressive even towards wheat genotypes that have previously been resistant to blast. Genomic DNA from 16MoT01 was sequenced using Oxford Nanopore long read sequencing, assembled with Canu, and polished using Illumina reads, resulting in a finished chromosome-level assembly consisting of seven core-chromosomes, a mini-chromosome, and a mitochondrial genome. When compared to the reference genome of strain B71, the core-chromosomes show high similarity and the mini-chromosome shows a high level of divergence. The presence of mini-chromosomes will be confirmed through contour-clamped electric field (CHEF) gel electrophoresis. The CHEF protocol was developed using genomic DNA from a rice blast fungus. This assembly provides another reference genome and potential insights into what makes this strain so aggressive.Item Open Access Identifying Beetle Species Using Machine Learning(2019) Whitten, SamanthaMachine learning Artificial Intelligence (AI) hold the potential to benefit farmers and the environment. Computer models can identify lady beetles in images, and, with more training, possibly determine their presence in crop fields. As predators, lady beetles could be a strong indicator of aphid infestations. Using this information and Al technology, farmers could simultaneously reduce costs and environmental damage by having the ability to identify an infested area and focus pesticide applications on a specified section rather than on an entire field,. Before we reach this point, we must determine whether Al or human identification is more reliable and efficient.Item Open Access Sorghum Carotenoid Variation(2019) Bach, Tory; Bashir, Elfaddil; Cruet-Burgos, Clara; Rhodes, DavinaPurpose The purpose of this research is to understand the heritability and genetic controls of sorghum grain carotenoids in order to develop a biofortification plan. Hypothesis and Predictions • Hypothesis 1: Carotenoids in a genetically diverse sorghum association panel grown in a temperate humid environment are highly heritable. o Prediction 1: There will be a significant correlation in carotenoid content between sorghum grown in 2015 and 2016 measured by high-performance liquid chromatography (HPLC). o Prediction 2: Genome-wide association studies (GWAS) will identify some of the same quantitative trait loci (QTL) in each year, in particular zeaxanthin epoxidase (ZEP).
