<p>  </p> <p>Spotted-wing Drosophila (SWD), <em>Drosophila suzukii</em> (Matsumura), is an economically-important pest of small fruits worldwide. Currently, timing of management is based on morphological identification of adult flies captured in baited monitoring traps; however, distinguishing SWD from other native drosophilids in traps is a time-consuming process that requires magnification. And a degree-day model that could help small fruit growers understand and predict the seasonal activity of this pest has not been developed for Indiana. Due to the low tolerance for maggots in fruit market, most small fruit growers rely on intensive, insecticide applications on a calendar-based schedule without guidance on the activity levels of SWD. </p> <p>A total of 6,051 SWD adults were monitored weekly using commercial Scentry traps at three highbush blueberry orchards during May to August. I applied the published SWD developmental thresholds of 7.2 °C (lower) and 31.5 °C (upper) and the single-sine method to calculate accumulated degree days in the year of 2021 and 2022. A predictive model from two years of data at three locations exhibited an S-shaped curve, with 5%, 25%, and 50% of adults detected at ~907, 1,293, and 1,523 CDD, respectively. By examining infestations in three varieties, ‘Bluecrop’, ‘Blueray’, and ‘Elliot’, I found that blueberry infestation rate increased as the trap captures increased. The use of early-ripening highbush blueberry varieties can reduce infestation and regardless of variety, as berries became softer, the number of SWD egg scars in berries increased.</p> <p>DNA-based diagnostic methods, like loop-mediated isothermal amplification (LAMP), have the potential to improve SWD detection by replacing morphological identification with DNA-based identification. Positive results of the LAMP assay are based on a visible color change from pink to yellow when focal DNA is present. I tested the reliability of LAMP results using SWD DNA and then evaluated the sensitivity of LAMP in discriminating between SWD and two native drosophilids common captured in monitoring traps in Indiana, <em>Drosophila affinis</em> and <em>D. simulans</em>. I found the LAMP assay can quickly and accurately identify SWD with as little as 0.1 ng/μl of DNA. Following optimization, the assay also suggested success in discriminating between SWD and these two native species: it only requires an individual fly, DNA extraction is not necessary. </p> <p>By better predicting seasonal SWD activity and optimizing DNA-based diagnostics for this pest, this study can help improve the timely detection of SWD and the management in small fruit systems. </p>

<p dir="ltr">Palmer amaranth (Amaranthus palmeri S. Watts) and waterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer] are two of the most troublesome weeds in U.S. soybean production and the auxin herbicides dicamba and 2,4-D, are currently used extensively for postemergence control of these species. In some cases, complete control of weeds at the time of auxin application is not achieved due to adverse environmental conditions, plant factors or misapplications. In these instances, a subsequent postemergence herbicide may be required to control any plant that survived the initial auxin herbicide application. This research was conducted to determine the efficacy and optimal successive time interval between applications of viable postemergence herbicides in soybean on Palmer amaranth and waterhemp plants surviving a previous application of 2,4-D or dicamba. Results from this research indicated that respraying a failed auxin herbicide application with a subsequent auxin herbicide, especially dicamba, was less effective than respraying with glufosinate or fomesafen to control waterhemp in addition to being a less desirable approach for resistance management. Additionally, respray herbicide applications should target 7 to 14 d after the initial failed herbicide application on waterhemp for optimal overall efficacy. When dicamba was the initial herbicide sprayed on Palmer amaranth, 94% or greater control was achieved with glufosinate in 2019 on a 7- and 14-d respray interval, which was greater than the efficacy observed with either dicamba or 2,4-D (< 82%). In 2020, these differences in herbicide efficacy were not evident within these time intervals. These general trends in treatment differences were also manifested in the data for plant height, biomass and viable apical meristems. When 2,4-D was the initial herbicide sprayed on Palmer amaranth, fomesafen and glufosinate applications on a 7-d respray interval and glufosinate on a 14-d respray interval resulted in greater control than 2,4-D in 2019. All other trends in herbicide treatments and time intervals were consistent with dicamba applied as the initial herbicide. Another part of his research was conducted with the objective of quantifying herbicide spray solution deposition and herbicide efficacy on waterhemp growing in different densities plant densities: low, high-thinned and high densities. In both field and greenhouse experiments, spray deposition (µl cm-2) on waterhemp leaves was up to 53% less on plants grown in high density compared to the other density treatments. Even though no differences in herbicide deposition between low and the high-thinned densities were observed, there were differences in herbicide efficacy. When applied to plants growing in low density, applications of glufosinate, fomesafen and topramezone reduced weed biomass to a greater extent than plants growing in the high-thinned density. Following herbicide damage to the apical meristem, plants growing in high-density produced new branches from axillary buds that were previously dormant, whereas plants growing in the low density already had axillary branches initiated from these buds and did not provide an opportunity for new shoot growth. In general, no differences in herbicide efficacy were observed across weed densities following dicamba applications. Source-to-sink translocation of dicamba to previously active meristems, or axillary buds that broke dormancy after the herbicide application, may have compensated for less spray solution interception on plants growing in high density. Lower levels of postemergence herbicide efficacy in high density weed populations are not only influenced by spray deposition differences, but also by changes in plant growth and apical dominance. This research provides further evidence that justifies the need for weed managers to reduce weed densities as much as possible, via non-chemical or soil residual herbicides (preemergence), as much as possible to optimize the efficacy of foliar herbicide applications.</p>

No description available.

No description available.

Weed resistance to control measures, particularly herbicides, is a growing problem in agriculture. In the case of herbicides, resistance is sometimes connected to genetic changes that directly affect the target site of the herbicide. Other cases are less straightforward where resistance arises without such a clear-cut mechanism. Understanding the genetic and gene regulatory mechanisms that may lead to the rapid evolution of resistance in weedy species is critical to securing our food supply. To study this phenomenon, we exposed young Arabidopsis plants to sublethal levels of one of four weed management stressors, glyphosate herbicide, trifloxysulfuron herbicide, mechanical clipping, and shading. To evaluate responses to these stressors we collected data on gene expression and regulation via epigenetic modification (methylation) and small RNA (sRNA). For all of the treatments except shade, the stress was limited in duration, and the plants were allowed to recover until flowering, to identify changes that persist to reproduction. At flowering, DNA for methylation bisulfite sequencing, RNA, and sRNA were extracted from newly formed rosette leaf tissue. Analyzing the individual datasets revealed many differential responses when compared to the untreated control for gene expression, methylation, and sRNA expression. All three measures showed increases in differential abundance that were unique to each stressor, with very little overlap between stressors. Herbicide treatments tended to exhibit the largest number of significant differential responses, with glyphosate treatment most often associated with the greatest differences and contributing to overlap. To evaluate how large datasets from methylation, gene expression, and sRNA analyses could be connected and mined to link regulatory information with changes in gene expression, the information from each dataset and for each gene was united in a single large matrix and mined with classification algorithms. Although our models were able to differentiate patterns in a set of simulated data, the raw datasets were too noisy for the models to consistently identify differentially expressed genes. However, by focusing on responses at a local level, we identified several genes with differential expression, differential sRNA, and differential methylation. While further studies will be needed to determine whether these epigenetic changes truly influence gene expression at these sites, the changes detected at the treatment level could prime the plants for future incidents of stress, including herbicides. / Doctor of Philosophy / Growing resistance to herbicides, particularly glyphosate, is one of the many problems facing agriculture. The rapid rise of resistance across herbicide classes has caused some to wonder if there is a mechanism of adaptation that does not involve mutations. Epigenetics is the study of changes in the phenotype that cannot be attributed to changes in the genotype. Typically, studies revolve around two features of the chromosomes: cytosine methylation and histone modifications. The former can influence how proteins interact with DNA, and the latter can influence protein access to DNA. Both can affect each other in self-reinforcing loops. They can affect gene expression, and DNA methylation can be directed by small RNA (sRNA), which can also influence gene expression through other pathways. To study these processes and their role in abiotic stress response, we aimed to analyze sRNA, RNA, and DNA from Arabidopsis thaliana plants under stress. The stresses applied were sublethal doses of the herbicides, glyphosate and trifloxysulfuron, as well as mechanical clipping and shade to represent other weed management stressors. The focus of the project was to analyze these responses individually and together to find epigenetic responses to stresses routinely encountered by weeds. We tested RNA for gene expression changes under our stress conditions and identified many, including some pertaining to DNA methylation regulation. The herbicide treatments were associated with upregulated defense genes and downregulated growth genes. Shade treated plants had many downregulated defense and other stress response genes. We also detected differential methylation and sRNA responses when compared to the control plants. Changes to methylation and sRNA only accounted for about 20% of the variation in gene expression. While attempting to link the epigenetic process of methylation to gene expression, we connected all the data sets and developed computer programs to try to make correlations. While these methods worked on a simulated dataset, we did not detect broad patterns of changes to epigenetic pathways that correlated strongly with gene expression in our experiment's data. There are many factors that can influence gene expression that could create noise that would hinder the algorithms' abilities to detect differentially expressed genes. This does not, however, rule out the possibility of epigenetic influence on gene expression in local contexts. Through scoring the traits of individual genes, we found several that interest us for future studies.

<p dir="ltr">Waterhemp (<i>Amaranthus tuberculatus</i>)<i> </i>is one of the most problematic weeds in soybean production in the United States. The ability of waterhemp to quickly evolve resistance threatens the utility of many herbicides. The introduction of Xtend^®and Xtendflex^®soybeans allow for the in-season application of dicamba and glufosinate. With an increase in dicamba use in soybeans plus its continued use in corn, there have been many reports of dicamba failure on waterhemp.</p><p dir="ltr">Greenhouse dose response experiments were conducted to screen six populations of waterhemp for resistance to dicamba. Each population was compared to a known sensitive and known resistant population, with 50% growth reduction (GR₅₀) values of 39 g ae ha^-1and 226 g ae ha^-1, respectively. Low-level dicamba resistance was identified in all populations, as they had GR₅₀values that were different from the known sensitive and R:S ratios that varied from 1.7 to 4.4. Additionally, all six populations exhibited at least 50% survival at a 1/2X rate of dicamba where the sensitive only had 30% survival. Therefore, we can conclude that dicamba resistance in waterhemp is present in multiple counties in Indiana.</p><p dir="ltr">In addition to characterizing populations from Indiana, a growth monitoring study was conducted to determine how emergence timing impacted waterhemp growth. In 2021, plants that emerged in the earliest cohort were taller, had more branches, and accumulated more biomass in comparison to later emerging plants at six weeks after flagging. In 2022, drought conditions throughout the month of June impacted growth of earlier emerging plants, and waterhemp that emerged in the latest cohort were taller, had more branches, and accumulated more biomass than earlier emerging cohorts at six weeks after flagging. Seed yields per plant were low in both years, but all cohorts were able to produce seed. This research concludes that in years when soil sufficient moisture is available, earlier emerging waterhemp plants are competitive with crops and later emerging plants can still produce seed.</p><p dir="ltr">Additionally, field trials were conducted to determine herbicide programs in the Enlist^® and Xtendflex^® soybean systems that would best control a waterhemp population with multiple herbicide resistance. At 21 days after the second postemergence application, waterhemp control was highest in two pass systems. The addition of pyroxasulfone to the second postemergence application increased control of waterhemp in the Xtendflex^® system. Waterhemp densities were the lowest and soybean yield was the highest in two pass herbicide programs for both systems. The results indicate that waterhemp resistant to chemistries in HRAC Groups #2, #4, #5, #9, #14, and #27 was most effectively controlled by programs with two herbicides applications, either a preemergence followed by postemergence or two pass postemergence, and included 2,4-D and glufosinate in the postemergence application(s).</p><p dir="ltr">Finally, a waterhemp population from Francesville, IN was characterized for herbicide resistance via a series of field, greenhouse, and laboratory experiments. Preliminary laboratory analysis confirmed resistance to herbicide actives in the HRAC Groups #2 and #14 via target site mutations and to Group #9 via gene amplification. Field research trials indicated inadequate waterhemp control with preemergence applications of pendimethalin and atrazine and postemergence applications of herbicide actives from Groups #2, #9, #14, and #27 as well as glufosinate and dicamba. Greenhouse dose response experiments revealed GR₅₀values for the Francesville population that were significantly higher for dicamba, mesotrione, and topramezone than the known sensitive. R:S ratios of 4.4, 3.3, and 1.8, were documented for dicamba, mesotrione, and topramezone, respectively. Data from all experiments demonstrated that the Francesville population is resistant to herbicide actives in Groups #2, #4, #5, #9, #14, and #27.</p>

Doctor of Philosophy / Department of Agronomy / Kassim Al-Khatib / Mitchell R. Tuinstra / Sorghum acreage is declining throughout the United States because management options and yield have not maintained pace with maize improvements. The most extreme difference has been the absence of herbicide technology development for sorghum over the past twenty years. The objectives of this study were to evaluate the level of resistance, type of inheritance, and causal mutation of wild sorghums that are resistant to either acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicides or acetohydroxyacid synthase (AHAS)-inhibiting herbicides. ACCase-inhibiting herbicides used in this study were aryloxyphenoxypropionate (APP) family members fluazifop-P and quizalofop-P along with cyclohexanedione (CHD) family members clethodim and sethoxydim. The level of resistance was very high for APP herbicides but low to nonexistent to CHD herbicides. With genetic resistance to APP herbicides, the resistance factors, the ratio of resistance to susceptible, were greater than 54 to 64 for homozygous individuals and greater than 9 to 20 for heterozygous individuals. Resistance to CHD herbicides was very low with resistance factors ranging from one to about five. Genetic segregation studies indicate a single gene is the cause of resistance to APP herbicides. Sequencing identified a single mutation that results in cysteine replacing tryptophan (Trp-2027-Cys). Trp-2027-Cys has previously been reported to provide resistance to APP but not CHD herbicides. The other wild sorghum evaluated in this study was resistant to AHAS-inhibiting herbicides including imidazolinone (IM) family member, imazapyr, and sulfonylurea (SU) family member, nicosulfuron. Resistance factors in this genotype were very high, greater than 770 for the IM herbicide and greater than 500 for the SU herbicide, for both herbicide chemical families. Genetic segregation studies demonstrate that resistance was controlled by one major locus and two modifier loci. DNA sequencing of the AHAS gene identified two mutations, Val-560-Ile and Trp-574-Leu. Val-560-Ile is of unknown importance, but valine and isoleucine are similar and residue 560 is not conserved. Trp-574 is a conserved residue and Leu-574 is a known mutation that provides strong cross resistance to IM and SU herbicides. The results of these studies suggest that these sources of APP, SU, and IM resistance may provide useful herbicide resistance traits for use in sorghum.

The invasion of ecosystems by alien species is a growing threat to the delivery of ecosystem services. This study explored the spatial distribution of water hyacinth in the Benoni Lakes and made analysis of its impact on water availability and usability in order to understand the evolution and its propagation rates. The study used satellite imagery for lake level modelling using Remote Sensing and Geographical Information Systems for calculations of area covered by weeds in each lake from 2002 to 2012.The modelling approach illustrates the potential usefulness in projecting invasive plants under climate change and enabled the quantification of long term changes in aquatic weeds. The results showed that aquatic infestations in lakes may be used as powerful predictors of correlations between plant abundance and climate change. The study therefore informs decision makers to identify areas where invasion is likely to occur and increase surveillance for early invaders. / Environmental Sciences / M. Sc. (Environmental Management)

<br /> Vários compostos químicos são usados para o controle de pragas e doenças na agricultura com a finalidade de aumentar a produtividade. É de conhecimento científico que tais compostos afetam negativamente a saúde humana e animal por meio da contaminação dos alimentos e do meio ambiente. Assim, o uso de substâncias obtidas da própria natureza para o combate de pragas e plantas invasoras é uma alternativa para o controle e, consequente, prevenção da contaminação ambiental. Neste trabalho foram avaliados os extratos aquosos das folhas da leguminosa feijão-de-porco (Canavalia ensiformis) como bioerbicida pós-emergente aplicado no controle de plantas invasoras em cultura de soja e seus efeitos no solo. Salienta-se que não há informações sobre os efeitos desses bioerbicida no solo. Os compostos fenólicos, em especial os ácidos fenólicos, têm ação inibitória no crescimento de plantas invasoras. O processo de extração dos compostos fenólicos foi feito em um sistema de digestão por micro-ondas, com aproximadamente 2 g de material vegetal seco, seguida de injeção cromatográfica. Para otimização do procedimento de extração via micro-ondas os parâmetros avaliados foram: tempo de irradiação, temperatura e rampa aplicada. Foram realizadas determinações cromatográficas para identificação e quantificação dos compostos fenólicos: rutina, ácido clorogênico, ácido ferúlico e naringenina presentes nas folhas do feijão-de-porco por HPLC-UV, mediante metodologia de extração por micro-ondas. Todo o trabalho foi desenvolvido de acordo com os requisitos de gestão da qualidade referentes às normas NBR ISO/IEC 17025 e BPL. / <br /> Several chemical compounds are used for pest and disease control in agriculture in order to increase productivity. It is well know that such pesticides adversely affect human and animal health through contamination by food and environment. Thus, the use of substances obtained from nature itself to combat pests and weeds is an alternative for the control of those and, consequently, prevent environmental contamination. This work were assessed aqueous extracts of jack bean leaves (Canavalia ensiformis) as a post-emergent bioherbicide applied in weed control in soybean crops and its effects on the soil. It is noteworthy there is not information on the effects of these bioherbicides on the soil. Phenolics compounds, notably, phenolics acids, have inhibitory action on the growth of weeds. The process of extraction of phenolic compounds was carried out in a digestion system by microwave, using approximately 2 g dry plant material, followed by chromatographic injection. For optimization of the extraction procedure by microwave-assisted extraction the factors evaluated were irradiation time, temperature and ramp time. Chromatographic determinations were performed for identification and quantification of the phenolic compounds: rutin, chlorogenic acid, ferulic acid and naringenin present in the Canavalia ensiformis leaves by HPLC-UV, through microwave extraction methodology. All the study was developed in compliance with the quality management concepts covered in NBR ISO/IEC 17025 and GLP.

O Huanglongbing (HLB) é uma das mais temidas doenças da citricultura mundial, associada a bactérias do gênero Candidatus Liberibacter, que foram detectadas no Brasil em 2004. Em 2008, detectou-se outra bactéria associada a sintomas de HLB no Estado de São Paulo, que foi caracterizada como sendo um fitoplasma do grupo 16 SrIX. Fitoplasmas são molicutes fitopatógenos restritos ao floema de plantas, disseminados por insetos vetores. O presente trabalho buscou identificar cigarrinhas potencialmente vetoras do fitoplasma associado ao HLB e plantas hospedeiras desses insetos, bem como desenvolver uma técnica de quantificação de DNA desse patógeno em insetos e plantas. Amostragens de cigarrinhas foram realizadas quinzenalmente por 12 meses em dois pomares de laranja com histórico de ocorrência do fitoplasma 16SrIX na região norte do Estado de São Paulo, usando-se armadilhas adesivas amarelas em duas alturas (0,3 e 1,5 m) da copa de árvores cítricas, e rede de varredura na vegetação espontânea. Dados faunísticos identificaram uma espécie de Agalliinae (Agallia albidula Uhler) e três de Deltocephalinae, [Balclutha hebe (Kirkaldy), Planicephalus flavicosta (Stål) e Scaphytopius (Convelinus) marginelineatus (Stål)], como os cicadelídeos (Hemiptera: Cicadellidae) mais abundantes e frequentes nas áreas estudadas. Essas espécies predominaram na amostragem com rede de varredura e na menor altura de coleta com armadilhas adesivas, indicando comportamento de alimentação em vegetação rasteira. Com observações visuais, verificou-se associação das espécies com certas plantas invasoras, e influência da composição florística da vegetação rasteira sobre a abundância das cigarrinhas. S. marginelineatus e P. flavicosta ocorreram com maior frequência em Sida rhombifolia L. e Althernantera tenella Colla, respectivamente, enquanto que A. albidula foi predominante em Conyza bonariensis (L.) Cronq., e B. hebe ocorreu exclusivamente em gramíneas, principalmente Panicum maximum Jacq.. Plantas invasoras amostradas nas áreas foram testadas para a presença do fitoplasma 16SrIX, porém sem resultados positivos. No entanto, amostras de campo da cigarrinha S. marginelineatus foram positivas por PCR e sequenciamento para o referido fitoplasma. Indivíduos de S. marginelineatus criados em laboratório e mantidos por um período de acesso à aquisição de 72 h em citros infectado com o fitoplasma 16SrIX, foram capazes de transmití-lo para citros, após 21 dias de latência, porém com baixa eficiência (0,5%). Por meio de PCR quantitativo desenvolvido para esse fitoplasma, verificou-se baixo título do patógeno tanto em S. marginelineatus, quanto em plantas cítricas infectadas, o que pode explicar, pelo menos em parte, a baixa eficiência de transmissão pelo inseto tendo citros como fonte. Isto sugere a existência de outros hospedeiros mais adequados como fontes de inóculo para aquisição do fitoplasma por S. marginelineatus ou outro vetor ainda desconhecido. / Huanglongbing (HLB) is a severe citrus disease associated to phloemlimited bacteria in the genus Candidatus Liberibacter, which were detected in Brazil in 2004. In 2008, another bacterium was found in association with HLB symptom in the São Paulo State, and characterized as a phytoplasma belonging to 16SrIX group. Phytoplasmas are vector-borne phytopathogenic mollicutes that inhabit plant sieve elements. The goals of this study were to identify potential leafhopper vectors of the HLB-associated phytoplasma and their host plants, as well as to establish a real-time PCR procedure for pathogen quantification in vectors and plants. Leafhoppers were sampled fortnightly for 12 months by yellow sticky cards placed at two heights (0.3 and 1.5 m) on the citrus tree canopy and by sweep net in the ground vegetation of two sweet orange groves with history of infection by the 16SrIX phytoplasma, in the northern region of São Paulo State. Faunistic analyses indicated 1 Agalliinae (Agallia albidula Uhler) and 3 Deltocephalinae [Balclutha hebe (Kirkaldy), Planicephalus flavicosta (Stål) e Scaphytopius (Convelinus) marginelineatus (Stål)] species that were the most abundant and frequent leafhoppers (Hemiptera: Cicadellidae) in the experimental areas. These species predominated in sweep net and in sticky traps catches at 0.3 m above soil, showing that they inhabit the ground vegetation. Visual observations indicated a strong association of leafhopper species with some weeds and the influence of weed species composition on leafhopper abundance in the ground vegetation. S. marginelineatus and P. flavicosta were more frequent on Sida rhombifolia L. and Althernantera tenella Colla, respectively, while A. albidula was observed more often on Conyza bonariensis (L.) Cronq., and B. hebe occurred solely on grasses, more abundantly on Panicum maximum Jacq. Fourteen weed species sampled in the area were PCR tested for infection by the 16SrIX phytoplasma, but none was found infected. Nevertheless, 3 out of 30 field-collected samples (10 adults per sample) of S. marginelineatus tested positive for this phytoplasma by PCR and sequencing. Healthy lab-reared adults of S. marginelineatus were able to transmit inefficiently (0,5%) the 16SrIX phytoplasma to healthy citrus after a 72-h acquisition access period on infected citrus plants followed by a 21-day latent period on S. rhombifolia plants. By using the qPCR method developed for this phytoplasma, a very low pathogen titer was found both in S. marginelineatus and in infected citrus plants, which may explain, at least partially, the low transmission efficiency by this vector using citrus as a source plant. It also suggests that existence of alternative hosts that might be more adequate as inoculum sources for phytoplasma acquisition and spread by S. marginelineatus or another vector yet to be discovered.