The continued spread of glyphosate-resistant common waterhemp [Amaranthus tuberculatus (Moq.) Sauer (syn. rudis)] and Palmer amaranth [Amaranthus palmeri (S. Wats.)] have complicated weed control efforts in soybean and corn production in Illinois. A thorough understanding of the weed biology of these species is fundamental in developing effective weed management strategies. The determination of emergence patterns as well as the influence of tillage practices on soil microclimate and soil seed bank will allow control strategies to be implemented at the most effective timing. Field experiments were conducted in southern Illinois throughout the growing season of 2013 and 2014 on two separate sites with populations of common waterhemp and Palmer amaranth. Three tillage treatments were evaluated: no-tillage; early tillage, preferably performed around a recommended soybean planting date of May 1st; and late tillage, preferably performed on June 1st to simulate a late soybean planting. Amaranthus seedlings were identified and enumerated in the center 1 m2 quadrat of each plot within a 7-day interval from April through November or first frost. All weed seedlings were removed from the plot area after each enumeration. Soil temperature and soil moisture were recorded hourly throughout the experiment using data loggers established in the plot area. First emergence of common waterhemp occurred earlier in the season than did Palmer amaranth. In 2013, initial emergence of common waterhemp and Palmer amaranth was observed at the first and second week of May, respectively. In 2014, initial common waterhemp emergence was observed in late April, while Palmer amaranth initial emergence was similar to previous year. Palmer amaranth emerged over a longer period compared to waterhemp. By the end of June, 90% of common waterhemp had emerged regardless of tillage or year. By the same measure, Palmer amaranth emergence was extended to the third week of July and second week of August in 2013 and 2014, respectively. Soil temperature did not differ across tillage treatments in both years. On the other hand, differences in soil moisture were observed, mostly over two weeks following each tillage operation. The single best predictor for common waterhemp emergence was soil temperature (weekly highs and lows) followed by soil moisture. For Palmer amaranth emergence the single best predictor was spikes in soil moisture (high for the week). In 2013, common waterhemp emergence was initially positively and later in the growing season negatively interacted with maximum temperature 13 days prior to counts, with temperatures above 30 C observed with decreased emergence (R2 = 0.35). In the same year spikes in soil moisture interacted with Palmer amaranth emergence were those observed 11 days before each seedling enumeration date (R2 = 0.30). In 2014, with first common waterhemp emergence in April, a positive interaction to high soil temperature was initially observed followed by a positive interaction to minimum temperatures later in the season (R2 = 0.55). Spikes in soil moisture observed 2 weeks prior to emergence and weekly high temperatures 8 days prior to emergence were the best predictors of Palmer amaranth emergence in 2014 (R2 =0.37). Soil seed bank depletion was also estimated by comparing field emergence with greenhouse experiment results of soil seed bank estimation. Greater emergence of common waterhemp from the soil seed bank was observed in early tillage in 2013 and no-tillage in 2014 than late tillage, respectively; for Palmer amaranth, the greatest emergence from the soil seed bank was observed in no-tillage and late tillage in 2013, and no-tillage, in 2014. The emergence patterns observed in this research suggest that although common waterhemp and Palmer amaranth exhibit discontinuous emergence throughout the growing season, greater attention should be placed on managing peaks of emergence from late April to late July, which is critical to provide a foundation for early-season weed management. Furthermore, knowledge regarding the emergence patterns of common waterhemp and Palmer amaranth combined with monitoring environmental factors such as soil moisture and soil temperature may assist efforts for scouting fields to determine the likely presence of these weed species. The timing of viable postemergence herbicide options for control of glyphosate-resistant waterhemp and Palmer amaranth is critical and monitoring weather patterns to direct scouting efforts may improve the timeliness of these postemergence applications.

The expression of glyphosate resistance can vary within single field populations of common waterhemp and Palmer amaranth. This variability in expression can translate into control ranging from 20 to 80%, which could be the difference in a minor versus a major failure in weed management. Certain application parameters that have been previously associated with glyphosate efficacy, such as glyphosate application time of day and plant stress may exacerbate this variability and lead to failed control of plants on the lower end of the resistance spectrum. Greenhouse research was conducted in 2011 to determine the influence of glyphosate application time of day on the expression of resistance in common waterhemp and Palmer amaranth. Control of both glyphosate-susceptible (GS) and -resistant (GR) weed species showed similar trends in response to glyphosate with respect time of application. Decreased sensitivity of all Amaranthus biotypes was greatest at 9:00 pm and may be attributed to an observed shift in leaf orientation from horizontal to vertical at the time of glyphosate application in response to low-light conditions. The altered leaf orientation most likely reduced herbicide spray coverage. The magnitude of resistance, the difference in the sensitivity of the resistant versus susceptible biotypes, was unaffected by glyphosate application time of day; however, these results indicate that even in resistant populations glyphosate applied at suboptimal times of day such as the evening can cause a further increase in weed escapes from glyphosate. Greenhouse and field experiments were conducted in 2011 and 2012 to determine the influence the soil nutrient amendments on glyphosate sensitivity and growth rate and of GS and GR common waterhemp and Palmer amaranth. In both the GR and GS biotypes of common waterhemp the sensitivity to glyphosate was increased as fertilizer was introduced. However, only the sensitivity of the susceptible biotype of Palmer amaranth was increased with the addition of fertilizer. The lack of response in the GR Palmer amaranth population to fertilizer can be associated with the fact that due to carrier volume limitations enough glyphosate could not be applied to achieve 50% control. The magnitude of resistance was decreased numerically with the addition of fertilizer in both weed species; however, only in common waterhemp was the magnitude of resistance significantly different with the use of high rates fertilizer. The use of fertilizer also had an influence on the growth rate and dormancy of axillary buds. Lateral branching (broken dormancy in axillary buds) was increased in both common waterhemp and Palmer amaranth with the addition of fertilizer. Converting dormant buds to active meristems favors glyphosate translocation and could be responsible for increased glyphosate efficacy. In the field, glyphosate efficacy in GR common waterhemp and Palmer amaranth was also increased with addition of fertilizer; however, this effect was variable. Optimizing the efficacy of glyphosate when applied to even mixed populations of GS and GR Palmer amaranth and common waterhemp can reduce surviving weeds that can produce seed and perpetuate the frequency of glyphosate resistance in the field. Furthermore, greater efficacy of glyphosate may translate into relatively less significant failures in glyphosate applications allowing for successful rescue herbicide treatments and minimal impact on crop yield compared with a complete glyphosate failure with dramatic implications on reduced crop yield and increased weed seed production.

Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.

Master of Science / Department of Agronomy / Johanna A. Dille / Corn yield potential is limited by water deficit stress and limited soil nitrogen. Field and greenhouse experiments were conducted near Manhattan, KS in 2005 and 2006. The field experiment evaluated the influence of nitrogen (N) rate and increasing Palmer amaranth (PA) density grown alone and in competition with corn in two moisture environments. In 2006 the dryland environment was very drought stressed, while 2005 had more intermediate conditions. Weed-free corn yields were approximately half in dryland environments compared to the irrigated environment across years. Increasing PA density increased corn yield loss similarly in both 2005 environments and in 2006 dryland environment across all N rates. In the 2006 irrigated environment corn yield loss was increased by decreasing N rate and increasing PA density. Maximum predicted yield loss at high PA densities in both 2005 environments was 20-54% while in 2006 dryland environment, maximum yield loss was 95% and in the irrigated environment was 62%. In general, soil moisture environment was more critical than N rate or PA density when determining potential corn yield. In the greenhouse study a factorial arrangement of two irrigation methods and five crop-weed combinations (corn, PA, GF, corn/PA, and corn/GF) was established with two replications and three runs conducted. Two plants were grown in 25.4 cm diameter PVC pipe cut into 91.5 cm lengths. Irrigation application method included a surface and subsurface application. Plants were harvested at the V10 corn growth stage. No differences were detected between irrigation methods with respect to above- or below ground biomass production. Corn aboveground biomass was decreased by the presence of corn or PA but not GF. Below ground biomass information was presented as column totals because species could not be separated. There was no impact on root to shoot ratio, total below ground biomass, rooting depth, or root area across the crop-weed combinations except for the GF monoculture columns which were lower than all other crop-weed combinations. Future research needs to examine the light interception of corn and PA when grown at different N rates along with examining the influence of surface and subsurface irrigation practices on crop weed interactions and weed seed germination in a field setting.

The resistance of Palmer amaranth (PA) and the tolerance (natural resistance) of pitted morningglory (PM) to glyphosate have made these species among the most common and troublesome weeds in the southeastern U.S. since the adoption of glyphosate-resistant (GR) crops. Populations of GR PA (R1 and R2) were identified in Mississippi. The inheritance of glyphosate resistance was examined in reciprocal crosses (RC) between glyphosate-resistant (R) and -susceptible (S) parents (Female-S × Male-R, S/R, and Female-R × Male-S, R/S), and second reciprocal crosses (2RC) (Female-S/R × Male-S/R, S/R//S/R, and Female-R/S × Male-R/S, R/S//R/S). Dose-response assays resulted in 17- to 4old resistance to glyphosate compared with S. Population S accumulated 325- and 8-times more shikimate at the highest glyphosate dose than in R1 and R2, respectively. cDNA sequence analysis of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene indicated no target site mutation. Genomes of R1, R2, RC, and 2RC contained from 1- to 59old more copies of EPSPS gene than S; EPSPS was highly expressed in R1 and R/S, but was poorly expressed in S, S/R, and R2. EPSPS activity was lower in S and S/R than in R and R/S, glyphosate absent; all were inhibited by glyphosate. Western Blot analysis confirmed an increased EPSPS protein level to EPSPS copy number correlation. Thus, the level of resistance was decidedly influenced by the direction of the cross. R and S female plants were reproductively isolated and seed were still produced, suggesting that PA can produce seed both apomictically and sexually (facultative apomixis). This mode of reproduction determined the low copy number inheritance, as well as guaranteeing the GR trait stability in the R populations. Dose-response assays resulted in 2.6old variability in tolerance to glyphosate between the most tolerant (MT) and the least tolerant (LT) PM populations. The level of tolerance positively correlated with the time of exposure to GR-crop system. Less shikimate was recovered in MT as compared to LT. Levels of aminomethylphosphonic acid (AMPA) were not different between populations and sarcosine was not present in either populations. Consequently, metabolism of glyphosate to AMPA or sarcosine is not a common factor in explaining natural resistance levels.

The continued spread of Palmer amaranth (Amaranthus palmeri S. Wats.) throughout the southern and midwestern United States is a result of herbicide-resistant populations. Besides being the most troublesome weed specie in several agronomic crops, Palmer amaranth is also host to economically important pests such as tarnished plant bug (Lygus lineolaris Palisot de Beauvois). Pesticide application methodology that maximizes efficacy while reducing selection pressure is needed to combat herbicide-resistant Palmer amaranth. Pulse width modulation (PWM) sprayers are used for pesticide application with the goal of maintaining product efficacy while mitigating spray drift. Additionally, alternative off-season weed management practices such as flooding could be adopted to optimize soil seedbank depletion. Therefore, evaluation of spray droplet size and flooding period on Palmer amaranth control and seed germination was conducted. The objectives of this research were to: (1) evaluate the influence of spray droplet size on lactofen and acifluorfen efficacy on Palmer amaranth using a PWM sprayer, (2) develop prediction models to determine spray droplet size that provides the greatest level of Palmer amaranth control, (3) evaluate the impact of flooding period and seed burial depth on Palmer amaranth seed germination in different soil textures, and (4) analyze the impact of nitrogen fertilizer application rate on the attractiveness of Palmer amaranth to tarnished plant bug. Results show that spray droplet size does not affect lactofen efficacy on Palmer amaranth, thus, coarser spray droplets are recommended to increase spray drift mitigation efforts. In contrast, acifluorfen applied with 300 μm (medium) spray droplets provided the greatest Palmer amaranth control. Furthermore, prediction models indicated that greater model accuracy was obtained when adopting a location-specific weed management approach. Flooding periods of 3, 4, and 5 months reduced Palmer amaranth seed germination across burial depths and soil textures. Therefore, fall-winter flooding may be adopted as an effective practice for soil seedbank depletion. Results also demonstrated that nitrogen fertilizer application rate does not consistently impact Palmer amaranth attractiveness to tarnished plant bug.

Weeds pose a challenge to cotton production, and herbicides have been the primary means of control. However, there is growing concern over weed resistance to herbicides. To address this issue, we evaluated three cover crop species and six cotton accessions for weed suppression. The study found that hairy vetch, wheat, and B16 cotton CS line effectively suppressed Amaranthus species, while MNTN 4-15, B16, hairy vetch, and wheat were correlated with the highest cotton yield. Cover crops were also analyzed for chlorogenic acid content, with wheat, MNTN 4-15, and hairy vetch producing the highest amounts. The greenhouse tray study showed that wheat and hairy vetch cover crops were among the best treatments for weed suppression. These findings suggest that cover crops may provide effective weed control and improve crop yield.

Herbicide resistant weeds are driving implementation of integrated weed management (IWM). A new tactic to manage weeds is harvest weed seed control (HWSC), which targets weed seeds retained on the plant at crop harvest and either destroys, removes, or concentrates them. Research is limited on the effectiveness of HWSC in US cropping systems. For HWSC to be effective it is important to know when and how many seed are shed from a weed species in relation to crop harvest. Research was conducted to quantify when weed seed are shattered from 6 economically important weed species, four broadleaf (redroot pigweed, common ragweed, common lambsquarters, and common cocklebur) and two grass species (large crabgrass and giant foxtail). Results indicate that among summer annuals, broadleaf species retain larger proportions of their seed compared to grass species at the first opportunity for soybean harvest. As harvest was delayed, more seeds shattered from all species evaluated, indicating timely harvest is critical to maximizing HWSC effectiveness. Studies were conducted on grower fields in Virginia to evaluate the effectiveness of HWSC (field residue and weed seed removal). Results indicate that HWSC can significantly reduce populations of Italian ryegrass in wheat and common ragweed in soybean in the next growing season, but reductions were not observed for Palmer amaranth in soybean. Investigating IWM system for common ragweed control in soybean, HWSC was found to be less effective than soybean planting date (i.e. double cropping after wheat) at reducing common ragweed populations. However, the effectiveness of HWSC varied by location. If HWSC adoption were to become widespread, weeds could adapt by shedding seed earlier in the season. Research was conducted by growing Palmer amaranth populations from across the eastern US in a common garden. Currently there are differences in flowering time and seed shatter among Palmer amaranth populations based on the location of the maternal population, indicating potential for adaptation. This research demonstrates that HWSC is a viable option for weed management in US cropping systems but needs to be stewarded like any other weed management tool. / Doctor of Philosophy / Herbicide resistance in weeds is a growing problem in the US and around the world. Alternative methods of weed control must be adopted to maintain crop yields in the presence of herbicide-resistant weeds. Researchers and extension specialists strongly advise growers to adopt an integrated weed management (IWM) approach. Integrated weed management involves implementing multiple weed control tactics during a growing season. By using multiple methods of weed control within a given season the chances of weeds becoming resistant or adapting to any single tactic is reduced. Harvest weed seed control (HWSC) is a new tactic developed in Australia in response to herbicide resistance. HWSC targets weed seeds retained on the plant at crop harvest. In a normal crop harvest, the combine removes the grain and spreads crop residues (leaves, stalks, and other plant parts), including weed seeds, back across the field. When HWSC is implemented, weed seeds are destroyed (narrow windrow burning, cage mills) or concentrated and potentially removed from the field (chaff carts, direct bale, chaff lining). Thus, HWSC limits the number of weed seeds returned to the soil seed bank. There is limited research on HWSC and its integration with other tactics, in US cropping systems. For HWSC to be effective it is necessary for weed seeds to be retained on the mother plant in sufficient quantities at crop harvest. Research was conducted in Virginia to determine when weed seeds are shattered during the soybean growing season for 6 economically important weed species, four broadleaf (redroot pigweed, common ragweed, common lambsquarters, and common cocklebur) and two grass species (large crabgrass and giant foxtail). The broadleaf species retained >85% of their seed until the first opportunity for soybean harvest (mid-October). In the grass species, more seed shattered prior to soybean harvest with 50% of large crabgrass and 74% of giant foxtail seed being retained at the first opportunity for soybean harvest. When harvest was delayed seed continued to shatter and less was captured using HWSC. This research indicates broadleaf species are more suitable candidates for HWSC than grass species, among summer annuals. Further research on the ability of seed to germinate in relation to when seeds were shed was conducted on redroot pigweed, common ragweed and common lambsquarters. Results indicate that there are variable effects on germination of these species depending on when they were shed. HWSC was implemented on grower fields to assess the impact on weed populations of 3 weed species (Italian ryegrass, common ragweed, and Palmer amaranth). These experiments compared conventional harvest and HWSC (field residue and weed seed removal) when all other management strategies were the same within that field. Italian ryegrass tiller density in wheat varied by location but was reduced up to 69% in the spring following implementation of HWSC. By wheat harvest, HWSC reduced Italian ryegrass seed head density 67% at one location compared to conventional harvest. In soybean, common ragweed densities were reduced by 22 and 26% prior to field preparation and postemergence herbicide applications, respectively, in the HWSC plots compared to the conventional harvest plots. No differences were observed in common ragweed density by soybean harvest. No differences were observed with Palmer amaranth densities at any point during the soybean growing season. This research show that HWSC can reduce weed populations but is variable and additional research is still needed. IWM experiments were established across Virginia to compare soybean planting date (full season or double cropped), + cover crop (cereal rye/wheat or no cover), and + HWSC (field residue removal) to evaluate the best management strategy for common ragweed in soybean. Across all locations, double cropping soybean behind wheat had the greatest impact on common ragweed densities at the end of the first season. The impact of double cropping soybeans on common ragweed population is due to the emergence pattern of common ragweed; majority of common ragweed emerges prior to planting double cropped soybean (mid-June to early-July). HWSC was variable and only reduced common ragweed density at one of three locations. Widespread adoption of HWSC could place a selection pressure on weeds to shatter seed earlier in the season. A common garden experiment was conducted in Blacksburg, VA to assess Palmer amaranth populations collected from central Florida to southern Pennsylvania for differences in flowering time, time to seed shatter, and other phenotypic traits. Results indicate that latitude of the maternal population influences time to first flower with a 0.53 d reduction in flowering time for every degree north in latitude the maternal population was collected from. The strongest predictor of Palmer amaranth flowering time was emergence date/daylength. For every day emergence was delayed the time to first flower was reduced by 0.31 and 0.24 d for female and male plants, respectively. Time from emergence or first flower to first seed shatter was reduced by 0.48 or 0.17 d, respectively, for each day emergence was delayed. These results indicate that differences exist currently among Palmer amaranth populations and the selection pressure of HWSC could push these populations to flower and shatter seed early.

Harvest weed seed control (HWSC) methods concentrate, remove, or destroy weed seeds captured by the combine during harvest. Furthermore, chaff lining uses a chute fitted on the back of a combine to concentrate chaff and weed seed therein into a narrow line. Since chaff amount increases with crop yield, studies aimed to determine how varying crop yield and the associated chaff amount will affect chaff lining control of select weed species, while also examining subsequent crop performance. Objective 1 of this work focused on wheat chaff lining (WCL), and objective 2 studied soybean chaff lining (SCL). Weed species of interest included wild mustard (Sinapis arvensis L.) and Italian ryegrass (Lolium perenne ssp. multiflorum L. Husnot) in WCL and Palmer amaranth (Amaranthus palmeri S.) and common ragweed (Ambrosia artemisiifolia L.) subject to SCL. Each weed species was evaluated in separate experiments, and the SCL experiment included an additional factor of with and without a cereal rye cover crop treatment. Chaff lines mimicked harvest across a range of wheat and soybean yields, with equal weed seed additions (based on existing fecundity and seed shatter phenology data) to each chaff line. A conventional harvest (control) and an outside-the-chaff-line treatment were included, where total fecundity or weed seed rain occurring prior to harvest based on weed species were broadcast respectively. Inhibition of crop and weed emergence as a function of yield and the associated chaff amount was also investigated in the greenhouse. Crop yield across treatments at the field scale (accounts for both chaff lines and outside-the-chaff-line), was not affected in double-crop soybean following WCL and full-season soybean following SCL. Field scale wheat yield in WCL compared to conventional harvest was not different, increased, or decreased in 8, 3, and 1 site-years, respectively. WCL reduced total weed emergence over the combined double-crop soybean and winter wheat growing seasons by 43-54% at the field scale. SCL reduced common ragweed emergence in cereal rye by 64% and 85% in 2 of 3 locations across the soybean growing season. The cover crop did not reduce common ragweed emergence while it was growing, but residual mulch in soybean reduced emergence by 39%. No differences were observed in Palmer amaranth emergence during cereal rye growth, however cereal rye decreased total emergence by 41%. In 6 of 7 Palmer amaranth location-years, SCL decreased field scale weed emergence in soybean by 81%. These results indicate chaff may create an unfavorable environment for weed seed emergence. In both WCL and SCL, greater amounts of chaff caused larger reductions in weed emergence. Objective 3 focused on quantifying the above-ground biomass breakdown of soybean plants into chaff, straw, and seed fractions as they are processed and dispensed by various harvesters. Depending on HWSC system, chaff and straw residues may also be destroyed, removed, or concentrated. Therefore, chaff and straw nutrient composition was analyzed to evaluate the nutrient and economic consequences of HWSC. Our results show average soybean harvest index is 0.57:1. Furthermore, chaff and straw residues equal 13.4% and 68.5% of the seed weight, respectively. Using 5-year average fertilizer prices (2017 – 2021), replacement of N, P, K and S in chaff, straw, and the combination of both residues costs USD 1.58, USD 5.88, and USD 7.46, respectively. / Master of Science in Life Sciences / In conventional wheat and soybean production, the primary means of weed control is herbicides. If herbicide use is not diversified, a repeated selection pressure drives weeds to evolve resistance to such chemistries. Producers and researchers alike are constantly looking for new ways to combat weeds and herbicide-resistant issues. Originally developed to control nuisance weeds in Australia, harvest weed seed control (HWSC) offers promise in aiding our current herbicide resistance crisis. To further explain HWSC, it is important to know the harvesting mechanism. Many of the row crops including corn, soybean and wheat are harvested using a combine. Combines cut below or tear off plant material to capture the grain or seed which is processed via a threshing system and separated into three fractions: the seed, chaff, and straw. The grain is allocated to a storage bin and eventually removed from the field. In conventional harvest, the remaining crop residue is spread evenly behind the combine across the field to ensure a balanced distribution of organic matter, nutrients, and residue across the field. There is however more than chaff and straw being dispersed. Weeds present in the field at harvest whose seed is retained at crop maturity and at an elevation above the combine header height will inherently end up inside the combine. HWSC are methods intended to capitalize on the combine capturing weed seeds during harvest. Many HWSC approaches to managing weed seed exist, including destruction, removal and concentration of weed seed. Most of this research focuses on only one method of HWSC, chaff lining. Chaff lining utilizes a chute fitted onto the back of the combine and concentrates weed seed and the chaff fraction only into a narrow line behind the combine. Although not directly known, chaff may inhibit future weed emergence within the line due to a mulching effect, intraspecific competition, a greater degree of rotting and increased seed predators. The chute is inexpensive to construct, and there are no additional labor requirements at harvest making it an appealing HWSC option. There is a limited amount of research on chaff lining in North American cropping systems making it a prime HWSC candidate for this thesis. We were curious if chaff lining could benefit wheat and soybean farmers and if crop yield and the associated chaff amount deposited in chaff lines would have any impact on crops planted and weeds placed in lines. Our results indicate chaff lining does not cause field scale yield consequence in double-crop and full-season soybean following wheat and soybean chaff lining, respectively. The effect of wheat chaff lining on wheat field scale yield was variable, but only caused a yield decrease in 1 of 12 experimental locations. Reductions in weed emergence in chaff lining systems compared to conventional indicate chaff may alter the environment to be unfavorable for weed seed emergence. The final objective of this thesis investigates the economic cost of nutrient loss among HWSC systems. Using average fertilizer prices, the cost to apply N, P, K and S concentrated or lost during HWSC in chaff, straw, and the combination of both residues is USD 1.58, USD 5.88, and USD 7.46, respectively.

<p>Acetolactate synthase (ALS) inhibitors are a widely used class of selective herbicides used to control grass and broadleaf weeds. The repeated use of ALS-inhibiting herbicides has selected for biotypes of weeds resistant to ALS inhibitors, especially in the weeds most problematic to growers in the Midwest. While ALS inhibitor use seems futile, new mechanisms of herbicide action are not predicted to be commercialized in the near future to solve this problem. This leads to the main objective of this research, determining what value ALS inhibitors provide in controlling populations of weeds with resistance to ALS inhibitors. </p> <p>Field experiments with soil-applied (PRE) applications of ALS inhibitors on horseweed (<i>Erigeron canadensis</i>) and tall waterhemp (<i>Amaranthus tuberculatus </i>var. <i>rudis</i>) exhibited higher efficacy than would be expected given the frequency of the ALS resistance trait in the population. Whereas control of these species with POST-applied applications was similar or less than the proportion of the population characterized as susceptible using molecular techniques. Soil-applied applications, therefore, resulted in relatively greater control than POST applications in populations with known ALS-inhibitor-resistance mechanisms.</p> <p>Greenhouse experiments showed that overall resistance ratios were higher for PRE applications of ALS inhibitors in horseweed, tall waterhemp, and Palmer amaranth (<i>Amaranthus palmeri</i>). However, GR₅₀ values decreased for both susceptible and resistant biotypes for the PRE applications compared to POST, suggesting the biologically effective dose of these herbicides is lower in soil residual applications. This research found that PRE applications of ALS inhibitors resulted in some level of control on horseweed and tall waterhemp classified as resistant to ALS inhibitors due to the higher efficacy of PRE herbicide applications.</p> <p>Genetic analysis assessing the amino acid substitutions that confer resistance to ALS inhibitors in tall waterhemp confirmed a difference in selection pressure between PRE and POST applications and between ALS active ingredients in tall waterhemp. Applications of chlorimuron PRE at 11 g ai ha^-1selected for 35% homozygous W574L genotypes and at 44 g ha^-1 selected for 70% homozygous W574L genotypes. An increase of homozygous W574L individuals along with a decrease in heterozygous individuals from 65 (11 g ha^-1) to 29% (44 g ha^-1) suggests that W574L is semi-dominant in tall waterhemp and that high labeled rates of chlorimuron applied PRE can partially overcome the heterozygous W574L-resistance mechanism. In horseweed, no difference in selection pressure was observed between application timing or between chlorimuron or cloransulam. A new mutation conferring ALS-inhibitor resistance in horseweed was discovered, a Pro197Leu amino acid substitution, with resistance ratios of 21X to chlorimuron and 8.6X to cloransulam. These resistance ratios are slightly less than those reported for the Pro197Ala and Pro197Ser amino acid substitutions in conferring ALS-inhibitor resistance in horseweed. </p> <p>Finally, a survey of 42 populations of tall waterhemp in Indiana counties with confirmed ALS-inhibitor resistant populations of tall waterhemp found that all populations contained at least 16% individuals with the W574L amino acid substitution, 35 populations contained at least 1% individuals with the S653N substitution, and 9 populations contained at least 1% individuals with the S653T substitution. Taking into consideration the three mutations tested, 8 of the 42 populations tested contained <50% ALS-inhibitor resistant individuals within the population. Using the same tall waterhemp populations as collected in the survey, Next-Generation Sequencing was used to determine if other amino acid substitutions conferring resistance to ALS inhibitors existed. Results from WideSeq revealed that 10 other amino acid substitutions in the ALS protein may be conferring resistance in tall waterhemp in Indiana: A122T, A122N, A122S, P197T, P197L, P197H, D376E, and G654F. Further research from this survey also suggests that metabolic resistance to ALS inhibitors is likely a contributor to resistance in tall waterhemp in Indiana.</p> <p>This research suggests that ALS-inhibiting herbicides, more specifically chlorimuron, would provide the greatest contribution to management of tall waterhemp. Chlorimuron would perform best when used in soil residual applications and in populations of tall waterhemp containing either individuals susceptible to chlorimuron or individuals heterozygous for ALS inhibitor resistance conferred by the W574L mutation. This research also demonstrates the specificity of the amino acid substitutions in the ALS protein and by weed species to realize the benefit of these herbicides for management of weeds resistant to ALS inhibitors. Molecular characterization of target site resistance to ALS inhibitors has traditionally been considered relatively simple. However, we found 11 new amino acid substitutions that confer resistance to ALS inhibitors in horseweed and tall waterhemp. The complexity of ALS inhibitor resistance calls for the use of methods such as NGS to detect all potential resistance mutations in a timely manner and for the use of tests detecting metabolic resistance. Overall, this research demonstrates that ALS inhibitors still provide some utility for management of weed populations classified as resistant to ALS inhibitors and that the resistance mechanisms in horseweed and tall waterhemp are more numerous than previously reported. </p>