Browsing by Author "McKay, John, committee member"
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Item Embargo Climate change, soil carbon sequestration, and agricultural technology adoption: the case of deeper root system corn adoption and diffusion in the U.S. Corn Belt(Colorado State University. Libraries, 2024) Al Maamari, Aaisha, author; Graff, Gregory, advisor; Mooney, Daniel, committee member; Hill, Alexandra, committee member; McKay, John, committee memberTraditional agricultural practices and land use changes have resulted in greenhouse gas emissions back into the atmosphere, which negatively contributes to climate change. Traditional practices also reduce soil organic matter including soil carbon which is essential for soil health, maintenance of soil biological processes, and environmental sustainability. Currently, a range of agricultural conservation practices has come to be recommended and incentivized for soil carbon sequestration by either increasing carbon inputs and/or reducing carbon losses. These include practices such as reduced tillage, cover cropping, and crop rotations. Although private carbon markets have taken the initiative to provide incentive payments for carbon sequestration in agriculture, the adoption of SCS practices can be hindered by different socioeconomic, farm operational, and environmental constraints. In addition to currently recommended soil management practices, new crop genetic innovations, including perennial grain crops and annual crops, such as corn, with larger root systems or deep root traits are emerging as additional examples of SCS frontier technologies. The first chapter of this dissertation utilizes a joint adoption model to hypothetically examine the impact of socioeconomic, environmental, and farm variables on the probability of adopting either or both of currently recommended SCS practices and these novel genetic innovations, such as deeper root corn varieties. Moreover, deeper root system traits are expected to maintain yields under drought conditions. Deeper root system hybrids are also expected to be an effective agricultural technology for maintaining soil health as they can reduce soil erosion and increase soil organic matter. Existing drought tolerant (DT) corn varieties that have been commercially marketed for more than 10 years exhibit some of these same characteristics. Therefore, the adoption of existing DT hybrids is likely a good indication of the potential for the adoption of hybrids with further enhanced root systems. In the second chapter, we use state-level and field-level data for corn planted in the United States Corn Belt to examine the influence of climate change, soil characteristics, and production practices in the decision to adopt DT varieties. Seed industry data indicates that 44 percent of Corn Belt planted corn acres were allocated to a DT variety in 2021 and 58 percent were planted to DT in 2022. Results suggest that exposure to recent years' drought is a significant determinant of the adoption of DT corn. DT corn is more likely to be adopted in non-irrigated fields. We find that western Corn Belt states are more likely to increase the share of DT corn acres compared to eastern and central Corn Belt states, associated with lower precipitation values and higher drought severity. Thus, deeper root varieties are likely to be more attractive to farmers in western more arid regions of the Corn Belt, where associated soil carbon benefits of deeper root varieties are likely to be more limited. Anticipating that enhanced deeper root corn hybrids with public benefits may come to be treated as a conservation practice included under incentive payment programs, and understanding that soil carbon potential is heterogeneous, in the third chapter we consider the question of spatial targeting of payments. We develop three per acre payment scenarios under the benefit optimization approach to estimate and compare the metric tons of carbon inset under an optimal cropland acre enrolled in a carbon incentive program. The study uses cross section data for counties in the United States Corn Belt, a region with the largest number of productive cropland acres and higher potential carbon sequestration rates compared to other regions across the United States. Results show that if the carbon incentive program is designed to target the adoption of SCS practices that result in high, medium, and low SCS rates respectively, then we can expect that about 32, 24, and 19 million metric tons of carbon can be sequestered in Corn Belt croplands annually.Item Open Access Corn grower change for climate change: ex-ante economic analysis of adoption of enhanced root traits(Colorado State University. Libraries, 2019) Giraud, Angelique, author; Graff, Gregory, advisor; Mooney, Daniel, committee member; McKay, John, committee memberSustainable agriculture technologies of enhanced root corn possess the potential to offset more than half of the greenhouse gas emissions of the transportation sector if completely diffused. Weather variability resulting from climate change is predicted to decrease agricultural productivity. Enhanced corn root traits aim to mitigate and adapt to climate change by improving drought tolerance and soil quality and increasing carbon sequestration rates. Encouraging adoption is challenging among heterogeneous corn growers in an enormous market. Previous research on farmer preferences around four categories of benefits stemming from adoption of corn with enhanced root traits frames the motivation to detail profit margins influencing business decisions utilizing a linear programming model. Several scenarios of changes to cost, revenue, carbon sequestration, and water scarcity are analyzed to provide guidance for policy. Results indicate that a corn grower will not choose enhanced root corn when the only benefit is carbon sequestration with cost and revenue as sole drivers of the decision to adopt. As water scarcity progresses, drought tolerance becomes increasingly valuable, substantially shifting production decisions in favor of adoption of corn with enhanced root traits.Item Open Access Evaluating genetic mechanisms and performance characteristics of alternative oilseed crops for on-farm biofuel production in Colorado(Colorado State University. Libraries, 2015) Campbell, Brian J., author; Byrne, Patrick, advisor; Johnson, Jerry, advisor; Seshadri, Arathi, committee member; McKay, John, committee memberDryland winter wheat (Triticum aestivum) cropping systems dominate most of the agricultural landscape in Colorado’s semi-arid eastern plains. Since this area’s climate is characterized by frequent heat and drought, it is important to maximize water use efficiency to make agricultural lands as productive as possible. Adding a spring crop in rotation with winter wheat intensifies the rotation, increasing water use efficiency by up to 37%. Recent research has explored further intensifying this rotation by adding an oilseed crop into a wheat – spring crop – fallow rotation during the fallow period. Ideally, the oilseed crop acts as a cover crop for part of the season and leaves enough time at the end of the season to regenerate water in the soil profile before planting wheat in the fall. The oil from this crop can be used to produce on-farm biofuels, offsetting petroleum diesel costs without displacing high-value food crops. Additionally, the meal from this crop acts as a value-added byproduct by providing feed for livestock. Since traditional oilseeds such as soybean (Glycine max) and rapeseed (Brassica napus) do not perform well in Colorado, several alternative oilseeds have been tested to assess whether they can fill this niche. Camelina (Camelina sativa) has shown great potential, with high oil content and inherent resistance to many biotic and abiotic stressors. Other potential oilseeds include Brassica juncea and Brassica carinata, but both of these species have exhibited longer life cycles and lower yields than camelina. A major challenge to camelina production in Colorado is a susceptibility to heat stress during reproductive periods. Both short periods of intense heat stress and longer periods of mild heat stress can cause floral and seed abortion, resulting in reduced yield. In the current study, a quantitative trait locus (QTL) approach is used to identify heat and drought tolerance mechanisms and yield components, explore the extent of pleiotropy, epistasis, and linkage, and identify promising lines for study or production. Genetic resources for camelina are becoming more readily available and a newly developed genetic map with improved marker density was used for QTL discovery. Replicated field trials were performed during the 2014 growing season in Fort Collins and Greeley, Colorado, under differential irrigation treatments at each site to collect phenotypic data on a variety of traits. Sixteen new QTL were discovered from this data, along with nine QTL using data from Colorado trials of the same population in 2009 and 2010 performed by Enjalbert (2011). Seven QTL were discovered for yield, however, no QTL were found in more than two environments, indicating a lack of stable QTL for this trait. This was in contrast to results from Enjalbert (2011) where stable QTL for yield across environments were detected using the original, mainly AFLP generated, genetic map by Gehringer et al. (2006). This underscores the high amount of variation that can be caused by environment. QTL for other traits, such as plant height and days to flowering, were detected that were more robust, however, no QTL were detected with either data set that spanned more than three environments. Two loci were identified that affected multiple traits, supplying evidence of either pleiotropy or close linkage of genes. Several RIL performed well in multiple environments, indicating potential for production in Colorado, however, these lines were not in common with previous studies, so further trials will be needed to confirm consistently stable yields. In addition to the camelina QTL study, a two-year variety trial of Brassica carinata was performed in Fort Collins, CO during the 2013 and 2014 growing seasons under limited and full irrigation. Collaboration with the private Canadian oilseed company Agrisoma Biosciences spurred interest in reevaluating the potential of this alternative oilseed in Colorado cropping systems. Agrisoma Biosciences developed early flowering and early maturing germplasm that performs well in the Canadian prairie and is interested in testing their germplasm in new regions with potential for production. The company provided six lines for the trial, five experimental lines and one commercial check cultivar. Mean flowering time was over 13 days longer than previously tested African accessions that had been deemed too late flowering to be competitive in Colorado’s climate. Mean yields were low as well, at 669 kg ha⁻¹. The commercial check cultivar, A100, outperformed all of the experimental lines, with a mean yield of 1081 kg ha⁻¹ across environments. With a wide margin between the other lines and A100, this commercial cultivar was clearly more successful than any of the experimental lines. However, yields of this one cultivar were not sufficiently impressive to recommend on-farm testing of the crop.Item Open Access Minimum stomatal conductance: implications for describing the genetic control of transpiration(Colorado State University. Libraries, 2013) Reuning, Gretchen, author; Bauerle, William, advisor; McKay, John, committee member; Qian, Yaling, committee memberMinimum stomatal conductance (g0) makes a significant contribution to the rate of water loss in plants. The influence of g0 on water use efficiency (WUE) has implications for plant drought tolerance and adaptation, thus we propose that g0 can be used as a trait to describe the genetic control of water use in leaf transpiration models. In the model species, Arabidopsis thaliana, g0 exhibits both environmental and genetic variation. We explored one g0 quantitative trait locus (QTL) by measuring and simulating transpiration for two A. thaliana accessions Kas-1 and Tsu-1, as well as recombinant inbred lines (RILs) from a reciprocal cross of the two parental lines. Using a three-dimensional spatially explicit plant process model, MAESTRA, we aimed to: (1) test the accuracy of transpiration prediction for Kas-1 and Tsu-1 using measured g0 values, (2) parameterize MAESTRA with Tsu-1, Kas-1, and RIL g0 values to predict transpiration of RILs containing either Tsu-1 and Kas-1 alleles at the g0 QTL, and (3) determine if a relationship exists between g0 values under well-watered and drought conditions in A. thaliana. MAESTRA accurately predicted A. thaliana transpiration for Kas-1 and Tsu-1 accessions when parameterized with measured g0 values. There was no significant difference between measured and simulated transpiration estimates for both accessions, with Tsu-1 simulated transpiration 5.2% lower than the mean measured, and Kas-1 simulated transpiration 1.4% higher than measured. On average, Kas-1 transpired 73% as much water as Tsu-1. Due to the lack of specific knowledge of RIL physiology aside from g0, simulating RIL transpiration with varying g0 values yielded non-significant results. However, based on the simulated means for RIL transpiration using RIL, Kas-1, and Tsu-1 g0 values, we show that g0 parameterization predicts daily transpiration when all other parameters are held constant at Tsu-1 or Kas-1 measured and presumed physiology. This further points to the importance of g0 for transpiration predictions. Data on additional g0 QTL could aid in predicting transpiration from novel genotypes such as RILs containing multiple combinations of alleles from parental genotypes. We found that accessions with relatively high well-watered g0 values showed sharper declines in g0 during drought compared to accessions with lower g0 values under well-watered conditions (p < 0.0001). The use of plant physiological models for predicting transpiration of novel genetic lines will benefit from the further knowledge of the genetic control of g0.Item Open Access New insights into Pleistocene hominin butchery and tool choice from a 0.9 Ma fossil assemblage from the HEB site, Olduvai Gorge, Tanzania(Colorado State University. Libraries, 2021) Mwakyoma, Ipyana F., author; Pante, Michael C., advisor; Glantz, Michelle M., committee member; McKay, John, committee memberCut marks on animal bones have the potential to inform on hominin diet and tool use. Although these important traces of behavior appear as early as 3.4 Million years ago, they normally are rare in fossil assemblages in part due to the exceptional preservation of bone surfaces required to study them. Olduvai Gorge is unique in having many fossil assemblages with well-preserved cortical surfaces that allow identification and study of bone surface modifications. Most of these assemblages are from Beds I and II as fossil preservation is generally poor in the younger Beds. The present study analyzes the well-preserved fossil assemblage recovered from renewed excavations of the HEB site by the Olduvai Gorge Coring Project (OGCP). The HEB site is stratigraphically positioned in lower Bed IV, just above Tuff IVA, dating to ~0.9 Ma and was first excavated by Mary Leakey's team in 1962. These fossils exhibit a large number of cut marks and are in direct association with Acheulean tools; making this site important for inferring the feeding and tool use behavior of Homo erectus. Optical profilometry protocols developed by Pante et al (2017) were used to obtain 3D quantifiable micromorphological measurements of 256 experimentally created cutmarks, and 20 archaeological cutmarks from HEB site Olduvai Gorge. Focusing on the micromorphological measurements, this study used quadratic discriminant analyses models to classify the archaeological cutmarks from HEB site based on technology and raw materials types of the stone tools used to create those marks. The discriminant models on raw material types only, tool types only and both raw material and tool types had 64.8%, 77.3% and 68.4% classification accuracies respectively. Results from the models indicate that cut marks at HEB were made by using both flakes and biface tools, made from lava and quartzite raw materials. These results are consistent with Leakey (1994) excavations, which showed a significant prevalence of flakes and bifaces made from volcanic lava and quartzite raw materials. When interpreted in conjunction with butchery experiments, this study can help us understand hominin tool use and choices at HEB site, Olduvai Gorge - around 0.9 million years ago.Item Open Access QTL mapping of root and leaf traits associated with drought tolerance in a canola (Brassica napus l.) doubled haploid population(Colorado State University. Libraries, 2013) Mekonnen, Melaku Degefu, author; Byrne, Patrick, advisor; McKay, John, committee member; Seshadri, Arathi, committee memberDrought stress is one of the major constraints to canola production in Colorado, therefore, improved understanding of the inheritance and genetic variation for drought tolerance will help to develop cultivars that are adapted to the state. To learn more about traits associated with drought tolerance in canola we focused on root pulling force and carbon isotope discrimination with the objectives of: • Detecting the location, number, and effects of quantitative trait loci (QTL) associated with root pulling force and carbon isotope discrimination • Understanding the association of root pulling force and carbon isotope discrimination with yield components in well watered and water limited environments We used 148 doubled haploid lines of the DHYB population developed from the cross of a black seeded (DH12075) and a yellow seeded (YN01-429) parent. The experiment was conducted as a split-plot design with three replications in the 2011 and 2012 summer seasons. Two moisture regimes (wet and dry) constituted the main plot factor, with genotype as the subplot factor. A single individual plant per replication represented each genotype. Days to flowering, leaf relative water content, δ13C (the ratio of 13C to 12C), plant height, lateral branch number, lateral root number, thousand seed weight, seed yield per plant, root pulling force, and proportion of aborted siliques were measured, though not every trait was evaluated in each treatment or year. Phenotypic correlation among all pairs of traits and heritability of the traits under both treatments were estimated. QTL analysis was conducted for each trait and environment with R/qtl software. Analysis of variance revealed significant differences (P<0.001) among genotypes for days to flowering, plant height, and δ13C in both treatments and years. Transgressive segregation was observed for root pulling force, δ13C, days to flowering and plant height in both treatments and years. Root pulling force was significantly correlated with plant height (r = 0.32 to 0.54, P<0.001), fresh biomass (r = 0.17 to 0.58, P<0.001), and lateral root number (r = 0.21 to 0.42, P<0.001) in both years and under both moisture treatments. The strong positive correlation of root pulling force with the branch number and fresh biomass suggests that it can be used to detect genotypes with higher yield potential in drought. δ13C was positively correlated with days to flowering in each experiment and negatively correlated with seed yield per plant and thousand seed weight. In 2011 QTL were detected for days to flowering on linkage group 1, 2, 12T, and 16, and for the interaction between loci on linkage groups 1 and 16; some of the same QTL were also detected in 2012. In 2011, QTL for root pulling force were detected on linkage groups 3, 5, 11, 14T, and 18 and for the interaction between QTL on linkage groups 3 and 18. In 2012, consistent QTL were detected on linkage groups 11 and 18. The QTL for root pulling force co-localized with a fresh biomass QTL on linkage group 11 and with plant height on linkage group 14T. Five QTL for δ13C were detected on linkage groups 2, 9, 18, and 19 in different environments. In general QTL for δ13C were associated with QTL for days to flowering. No epistatic interactions were detected for the QTL detected in 2011 and 2012 for δ13C, suggesting strong additive gene action for δ13C. We found high heritability and relatively low QTL x environment interaction for root pulling force and δ13C; therefore, we suggest these traits can be used to select genotypes with a higher yield and biomass in dry environments. The study provides insights about root pulling force, δ13C and their relationships with yield, and yield related traits in canola. In order to utilize these traits in breeding for drought tolerance and marker assisted breeding further research on the relationship among these traits is imperative.Item Open Access Quantitative trait locus mapping of yield and yield components in canola (Brassica napus L.) under irrigated and rainfed treatments(Colorado State University. Libraries, 2012) Heiliger, Annie, author; Byrne, Patrick, advisor; Johnson, Jerry, committee member; McKay, John, committee memberRapeseed (Brassica napus L.) is an oilseed crop that has a variety of uses, including applications in industry as well as for food, feed, and fuel. Improved B. napus cultivars with decreased levels of two disease-causing compounds are known commonly as canola or double-low cultivars, and are approved for human and animal consumption in the U.S., Canada, and Europe. Canola is currently grown in the northern U.S. and in several areas of Canada and Europe, but has potential to be grown in other areas of the U.S., including Colorado, either for biodiesel or to be sold in a canola commodity food oil market at the discretion of the seed producer. Additionally, the cake meal left after oil extraction has a high protein concentration and can be added as a supplement to animal feed. In recent years, water availability for crop production in the western U.S. has declined due to competition with non-agricultural water uses, and the increasing demands for water will likely increase with global climate change. Therefore, in order to be sustainable, crops grown in Colorado must be high-yielding with limited or no irrigation inputs, and consequently canola cultivars adapted to the semi-arid climate of Colorado and the U.S. High Plains will need to be drought tolerant. To provide information relevant to improving adaptation of canola to Colorado conditions, a study was conducted with the following objectives: 1) to evaluate yield, yield components, and days to flowering (DTF) in two doubled haploid (DH) canola mapping populations under rainfed and irrigated conditions; 2) to determine relationships among yield and yield components by analyzing trait correlations and to study trait inheritance patterns; 3) to determine areas of the B. napus genome that are implicated in yield and yield component traits under both rainfed and irrigated conditions by quantitative trait locus (QTL) analysis; and 4) to study the sensitivity of yield and yield component traits to drought stress by performing analysis of variance and by performing a QTL analysis on the difference in trait values from the rainfed and irrigated treatments. Two DH canola mapping populations were grown in side-by-side irrigated and rainfed treatments near Fort Collins, Colorado: population SE1 in 2010 (n=183) and population DHYB (n=150) in 2011. DTF, seed yield, and yield-related traits were measured in order to understand relationships among these traits under different water regimes, to study trait heritabilities, and to better understand genotype, treatment, and treatment by genotype interaction effects. QTL mapping was conducted separately for each treatment in each population using R-QTL software to detect additive and epistatic effects. Yield components that were studied included siliques per main inflorescence (SMI), seeds per silique (SS), and thousand seed weight (TSW). Seed coat color was also classified for the DHYB population. Analysis of variance revealed an influence of genotype (P<0.0001) on all traits in both populations, treatment effects on seed yield, SMI, and SS (P<0.05) in the SE1 population, and treatment effects on seed yield, SMI, TSW, and DTF in the DHYB population. Genotype by treatment interactions were significant (P<0.01) for all traits in the SE1 population and for seed yield and TSW (P<0.05) in the DHYB population. In the 2010 study, three DTF QTL were detected that colocated with most of the other QTL, demonstrating the strong influence of flowering time on seed yield and yield components in this population. These QTL explained 73 and 65 percent of phenotypic variance for DTF in the wet and dry treatments, respectively, in a multiple QTL model. Several novel QTL were detected in the 2011 study, including a locus on LG 17 that explained 7.54% of trait variation for seed yield in the dry treatment and a locus on LG 16 that explained 11.41% of seed yield in the wet treatment. A novel QTL for SS was detected on LG 7 in both treatments. Two QTL reported for DTF in the wet treatment on LGs 14 and 18 are novel, as are two QTL for SMI in the dry treatment. Of the yield components studied, SS consistently had the lowest amount of genotype by treatment interaction and direct treatment effects in both populations, as well as high heritability estimates in both populations. SS also correlated positively and significantly (P<0.05) with seed yield in both years of the study. Additionally, the QTL detected for SS in the 2011 study were the same for the wet and dry treatments, indicating QTL stability. It is our conclusion that SS is a good candidate for direct selection in a breeding program, and that he QTL reported for SS could also be useful for marker-assisted selection for improved yields in Colorado.Item Open Access The evolution of selenium hyperaccumulation in Stanleya (Brassicaceae)(Colorado State University. Libraries, 2014) Cappa, Jennifer JoCarole, author; Simmons, Mark P., advisor; Pilon-Smits, Elizabeth A. H., advisor; Angert, Amy L., committee member; McKay, John, committee memberElemental hyperaccumulation is a fascinating trait found in at least 515 angiosperm species. Hyperaccumulation is the uptake of a metal/metalloid to concentrations 50-100x greater than surrounding vegetation. This equates to 0.01-1% dry weight (DW) depending on the element. Studies to date have identified 11 elements that are hyperaccumulated including arsenic, cadmium, cobalt, chromium, copper, lead, manganese, molybdenum, nickel, selenium (Se) and zinc. My research focuses on Se hyperaccumulation in the genus Stanleya (Brassicaceae). The threshold for Se hyperaccumulation is 1,000 mg Se kg-1 DW or 0.1% DW. Stanleya is a small genus comprised of seven species all endemic to the western United States. Stanleya pinnata is a Se hyperaccumulator and includes four varieties. I tested to what extent the species in Stanleya accumulate and tolerate Se both in the field and in a common-garden study. In the field collected samples only S. pinnata var. pinnata had Se levels >0.1% DW. Within S. pinnata var. pinnata, I found a geographic pattern related to Se hyperaccumulation where the highest accumulating populations are found on the eastern side of the Continental Divide. In the greenhouse S. pinnata var. pinnata accumulated the most Se within the genus, in both the young leaves and roots. I also discovered a polyploidy event within S. pinnata. All varieties of S. pinnata collected on the western slope of the Rocky Mountains were tetraploid and all but one population collected from the eastern slope of the Rocky Mountains were diploid. However, when tested, genome size did not correlate with Se hyperaccumulation capacity in S. pinnata. I isolated DNA from the field collected leaves and conducted a phylogenetic analysis using four nuclear gene regions and fifteen morphological characters. Using the phylogeny, I conducted an ancestral-reconstruction analysis to predict the ancestral states for Se related traits in a parsimony framework. I infer from the results that tolerance preceded hyperaccumulation in the evolution of Se hyperaccumulation in Stanleya and that hyperaccumulation evolved in an ancestor of the S. pinnata/bipinnata clade. Lastly, I conducted a comparative transcriptomic analysis between S. pinnata var. pinnata and S. elata, a non-hyperaccumulator. I found higher transcript levels for many of the enzymes involved in sulfur (S) transport and assimilation in S. pinnata relative to S. elata. Surprisingly, I found high constitutive expression for many of the S assimilation enzymes in the roots of S. pinnata, particularly an isoform of ATP sulfurylase. I also found high constitutive expression for sulfate transporter 1;2 in the roots of S. pinnata. Based on these data I infer that S. pinnata assimilates Se in the root and that sulfate transporter 1;2 and ATP sulfurylase 2 may be key enzymes in Se hyperaccumulation in S. pinnata. Taken together these data, in conjunction with previous work, help provide a better understanding of the evolution of Se hyperaccumulation in Stanleya at the physiological, phylogenetic and transcriptional levels.Item Open Access Toward effective high-throughput georeferencing over voluminous observational data in the domain of precision agriculture(Colorado State University. Libraries, 2018) Roselius, Maxwell L., author; Pallickara, Sangmi Lee, advisor; Pallickara, Shrideep, committee member; McKay, John, committee memberRemote sensing of plant traits and their environment facilitates non-invasive, high-throughput monitoring of the plant's physiological characteristics. Effective ingestion of these sensing data into a storage subsystem while georeferencing phenotyping setups is key to providing timely access to scientists and modelers. In this thesis, we propose a high-throughput distributed data ingestion framework with support for fine-grained georeferencing. The methodology includes a novel spatial indexing scheme, the nested hash grid, for fine-grained georeferencing of data while conserving memory footprints and ensuring acceptable latency. We include empirical evaluations performed on a commodity machine cluster with up to 1TB of data. The benchmarks demonstrate the efficacy of our approach.Item Open Access Use of traveling salesman problem solvers in the construction of genetic linkage maps(Colorado State University. Libraries, 2015) Allen, Zachariah A., author; Whitley, Darrell, advisor; McConnell, Ross M., committee member; McKay, John, committee memberConstruction of genetic linkage maps is an important tool for Biology. Researchers use a variety of laboratory techniques to extract genetic marker data from an experimental cross of a species of interest and then use these data to group the markers into chromosomes, and then construct maps of the locations of the markers within the chromosomes. This in turn allows them to determine which sections of the chromosomes are responsible for variation in agricultural, medical or other traits of interest. The current methods of constructing genetic linkage maps are tedious and time-consuming. This thesis presents a method of utilizing the Hamiltonian path problem (HPP) to solve the problem of genetic linkage mapping. Since solvers already exist for the traveling salesman problem (LKH and Concorde), by casting the linkage mapping problem as a HPP we can use these solvers to efficiently find the solution. To do this, the recombination frequencies between genetic markers are treated as internode weights and the TSP solution gives the lowest-cost path through the markers. By adding a dummy marker with zero weight to all other markers, the TSP solution is made equivalent to a HPP. The primary difficulty in constructing a linkage map is the fact that all data sets are noisy: errors in laboratory techniques create uncertainty in the relationships between genetic markers, so a straightforward HPP solution is not sufficient. This thesis describes a method of using the HPP to separate the raw data into clusters so that the researcher can be sure that the chromosomes are well-separated, the clusters can then be assembled into complete chromosomes using existing TSP solvers. The results show that this method produces results which are equally as good as the prevalent software in the field, while drastically decreasing the time required to run an analysis.Item Open Access Utilizing plant genetic resources for pre-breeding of water-efficient sorghum: genetics of the limited transpiration trait(Colorado State University. Libraries, 2022) Cerimele, Gina, author; Morris, Geoffrey, advisor; Cotrufo, Francesca, committee member; McKay, John, committee memberShifting precipitation patterns driven by the changing climate threaten productivity of dryland agricultural systems. Increasing the efficiency of water use by crops grown in dryland regions, such as sorghum (Sorghum bicolor), is a target for plant breeding to address this issue. c variants conferring efficient water use in sorghum may be found within collections of plant genetic resources (PGR). However, tropical sorghum PGR require adaptation to the target temperate environment to begin the pre-breeding trait discovery process. The landmark Sorghum Conversion Program unlocked diverse sorghum genetics for temperate breeding by adapting tropical African lines to temperate height and maturity standards. In the U.S. Sorghum Belt, spanning South Dakota to central Texas, the limited transpiration (LT) trait could provide growers a 5% yield increase in water-limited conditions with high vapor pressure deficit (VPD) according to crop modeling. To transfer the LT trait into commercial breeding programs, an elite donor line must be developed. Characterizing the genetic architecture of LT informs markers and breeding strategy for development of an elite donor. To characterize the genetic architecture of LT, two biparental recombinant inbred line (RIL) mapping families were developed from crossing putative LT parents SC979 and BTx2752 by putative non-LT parent RTx430. For this study, the families were grown together as a mapping population in three locations (continental-humid eastern Kansas, semi-arid western Kansas, and semi-arid Colorado) in one year. The families were phenotyped for the LT trait using UAS- collected thermal imaging and canopy temperature as a proxy. The families were initially designed with the goal of controlling phenotypic covariates of canopy temperature associated with height and flowering time, like neighbor-shading and artifactual temperature inflation related to panicle imaging. To test whether the family design controlled for height and flowering time covariates, the populations were phenotyped for both traits. High broad-sense heritability (H2) > 0.86 for all traits and families across locations indicates that the traits are not fixed. However, phenotypic distributions reveal that most lines are within an agronomically-relevant range that limits confounding covariates. Using DArTseq-LD genotyping data, GWAS analyses of height and flowering time reveal putatively significant marker-trait associations (MTA) with known loci underlying height and maturity in sorghum. These results collectively indicate that, while genetic variation for height and flowering exist in the LT mapping families, the resulting phenotypes are homogeneous enough to be suitable for LT genetic mapping. To test hypotheses on the monogenic, oligogenic, or polygenic architecture of the LT trait, canopy temperature data collected by the UAS-thermal imaging missions was used. Non-zero H2 of canopy temperature in most location-timepoints indicates genetic variation is present for LT in the population. Continuous phenotypic distributions imply a quantitative architecture. GWAS analyses revealed moderate marker-trait association peaks visible within timepoints and across locations, indicating oligogenic architecture of LT. Some of those peaks also colocalize with sorghum homologs of aquaporin genes in Arabidopsis thaliana, suggesting that aquaporin variation could be a molecular basis underlying the trait. These results provide a basis for marker-assisted selection in developing an LT donor line.