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Browsing by Author "Richards, Christopher, committee member"

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    Inferring mating behavior and reproductive success of (Agkistrodon contortrix) using molecular parentage assignment tests
    (Colorado State University. Libraries, 2012) Kendall, Jennifer, author; Savidge, Julie A., advisor; Douglas, Michael E., advisor; Douglas, Marlis R., committee member; Richards, Christopher, committee member; Givens, Geoffrey, committee member
    Historically, behavioral and ecological research on snakes has been limited due to the secretive and cryptic nature of these species. Readily available molecular techniques have enhanced the study of reproductive behavior and advanced our understanding of mating patterns (such as multiple paternity) that were previously deemed ambiguous. Instead they have been revealed as often prevailing and strongly influential on genetic population structure. Underlying biological questions about the social and behavioral movements associated with mating can be addressed by correlating the results of population genetic analyses with known social structure and can be used to make inferences regarding landscape genetics and gene flow. During a three-year (2001--2003) ecological study of a geographically isolated population of Northern Copperhead (Agkistrodon contortrix) in Meriden, Connecticut, U.S.A., blood samples from 254 individuals (117 adults and 137 juveniles) were collected for extraction and amplification of genomic DNA. Five microsatellite DNA markers, derived from species closely related to the study organism, were used to identify individuals in the population and to infer paternity. These analyses revealed aspects of mate selection, reproductive ecology, and sociality in Northern Copperhead. No spatial genetic structure among dens could be determined with the available data and thus influence of den structure on mating patterns could not be inferred. In contrast, genetic structure in the form of three distinct genetic clusters was identified within the population. Paternity tests identified a nonrandom mating pattern by which individuals showed a clear pattern of intra-cluster mating. Causation underlying this phenomenon remains unclear, as further ecological and genetic data would be needed.
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    Mapping Rhizoctonia root and crown rot resistance from sugar beet germplasm FC709-2 using new genomic resources
    (Colorado State University. Libraries, 2024) Metz, Nicholas, author; Mason, Esten, advisor; Dorn, Kevin, committee member; Richards, Christopher, committee member; Gaines, Todd, committee member
    Sugar beet (Beta vulgaris subsp. Vulgaris) provides about 35% of the refined sugar globally, and over half of the domestic production in the United States. Sugar beet are primarily grown in temperate climates from plantings in late spring and harvest in the fall. In the United States sugar beets are grown in four diverse regions: the upper Midwest (Minnesota and North Dakota), the far west (California, Idaho, Oregon, and Washington, the Great Plains (Colorado, Nebraska, Montana, and Wyoming), and the Great Lakes (Michigan). Multiple pests and pathogens continue to threaten tonnage and recoverable sugar yields. These are controlled through planting genetically resistant cultivars, agronomic cultural practices and chemical applications throughout the growing season. With a shrinking set of chemical and cultural control options to manage these production threats, the need for continued improvement upon host plant resistance is important. Decades of global breeding efforts to improved disease tolerance in sugar beet has been effective, but molecular and genomic guided breeding and disease resistance characterization in sugar beet is only now emerging. The most important root pathogen in sugar beet is Rhizoctonia Root and Crown Rot (RRCR) caused by the fungal pathogen Rhizoctonia solani. This disease is estimated to cause up to 50% localized losses, and regularly causes 57 million dollars in economic losses per year despite the use of tolerant varieties, chemical control, and cultural practices. Public sugar beet pre-breeding has developed hundreds of widely utilized lines with novel traits and combinations of traits, including for RRCR resistance. One such line, FC709-2, displayed exceptional tolerance to Rhizoctonia solani released from the United States Department of Agriculture sugar beet breeding program in Fort Collins, Colorado. This germplasm line is base for many RRCR resistant cultivars used by growers around the world. In this study, new germplasm, genetic, and genomic resources revolving around FC709-2 were developed. These resources include a new germplasm line derived from the purification of FC709-2. By using stricter selection pressure and single seed decent a more homogenous seed lot was created to be used by other breeding programs. A new reference genome created from a single highly RRCR resistant plant using the most recent sequencings and bioinformatic technologies will be used to discover genes that are responsible for a wide array of plant interactions. Last, novel QTLs associated with RRCR resistance were discovered using a bi-parental mapping population and bulk segregate analysis. Collectively, these results show that discovering novel RRCR resistance genes in a highly resistant germplasm line using a purpose-built reference genome is a streamlined and accurate method. With these new resources in place researchers around the world can use them to discover the genes responsible for RRCR resistance, create markers for more accurate selections, and follow the methods described to be implemented in other plant breeding programs.
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    Paralogy or reality? Exploring gene assembly errors in a target enrichment dataset
    (Colorado State University. Libraries, 2022) Rosén, Austin, author; Simmons, Mark P., advisor; Ackerfield, Jennifer, committee member; Richards, Christopher, committee member; Stewart, Jane, committee member
    De novo gene assembly of short read data is inherently difficult – similar to the process of assembling a jigsaw puzzle. I describe three errors that occurred with the assembly of target enrichment data in the genus Cirsium (Asteraceae): inconsistent contig selection, artificial recombination, and inconsistent intron determination leading to over-alignment of non-homologous nucleotides. These errors occurred in 39% of loci in the dataset and were often a by-product of undetected paralogs: assembled loci that likely contained paralogous or homoeologous sequences but did not trigger default paralog warnings by the assembly program, HybPiper. Default HybPiper thresholds for identifying paralogy during the assembly process were insufficient to filter such loci. A custom target file was created in which putative paralogs were separated into independent loci. The custom target file was successful in reducing, but not eliminating, assembly errors in the dataset. A final iteration of quality control was performed to create a dataset largely free of assembly errors. However, phylogenetic inferences applied to this final cleansed dataset were unable to resolve the taxonomic relationships between the sampled specimens. Rather, these results affirm that Cirsium is a taxonomically problematic genus and may require population-level genetic data or integrative taxonomy approaches to delimit species boundaries.
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    Viability and invasive potential of hybrids between yellow toadflax (Linaria vulgaris) and dalmatian toadflax (Linaria dalmatica)
    (Colorado State University. Libraries, 2012) Turner, Marie F. S., author; Ward, Sarah, advisor; Richards, Christopher, committee member; Steingraeber, David, committee member; Beck, George, committee member; Sing, Sharlene, committee member
    Although outcomes of hybridization are highly variable, it is now considered to play an important role in evolution, speciation, and invasion. Hybridization has recently been confirmed between populations of yellow (or common) toadflax (Linaria vulgaris) and Dalmatian toadflax (Linaria dalmatica) in the Rocky Mountain region of the United States. The presence of hybrid toadflax populations on public lands is of concern, as both parents are aggressive invaders already listed as noxious weeds in multiple western states. A common garden experiment was designed to measure differences in quantitative (shoot length, biomass, flowering stems, seed capsule production) phenological (time of emergence, first flowering and seed maturity) and ecophysiological (photosynthesis, transpiration and water use efficiency (WUE)) traits for yellow and Dalmatian toadflax, F1 and BC1 hybrids, as well as natural field-collected hybrids from two sites. Genotypes were cloned to produce true replicates and the entire common garden was also replicated at two locations (Colorado and Montana); physiological data were collected only in Colorado. All genotypes grew larger and were more reproductively active in Colorado than in Montana, and hybrids outperformed parent taxa across vegetative and reproductive traits indicating heterosis. Hybrids also emerged earlier, but did not flower or set seed sooner than parent taxa, and all genotypes set seed more quickly in Montana than in Colorado indicating a strong environmental influence on this trait. There were indications that for some traits, yellow toadflax alleles conferred a relative advantage in Montana and Dalmatian toadflax alleles conferred a similar advantage in Colorado. Natural hybrids collected from Montana had higher rates of overall germination than any other class, suggesting selection for transgressive germination; they also emerged earlier in the Montana common garden suggesting possible local adaptation. Aside from these indications of GxE , general patterns of genotypic class performance remained relatively consistent across sites. Ecophysiological patterns were intermediate: yellow toadflax had the highest rates of photosynthesis and WUE; Dalmatian toadflax had the lowest rates of these two metrics and hybrid rates were distributed between them. Plants with higher rates of photosynthesis and transpiration reached phenological stages earlier than those with lower rates. For natural hybrids, the direction of the correlation between ecophysiological traits and quantitative and phenological traits changed depending on when the physiological data was collected. Overall, results indicate most toadflax hybrids may have increased fitness relative to their parents as well as multiple phenotypic attributes which may enable them to expand and invade. However, which of these specific genotypes become invasive will also depend on the direction of crossing and location at which hybridization occurs. Given the observed heterosis, transgressive trait expression, a lack of other apparent phenotypic shortcomings and the potential impacts of hybridization on current mechanisms of control, known hybridization sites, as well as other locations where yellow and Dalmatian toadflax are co-invading should be prioritized for management.