Master of Science / Department of Entomology / Jeremy L. Marshall / Sexual conflict is a process that occurs when the evolutionary interests of the sexes is not aligned. The theory began with Darwin in the 1800’s. His observations of sexual dimorphism and traits which did not seem to follow the rules of natural selection led him to the theory of sexual selection. Sexual selection resolved some of the issues which were noted in the evolutionary processes he observed but not all of them. For example, it did not explain traits which increased the male optimum fitness while decreasing the female optimum fitness. It was decades before the concept of sexual conflict was formulated, and even longer before the underlying mechanisms were understood. Sexual conflict is different than sexual selection and there are ways to differentiate which of these processes have occurred in a population. The main forms of sexual conflict are intralocus and interlocus conflict. These involve the interactions between alleles in the genome of the sexes. Intralocus conflict involves conflict at a single locus in the genome while interlocus conflict involves conflict between different loci. Interlocus conflict has been more extensively studied due to its association with sexually antagonistic coevolution (SAC). SAC draws the attention of scientists due to the possibility it is related to the fundamental biological process of speciation. Sexual conflict targets certain traits at defined periods in the mating process. These periods include first, the precopulatory stage which is before the act of copulation begins. Second, there is the stage during copulation but before fertilization of the embryo. Finally, there is the postcopulatory postzygotic stage which is after copulation has ended and fertilization has occurred. Each of these points in the process of mating has traits or behaviors which sexual conflict may target. This review concludes with a proposed experiment to determine if sexual conflict is occurring in a group of four genera of mosquitoes. The experiment utilizes the attributes of sexual conflict to differentiate between other processes. A major component is the consequence of mating systems on selective processes to determine if sexual conflict is involved in the evolution of male accessory gland proteins.

Doctor of Philosophy / Department of Biology / Alexander E. Beeser / Multiple signaling pathways regulate development of the posterior zebrafish body, which is derived from a population of progenitor cells called the tailbud, a structure formed at the end of gastrulation. Fate specification and differentiation are closely linked with cell migration to ensure that, as some cells exit the tailbud and differentiate, other cells are retained in the tailbud as undifferentiated precursors to support later growth. The role of BMP signaling in specifying cell fate in the tailbud has been well-characterized. Among the lost ventral tissues like ventral tailfin and cloaca, embryos with compromised BMP signaling produce a curious phenotype-a ventrally located secondary tail containing both somitic muscle and notochord. This phenotype is proposed to be a fate-patterning defect when the BMP gradient lowered to a precise level. However, this morphogen mode is insufficient to explain secondary tail formation without considering BMP also regulates morphogenetic movements during gastrulation, promoting the convergence of lateral mesodermal cells towards the dorsal axis. In this study, we provide evidence that BMP signaling continues to mediate cell movements during tail development. Our data indicate that BMP signaling is activated in the ventroposterior tailbud to promote cell migration during tailbud protrusion, and that it is the defective migration of these cells which ultimately leads to bifurcation of the CNH domain, a presumptive stem cell pool in the tailbud, and formation of a secondary tail in BMP mutants. In parallel, the morphogenesis of tailbud cells is known to be under the control of noncanonical Wnt signaling, although the exact nature of the defect remains unclear. We find that inhibition of noncanonical Wnt signaling also leads to secondary tail formation. Additionally, we show that noncanonical Wnt signaling interacts with BMP signaling to maintain CNH integrity by affecting cadherin localization in CNH cells, possibly disrupting cell cohesion. We propose a model that BMP and a noncanonical Wnt pathway regulate tail morphogenesis by controlling cell migration and cell adhesion within the tailbud.

Doctor of Philosophy / Genetics Interdepartmental Program / Bikram S. Gill / Threshability is an important agronomic trait in wheat as free-threshing forms facilitate mechanical threshing of grain. All wild relatives of wheat have tough glumes and are non-free-threshing, whereas most cultivated wheats have soft glumes and are free-threshing. Two genetic loci are known to govern the threshability trait in bread wheat. The Q gene located on chromosome 5AL and glume tenacity genes located on homoeologous group-2 chromosomes seem to interact to produce a free-threshing phenotype. Although, the Q gene was found to be a member of APETALLA 2 (AP2) class of transcription factors, the molecular nature of the tough glume genes remains unknown. In the present study, genetic and molecular characterization of two of the threshability genes in wheat was undertaken. The soft glume (sog) gene of diploid wheat and tenacious glume (Tg) gene of hexaploid wheat were characterized and mapped on short arm of chromosome 2Am and 2D respectively. Comparative mapping of sog and Tg genes suggested their independent origins. The sog gene was mapped in a low-recombination region near the centromere on 2AmS. Genomic targeting using deletion bin mapped ESTs assigned the Tg gene to a 4.9 cM interval in the distal 16% of short arm of chromosome 2D. In order to find additional markers for fine-mapping the Tg gene, macrocolinearity between rice and wheat was explored in the Tg region. Although synteny between rice and wheat was found to be conserved in the distal region of chromosome 2DS, the genomic region encompassing the Tg gene in wheat showed some rearrangements relative to rice. Molecular characterization of ethyl methanesulfonate-induced free-threshing mutants in two different non-free-threshing backgrounds revealed point mutations as well as variable sized deletions at Tg locus. Targeting of Tg to the high-recombination gene-rich region in wheat and availability of several genomic resources from the present study will aid in the cloning and further characterization of this important agronomic gene.

Master of Science / Department of Statistics / Gary L. Gadbury / QTL (quantitative-trait locus) analysis aims to locate and estimate the effects of genes that are responsible for quantitative traits, such as grain protein content and yield, by means of statistical methods that evaluate the association of genetic variation with trait (phenotypic) variation. Quantitative traits are typically polygenic, i.e., controlled by multiple genes, with varying degrees of in uence on the phenotype. Several methods have been developed to increase the accuracy of QTL location and effect estimates. One of them, multiple interval mapping (MIM) (Kao et al. 1999), has been shown to be more accurate than conventional methods such as composite interval mapping (CIM) (Zeng 1994). Other QTL analysis methods have been developed to perform additional analyses that might be useful for breeders, such as of pleiotropy and QTL-by-environment (QxE) interaction. It has been shown (Jiang and Zeng 1995) that these analyses can be carried out with a multivariate extension of CIM (MT-CIM) that exploits the correlation structure in a set of traits. In doing so, this method also improves the accuracy of QTL location detection. This thesis describes the multivariate extension of MIM (MT-MIM) using ideas from MT-CIM. The development of additional multivariate tests, such as of pleiotropy and QxE interaction, and several methods pertinent to the development of MT-MIM are also described. A small simulation study shows that MT-MIM is more accurate than MT-CIM and univariate MIM. Results for real data show that MT-MIM is able to provide a more accurate and precise estimate of QTL location.

Master of Science / Department of Food Science / Elizabeth Boyle / Salmonellosis is one of the most important bacterial foodborne infections in the United States resulting in over 1 million illnesses and 375 deaths annually. Salmonella serotypes cause several types of disease in humans: gastroenteritis, enteric fever, septicemia, focal infections, and an asymptomatic carrier state. Salmonella-shedding pigs are known to constitute a risk factor for contamination of carcasses during the slaughter process. Vaccination has generally not been effective in the prevention of Salmonella, partially because of the rapid mutation rate. Previous research has indicated that >70% of farms tested in Iowa were positive for Salmonella during 2006-2009. Salmonella-colonized pigs are usually asymptomatic carriers of the bacterium and can shed upon exposure to stress causing contamination of pen-mates, trailers used for shipping, and lairage areas at processing facilities. Emergence and dissemination of antimicrobial-resistant pathogens, which antibiotics are commonly used in pig production, have become a public health concern worldwide. For this reason, alternative interventions need to be evaluated for effectiveness. The objective of this report was to determine if there is a genetic basis for host resistance or susceptibility to Salmonella through quantitative and/or molecular selection. Genetic improvement of disease resistance and/or tolerance in animals is a potentially effective intervention for addressing pre-harvest food safety issues. Previous research has demonstrated genetic control of the immune response to pathogens. Developing a strong innate response to infection, so the animal does not become ill or become a carrier, is the basis for a genetic intervention for Salmonella. Quantitative trait loci for humoral and innate immune response have been detected for E. coli through leucocyte counts, cytokine concentration, mitogen-induced proliferation, and levels of pre-infection antibody titers. Single nucleotide polymorphisms have been found and can be exploited for genetic improvement of the innate immune response in pigs when infected with Salmonella. Pigs that differentially express polymorphisms and persistently shed the bacteria versus pigs that do not shed or shed little can be used as criteria for selection when developing the intervention.

Master of Science / Department of Biology / Theodore J. Morgan / The organismal response to temperature represents one of the most ubiquitous processes that occur in the natural world, and this response is critical for survival in most habitats. Increased attention should be focused on how organisms cope with temperature extremes, either through adaptation, plasticity, or a combination of both, as climate models predict increased variations in temperature accompanied by novel thermal extremes. Drosophila melanogaster is an excellent resource for answering questions pertaining to how organisms persist in environmental extremes because they originated in central tropical Africa and have since colonized nearly the entire globe, exposing them to many novel thermal stressors. In this work I elucidated regions of the genome contributing to phenotypic variation in cold tolerance and thermal plasticity. A quantitative trait locus (QTL) approach was used, which involved phenotyping roughly 400 recombinant inbred lines (RILs) of D. melanogaster from the Drosophila Synthetic Population Resource (DSPR). The DSPR captures genetic variation from around the globe, allowing for precision mapping of cold tolerance and thermal plasticity QTL, while simultaneously determining the frequency of the QTL alleles. Upon development at both 18°C and 25°C, RILS were measured for a common cold tolerance metric, chill-coma recovery time (CCR), and a plasticity value was derived as the change in CCR between environments. Analysis of variance revealed significant effects of sex, line (RIL), treatment (temperature), and line by treatment interaction (GxE). Mapped QTL for chill-coma recovery time at 18°C and 25°C spanned the same regions as several studies previously reported, validating the automated phenotyping method used and the mapping power of the DSPR. QTL between CCR at 18°C and 25°C overlapped significantly, and QTL for thermal plasticity shared the similar regions as QTL for CCR, but also exhibited two non-overlapping QTL on the left arm of the third chromosome. This study demonstrated the tremendous amount of variation present in cold tolerance phenotypes and identified candidate regions of the genome that contribute to thermal plasticity and require further investigation.

Master of Science / Department of Biochemistry / Gerald Reeck / Aphids mount a remarkable salivary secretion to overcome plant host defenses. Our group has previously reported a gene unique to aphids enriched in the salivary glands of the pea aphid A. pisum, C002, which is required for successful feeding on its host plant Vicia fava. Here I present an analysis of genetic variation within the available EST data for C002 in pea aphids. From 596 total ESTs, 332 are full-length, and segregate into 8 validated haplotypes based on the criteria I set in place to access the quality of EST data. Additionally, Armet, is a putative multi-functional gene implicated as a neurotrophic factor during development, and as a part of the unfolded protein response during stress. I employ RNA interference in the model organism T. castaneum to determine the effect of transcript knockdown during development from early in-star larval stages, through pupation, and its effect on adult emergence. I report that knockdown of Armet transcript significantly hinders the ability for beetles to emerge from the pupae.

Doctor of Philosophy / Department of Plant Pathology / Bikram S. Gill / Segregation distortion describes the transmission of an allele or alleles of a heterozygous locus at a higher frequency than expected in a Mendelian ratio. From the organism's view, segregation distortion is the preferential retention of chromosomal blocks carrying genes beneficial to its fitness and reproductive viability. In wheat the best studied segregation distortes are those introduced from Aegilops species; these selfish genetic elements are named gametocidal (Gc) genes and the chromosomes carrying them are called Gc chromosomes. This genetic mechanism causes chromosome breakage in gametophytes lacking the Gc carrier chromosome, thus favoring its own retention in the genome. While the mode of action of the Gc genes is not yet known, they have been used extensively in wheat genetics for the development of deletion stocks, a key resource for elucidating the structure of physical regions containing important genes. The objective of this study was to develop the tools necessary to map the Gc2 gene derived from Ae. sharonensis and perform map-based cloning. Extensive physical and genetic mapping located the gametocidal gene on the distal 1% of the 4BL arm present in the T4BS[dot in middle of line]4BL-4S[sh superscript]#1L translocation chromosome. Comparative genomics using rice provided markers distal and proximal to the Gc2 locus; however, synteny broke down at the locus. The characterization of this chromosomal region has provided insight into its recombination frequency, synteny and composition; however, the dynamic architecture of the end of the chromosome has made comparative mapping of this region difficult.

Doctor of Philosophy / Department of Animal Sciences and Industry / David M. Grieger / Early in embryonic development a series of events occur whereby pluripotent cells undergo differentiation to give rise to the three germ layers and extraembryonic tissues of the developing conceptus. Nanog, Sox-2, and Oct-4 genes have been identified as having key roles in maintaining pluripotency in undifferentiated human and mouse cells but recent evidence suggests they may have different roles in farm animals. We cloned the coding sequence for porcine Nanog including 452 base pairs of the Nanog promoter, and partial coding sequences of Oct-4 and Sox-2. Embryos were flushed from sows 10, 12, 15, and 17 days post insemination. RNA was isolated from whole d-10 and -12 conceptuses, d-15 embryonic disk, distal and proximal extraembryonic tissue, and d-17 embryonic disk, distal and proximal extraembryonic tissue, and allantois for real-time PCR. RNA from d-40 maternal myometrium and endometrium, fetal placenta, and liver were also used in real-time PCR. The homeodomain and c-terminal tryptophan repeats are highly conserved in porcine Nanog compared to the mouse, human and bovine. In the promoter, the highly conserved Octamer and Sox binding sequences are also present. The Nanog expression pattern was different when compared to Oct-4 and Sox-2. Day-40 tissues demonstrated the highest expression including endometrium (7 fold) fetal liver (27 fold), placenta (40 fold) and myometrium (72 fold) when compared to day 15 distal extraembryonic tissue. Oct-4 and Sox-2 expression was lowest in d-40 tissues except for fetal liver which was 20 and 71 fold, respectively, higher than endometrium. Oct-4 levels were consistent in d-10, -12, and -15 conceptuses and disk but dropped 3 fold in d-17 disk. On the other hand, Sox-2 was upregulated a 1000 fold in the d-15 disk and 2000 fold in the d-17 disk when compared to the d-12 conceptus. Nanog may have other roles in than maintenance of pluripotency including a possible role in multipotent or progenitor stem cells. Expression of all 3 markers in fetal liver suggests a more primitive cell type is present such as hematopoietic stem cells.

Master of Science / Department of Agronomy / John P. Fellers / Allan K. Fritz / Water availability is commonly the most limiting factor to crop production, especially in drought prone areas like the Midwest. This study was conducted to map quantitative trait loci (QTL) involved in drought tolerance in wheat (Triticum aestivum L.) to enable their use for marker assisted selection (MAS) in breeding. A population of 122 F[subscript]7 derived recombinant inbred lines from a cross between Dharwar Dry and Sitta, spring wheat lines with contrasting drought tolerances, was analyzed using the amplified fragment length polymorphism (AFLP) technique and Diversity Array Technology (DArT) markers to create a QTL map. Of the 256 AFLP primer combinations evaluated, 151 were found to be polymorphic between the parents and were used to screen the population. A linkage map of 48 groups was created from the combined DArT markers, AFLP data, and SSR markers. This was used to create a QTL map which identified QTL in 24 of these groups. Using these markers for MAS in a breeding program could overcome the difficulties of selecting for drought tolerance. Another serious limitation to wheat production is leaf rust caused by the pathogen Puccinia triticina. Leaf rust causes between 1% and 20% yield loss on average and tends to be the worst in years with high yield potential. PI 289824 contains a single, dominant gene for seedling resistance mapping to chromosome 5BS and thought to be different from Lr52. An F[subscript]2 mapping population from a cross between PI 289824 and Jagger was used to try to identify markers very closely linked to the gene and therefore useful for MAS. The population presented some mapping challenges, but with the use of SSR and EST-STS markers, the gene was flanked. However, the markers were at too a great distance to be useful for mapping.