Browsing by Subject "genetic diversity"

Now showing 1 - 3 of 3
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    Genetic and Horticultural Characterization of Hydrangea quercifolia Bartr. (Oakleaf Hydrangea) Throughout its Natural Range of Occurrence
    (2020-06) Sherwood, Andrew
    Oakleaf hydrangea (Hydrangea quercifolia Bartr.) is an understory shrub native to the southeastern United States. The species occupies a small native range, and little is known about its genetic diversity, needs for conservation or range of phenotypic variation for horticultural traits. This study had two primary objectives. 1) To characterize the structure of the genetic diversity throughout the species range and begin to understand what factors contribute to this structure. 2) To characterize variation for horticulturally important traits. Samples were collected from 188 plants in 73 locations throughout the species range and were genotyped using genotyping by sequencing. A Structure analysis identified 6 genetic clusters which are geographically structured. Although these clusters are weakly differentiated, each has unique alleles. An environmental association analysis determined that environmental variables explain 11.3% of genetic diversity while population structure explains 13.5%. Further, 231 putative adaptive alleles were identified, the majority of which are correlated with precipitation related variables, indicating that precipitation has an impact on genetic diversity in H. quercifolia. Many historically documented populations were found to be either extirpated or at risk of extirpation. The genetic clusters on the southern extent of the species range are relatively small and contain putative adaptive alleles at relatively high allele frequencies. This highlights the importance of preserving representative germplasm from throughout the species range. Seed was collected from 55 populations throughout the species range for the horticultural characterization. Seed germination percentage was characterized in a greenhouse and growth chamber. Plant architecture was characterized as plant height, number of nodes, internode length, number of branches and plant width. Plant architecture was measured in potted and field grown plants in two locations. Tolerance to leaf spot (Xanthomonas campestris L.) was characterized in wild collected seedlings and cultivars by measuring disease severity under natural exposure to inoculum. Cold hardiness was characterized in two winters with a controlled freezing experiment. The first winter, seedlings were tested in January only and the second winter seedlings and cultivars were tested monthly throughout winter. Significant variation among wild populations and cultivars was found for all traits measured in all environments. Mean population seed germination percent ranged from 11% to 93% (mean=61% in greenhouse, 74% in growth chamber). Plant architecture varied by environment, with plants growing larger in Tennessee than in Minnesota. Plant height was correlated with collection site latitude (r=-0.66) with populations from the northeastern extent of the species range being the most compact and populations from Florida being the largest. Leaf spot severity varied significantly among populations and cultivars and was also correlated with latitude in the wild seedlings (r=0.70). Two populations in Florida were identified as sources of resistance to leaf spot while ‘Flemygea’ and ‘Alice’ were identified as having moderate tolerance to leaf spot. Cold hardiness varied among populations and cultivars and among months of the winter. Overall maximum cold hardiness was observed in February (mean LT50=-33.7°C), and several populations maintained an extreme level of cold hardiness into late winter. Midwinter cold hardiness also varied by latitude (r=-0.65). These results indicate that certain wild oakleaf hydrangea populations will be useful for introgressing novel variation into breeding programs.
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    Genetic structure and phenotypic differences among and within extant populations of Chrysanthemum arcticum L. and C. a. subsp. arcticum
    (2020-07) Liu, Yunjia
    Chrysanthemum arcticum L., Arctic daisy, (=Arctanthemum arcticum; =Dendranthema arcticum) and its two subspecies (C. arcticum L. subsp. arcticum, C. arcticum L. subsp. polaré Hulten), collectively the C. arcticum species complex, are the only chrysanthemum species native to North America. The species are of interest since they are salt tolerant, growing only along the oceans, with a groundcover habit and may possess other ornamental traits of value to chrysanthemum breeders. However, evidence of decline in species’ range of distribution were detected, which may be reducing the genetic diversity. Understanding the genetic diversity and population structure is important in order to develop conservation strategies and utilize valuable germplasm resources. Thus, we have collected and genotyped 529 genotypes in nine C. arcticum and 21 C. a. ssp. arcticum extant populations from the State of Alaska mainland and Attu Island (the westernmost Aleutian Island). Population genetic diversity was analyzed using 7,449 SNP markers from DArTseqLD. Simultaneously, 16 quantitative morphological traits and 5 qualitative morphological traits were investigated for phenotypic differences. Three distinct genetic clusters were detected by STRUCTURE 2.3.4 within C. arcticum populations and consistent results were obtained with Principal coordinate analysis (PCoA), Discriminant analysis of principal components (DAPC), and the Unweighted pair group method with arithmetic means (UPGMA), while a mixture of subgroups were present in C. a. subsp. arcticum populations genetic cluster analyses, which may be the result of gene flow among close populations capable of gene exchange (Chapter 2). The study on the species’ variation in morphological and diagnostic traits is of importance to enhance diagnostic traits for species identification and link morphological traits with single nucleotide polymorphism (SNP) markers. Soil samples revealed extremely high levels of Na, which confirmed that the species are salt-tolerant. Univariate ANOVAs revealed significant differences among species and morphological traits, similar to the genetic structure analysis for variation among populations within members of the C. arcticum species complex. Overlaps in the genetic cluster analysis for C. a. subsp. arcticum verified the possibility of a higher frequency of gene flow among Attu island collection sites (chapter 3).
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    Influenza Prime-Boost Vaccination, Diversity, And Evolution In Pigs
    (2022-03) Li, Chong
    Swine influenza is an important disease that affects pigs of all ages and impacts swine productivity and public health. Vaccination is the primary measure employed to control the disease, and it is widely implemented in pigs in the United States. However, controlling influenza infections is hard due to the high genetic and antigenic diversity of the influenza A virus (IAV). The continuous evolution and population dynamics of IAVs facilitates its circulation in endemically infected herds. The overall goal of this dissertation was to explore the application of multiple prime-boost vaccination protocols to prevent influenza infections in pigs, and characterize the immune response, the within-host evolution of IAV, and the emergence of novel reassortant influenza viruses in vaccinated pigs compared to unvaccinated pigs. We evaluated different prime-boost vaccination protocols in pigs co-challenged with H1 and H3 influenza subtypes using a seeder pig infection model under experimental conditions. We characterized the immune response, the within-host evolution, and the emergence of novel reassortant influenza viruses in the upper and lower respiratory tracts of pigs with different vaccination statuses. We found that the heterologous prime-boost vaccination protocols provided broader protection against multiple subtype IAVs in pigs. Pigs that received the heterologous prime-boost vaccination protocols showed more favorable disease outcomes than their comparison groups in reducing the number of IAV infected pigs, virus shedding, and inducing humoral immunity. We found that vaccination decreased the risk of influenza reassortment but not genetic variation as measured in the lungs of pigs co-infected with H1 and H3 subtypes. The results of IAV within-host diversity from the swine nasal cavities also showed that vaccination had a limited effect on the evolutionary selection processes across the entire IAV genome, possibly due to the short longevity of IAV infection in individual pigs. However, vaccination may have shifted the selection patterns of IAV variants at specific amino acid sites during the infection process. Besides, a large proportion of IAV variants generated in the pigs became lost during transmission events among immune pigs of the same room. In addition, we observed that multiple subtype IAVs could infect pigs consecutively and concomitantly, which facilitated virus reassortment and altered variant selection by flipping the interaction of the suite of mutations (epistasis), finally changing the overall diversity of virus populations in pigs. The studies in this dissertation revealed a tangled relationship between IAV vaccination, diversity, and evolution in pigs. The knowledge generated from this thesis will help design more effective IAV surveillance and control programs in pigs worldwide and prevent infections between pigs and people.