Browsing by Subject "Breeding"
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Item Genomewide Selection in Apple: Prediction and Postdiction in the University of Minnesota Apple Breeding Program(2019-10) Blissett, ElizabethAlthough marker assisted breeding is now considered routine in apple breeding programs, the adoption of genomewide selection is still in its infancy. Genomewide selection offers the potential to be a valuable tool to apple breeders. The first aim of this research was to assess the predictive ability of genomewide selection for fruit traits by testing an additive prediction model, a model fitting heterozygote effects, and a model fitting fixed effects for major QTL. The second aim of this research was to assess the utility of genomewide selection for fruit traits in the University of Minnesota apple breeding program. This comprised two main objectives, a comparison of selections based on genomewide predictions to selections made based on phenotypic selection and an analysis of the impact on predictive ability when full-sibs are included in the training data. This research finds that in general, a simple linear model is the most efficient choice for genomewide selection in apple unless major effect QTL are known, in which case including them as fixed effects may improve predictive abilities. We also confirmed that predictions made based on genomewide selection to be consistent with selections based on traditional phenotypic selection and that including five to 15 full-sibs from the test population in the training population data can improve predictive ability.Item Genomic provenance and genetic providence in domesticated barley(2015-08) Poets, AnaIn the context of plant improvement, it is important to identify the sources of genetic diversity that are available for use, and to understand how current genetic diversity is being utilized. Comparative population genetic analyses provide a means of identifying new sources of genetic variation as well as changes in allele frequencies governed by selection or demographic processes. Considering the broad geographic distribution of both wild and cultivated barley, it is likely that many traits have multiple origins. Thus, the identification of the source population that contributed to a specific chromosomal region in landraces can help identify genetic variants that contribute to agronomic traits. In Chapter 1, I use genotyping data for a set of 803 barley landrace and 277 wild barley accessions to address two primary questions (i) Do specific wild populations contribute disproportionately to barley landraces?, (ii) does the genetic contribution of wild populations to landraces vary across the genome or across the broad geographical range of landrace cultivation? I find that multiple wild populations contributed to the genetic composition of the landraces. Their contribution differs across the genome and across the geographic range. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to landraces. Barley was introduced to North America (NA) by early European colonist as early as 1602. Adaptation to diverse environments has involved many generations of selection towards ideal phenotypes. In Chapter 2, I analyze a data set comprised of 3,613 barley accessions representative of NA barley breeding programs. I aim to determine: (i) the patterns of recents and long-term selection, (ii) assess the effects of drift and linked selection, and (iii) identify the extent of gene flow among barley breeding programs. I identify loci known to be controlling major traits and a series of loci putatively involved in recent and older bouts of selection. There is clear evidence of genetic drift and linked selection acting in these populations. There is evidence of possible gene flow among populations with similar growth habit and inflorescence type.Item Identification and Characterization of Important Quantitative Trait Loci for Soluble Solids and Titratable Acidity for Germplasm in the University of Minnesota Apple Breeding Program(2020-12) Miller, BayleeApple fruit acidity and sweetness are two of the major trait components involved in apple seedling sensory evaluation. Published studies have alluded to some of the genetic components of apple fruit acidity and sweetness, but few have included an array of germplasm relevant to the University of Minnesota apple breeding program. With the release and subsequent frequent use of ‘Honeycrisp’ and ‘Minneiska’ apple cultivars as parents at the University of Minnesota, the germplasm set deviates from other breeding programs. In order to increase breeding efficiency and increase overall quality of apple seedlings, this study describes the genetic components of apple fruit acidity and sweetness and provides breeding insights to negate the creation of undesirable apple seedlings. This study uses data from 2010 to 2018 to characterize a wide but relevant array of germplasm, using six major families, three of which have ‘Honeycrisp’ as a parent, and three of which have ‘Minneiska’ as a parent. Three major loci associated with variation in titratable acidity content on linkage groups 1, 8, and 16, and two loci associated with variation in soluble solids content on linkage groups 1 and 13 were identified, and haplotypes were characterized for each locus. The conclusions from this study provide insights for designing crosses that create seedlings with desirable ranges of acidity and sweetness characteristics.Item Riparian bird communities along an urban gradient: effects of local vegetation, landscape biophysical heterogeneity, and spatial scale(2008-12) Pennington, Derric NevilleUrbanization is an important driver of ecosystem change that can have deleterious effects on regional native biodiversity. Yet we know little about the potential value of urbanizing areas for maintaining local and regional species diversity. Few studies have explicitly examined how the spatial arrangement and composition of biophysical elements within a metropolitan area contribute to the structure and composition of urban biodiversity. This thesis focuses on avian community responses and uses observational studies that consider local vegetation and landscape factors in order to further understanding of the ecological and conservation implications of urbanization across multiple temporal and spatial scales. A synthesis of three urban systems demonstrates the usefulness of gradient analysis approach for understanding fine-and coarse-scale processes influencing urban bird distributions. Results illustrate differences between two urban-to-rural gradient paradigms and the importance of conducting investigations at multiple spatial, temporal and biological scales. Recommendations are provided to improve our understanding of urban bird communities using gradient analyses and emphasize the future need to derive a common framework that incorporates the biophysical and social heterogeneity of urban systems. An urban gradient study of riparian bird communities within metropolitan Cincinnati, Ohio during spring migration found that bird species responses varied based on migratory strategies and across spatial scales. Long-distance Neotropical migrant species density, richness, and evenness responded most strongly to landscape and vegetation measures and were positively correlated with areas of wide riparian forests and less development within 250 m. Resident Neotropical migrants density, richness, and evenness increased with wider riparian forests (> 500 m) without buildings, while en-route migrants utilized areas having a wide buffer of tree cover (250 to 500 m) regardless of buildings; both resident and en-route landbirds were positively associated with native vegetation composition and mature trees. To better understand the relative importance of proximate versus landscape features and the influential spatial scales of these landscape features, I focused on breeding riparian bird species and the influences of two biophysical features of the urban environment - vegetation and built elements - within 1 km for the same riparian study area. At the proximate scale, native tree and understory stem frequency were the most important vegetation variables; native tree frequency had a positive influence on 35 species and a negative influence on 13 of the 48 species and native understory frequency had a positive influence on 27 species and a negative influence on 21 species. At the landscape scale, the vegetative features (both tree cover and grass cover) were most important variables included in competitive models across all species; tree cover positively influenced 15 species and negatively influenced 5 species and grass cover positively influenced 22 species and negatively influenced 5 species. Building density was an important variable for 13 species, and positively influenced 6 species and negatively influenced 7 species. In a comparison of multiple scales, models with only landscape variables were adequate for some species, but models combining local vegetation and landscape information were best or competitive for 42 of the 44 species. Local-vegetation-only models were rarely competitive. Combined models at small spatial scales (≤ 500 m) were best for 36 species of the 44 species and these models commonly included tree cover and building density. Only eight species had best models at larger scales (> 500 m); grass cover was most the important variable at larger scales. In conclusion, understanding the processes that create repeatable patterns in urban bird distributions is a challenge that requires investigation at multiple spatial, temporal, and biological scales. These findings provide managers and land-use planners with species-specific information and emphasize the importance of acknowledging both proximate and landscape influences in habitat modeling.Item Uncovering Hidden Phenotypes to Accelerate Domestication in Perennial Ryegrass for Seed Production(2022-10) Barreto Ortiz, JoanSeed dispersion, shattering, shedding, and lack of retention, all refer to the same dispersal mechanism in which reproductive organs detach from plant inflorescences upon maturity. This separation, or disarticulation, is mainly attributed to the development of an abscission layer which is genetically programmed. However, such detachment is just part of the seed dispersal phenomenon determined by a network of interactions between biotic and abiotic agents allowing gene flow over space and time. Understanding the genetics underlying seed dispersal has ecological and agricultural implications; while this phenomenon grants an evolutionary advantage to wild plants, it affects crop productivity and domestication of species with economic potential by severely reducing seed yield. In consequence, variation for dispersal-related traits has been selected over millennia through improving seed retention and yield, thus allowing the development of agriculture and consequent human societies. Nevertheless, genetic correlations among traits can limit the progress of selecting for a dispersal trait and generate unfavorable trade-offs. The presence of these correlations can be attributed to (i) the univariate approach that characterizes both selection methods and the study of multivariate phenotypes like inflorescence architecture and seed dispersal, and (ii) our limited ability to perceive and quantify the multidimensional phenotypic reality. These are the two foci of this introductory chapter, in which I use perennial ryegrass (Lolium perenne L.) as an example to discuss the need for a holistic understanding of the relationships between inflorescence morphology and seed dispersal, with an ultimate goal to improve seed yield and plant domestication.