The performance of hybrid progeny of outcrossing parents for a variety of important agronomic traits can be highly variable and differ substantially from the performance of either parent. Luxury commodities, such as strawberry, more than staples, have to find that balance been fruit quality (demand) and production quantity (supply). Strawberry breeding programs and other specialty crops have long relied on the production of superior hybrid progeny for success. Despite the cloud of mystery surrounding the intra-specific hybrid origins and complicated breeding history of cultivated Garden Strawberry (Fragaria x ananassa) and the importance of producing transgressive hybrid progeny, there is no consensus on the relevance or prevalence of heterosis in strawberry breeding programs. We have used a large collection of first-generation hybrids to characterize the genetics of heterosis in a commercial important population of strawberry.
The emergence of high-throughput, genome-scale approaches for identifying and genotyping DNA variants has been a catalyst for the development of the increasingly sophisticated whole-genome association and genomic prediction approaches, which together have revolutionized the study of complex traits in animal and plant populations. These approaches have uncovered a broad spectrum of genetic complexity across traits and organisms, from a small number of detectable loci to an unknown number of undetectable loci. The heritable variation observed in a population is often partly caused by the segregation of one or more large-effect (statistically detectable) loci. In chapter 1, I explored the consequences of inaccurate variance component estimation procedures and proposed a straightforward mathematical correction factor (kM) that depends only on degrees of freedom and the number of entries, is constant for a given experiment design, expands to higher-order genetic models in a predictable pattern, and yields bias-corrected estimates of marker-associated genetic variance and heritability.
Shape is a critical element of the visual appeal of strawberry fruit and influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is an inherently multi-dimensional, continuously variable trait, and not adequately described by a single categorical or quantitative feature. Morphometric approaches enable the study of complex, multi-dimensional forms but are often abstract and difficult to interpret. In chapter 2, I developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the Principal Progression of k Clusters (PPKC). We use these human-recognizable shape categories to select quantitative features extracted from multiple morphometric analyses that are best fit for genetic dissection and analysis. I generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches we applied in strawberry should apply to other fruits, vegetables, and specialty crops.
Genetic gains for yield have been dramatic in strawberry, an outcrossing allo octoploid, and have played a pivotal role in the expansion of production over the last half-century. Superior progeny of out-crossed parents in closed breeding programs are a necessity of the long-term longevity of such programs and the ubiquity of transgressive hybrid phenotypes has interested biologists for over a century and is of importance throughout crop species. Despite evidence for strong directional selection for high yielding cultivars, genetic improvement continues to an effective method to advance crop yields in this highly heterozygous species hypothesized to harbor significant genetic load. In chapter 3, I exposed the complex genomic architecture of yield and heterosis and revealed a putative heterozygosity Goldilocks zone of high performing hybrids, indicating a large genetic load of unfavorable alleles that breeders must constantly act balance with the presence of masking alleles or by concentrating the number of favorable alleles. These results suggested that strawberry breeders have had to strike a balance between the pressures of both inbreeding and outbreeding depression in order to produce novel breeding lines and cultivars. Our analyses underscore the importance of non-additive effects as a principal factor in determining variation in quantitative traits and provides a means to uncover the genetic architecture yield and heterosis in strawberry. Knowledge of the genetic architecture of quantitative traits contributes to our understanding of culturally and agronomically important traits and enhance the ability to make genetic gains.
|Advisor:||Knapp, Steven J.|
|Commitee:||Ross-Ibarra, Jeffery, Runcie, Daniel E., Tabb, Amy|
|School:||University of California, Davis|
|Department:||Horticulture and Agronomy|
|School Location:||United States -- California|
|Source:||DAI-B 82/5(E), Dissertation Abstracts International|
|Subjects:||Plant sciences, Genetics, Agriculture, Morphology, Bioinformatics, Horticulture|
|Keywords:||Heterosis, Morphometrics, Quantitative genetics, Strawberry fruit breeding, Variance components, Genomic prediction|
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