Polyploidy, or the presence of three or more complete genomes in a single organism, has occurred frequently in plants, especially in the angiosperm lineage. Allopolyploids, or polyploids resulting from the merging of different genomes in an interspecific hybrid, have often been shown to experience subgenome dominance. Subgenome dominance is the phenomenon where there is bias in the gene loss and expression between the different genomes in a polyploid, known as subgenomes. Despite the prevalence of polyploids and subgenome dominance, little is known about the factors and mechanisms that influence this process. Strawberry (Fragaria sp.) is emerging as a powerful model system to investigate polyploid subgenome dominance evolution due to the recent identification of the four extant diploid progenitor species of the cultivated octoploid strawberry (Fragaria x ananassa). Having the diploid progenitors in hand allows us to identify differences between the dominant subgenome, F. vesca, and the other three progenitors that may have an impact of subgenome dominance. One possible factor is transposable element (TE) abundance, as low TE density has been consistently associated with the dominant subgenome in allopolyploids. Epigenetic silencing of TEs by DNA methylation to suppress TE activity has been shown to result in decreased expression of neighboring genes and this lowered gene expression may affect the establishment of subgenome dominance. F. vesca will be used as a diploid model for the study of subgenome dominance in strawberry where I can examine how TE abundance and other factors influence gene expression in a single accession and in hybrid crosses between different accessions. Tracking changes in gene expression in the hybrids will allow us to examine how genomes with difference sizes and genomic factors interact. The results and insights observed from this study can then be applied to subgenome dominance research in octoploid strawberry. In addition to the germplasm and genomic resources, strawberries are also a high value crop and the loss of their production due to (a)biotic stressors results in the loss of millions of United States dollars annually. Using a population of octoploid strawberries segregating for salt tolerance, I will identify candidate genes related to salt tolerance. Together this work will identify factors and mechanisms related to subgenome dominance and use genotypic data in a practical breeding context.
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