Sour cherry (Prunus cerasus L., 2n = 2x = 32) is an allotetraploid fruit tree species native to Eastern Europe that resulted from the interspecific hybridization between the tetraploid ground cherry P. fruticosa Pall. (2n = 4x = 32) and the diploid sweet cherry P. avium L. (2n = 2x = 16). Sour cherry has been cultivated by humans for thousands of years, and the ability to clonally propagate through budwood cuttings means that many landraces have persisted for over 400 years and therefore their parental origins are unknown. Previous research on both crop and model polyploid species has shown that one subgenome of an allopolyploid may dominate the other(s) through a number of processes including gene expression bias and homoeologous exchanges and replacements favoring one subgenome over generations. By comparison, the subgenome dynamics of sour cherry have yet to be characterized. In the first chapter of this dissertation, I review the history of sour cherry, from the wild origins in Eastern Europe and Western Asia to the sour cherry industry in the US today, the current literature on polyploidy and its consequences for plant genomes and crop improvement, the progress made so far on sour cherry breeding and genetics in the modern era, and I give a brief overview of fruit development physiology for this crop. In the second chapter I present the first-ever reference genome of sour cherry, a chromosome-scale assembly of the sour cherry cultivar Montmorency that reveals three subgenomes, two inherited from the polyploid progenitor P. fruticosa (newly discovered to be allopolyploid, not auto- as previous literature suggests), and one inherited from the diploid progenitor P. avium. I was able to differentiate the subgenomes based on kmer content and further demonstrate the ancestral origin of the subgenomes through coding sequence phylogeny of a set of dormancy-associated MADS box genes associated with bloom timing in Prunus. The third chapter investigates the subgenome dynamics of a panel of four sour cherry landraces and two bred cultivars by examining homoeolog dosage and overall subgenome expression bias. I identified 24 unique homoeologous exchange events in three of the six accessions, five whole-homoeolog replacements in two of these three accessions, and subgenome expression bias in favor of the ground cherry-derived A and A’ subgenomes over the sweet cherry-derived B subgenome in all of the accessions. I partially validated the subgenome dosage of each accession using the previously-characterized S-alleles and demonstrated the implications of subgenome dosage and expression bias for a set of four expansins previously associated with fruit softening in sour cherry. Altogether this work represents substantial progress in genome resources and application of genomics techniques for sour cherry and a unique addition to the body of work on polyploid genomics.
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