LINKING GENES AND PHYSIOLOGY UTILIZING GENOMICS AND TRANSCRIPTOMICS APPROACHES IN SWEET CHERRY (PRUNUS AVIUM)
Koepke, Tyson Andrew
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Sweet cherry is an important horticultural crop in Washington. Sweet cherry trees are grown as composite plants where the scion is grafted onto a rootstock. Rootstock genotype influences tree yield potential (among other traits) largely by affecting floral bud numbers. A transcriptomics approach (differential display and 3'UTR sequencing) was used to examine the genetic mechanism of the rootstock's effect on floral bud initiation.The first section of this dissertation outlines the development of key genomic resources for sweet cherry. Utilizing both reference mapping and de novo genome assembly for the sweet cherry variety `Stella', 1.5 million single nucleotide polymorphisms were identified and 180Mb of genome were assembled respectively. The identified polymorphisms were screened and roughly 300,000 are located in peach genes and could be used as gene-based markers for future research. From this set, several genes involved in fruit ripening were found to contain nonsense mutations and could be the underlying cause for non-climacteric ripening in sweet cherry. Examining gene expression in developing floral buds of the scion, rootstock effects were identified through differential display and 3'UTR analyses. Differential display identified 207 transcripts that were putatively controlled by the rootstock genotype while 3'UTR identified 115 differentially expressed gene fragments. Several transcription factors including some with domains previously documented to control flowering were identified in these datasets and their expression levels were examined via qRT-PCR for verification.These studies have created vast amounts of information from both the sweet cherry genome and transcriptome. Many single nucleotide polymorphisms were identified and leveraged as DNA markers for screening sweet cherry populations. This demonstrated the rapid application of a small subset to aid sweet cherry breeding and population screening. Additionally, a computational program was developed to assess restriction sites in large datasets and used to convert the polymorphism information into cleaved amplified polymorphic sequence markers.Overall, the work described in this dissertation has laid the foundation for sweet cherry genomics research and identified several directions for future studies.