2019 ASHS Annual Conference

Complex changes in gene expression occur during postharvest storage of tree fruits and often precede or accompany changes in ripening and disorder development. Targeted gene expression analysis fundamentally relies upon prior knowledge of the targeted gene. In an effort to improve this prior knowledge, we developed a workflow that leverages transcriptome data to discover cultivar-specific gene sequences and then guide primer design for quantitative real-time polymerase chain reaction (qPCR). We find that potentially problematic polymorphisms occur frequently in genes of interest when candidate primer binding sites were selected using a mismatched reference genome. These polymorphisms can be accounted for when utilizing transcriptome data from the target cultivar. We applied our work flow to another tree fruit, Pyrus communis, for qPCR validation of RNA-seq data generated from ‘D’Anjou’, but analyzed using the ‘Bartlett’ reference genome.