Application of workflow designed to leverage transcriptome data for enhanced gene expression analysis in tree fruits

Authors: Hargarten, Heidi; SCHMIDT, REBECCA - FORMER ARS EMPLOYEE; KAHN, ELENA - FORMER ARS EMPLOYEE; Honaas, Loren

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/29/2018
Publication Date: 7/21/2019
Citation: Hargarten, H.L., Schmidt, R., Kahn, E., Honaas, L.A. 2019. Application of workflow designed to leverage transcriptome data for enhanced gene expression analysis in tree fruits. Plant and Animal Genome Conference. Meeting Abstract.

Interpretive Summary:

Technical Abstract: 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 using apple cultivars, leveraging publicly available transcriptome data to discover cultivar-specific gene sequences to guide primer design for quantitative real-time polymerase chain reaction (qPCR). We find that problematic polymorphisms occur frequently in cultivars of interest when candidate primer binding sites were selected using a reference genome of a different cultivar. These disruptive, cross-cultivar polymorphisms can be avoided when utilizing transcriptome data from the target cultivar. We validated our work flow with another tree fruit, Pyrus communis, and developed cultivar specific ‘D’Anjou’ qPCR primers selected ab initio from de novo assembled transcripts, to validate RNA-Seq data generated using a ‘Bartlett’ reference genome.