Location: Plant, Soil and Nutrition Research2012 Annual Report
1a. Objectives (from AD-416):
To identify gene expression patterns specific to individual disorders which can be developed into biomarkers for predicting apple fruit disorders, thus determining storage plans for fruit held in controlled atmosphere storage.
1b. Approach (from AD-416):
Facilitate RNAseq transcriptome analysis of apple tissues under conditions conducive to apple fruit postharvest disorders. We will harvest apple tissues, extract mRNA, create primer-tagged cDNA libraries, sequence said libraries via Illumina HighSeq, sort and trim sequences and process for quality, map to the public apple genome sequence and determine expression patterns via read counting. Resulting data will then feed into the larger NIFA funded apple consortium project for selection and development of biomarkers.
3. Progress Report:
This project is part of a broader multi-institutional effort directed toward eventual development of diagnostic tools for predicting apple fruit storage disorders negatively impacting fruit appearance or quality so that decisions can be made regarding optimal use of specific apple storage lots. For example, apple storage lots showing markers for late term apple fruit disorders might be targeted for early fresh use or sent to the processing stream if stored for a longer period so as to recover maximal product benefit. Specific activities under this project include testing of candidate gene expression patterns that may serve as early warning markers for various storage regimes and pre-storage treatments that might impact later development of fruit storage disorders. In the current year, we have developed extensive whole genome profile data from apples of various varieties and under a range of storage conditions and durations. We have identified a number of candidates for disorder marker use. These genes were then used to develop gene-specific probes for confirmation experiments designed to test their utility. This project is in all respects on schedule and on budget and indeed has exceeded objectives as advances in sequencing technology has allowed us to test more varieties, treatments and durations of storage than originally proposed.