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.
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 component include generation of comprehensive gene expression data for as many apple genes as possible during various storage regimes and pre-storage treatments that might impact later presentation of fruit storage disorders. In FY 2011, we have adapted RNA isolation and gene expression profiling techniques to apple and have completed the first of several planned treatments/gene expression profiling experiments. Data analysis from this first experiment is in progress. This project is in all respects on schedule and on budget. We do collaborate with researchers on the Cornell campus and with the USDA-ARS in Washington State who provide fruit tissues and perform storage treatments. One project meeting and multiple electronic meetings were held over the course of the year to insure project activities started asp planned and remained on track, problems were addressed and all project participants were current on activities occurring in cooperating laboratories. Project participants including project leaders and key technicians, postdocs and graduate students involved in the project meet quarterly via conference calls. Regular meetings between the leaders of the Ithaca, Cornell and Washington project leaders, phone conversations and email are used on a frequent basis as needed to address questions, technical problems, or to plan next steps when milestones are reached.