Location: Crops Pathology and Genetics Research
Project Number: 2032-22000-016-045-T
Project Type: Trust Fund Cooperative Agreement
Start Date: Oct 1, 2018
End Date: Dec 31, 2019
Objective:
1) Extract and sequence small RNA profile of almond trees exhibiting noninfectious bud failure.
2) Conduct bioinformatics analysis of the small RNA fraction.
Approach:
ARS scientist will collect shoots from Nonpareil and Carmel almond trees exhibiting BF and from control NonPareil plants without BF. Shoot samples will be collected from four trees at four seasons; spring, summer, fall and winter. This will provide us 64 samples. Collected samples will be stored at -800C.
Small RNA fraction will be isolated following the methods described in Chellappan et al., (2009) and cDNA Libaries will be generated for sequencing using Illumina platform.
We will map quality-filtered sRNA reads to coding-regions (ca. 27,852) and noncoding RNAs of peach (P. persica) genome (International Peach Genome Initiative et al., 2013) using the Burrows-Wheeler Aligner (BWA) and identify differentially expressed transcripts using Cufflinks (Trapnell et al., 2012). From this analysis, we will identify differentially regulated genes or sRNAs between BF trees compared to control. We will validate results of differentially expressed genes or sRNAs using real-time RT-qPCR.
