Differential Cacao Cultivar Gene Expression with RoDEO

Moniliophthora roreri, a fungal pathogen of cacao, causes frosty pod (FP) disease where fungal mycelial growth on the pod appears similar to frost.  To identify genes that could be critical to resistance to FP, we performed a time course of inoculation of a susceptible cultivar (Pound 7) and a resistant cultivar (UF273) with FP conidia. 

Pods on the trees were inoculated or mock inoculated, harvested at 8, 24 and 48 hours, RNA was isolated and sequenced on an Illumina HiSeq. 

The gene expression data were analyzed with RoDEO (Robust Differential Expression Operator), see http://researcher.watson.ibm.com/project/5513. RoDEO employs a non-parametric method assessing stable as well as differentially expressed genes, and is particularly resilient when dealing with a limited number of replicates. 

We observed robust cultivar-specific expression patterns that persist across time points and individuals plants. In addition, we identified genes whose expression is consistently different between the two cultivars, including genes linked to disease resistance.