Transcriptomic Analysis of ‘Garnem’ Rootstock By RNA-SEQ Reveals Genes and GENE Ontologies Involved in Drought Response

In light of new environmental conditions, accentuated by climate change, the impact of drought on agriculture has become critical. There is now a pressing need to select drought tolerant rootstocks that can adapt to limited water availability. Currently, molecular information about the response of Prunus rootstocks to drought stress is limited. We performed a time course RNAseq-based transcriptome analysis of roots in an almond x peach hybrid [P. amygdalus Batsch, syn P. dulcis (Mill.) x P. persica (L.) Batsch] using an Illumina platform. To induce drought stress, plants of ‘Garnem’ genotype were subjected to a PEG 6000 solution. Root samples were collected from control and stressed plants at 0, 2 and 24h for transcriptome analysis. Transcriptome data were assembled into contigs, which were mapped against the P. persica reference genome (v 2.0) for 0h control, 2h control, 2h stress, 24h control and 24h stress time points. We conducted pairwise comparisons between control and stressed samples and the different time points. RPKM values were calculated, and genes with at least a five-fold difference in expression in each of the pairwise comparisons were functionally annotated using Blast2GO. The analysis revealed gene ontology and signalling pathway information about the significantly up- and down-regulated genes during drought response. qRT-PCR validation of RNAseq results was conducted for 16 genes. Finally, an orthologous study was conducted with different plant species in order to understand the evolutionary process of these validated genes. Phylogenetic trees generated using a maximum-likelihood approach revealed different evolutionary patterns for genes of interest.