Comparative Transcriptomics of Two Grapevine Species

A fundamental goal of my research program is to understand the genomic basis of adaptation to the abiotic environment in long-lived plant species.  To this end, we are studying two North American grapevine species, Vitis riparia and V. rupestris, close relatives that have diverged morphologically, genetically, and with respect to the environmental variables characterizing their geographic ranges.   To understand divergence in response to abiotic conditions, we conducted an RNA-seq experiment in a common garden that included three clones each of three V. riparia genotypes and three V. rupestris genotypes.  Leaves were frozen on site, and RNA extraction, cDNA library construction, and single-end sequencing were completed separately for each clone at each time point. Transcript abundances among species, among genotypes, and across time points were compared using Welch’s T test under default and conservative parameter sets.  Results identified gene regions that were consistently differentially expressed in all accessions of V. riparia and V. rupestris at both time points, providing a window into species level differences.  Comparisons among time points revealed considerable, species-specific temporal variation in gene expression. Sequence variation underlying differentially expressed transcripts displayed contrasting mutation patterns in high-abundance transcripts in V. riparia vs. V. rupestris. Taken together, these data provide evidence for genomic differentiation and gene expression differences among V. riparia and V. rupestris, close relatives adapted to unique abiotic conditions in nature.  Because V. riparia and V. rupestris are commonly used rootstock species, basic science reported here may have applications in rootstock use strategy and breeding.