The Hunt for Adaptive Variation in Wild Grapevine; Sequencing, Assembly, and Annotation of North American Vitis Reference Transcriptomes

Wild grapevine species play an important role in the development of grapevine varieties for regions where environmental stresses limit production.  As climate change impacts current production regions, hybrids produced between cultivated and wild species will likely play a major role in the stability of the grapevine industry in environmentally marginal production regions.  In an effort to better utilize wild grapevine species for trait identification and cultivar development, we have constructed de novo reference transcriptomes for wild grapevine.  The reference collection includes multiple genotypes of seven important wild species; V. aestivalis (3), V. amurensis (2), V. cinerea (3), V. labrusca (3), V. riparia (3), V. rupestris (4), and V. vulpina (3).  Multi-tissue libraries were constructed from leaf, root, bud, tendril, rachis, flower, unripe berry, and ripe berry tissues.  In addition to these environmentally untreated samples, leaves from one genotype of each species was subjected to both a chilling and a freeze treatment. Samples were sequenced on a HiSeq2500 for 100bp paired-end sequencing producing between 118M-212M reads per species.  Sequence reads were assessed for quality and the Trinity analysis pipeline was used to generate reference transcriptomes.  BLAST and BLAST2GO were used to annotate contigs, cluster genes, and identify homologs between species.  Results of the project to date indicate contig alignment and annotation to 92% of the predicted V. vinifera transcripts present in the V2-annotation.  In parallel, the STAR and GATK pipelines were used to assess genetic variation and identify SNP loci from the transcriptomes of these genotypes.