Abstract
BackgroundGrape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.ResultsWe performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.ConclusionThe three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1442-3) contains supplementary material, which is available to authorized users.
Highlights
Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production
Through functional analysis of the cis-natural antisense transcript (cis-Natural antisense transcripts (NATs)) pairs we identified in the three Chinese wild grapes, we found those related to abiotic stress responses were significantly enriched
The enrichment of stress-related processes in distinct genes is consistent with the hypotheses that wild plants, which are often exposed to an adverse environment, such as extreme temperatures, aberrant pH, toxic chemicals and pathogens, tend to have accelerated adaptive evolution of stress genes [52], while during domestication, a large number of stress and defense-related genes are lost in the cultivated species, which might be due to the many years of cultivation and selection that have focused on desirable fruit qualities at the expense of disease resistance [6]
Summary
Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Grapes are among the most valuable fruit crops, grown on about 7 million ha with an annual production of approximately 67 million tonnes worldwide [1]. There are over 60 species of Vitis around the world [2] and Vitis vinifera is the most widely planted grapevine. Jiao et al BMC Genomics (2015) 16:223 high genetic diversity from wide progenitors [8]; most European cultivars are susceptible to many fungal diseases. The widely planted grape cultivars are very sensitive to diverse pathogens. Genetic engineering of disease resistance in grape has become an increasing need and this can be facilitated by the use of wild Vitis resources
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
