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Title: A phylogenomic analysis of the grape genus (Vitis) reveals broad reticulation and concurrent diversification during quaternary climate change

Author
item WAN, YIZHEN - Northwest Agricultural & Forestry University
item Schwaninger, Heidi
item Baldo, Angela
item Labate, Joanne
item SIMON, CHARLES - Former ARS Employee
item Zhong, Gan-Yuan

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/28/2013
Publication Date: 7/5/2013
Citation: Wan, Y., Schwaninger, H.R., Baldo, A.M., Labate, J.A., Simon, C., Zhong, G. 2013. A phylogenomic analysis of the grape genus (Vitis) reveals broad reticulation and concurrent diversification during quaternary climate change. BMC Evlutionary Biology. 13:141.

Interpretive Summary: Grapes (Vitis vinfera) are the world’s most valuable fruit crop with many healthful properties that are of great interest to the consumers and the public. Grape crops are under strong pest and disease pressure and restricted by abiotic factors such as cold temperatures. The genus contains upward of 60 wild species relatives that harbor genes to resist these challenges and also genes for novel fruit characteristics. To better conserve and utilize these genetic resources for grape improvement, we studied the genetic structure, relationships, and evolutionary history of the genus. We compared 309 DNA sequences composed of 27 gene fragments of 43 species and found that grapes formed a well connected gene pool until it fragmented due to climatic and tectonic changes about 1.8 million years ago. The major groups differentiated, adapted to their local conditions and formed the Asian, European and North American centers of diversity. We identified candidate markers for species identification and corrected the names of a number of misidentified accessions in the USDA-Agricultural Research Service Vitis Clonal Repositories maintained at Davis, California and Geneva, New York, respectively. Our results reveal the existence of tremendous amount of genetic wealth in the genus to be exploited for grape improvement, and provide valuable knowledge for species delineation, germplasm conservation and utilization.

Technical Abstract: Grapes are the most economically important fruit crop. Long-term sustainability and improvement of this crop depend on genetic prospecting for traits in the wild species all of which are facilitated by understanding phylogenetic relationships. This is the first comprehensive study to date that uses genomic DNA sequence to elucidate 1) a phylogenetic hypothesis of the genus Vitis, 2) the tempo and mode of evolution within Vitis, 3) the systematics of Vitis spp. in the light of phylogeny and biogeographic history, and 4) a framework for species delineation, germplasm conservation and use. We selected 309 accessions from 43 Vitis species and four outgroups drawn from across the genus’ native northern hemisphere distribution, examined ~11 kb of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times (Ks). The 38-chromosome Vitis were a strongly supported monophyletic clade, there was substantial support for species, and less for the higher-level groupings. The initial divergence of the 38-chromosome ingroup from the 40-chromosome outgroup occurred ~ 3 Ma while the ingroup clade divergences occurred about 1.8 Ma, suggesting fragmentation of ancestral range, differentiation of species in the context of Quaternary tectonic and climatic changes and adaptations to environmental heterogeneity. Tenuous evidence suggested a distributional trend from North America to Asia. Network analysis suggested broad reticulation across the Vitis ancestral gene pool and extending into recent times may have contributed to today’s reproductive compatibility within the subgenus. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications such as series, reveal the tremendous amount of genetic wealth in the genus to be exploited for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.