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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #348458
Title: High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections

Author
item KLEIN, LAURA - St Louis University
item MILLER, ALLISON - St Louis University
item CIOTIR, CLAUDIA - St Louis University
item HYMA, KATIE - Cornell University
item MIGICOVSKY, ZOE - Dalhousie University
item URIBE-CONVERS, SIMON - University Of Michigan
item Londo, Jason

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2018
Publication Date: 3/12/2018
Citation: Klein, L., Miller, A.J., Ciotir, C., Hyma, K., Migicovsky, Z., Uribe-Convers, S., Londo, J.P. 2018. High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. American Journal of Botany. 105(2):215-226.

Interpretive Summary: Grapes are one of the most economically important fruit crops worldwide, with the vast majority of production derived from a single, Mediterranean species, Vitis vinifera. Expansion of grapevine production into new regions such as the North and Eastern portions of the United States, as well as changing pressures from changing climate makes growing V. vinifera challenging. As a result, grapevine breeders hybridize V. vinifera with wild grapevine species to incorporate new adaptive traits. Genetic relationships between grapevine species have long been a topic of study but relationships between species remain unclear. This study was performed to addresses these issues by examining the living collections of wild grapevine maintained by the USDA-ARS germplasm repository system using 11,020 genome wide genetic markers. Analysis of the genetic relatedness of these samples confirms that the genus Vitis arose as a single evolutionary process (monophyly) as well as seperates species and species groups within the North American clade. In addition to providing this evolutionary framework for wild grapevine species, the results of this study were used to help assign species names to previously unknown vines growing in the germplasm as well as correct misidentified accessions. This work provides the basis for ongoing germplasm enhancement as it creates the genetic framework for identifying novel genetic variation and incorporating new, unsampled populations into the repository system for future breeding efforts.

Technical Abstract: Grapes are one of the most economically important berry crops worldwide, with the vast majority of production derived from the domesticated Eurasian species Vitis vinifera. Expansion of production into new areas, development of new cultivars, and concerns about adapting grapevines for changing climates necessitate the use of wild grapevine species in breeding programs. Diversity within Vitis has long been a topic of study; however, questions remain regarding relationships between species. Further, the identity of some living accessions are unclear. This study generated 11,020 single nucleotide polymorphism (SNP) markers for more than 300 accessions in the USDA-ARS grape germplasm repository using genotyping-by-sequencing. Resulting datasets were used to reconstruct evolutionary relationships among several North American and Eurasian Vitis species and to suggest taxonomic labels for previously unidentified and misidentified germplasm accessions based on genetic distance. Maximum likelihood and species tree analyses of SNP data support the monophyly of Vitis, subg. Vitis, a Eurasian subg. Vitis clade, and a North American subg. Vitis clade. Data delineate species groups within North America. In addition, analysis of genetic distance suggested taxonomic identities for 20 previously unidentified Vitis accessions and for 28 putatively misidentified accessions. This work advances understanding of Vitis evolutionary relationships and provides the foundation for ongoing germplasm enhancement. It supports conservation and breeding efforts by contributing to a growing genetic framework for identifying novel genetic variation and for incorporating new, unsampled populations into the germplasm repository system.