title: Genomic ancestry estimation quantifies use of wild species in grape breeding.
abstract: Grapes are one of the world's most valuable crops and most are made into wine. Grapes belong to the genus Vitis, which includes over 60 inter-fertile species. The most common grape cultivars derive their entire ancestry from the species Vitis vinifera, but wild relatives have also been exploited to create hybrid cultivars, often with increased disease resistance.
  
  
  
  We evaluate the genetic ancestry of some of the most widely grown commercial hybrids from North America and Europe. Using genotyping-by-sequencing (GBS), we generated 2482 SNPs and 56 indels from 7 wild Vitis, 7 V. vinifera, and 64 hybrid cultivars. We used a principal component analysis (PCA) based ancestry estimation procedure and verified its accuracy with both empirical and simulated data. V. vinifera ancestry ranged from 11 % to 76 % across hybrids studied. Approximately one third (22/64) of the hybrids have ancestry estimates consistent with F1 hybridization: they derive half of their ancestry from wild Vitis and half from V. vinifera.
  
  
  
  Our results suggest that hybrid grape breeding is in its infancy. The distribution of V. vinifera ancestry across hybrids also suggests that backcrosses to wild Vitis species have been more frequent than backcrosses to V. vinifera during hybrid grape breeding. This pattern is unusual in crop breeding, as it is most common to repeatedly backcross to elite, or domesticated, germplasm. We anticipate our method can be extended to facilitate marker-assisted selection in order to introgress beneficial wild Vitis traits, while allowing for offspring with the highest V. vinifera content to be selected at the seedling stage.
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
authors.forename: Zoë
authors.initials: Z
authors.lastname: Migicovsky
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.|Anandia Labs, 2259 Lower Mall, Vancouver, BC, Canada.
authors.forename: Jason
authors.initials: J
authors.lastname: Sawler
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
authors.forename: Daniel
authors.initials: D
authors.lastname: Money
authors.affiliation: JKI Institute for Grapevine Breeding, Geilweilerhof, Germany.
authors.forename: Rudolph
authors.initials: R
authors.lastname: Eibach
authors.affiliation: Department of Biology, Saint Louis University, Saint Louis, MO, USA.
authors.forename: Allison J
authors.initials: AJ
authors.lastname: Miller
authors.affiliation: Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Luby
authors.affiliation: Agriculture & Agri-Food Canada, Atlantic Food & Horticulture Research Centre, Kentville, NS, Canada.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jamieson
authors.affiliation: USDA-ARS, National Clonal Germplasm Rep, Davis, CA, USA.
authors.forename: Dianne
authors.initials: D
authors.lastname: Velasco
authors.affiliation: Jost Vineyards, 48 Vintage Lane, Malagash, NS, Canada.
authors.forename: Sven
authors.initials: S
authors.lastname: von Kintzel
authors.affiliation: Warner Vineyards, 391 Thorpe Rd, RR#2, Centreville, NS, Canada.
authors.forename: John
authors.initials: J
authors.lastname: Warner
authors.affiliation: Wührer Vineyards, 187 Highway 221, RR#1, Kingston, NS, Canada.
authors.forename: Walter
authors.initials: W
authors.lastname: Wührer
authors.affiliation: Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Brown
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada. sean.myles@dal.ca.
authors.forename: Sean
authors.initials: S
authors.lastname: Myles
mesh_terms: D001947:Breeding; D018556:Crops, Agricultural; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D005838:Genotype; D006824:Hybridization, Genetic; D027843:Vitis / Q000235:genetics*