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. 2016 Jun 30;17:478.
doi: 10.1186/s12864-016-2834-8.

Genomic Ancestry Estimation Quantifies Use of Wild Species in Grape Breeding

Free PMC article

Genomic Ancestry Estimation Quantifies Use of Wild Species in Grape Breeding

Zoë Migicovsky et al. BMC Genomics. .
Free PMC article


Background: 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.

Results: 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.

Conclusions: 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.


Fig. 1
Fig. 1
PCA-based ancestry estimation using 2482 SNPs and 56 indels for 7 wild Vitis, 7 V. vinifera, and 64 hybrid samples. a PCs were generated using wild Vitis and V. vinifera samples. The proportion of the variance explained by each PC is shown in parentheses along each axis. Hybrids were projected onto the axes. b Boxplots of PC1 values for wild Vitis, V. vinifera, and hybrid cultivars as well as a visual description of the calculation used for ancestry estimation. Further details are found in the Methods
Fig. 2
Fig. 2
Simulation of hybrids (10,000 of each). a Simulated hybrids including F1 hybrids, F1 backcrossed to V. vinifera and F1 backcrossed to wild Vitis were projected onto axes generated using wild Vitis and V. vinifera samples b Distribution of ancestry estimates for simulated populations
Fig. 3
Fig. 3
Estimated V. vinifera content in 64 commercial grape hybrids. Estimates are based on 2538 sites. a Distribution of V. vinifera ancestry estimates in hybrids (b) V. vinifera ancestry estimates for each cultivar. Bars are colored if a hybrid cultivar’s ancestry estimate falls within the 95 % confidence interval of a F1, F1 x wild Vitis, or F1 x V. vinifera cross, based on simulated values. Dotted lines indicate mean values for the wild Vitis and V. vinifera samples

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