Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape

Abstract

Despite the commercial importance of the Concord grape, its origin has remained unresolved for over 150 years without a comprehensive phylogenetic analysis. In this study we aimed to reconstruct the evolutionary history of the Concord grape using sequence data from four nuclear markers (AT103, GAI1, PHYA, and SQD1), six plastid markers (matK, psbA-trnH, petN-trnC, ycf1, trnL-F, and trnS-G), and the plastid genome. We sampled extensively the Vitis species native to northeastern North America as well as representative species from Europe and Asia, including the commercially important Vitis vinifera (wine grape), a native European species with hermaphroditic flowers, and its wild progenitor, V. vinifera subsp. sylvestris. We also sequenced the plastid genome of one accession of the Concord grape and compared the plastid genome data to the recently published data set of Vitis plastomes. Phylogenetic analyses of the plastid and nuclear data using maximum likelihood and Bayesian inference support the hybrid origin of the Concord grape. The results clearly pinpoint the wine grape, V. vinifera, as the maternal donor and the fox grape, Vitis labrusca, which is common in northeastern North America, as the paternal donor. Moreover, we infer that the breeding history of the Concord grape must have involved the backcrossing of the F1 hybrid with the paternal parent V. labrusca. This backcrossing also explains the higher morphological similarity of the Concord grape to V. labrusca than to V. vinifera. This study provides concrete genetic evidence for the hybrid origin of a widespread Vitis cultivar and is, therefore, promising for similar future studies focused on resolving ambiguous origins of major crops or to create successful hybrid fruit crops.

Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

“…Given the cytonuclear discordance of the phylogenetic position of this V. labrusca sample from Ma et al (2018) and the evidence listed below, it is highly likely that the particular sample was a hybrid. This particular tissue sample of V. labrusca was obtained as a cultivar in Henan, China as indicated by Ma et al (2018), and it may be a horticulture hybrid between V. labrusca and V. vinifera , likely the Concord grape, which is known as Vitis × labruscana L.H.Bailey (Moore & Wen, 2016; Wen et al, 2020). Furthermore, the phyparts analyses showed that only 72 SCNs supported the sister relationship between this V. labrusca sample and V. vinifera , contrasting to the 196 conflicting SCNs.…”

Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming

“…The incongruence detected between our plastid result and these two nuclear topologies may be due to the hybridization events during the diversification of the Yulania and Michelia clades and their close relatives. Hybridizations have played an important role in the evolution of Magnoliaceae (Kim et al, 2019) and many other lineages of angiosperms (Wen et al, 2018(Wen et al, , 2020Liu et al, 2019Liu et al, , 2020aLiu et al, , 2020b.…”

Back to the Origins: Background and Perspectives of Grapevine Domestication

“…Moreover, there is little knowledge about the phylogenetic relationships between V. vinifera and other grapes. Some authors have proposed the origin of an ancient Eurasian clade [79,85] and V. jacquemontii R. Parker could be the sister species of V. vinifera [88]. The identification and characterisation of closely related wild grapes can have important repercussions also from an agronomic perspective.…”

“…Moreover, incomplete lineage sorting [ 81 ] or introgression [ 73 ] could have confuse phylogeny between close relatives. An increasing number of plastid DNA sequences were used to explain the evolution of some Vitis taxa [ 79 , 82 , 83 , 84 ] as well as to support the reconstruction of the pedigree of some cultivars [ 85 ]. Today, next-generation sequencing technologies offer an unprecedented access to complete genome sequences and to investigate the plastomes has been proven to be a good procedure to infer new evolutive lines [ 86 , 87 ].…”