Phylogenomics, biogeography, and adaptive radiation of grapes

Ma, Zhi‐Yao; Wen, Jun; Ickert‐Bond, Stefanie M.; Nie, Ze‐Long; Chen, Lei; Liu, Xiu‐Qun

doi:10.1016/j.ympev.2018.08.021

Cited by 53 publications

(79 citation statements)

References 74 publications

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“…However, our results are consistent with the Vitis genus being slow-evolving [ 28 , 29 ]. The radiation the Vitis genus (including subgenera Vitis and Muscadinia ) from a dioecious ancestor took place 28 to 54 MY ago [ 30 , 31 ]. Previous work suggested that the V. sylvestris sex locus might be shared with other Vitis species [ 4 , 6 ].…”

Section: Discussionmentioning

confidence: 99%

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

et al. 2020

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Background: A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results: We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions: We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.

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Section: Discussionmentioning

confidence: 99%

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

et al. 2020

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“…We further surveyed more than 1300 accessions belonging to 16 Vitis species of USDA Vitis germplasm for the presence or absence of the AMAT promoter indels by genomic PCR with indel specific primers (Table S17 and Supplementary note 2). We also searched the publically available genome sequencing data of 123 V. vinifera cultivars, 44 V. sylvestris accessions, 48 Vitis hybrids, and 128 accessions covering 48 wild Vitis species for these AMAT structral variations 23,27,28,[39][40][41][42][43][44] (Table S18). AMAT alleles with absence of the 426-bp and 42-bp sequences were detected only in V. labrusca and its related hybrids (Tables S17 and S18).…”

Section: Promoter Indels and Their Impacts On Amat Expressionmentioning

confidence: 99%

A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’

et al. 2020

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'Concord', the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L., possesses a special 'foxy' aroma predominantly resulted from the accumulation of methyl anthranilate (MA) in berries. This aroma, however, is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V. vinifera. Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key 'foxy' aroma gene, anthraniloyl-CoA:methanol acyltransferase (AMAT), that is responsible for MA biosynthesis. We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in 'Concord' and other V. labrusca-derived grapes. These promoter variants, all with direct and inverted repeats, were further confirmed in more than 1,300 Vitis germplasm. Moreover, functional impact of these indels was validated in transgenic Arabidopsis. Superimposed on the promoter regulation, large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V. vinifera grapes. Elucidation of the AMAT genetic regulation advances our understanding of the 'foxy' aroma trait and makes it genetically trackable and amenable in grapevine breeding.

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“…Notably, there is incongruence among studies concerning the monophyly of the taxa of Vitis subgenus Vitis in North America (cf. Wan et al, 2013;Liu et al, 2016;Ma et al, 2018a;Wen et al, 2018a). Nevertheless, several studies have resolved Vitis subgenus Vitis into two main clades corresponding to their geographic distributional areas in Eurasia and North America (e.g., Zecca et al, 2012;Klein et al, 2018;Ma et al, 2018b;Wen et al, 2018a).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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.

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Phylogenomics, biogeography, and adaptive radiation of grapes

Cited by 53 publications

References 74 publications

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’

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

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