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Thread: Grape domestication

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    Grape domestication

    Nathan Wales et al., The limits and potential of paleogenomic techniques for reconstructing grapevine domestication, Journal of Archaeological Science, Volume 72, August 2016, Pages 57–70 http://www.sciencedirect.com/science...05440316300772

    In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE–1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.

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    Interested in what else could be out there on this topic? Here is one other example, unfortunately also behind a pay wall, apart from its abstract.

    Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms, by R. ARROYO-GARCÍA et al (2006)
    http://onlinelibrary.wiley.com/doi/1...6.03049.x/full
    The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a ‘wine culture’, have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species’ distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.

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    Quote Originally Posted by Saetro View Post
    Interested in what else could be out there on this topic? Here is one other example, unfortunately also behind a pay wall, apart from its abstract.
    The lead author has made the paper available in full via https://www.researchgate.net/ and also in pdf from https://www.ars.usda.gov . Just Google on the title.

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    More recent is the paper Myles, S. et al. 2011. Genetic structure and domestication history of the grape, PNAS, 108 (9), 3530–3535. http://www.pnas.org/content/108/9/3530.abstract

    The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.
    That is the one I cite in AJ. I am not sure that the paper I reported in the OP is getting us a lot further, but it seemed worth mentioning.

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    I had attempted to raise this topic in a 2014 thread here http://www.anthrogenica.com/showthre...ll=1#post44053, after which I swapped several emails with Patrick E. McGovern at Penn. His 2006 book Ancient Wine is well known, but far from the last word he has uttered on the subject. Here is an informal update from 2015: http://www.penn.museum/sites/biomole...eology/?p=1913

    I'm pleased to see Jean's link (in the OP here) to a paper dated two months in the future. Not that I understand chloroplast genomics, at all -- but somebody is at least looking. The last sentence of this new abstract (I'll quote it below) is reminiscent of the propaganda we were seeing for NextGen sequencing of human nuclear DNA, just a couple of years ago; and that optimism has turned out to have been largely correct -- if anything, understated.

    Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.

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    Quote Originally Posted by Jean M View Post
    The lead author has made the paper available in full via https://www.researchgate.net/ and also in pdf from https://www.ars.usda.gov . Just Google on the title.
    I usually find Google Scholar brings up these accessible equivalents, but not in this case.
    I will need to broaden my search techniques in future.

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    I remember reading before that Georgia in the South Caucasus is thought to be an area of very early grape cultivation and wine making as well.

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    Quote Originally Posted by J Man View Post
    I remember reading before that Georgia in the South Caucasus is thought to be an area of very early grape cultivation and wine making as well.
    I go for the South Caucasus in AJ:

    Grapes grew wild on the southern shores of the Black and Caspian Seas, climbing trees like lianas. They seem to have been first cultivated on the sunny southern slopes of the Caucasus.[McGovern 2003 and 2009.] The earliest complete winery was found in a cave in southern Armenia, close to Iran, complete with press, fermentation vats and storage jars. The species of grape was confirmed to be the domesticated variety. The complex has been radiocarbon-dated to 4100-4000 BC.[Barnard 2011.] A genetic study of varieties of grape vine supports an origin of grape domestication in the Near East.[Myles 2011.]

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    Georgia is often mentioned as the region of grape domestication and earliest wine-making. Georgia keeps their traditional wine making having unique grape variety aging their wines in clay vessels known as Kvevri. Europeans age their red wines in oak barrels.

    Georgian Kveri https://en.wikipedia.org/wiki/Kvevri



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    I just ran across a 2012 lecture by Patrick McGovern (mentioned previously in this thread) that looks promising. Will watch it in the next few days, if not hours. I have enjoyed two of his books, so I expect it will be both informative and kind of droll. https://www.youtube.com/watch?v=8K4Avq751ts

    Edit: Having now viewed it, I recommend it highly. At the end there's a link to a 2013 lecture, that I have not watched. But since I can still link it in the same post, I shall: https://www.youtube.com/watch?v=4eYztv0ZAEQ#t=0.232208
    Last edited by razyn; 07-12-2016 at 04:18 AM.

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