Xie Huahan, Konate Moumouni, Sai Na, Tesfamicael Kiflu G, Cavagnaro Timothy, Gilliham Matthew, Breen James, Metcalfe Andrew, Stephen John R, De Bei Roberta, Collins Cassandra, Lopez Carlos M R
Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia.
The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia.
Front Plant Sci. 2017 Oct 30;8:1860. doi: 10.3389/fpls.2017.01860. eCollection 2017.
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
了解葡萄如何感知并适应不同环境，将有助于我们深入了解如何更好地管理作物品质。越来越多的证据表明，表观遗传机制是环境与基因型之间的关键界面，最终影响植物的表型。此外，现在人们普遍认为，表观遗传机制是作物品种选择过程中有用变异的来源，可能会影响作物表现。虽然DNA甲基化对植物表现的贡献在其他主要作物中已得到广泛研究，但在葡萄方面的研究却很少。为了研究南澳大利亚巴罗萨六个葡萄酒次区域种植的22个设拉子葡萄园的遗传和表观遗传多样性。使用甲基化敏感扩增多态性（MSAP）来获得DNA甲基化的整体模式。观察到的表观遗传图谱显示出高度的分化，尽管葡萄园和次区域之间的遗传分化较低，但仍按其来源地区对葡萄园进行了分组。葡萄园之间的成对表观遗传距离表明，检测到的变异的主要贡献者（23 - 24%）与葡萄园在南北轴上的分布有关。对采用相同修剪系统的葡萄园甲基化图谱进行分析，增加了地理距离与表观遗传距离之间观察到的正相关性，表明修剪系统会影响葡萄园间的表观遗传分化。最后，通过测序进行的甲基化敏感基因分型在葡萄叶片中鉴定出3598个差异甲基化基因，这些基因被分配到1144个独特的基因本体术语中，其中8.6%与对环境刺激的反应有关。我们的结果表明，巴罗萨内部葡萄园和次区域之间的DNA甲基化差异受地理位置影响，在较小程度上也受修剪系统影响。最后，我们讨论了表观遗传变异如何作为一种工具来理解并潜在地调节葡萄中的风土。
