Fondap Center for Genome Regulation, Av, Blanco Encalada 2085, 3rd floor, Santiago, Chile.
BMC Plant Biol. 2014 Jan 7;14:7. doi: 10.1186/1471-2229-14-7.
Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as differential characteristics for berry size, cluster architecture and berry chemical profile, among others. 'Sultanina' plays a pivotal role in modern table grape breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for the de novo assembly of its highly heterozygous genome.
Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in 'Sultanina' and six SNPs in other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait for table grapes.
This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted breeding in table grapes.
葡萄（Vitis vinifera L.）是最重要的地中海水果作物，用于生产葡萄酒和烈酒，以及食用葡萄和葡萄干。葡萄酒和食用葡萄品种代表了两个具有不同起源和驯化历史的不同种质资源库，以及浆果大小、簇结构和浆果化学成分特征等方面的差异。“Sultanina”在现代食用葡萄育种中起着关键作用，提供了无核的主要来源。该品种也是鲜食和葡萄干生产中种植最多的品种之一。鉴于其重要性，我们对其进行了测序，并实施了一种新的策略来从头组装其高度杂合的基因组。
我们的方法产生了一个 466Mb 的草图基因组，回收了葡萄参考基因组中存在的 82%的基因；此外，我们还鉴定了 240 个新基因。鉴定出大量的结构变异和单核苷酸多态性。其中，在“Sultanina”中实验验证了 45 个（21 个 SNP 和 24 个 INDEL），在其他 23 个食用葡萄品种中验证了 6 个 SNP。转座元件约占参与结构变异的重复序列的 80%，超过 2000 个基因的结构受到这些变异的影响。其中一些基因可能与胚胎发育有关，表明它们可能与无核性有关，无核性是食用葡萄的一个关键特征。
这项工作产生了葡萄的第一个结构变异和 SNP 目录，为该关键水果作物的基因组研究提供了一个新的、非常强大的工具，特别是在支持食用葡萄的标记辅助育种方面非常有用。
