Institut National de la Recherche Agronomique (INRA) Unité Mixte de Recherche (UMR) 1097 Diversité et Adaptation des Plantes Cultivées, F-34060 Montpellier, France.
Genetics. 2009 Nov;183(3):1127-39. doi: 10.1534/genetics.109.103929. Epub 2009 Aug 31.
The combination of QTL mapping studies of synthetic lines and association mapping studies of natural diversity represents an opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping, which often leads to wide intervals encompassing numerous genes, it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape, a newly sequenced genome, to decipher the genetic architecture of anthocyanin content. Grapes may be either white or colored, ranging from the lightest pink to the darkest purple tones according to the amount of anthocyanin accumulated in the berry skin, which is a crucial trait for both wine quality and human nutrition. Although the determinism of the white phenotype has been fully identified, the genetic bases of the quantitative variation of anthocyanin content in berry skin remain unclear. A single QTL responsible for up to 62% of the variation in the anthocyanin content was mapped on a Syrah x Grenache F(1) pseudo-testcross. Among the 68 unigenes identified in the grape genome within the QTL interval, a cluster of four Myb-type genes was selected on the basis of physiological evidence (VvMybA1, VvMybA2, VvMybA3, and VvMybA4). From a core collection of natural resources (141 individuals), 32 polymorphisms revealed significant association, and extended linkage disequilibrium was observed. Using a multivariate regression method, we demonstrated that five polymorphisms in VvMybA genes except VvMybA4 (one retrotransposon, three single nucleotide polymorphisms and one 2-bp insertion/deletion) accounted for 84% of the observed variation. All these polymorphisms led to either structural changes in the MYB proteins or differences in the VvMybAs promoters. We concluded that the continuous variation in anthocyanin content in grape was explained mainly by a single gene cluster of three VvMybA genes. The use of natural diversity helped to reduce one QTL to a set of five quantitative trait nucleotides and gave a clear picture of how isogenes combined their effects to shape grape color. Such analysis also illustrates how isogenes combine their effect to shape a complex quantitative trait and enables the definition of markers directly targeted for upcoming breeding programs.
利用合成系的 QTL 作图研究和自然多样性的关联作图研究相结合，为阐明数量性状的遗传基础变异提供了机会。通过 QTL 作图提供的定位信息，通常会导致包含众多基因的广泛区间，现在可以直接针对负责完全测序基因组中观察到的变异的候选基因，并通过关联遗传学测试它们的效果。在葡萄中，一种新测序的基因组，采用这种方法来破译花色苷含量的遗传结构。葡萄可以是白色或有色的，根据浆果皮中积累的花色苷量，从最浅的粉红色到最深的紫色色调不等，这是葡萄酒质量和人类营养的关键特征。尽管白色表型的决定因素已经完全确定，但浆果皮中花色苷含量的数量变化的遗传基础仍不清楚。在 Syrah x Grenache F(1)拟测交中，一个单一的 QTL 负责花色苷含量变异的 62%。在 QTL 区间内鉴定的葡萄基因组中的 68 个基因中，根据生理证据选择了一个 Myb 型基因簇(VvMybA1、VvMybA2、VvMybA3 和 VvMybA4)。从自然资源的核心群体(141 个个体)中，发现 32 个多态性与显著关联，并且观察到了扩展的连锁不平衡。使用多元回归方法，我们证明 VvMybA 基因中的五个多态性(一个反转录转座子、三个单核苷酸多态性和一个 2bp 插入/缺失)除了 VvMybA4 外，除了 VvMybA4 外，都解释了观察到的 84%的变异。所有这些多态性导致 MYB 蛋白的结构变化或 VvMybAs 启动子的差异。我们得出结论，葡萄花色苷含量的连续变异主要由三个 VvMybA 基因的一个单基因簇解释。利用自然多样性有助于将一个 QTL 缩小到一组五个数量性状核苷酸，并清楚地说明了同系物如何结合它们的效应来塑造葡萄的颜色。这种分析还说明了同系物如何结合它们的效应来塑造一个复杂的数量性状，并能够定义直接针对未来育种计划的标记。
