Kong Junhua, Xu Xiaobo, Carbonell-Bejerano Pablo, Wang Haiqi, Wang Yi, Wang Yongjian, Fan Peige, Weigel Detlef, Hong Yiguo, Liang Zhenchang, Gallusci Philippe, Dai Zhanwu
State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
China National Botanical Garden, Beijing 100093, China.
Plant Physiol. 2025 Aug 4;198(4). doi: 10.1093/plphys/kiaf340.
DNA methylation plays an important role in mediating the phenotypic variations observed in many traits and plants. In this study, we explored the origin of berry flesh color at the metabolic, transcriptional, and epigenetic levels. To this end, a comprehensive multiomics analysis of grape (Vitis vinifera L.) berry flesh was carried out in an F1 breeding population segregating for white- and red-fleshed siblings. The results showed that differences in DNA methylation levels at the MYBA1 promoter could effectively distinguish the white- and red-fleshed varieties. More precisely, an approximately 1-kb region in the MYBA1 promoter was hypermethylated in white-fleshed genotypes compared with the red-fleshed genotypes. This variation in methylation level was consistent among leaves, berry skin, and flesh for a given genotype, and was inherited by the F1 generation arising from crosses between parents with different phenotypes. A targeted increase in the DNA methylation levels in the MYBA1 promoter led to decreased MYBA1 expression and anthocyanin levels in transgenic grapevine hairy roots, indicating that anthocyanin biosynthesis is modulated by differential methylation at this locus. Taken together, these results suggest that the variation in methylation at the MYBA1 promoter is stable, heritable and co-segregates with grape flesh color, providing a pertinent epiallelic variation that could be used as a breeding marker to select for grape flesh color. Our findings also offer insights into the mechanisms regulating anthocyanin accumulation in grape flesh.
DNA甲基化在介导许多性状和植物中观察到的表型变异方面发挥着重要作用。在本研究中，我们从代谢、转录和表观遗传水平探究了葡萄果肉颜色的起源。为此，我们在一个F1育种群体中对葡萄（Vitis vinifera L.）果肉进行了全面的多组学分析，该群体中白肉和红肉的兄弟姐妹发生了性状分离。结果表明，MYBA1启动子处DNA甲基化水平的差异能够有效区分白肉和红肉品种。更确切地说，与红肉基因型相比，白肉基因型中MYBA1启动子内大约1 kb的区域发生了高甲基化。对于给定的基因型，这种甲基化水平的变化在叶片、浆果表皮和果肉中是一致的，并且由具有不同表型的亲本杂交产生的F1代遗传。靶向增加MYBA1启动子中的DNA甲基化水平会导致转基因葡萄毛状根中MYBA1表达和花青素水平降低，这表明花青素生物合成受该位点的差异甲基化调控。综上所述，这些结果表明，MYBA1启动子处甲基化的变化是稳定的、可遗传的，并且与葡萄果肉颜色共分离，提供了一个相关的表观等位基因变异，可作为选择葡萄果肉颜色的育种标记。我们的研究结果还为调控葡萄果肉中花青素积累的机制提供了见解。
