Centro de Biotecnología y Genómica de Plantas (CBGP-INIA), CSIC - Universidad Politécnica de Madrid, Campus Montegancedo, Madrid, Spain.
Environmental Epigenetics and Genetics Group (EEGG), Department of Horticulture, College of Agriculture, Food and environment, University of Kentucky, Lexington, KY, USA.
BMC Plant Biol. 2024 Jun 6;24(1):504. doi: 10.1186/s12870-024-05197-z.
The domestication process in grapevines has facilitated the fixation of desired traits. Nowadays, vegetative propagation through cuttings enables easier preservation of these genotypes compared to sexual reproduction. Nonetheless, even with vegetative propagation, various phenotypes are often present within the same vineyard due to the accumulation of somatic mutations. These mutations are not the sole factors influencing phenotype. Alongside somatic variations, epigenetic variation has been proposed as a pivotal player in regulating phenotypic variability acquired during domestication. The emergence of these epialleles might have significantly influenced grapevine domestication over time. This study aims to investigate the impact of domestication on methylation patterns in cultivated grapevines. Reduced-representation bisulfite sequencing was conducted on 18 cultivated and wild accessions. Results revealed that cultivated grapevines exhibited higher methylation levels than their wild counterparts. Differential Methylation Analysis between wild and cultivated grapevines identified a total of 9955 differentially methylated cytosines, of which 78% were hypermethylated in cultivated grapevines. Functional analysis shows that core methylated genes (consistently methylated in both wild and cultivated accessions) are associated with stress response and terpenoid/isoprenoid metabolic processes. Meanwhile, genes with differential methylation are linked to protein targeting to the peroxisome, ethylene regulation, histone modifications, and defense response. Collectively, our results highlight the significant roles that epialleles may have played throughout the domestication history of grapevines.
葡萄的驯化过程促进了所需性状的固定。如今，与有性繁殖相比，通过扦插进行营养繁殖更便于保存这些基因型。然而，即使采用营养繁殖，由于体细胞突变的积累，同一葡萄园通常也会存在各种表型。这些突变并不是影响表型的唯一因素。除了体细胞变异，表观遗传变异也被认为是调节驯化过程中获得的表型可变性的关键因素。随着时间的推移，这些表观等位基因的出现可能对葡萄驯化产生了重大影响。本研究旨在探讨驯化对栽培葡萄甲基化模式的影响。对 18 个栽培和野生品种进行了简化重亚硫酸盐测序。结果表明，与野生品种相比，栽培葡萄的甲基化水平更高。野生和栽培葡萄之间的差异甲基化分析共鉴定出 9955 个差异甲基化胞嘧啶，其中 78%在栽培葡萄中呈超甲基化。功能分析表明，核心甲基化基因（在野生和栽培品种中均一致甲基化）与应激反应和萜类/异戊二烯代谢过程有关。同时，差异甲基化基因与过氧化物酶体的蛋白质靶向、乙烯调节、组蛋白修饰和防御反应有关。总之，我们的研究结果强调了表观等位基因在葡萄驯化历史中可能发挥的重要作用。
