Rothkegel Karin, Sandoval Paula, Soto Esteban, Ulloa Lissette, Riveros Anibal, Lillo-Carmona Victoria, Cáceres-Molina Javier, Almeida Andrea Miyasaka, Meneses Claudio
Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.
Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
Front Plant Sci. 2020 Jul 17;11:1115. doi: 10.3389/fpls.2020.01115. eCollection 2020.
Temperate deciduous fruit tree species like sweet cherry () require long periods of low temperatures to trigger dormancy release and flowering. In addition to sequence-based genetic diversity, epigenetic variation may contribute to different chilling requirements among varieties. For the low chill variety 'Royal Dawn' and high chill variety 'Kordia', we studied the methylome of floral buds during chilling accumulation using MethylC-seq to identify differentially methylated regions (DMRs) during chilling hours (CH) accumulation, followed by transcriptome analysis to correlate changes in gene expression with DNA methylation. We found that during chilling accumulation, DNA methylation increased from 173 CH in 'Royal Dawn' and 443 CH in 'Kordia' and was mostly associated with the CHH context. In addition, transcriptional changes were observed from 443 CH in 'Kordia' with 1,210 differentially expressed genes, increasing to 4,292 genes at 1,295 CH. While 'Royal Dawn' showed approximately 5,000 genes differentially expressed at 348 CH and 516 CH, showing a reprogramming that was specific for each genotype. From conserved upregulated genes that overlapped with hypomethylated regions and downregulated genes that overlapped with hypermethylated regions in both varieties, we identified genes related to cold-sensing, cold-signaling, oxidation-reduction process, metabolism of phenylpropanoids and lipids, and a MADS-box gene. As a complementary analysis, we used conserved and non-conserved DEGs that presented a negative correlation between DNA methylations and mRNA levels across all chilling conditions, obtaining Gene Ontology (GO) categories related to abiotic stress, metabolism, and oxidative stress. Altogether, this data indicates that changes in DNA methylation precedes transcript changes and may occur as an early response to low temperatures to increase the cold tolerance in the endodormancy period, contributing with the first methylome information about the effect of environmental cues over two different genotypes of sweet cherry.
像甜樱桃（）这样的温带落叶果树品种需要长时间的低温来触发休眠解除和开花。除了基于序列的遗传多样性外，表观遗传变异可能导致不同品种间的需冷量差异。对于低需冷量品种‘皇家黎明’和高需冷量品种‘科迪亚’，我们使用甲基化C测序（MethylC-seq）研究了低温积累过程中花芽的甲基化组，以确定低温小时数（CH）积累过程中的差异甲基化区域（DMR），随后进行转录组分析，将基因表达变化与DNA甲基化相关联。我们发现，在低温积累过程中，‘皇家黎明’在173 CH时和‘科迪亚’在443 CH时DNA甲基化增加，且大多与CHH背景相关。此外，在‘科迪亚’中，从443 CH时观察到转录变化，有1210个差异表达基因，到1295 CH时增加到4292个基因。而‘皇家黎明’在348 CH和516 CH时有大约5000个基因差异表达，显示出每种基因型特有的重编程。从两个品种中与低甲基化区域重叠的保守上调基因和与高甲基化区域重叠的下调基因中，我们鉴定出了与冷感知、冷信号传导、氧化还原过程、苯丙烷类和脂质代谢以及一个MADS-box基因相关的基因。作为补充分析，我们使用了在所有低温条件下DNA甲基化与mRNA水平呈负相关的保守和非保守差异表达基因（DEG），获得了与非生物胁迫、代谢和氧化应激相关的基因本体（GO）类别。总之，这些数据表明DNA甲基化变化先于转录变化，可能作为对低温的早期反应发生，以在内休眠期提高耐寒性，提供了关于环境线索对两种不同甜樱桃基因型影响的首个甲基化组信息。
