We investigated genome-wide DNA methylation and transcriptome (RNA-seq) profiling for tuber shape variation in potato. Mother plant (M1, round) and tissue culture-derived clonal variant plant (M2, elongated) were used. Total number of DNA methylation sites at cytosine contexts (CpG, CHG and CHH) was higher in M2 than M1, where CHH was the highest followed by CHG and CpG. Differential methylation regions (DMRs) analysis in M1 (control) and M2 revealed maximum DMRs number on chromosome 5 in CHG context and hypo-methylation was higher than hyper-methylation. Further, transcriptome analysis revealed that a total of 20,747 genes were differentially expressed between M1 (control) and M2, of which 280 (over-expressed) and 612 (under-expressed) genes were statistically significant (p ≤ 0.05). The gene ontology (GO) annotation showed predominance of molecular function, whereas signal transduction and carbohydrate metabolism were major KEGG (Kyoto encyclopedia of genes and genomes) pathways. RNA-seq gene expression was validated for the ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Based on the comparative analysis, we observed a few candidate genes associated with tuber developmental processes such as phytohormones-related (e.g. SAUR family protein, abscisic acid environmental stress-inducible protein TAS14), sugar metabolism (e.g. UDP-glucosyltransferase, glycosyltransferase family GT8 protein), transcription factors (e.g. F-box family protein, MYB, WRKY, MADS-box), stress-responsive proteins (e.g. early-responsive to dehydration 3, cytochrome P450, proline-rich protein) and cell wall modifying genes (e.g. endo-1,4-beta-glucanase, glycine-rich cell wall structural protein 1.8, 3-ketoacyl-CoA synthase 10). Our study suggests that these candidate genes probably play key roles in tuber shape variation in potato.

我们调查了马铃薯中块茎形状变异的全基因组DNA甲基化和转录组（RNA-seq）分析。使用了母本植物（M1，圆形）和组织培养衍生的克隆变异植物（M2，拉长的）。M2中胞嘧啶环境中的DNA甲基化位点总数（CpG，CHG和CHH）高于M1，其中CHH最高，其次是CHG和CpG。M1（对照）和M2中的差异甲基化区域（DMR）分析显示，CHG上下文中5号染色体上的最大DMR数量，低甲基化程度高于高甲基化程度。此外，转录组分析显示，在M1（对照）和M2之间总共有20,747个基因差异表达，其中280个（过表达）和612个（过表达）基因在统计学上具有显着性（p ≤0.05）。基因本体论（GO）注释显示出分子功能的优势，而信号转导和碳水化合物代谢是主要的KEGG（基因和基因组京都百科全书）途径。通过实时定量聚合酶链反应（RT-qPCR）分析验证了十个选定基因的RNA-seq基因表达。在比较分析的基础上，我们观察到了一些与块茎发育过程相关的候选基因，例如植物激素相关（例如SAUR家族蛋白，脱落酸环境胁迫诱导型蛋白TAS14），糖代谢（例如UDP-葡萄糖基转移酶，糖基转移酶家族GT8蛋白）。 ），转录因子（例如F-box家族蛋白，MYB，WRKY，MADS-box），压力响应蛋白（例如对脱水的早期响应3，细胞色素P450，富含脯氨酸的蛋白）和细胞壁修饰基因（例如，endo-1,4-β-葡聚糖酶，富含甘氨酸的细胞壁结构蛋白1.8、3-酮酰基-CoA合酶10）。我们的研究表明，这些候选基因可能在马铃薯块茎形状变异中起关键作用。