Bragato Research Institute, Blenheim, Marlborough, New Zealand.
Plant and Food Research Ltd, Lincoln, Canterbury, New Zealand.
BMC Genomics. 2021 Sep 20;22(1):676. doi: 10.1186/s12864-021-07973-9.
Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific ('terroir') differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.
We found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes.
This multi-'omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement.
体细胞变异是克隆繁殖作物中表型多样性的一个有价值的来源。在葡萄中，几个世纪以来它一直通过克隆繁殖，其重要的表型，如白色浆果颜色，是由转座因子引起的遗传变化的结果。此外，表观等位基因的形成可能在决定葡萄的地理特异性（“风土”）差异方面发挥作用，从而最终影响葡萄酒。这种基因组的可塑性可能通过体细胞胚胎发生被用于作物改良，但这取决于对这些培养物中转座因子（TE）表达和沉默的表观遗传调控的物种特异性理解。出于这个原因，我们使用全基因组亚硫酸氢盐测序、mRNA 测序和小 RNA 测序来研究胚胎发生愈伤组织中的表观遗传状态和 TE 的表达，与叶组织进行比较。
我们发现，与叶组织相比，葡萄胚胎发生愈伤组织培养物积累了相对较高的全基因组 CHH 甲基化，特别是在异染色质区域。这种从头甲基化与大量高复制 TE 家族的转录本以及相应的 24 nt 异染色质 siRNA 有关。位于基因内的 TE 特异性 CHG 区的甲基化相对较低，并且基因内 TE 位点的表达与这些基因的表达高度相关。
这项对葡萄胚胎发生愈伤组织与叶组织的多组学分析显示，TE 具有高水平的全基因组转录，同时这些序列发生 RNA 依赖性 DNA 甲基化。这为从胚胎发生培养物再生的植物中体细胞变异和表观等位基因形成的基因组条件提供了深入了解，当使用这些组织进行植物繁殖和遗传改良时，这是一个重要的考虑因素。
