Liu Sitong, Wang Xinfeng, Ding Ning, Liu Yutong, Li Ning, Ma Yiqiao, Zhao Jing, Wang Zhenhui, Li Xiaomeng, Fu Xueqi, Li Linfeng
School of Life Sciences, Jilin University, Changchun 130012, China.
Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
Plants (Basel). 2021 Dec 27;11(1):79. doi: 10.3390/plants11010079.
Plants have the salient biological property of totipotency, i.e., the capacity to regenerate a whole plant from virtually any kind of fully differentiated somatic cells after a process of dedifferentiation. This property has been well-documented by successful plant regeneration from tissue cultures of diverse plant species. However, the accumulation of somaclonal variation, especially karyotype alteration, during the tissue culture process compromises cell totipotency. In this respect, Chinese ginseng ( C. A. Mey.) is an exception in that it shows little decline in cell totipotency accompanied by remarkable chromosomal stability even after prolonged tissue cultures. However, it remains unclear whether chromosomal level stability necessarily couples with molecular genetic stability at the nucleotide sequence level, given that the two types of stabilities are generated by largely distinct mechanisms. Here, we addressed this issue by genome-wide comparisons at the single-base resolution of long-term tissue culture-regenerated plants. We identified abundant single nucleotide polymorphisms (SNPs) that have accumulated in cultured ginseng callus and are retained in the process of plant regeneration. These SNPs did not occur at random but showed differences among chromosomes and biased regional aggregation along a given chromosome. In addition, our results demonstrate that, compared with the overall genes, genes related to processes of cell totipotency and chromosomal stability possess lower mutation rates at both coding and flanking regions. In addition, collectively, the mutated genes exhibited higher expression levels than non-mutated genes and are significantly enriched in fundamental biological processes, including cellular component organization, development, and reproduction. These attributes suggest that the precipitated molecular level genetic variations during the process of regeneration in are likely under selection to fortify normal development. As such, they likely did not undermine chromosomal stability and totipotency of the long-term ginseng cultures.
植物具有显著的全能性生物学特性，即经过去分化过程后，几乎任何一种完全分化的体细胞都有能力再生出完整植株。多种植物物种的组织培养成功再生植株，充分证明了这一特性。然而，组织培养过程中体细胞克隆变异的积累，尤其是核型改变，会损害细胞全能性。在这方面，人参（C. A. Mey.）是个例外，即使经过长时间的组织培养，其细胞全能性几乎没有下降，同时染色体稳定性也很显著。然而，鉴于这两种稳定性是由截然不同的机制产生的，染色体水平的稳定性是否必然与核苷酸序列水平的分子遗传稳定性相关，仍不清楚。在此，我们通过对长期组织培养再生植株进行单碱基分辨率的全基因组比较来解决这个问题。我们鉴定出大量在培养的人参愈伤组织中积累并在植株再生过程中保留下来的单核苷酸多态性（SNP）。这些SNP并非随机出现，而是在染色体之间存在差异，并且沿给定染色体呈现出偏向性的区域聚集。此外，我们的结果表明，与整体基因相比，与细胞全能性和染色体稳定性过程相关的基因在编码区和侧翼区的突变率较低。此外，总体而言，突变基因的表达水平高于未突变基因，并且在包括细胞组分组织、发育和繁殖在内的基本生物学过程中显著富集。这些特性表明，人参再生过程中沉淀的分子水平遗传变异可能处于选择之下，以强化正常发育。因此，它们可能并未破坏长期人参培养物的染色体稳定性和全能性。
