Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor.
Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor.
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DOI：
10.1371/journal.pgen.1010479
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发表时间：
2022-11
期刊：
影响因子：
4.5
通讯作者：
中科院分区：
文献类型：
--
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克隆繁殖经常用于商业植物育种和生物技术计划，因为它最大限度地减少遗传变异，但观察到具有稳定表型变化的克隆植物并不罕见，这种现象称为体细胞克隆变异。一些研究已经将再生过程中诱导的表观遗传修饰与这种新获得的表型变异联系起来。然而，决定体细胞克隆变异程度的因素和支持这一过程的分子变化仍然知之甚少。为了解决我们知识中的这一差距，我们比较了使用两种不同的胚胎转录因子- RWP-RK结构域包含4（RKD 4）或叶子叶2（LEC 2）和来自两种表观遗传学上不同的创始人组织的体细胞胚胎发生的克隆繁殖的拟南芥植物。我们发现，外植体的表型（遗传）状态和再生协议发挥关键作用，塑造克隆植物的分子和表型景观。再生植株中的表型变异在很大程度上可以通过组织特异性DNA甲基化印记的遗传来解释，这些DNA甲基化印记与克隆植物有性后代中的特异性转录和代谢变化相关。例如，再生体特别受到根特异性表观遗传印记遗传的影响，这与叶片中水杨酸积累增加和加速植物衰老有关。总的来说，我们的数据揭示了支持克隆植物种群中出现和积累的表型和分子变异的特定途径。克隆繁殖通常用于植物中繁殖选定的基因型并帮助遗传/基因组操作。虽然克隆最大限度地减少了遗传变异，但克隆植物通常会显示表型变化，这种现象称为体细胞克隆变异，在多次有性生殖循环后有时会保持稳定。克隆植物表现出的新获得的表型变异与再生过程中诱导的非遗传修饰有关，尽管这些修饰的确切性质和涉及的因素仍然知之甚少。通过两种不同的方法产生克隆植物，并使用两种不同的组织-根和叶-，我们表明，克隆植物中发现的表型变异与创始人组织中已经存在的DNA甲基化标记的遗传变化有关。此外，这些新的表型与基因表达和代谢变化的特定模式相关。我们的研究结果揭示了支持克隆植物种群中出现和积累的新表型和分子变异的特定途径。
Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations. Clonal propagation is commonly used in plants to propagate selected genotypes and to aid genetic/genomic manipulation. Although cloning minimizes genetic variation, clonal plants commonly display phenotypic changes, a phenomenon known as somaclonal variation, that are at times stable after multiple cycles of sexual reproduction. The newly acquired phenotypic variation exhibited by clonal plants has been linked to non-genetic modifications induced during the regeneration process, though the precise nature of these modifications and the factors implicated remain poorly understood. By generating clonal plants through two different methods and using two distinct tissues–roots and leaves–, we show that the phenotypic variation found in clonal plants is linked to heritable changes in DNA methylation marks already present in the founder tissues. Further, these novel phenotypes are associated with specific patterns of gene expression and metabolic changes. Our findings unveil specific pathways underpinning new phenotypic and molecular variation that arises and accumulates in clonal plant populations.
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影响因子：
6.9
作者：
Chwialkowska K;Nowakowska U;Mroziewicz A;Szarejko I;Kwasniewski M
通讯作者：
Kwasniewski M
影响因子：
7.7
作者：
Dubin MJ;Zhang P;Meng D;Remigereau MS;Osborne EJ;Paolo Casale F;Drewe P;Kahles A;Jean G;Vilhjálmsson B;Jagoda J;Irez S;Voronin V;Song Q;Long Q;Rätsch G;Stegle O;Clark RM;Nordborg M
通讯作者：
Nordborg M
DOI：
10.1073/pnas.1716945115
发表时间：
2018-02-27
影响因子：
11.1
作者：
Gallego-Bartolomé J;Gardiner J;Liu W;Papikian A;Ghoshal B;Kuo HY;Zhao JM;Segal DJ;Jacobsen SE
通讯作者：
Jacobsen SE
拟南芥中疯狂域蛋白的结合模式的比较分析。
影响因子：
5.3
作者：
Aerts N;de Bruijn S;van Mourik H;Angenent GC;van Dijk ADJ
通讯作者：
van Dijk ADJ
影响因子：
64.5
作者：
Calarco JP;Borges F;Donoghue MT;Van Ex F;Jullien PE;Lopes T;Gardner R;Berger F;Feijó JA;Becker JD;Martienssen RA
通讯作者：
Martienssen RA