College of Bioengineering, Henan University of Technology, Lianhua Street 100, Zhengzhou High-technology Zero, Zhengzhou, 450001, Henan, China.
College of Crop Sciences, Fujian Agriculture and Forestry University, Jinshan Road, Cangshan District, Fuzhou, 350002, China.
Plant Cell Rep. 2018 Apr;37(4):611-625. doi: 10.1007/s00299-018-2255-z. Epub 2018 Jan 17.
The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.
在再植根的转录组谱分析中，发现关键基因表达模式的变化促进了重要的代谢途径、抗氧化和病原体防御系统的发展，调整了植物激素信号并抑制了木质素的生物合成。当药用植物牛膝被重新种植到先前种植同一作物的田间时，其产量可以显著提高，但这种所谓的“再植效益”的生物学基础尚不清楚。在这里，使用 RNA-seq 技术来鉴定负责效益的候选基因。从第一年种植（正常生长，NG）和第二年再植（连续单一种植，CM）的根中提取 mRNA 制备的 RNA-seq 文库的分析产生了约 40.22GB 的测序数据。经过从头组装，生成了 87256 个具有 1060bp 平均长度的 unigene。在这些 unigene 中，有 55604 个被公共数据库注释，有 52346 个编码序列和 2881 个转录因子被鉴定。NG 和 CM 文库之间的对比产生了一组 3899 个差异转录基因（DTG）。通过生物信息学和 qRT-PCR 方法进一步分析与再植效益相关的 DTGs 及其表达谱。NG 和 CM 转录组之间的主要差异包括参与糖酵解/糖异生、谷胱甘肽代谢和抗氧化防御的基因编码产物，在植物/病原体相互作用、植物激素信号和苯丙烷生物合成方面。这表明，再植材料具有更强的防御系统、激素信号的平衡调节和木质素形成的抑制作用，从而促进了根系的生长和发育。该研究为更好地理解再植效益的分子机制提供了重要的见解，并为开发增强药用植物效果的方法提供了可能的应用。
