中国农业科学 ›› 2025, Vol. 58 ›› Issue (6): 1195-1209.doi: 10.3864/j.issn.0578-1752.2025.06.011

• 园艺 • 上一篇    下一篇

基于跨物种转录组解析影响不定根发生的保守基因

谢露露(), 李福, 张思远, 高建昌()   

  1. 中国农业科学院蔬菜花卉研究所/蔬菜生物育种全国重点实验室,北京 100081
  • 收稿日期:2024-08-17 接受日期:2024-11-07 出版日期:2025-03-25 发布日期:2025-03-25
  • 通信作者:
    高建昌,E-mail:
  • 联系方式: 谢露露,E-mail:xielulu@caas.cn。
  • 基金资助:
    国家自然科学基金(31902004); 中国农业科学院科技创新工程(CAAS-ASTIP-IVFCAAS)

Analysis of Conserved Genes in Adventitious Root Formation Based on Cross Species Transcriptomes

XIE LuLu(), LI Fu, ZHANG SiYuan, GAO JianChang()   

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding, Beijing 100081
  • Received:2024-08-17 Accepted:2024-11-07 Published:2025-03-25 Online:2025-03-25

摘要:

【目的】 不定根(adventitious root)有利于扩大根系和增强抗逆性,其诱导发生已广泛应用于作物的无性繁殖技术中。通过比较不同物种不定根发生的差异表达基因,分析其中的跨物种保守基因,为全面了解不定根发生的调控机制提供候选基因。【方法】 基于公共数据库中矮牵牛、康乃馨、黄瓜、欧美杨、荞麦的不定根发生转录组,采用HISAT和Cufflinks转录组分析流程计算基因转录本丰度,使用DESeq2统计和筛选差异表达基因。将同源比对获得的每个物种差异表达基因(拟南芥最似同源基因),通过集合分析获得处于交集中的基因,进行AmiGO功能注释和富集分析。并使用qPCR对5个物种以外作物的不定根发生相关表达模式进行检验。【结果】 共获得保守上调基因15个,参与胁迫响应、细胞分裂、过氧化物、甲羟戊酸等调控路径。下调的保守基因和路径则主要参与离子和化合物稳态调节功能。上调的保守基因随不定根发育进程呈现出两类表达模式(Ⅰ和Ⅱ),NRT3.1WRKY75在诱导24 h之前,即不定根原基产生时达到峰值(Ⅰ类),而CYCB2;4KNOLLE表达量在诱导后48—96 h,即不定根凸出表皮时逐渐升高并维持到伸长期(Ⅱ类)。在番茄、西瓜、玉米的不定根诱导发生过程中检验保守基因的表达水平,在试验的双子叶植物类作物番茄、西瓜中,保守基因的表达模式一致,在试验的单子叶类作物玉米中,序列相似性高的WRKY75CYCB2;4KNOLLE具有相似的表达模式,序列相似性低的NRT3.1则不同。【结论】 在不同物种、不同组织、不同诱导条件下,不定根诱导发生都有赖于胁迫响应和细胞分裂等保守路径和基因的功能发挥。保守上调基因NRT3.1WRKY75CYCB2;4KNOLLE可作为不定根发生的候选基因,在一些双子叶物种中进行深入分析。

关键词: 不定根发生, 不定根诱导, 跨物种转录组, 保守基因分析, 单子叶植物, 双子叶植物

Abstract:

【Objective】 Adventitious root helps expanding root system and enhancing resistance, and its induction is widely used in asexual propagation of crops. Comparisons of the differentially expressed genes associated with adventitious root formation in different species, and analyze the conserved genes among them, so as to provide candidate genes for the comprehensive understanding of the regulatory mechanism of adventitious root formation. 【Method】 Based on the transcriptomes of adventitious root formation of Petunia hybrida, Dianthus caryophyllus, Cucumis sativus, Populus euramericana, and Fagopyrum esculentum that downloaded from the public database, we obtained transcript abundance via HISAT2 and Cufflinks pipeline, and counted and screened the differentially expressed genes by DESeq2. The homologs most similar to Arabidopsis and differentially expressed genes in each species were obtained by homologous alignment. The genes in the intersection set were obtained by set analysis, and their functional annotation and enrichment analysis were carried out in AmiGO. And qPCR was used to examine the expression patterns related to adventitious root development in crops other than these five species.【Result】 A total number of 15 conserved up-regulated genes were obtained from five species, which were mainly participate in stress response, cell division, peroxidase and mevalonate synthesis pathways. The conserved down-regulated genes and pathways mainly participate in the regulation of ion and chemical homeostasis. With the development of adventitious roots, two types (ⅠandⅡ) of expression patterns of up-regulated genes were seen. NRT3.1 and WRKY75 peaked at the early induction stage of 24 hours (typeⅠ), at the period of the adventitious root primordium formation. While the expression levels of CYCB2;4 and KNOLLE increased gradually in the later induction stage of 48-96 hours and extending to the elongation stage (typeⅡ), at the period of the adventitious root protruding beyond the periderm. Consistent patterns of the expression levels of conserved genes during the induction of adventitious roots were identified in tomatoes and watermelons, which belong to dicotyledon. While in monocotyledon like maizes, genes with higher similarity, such as WRKY75, CYCB2;4, and KNOLLE, performed similar patteren, except for NRT3.1. 【Conclusion】 Regardless of various species, tissues, and treatments, the adventitious root formation relies on the conserved pathways and genes involved in stress response and cell division. The conserved up-regulated genes NRT3.1, WRKY75, CYCB2;4, KNOLLE can be used as candidate genes for adventitious root formation for in-depth analysis in many dicotyledonous species.

Key words: adventitious root formation, adventitious root induction, cross species transcriptome, conserved genes analysis, monocotyledon, dicotyledon