Acta Agriculturae Boreali-Sinica ›› 2022, Vol. 37 ›› Issue (2): 171-182. doi: 10.7668/hbnxb.20192621

Special Issue: Tomato Biotechnology

• Resources & Environment·Plant Protection • Previous Articles     Next Articles

Identification and Expression Analysis of Bacterial Wilt Response Genes Based on RNA-seq in Tomato

SHI Jianlei1,2, XIONG Zili1, SU Shiwen1, WANG Kelei1, ZAI Wenshan1   

  1. 1.Wenzhou Vocational College of Science and Technology,Wenzhou 325006,China
    2.College of Agriculture,Fujian Agriculture and Forestry University,Fuzhou 350002,China
  • Received:2021-11-07 Published:2022-04-28

基于RNA-seq的番茄青枯病响应基因鉴定与表达分析

史建磊1,2, 熊自立1, 苏世闻1, 王克磊1, 宰文珊1   

  1. 1.温州科技职业学院,浙江 温州 325006
    2.福建农林大学 农学院,福建 福州 350002
  • 作者简介:
    作者简介:史建磊(1982—),男,河北张家口人,副教授,硕士,主要从事园艺作物遗传育种与生物技术研究。
  • 基金资助:
    温州市农业新品种选育协作组项目(2019ZX007)

Abstract:

To explore bacterial wilt resistance genes,RNA sequencing was used to characterize the transcriptomes of resistant and susceptible tomato inbred lines with Ralstonia solanacearum inoculation(RsI).The results showed that a total of 75.02 Gb high-quality data were generated in 12 libraries.With the fold change(FC)≥2 and false discovery rate(FDR)<0.01 as the standard,970 and 695 differentially expressed genes(DEGs)were identified in the two tomato lines,respectively.The 1 312 DEGs accounted for 3.71% of the total.Among them,the numbers of up-regulated genes were 457 and 450,respectively,totaling 693;the numbers of down-regulated genes were 513 and 245,respectively,totaling 621.Among these DEGs,836 genotype-specific DEGs were highlighted.These DEGs were mainly divided into 47 functional groups such as metabolism,regulation,response,binding,and catalysis,and 88 metabolic pathways such as DNA replication,secondary metabolite synthesis,plant-pathogen interaction,and signal transduction by GO and KEGG annotation.Specifically,4 NBS resistance genes,6 plant-pathogen interaction genes,11 plant hormone signal transduction genes,22 defense response genes,32 protein kinases,65 transcription factors,and several other important functional genes were involved,indicating that they played important roles in response to Rs.Promoter analysis revealed that these genes possessed multiple defense and stress response elements.The output was confirmed using RT-qPCR for 50 representative genes.It was found that more than half of the genes were consistent with RNA-seq in expression.Solyc02g086980.3 and Solyc04g011670.3 might be involved in the resistance response,whereas Solyc01g073985.1,Solyc09g092580.4,Solyc09g098100.4,and Solyc10g081300.1 might be the opposite.Together,these gene expression profiles serve as fundamental information to understand the potential molecular basis in the response to Rs in tomato,and facilitate the application of related resistance genes in breeding.

Key words: Tomato, Ralstonia solanacearum, Transcriptome, Differentially expressed genes, Gene annotation, Quantitative expression

摘要:

为了挖掘番茄青枯病抗性基因,对青枯菌侵染前后的不同番茄自交系进行转录组测序(RNA-seq)。结果发现,在12个样本中共获得75.02 Gb的高质量数据,以差异倍数(FC)≥2且错误发现率(FDR)<0.01为标准,在抗、感番茄中分别获得970,695个差异表达基因(DEGs),共计1 312个,占基因总数的3.71%。其中,上调基因数目分别为457,450个,共计693个;下调基因数目分别为513,245个,共计621个。这些DEGs中,有836个材料特异DEGs。通过GO和KEGG注释,这些DEGs主要分为代谢、调控、响应、结合和催化等47个功能组和DNA复制、次生物质合成、植物-病原物互作、信号转导等88个代谢通路,涉及4个NBS类抗病基因、6个植病互作基因、11个植物激素信号转导基因、22个防御反应基因、32个蛋白激酶、65个转录因子和多个其他重要功能基因,表明这些基因在响应Rs方面扮演着重要角色。启动子分析发现,这些基因含有多个防御与胁迫响应相关元件。选取50个代表基因进行RT-qPCR验证,发现超过1/2的基因表达变化趋势与RNA-seq结果一致。Solyc02g086980.3和Solyc04g011670.3可能参与抗病反应,Solyc01g073985.1、Solyc09g092580.4、Solyc09g098100.4和Solyc10g081300.1可能参与感病反应。这些基因表达谱有助于认识番茄青枯病抗性分子基础,进而加快基因改良和分子育种应用。

关键词: 番茄, 青枯菌, 转录组, 差异表达基因, 基因注释, 定量表达