Journal of Plant Growth Regulation

, Volume 38, Issue 4, pp 1507–1515 | Cite as

Transcriptomic Profiling of Rice Seedlings Inoculated with the Symbiotic Fungus Trichoderma asperellum SL2

  • Febri DoniEmail author
  • F. Fathurrahman
  • Muhamad Shakirin MispanEmail author
  • Nurul Shamsinah Mohd Suhaimi
  • Wan Mohtar Wan Yusoff
  • Norman Uphoff


The fungal species Trichoderma is reported to have a significant impact on the growth and physiological performance of rice plants. However, the molecular mechanisms that induce these effects remain unspecified. Using next-generation sequencing technology, this study compared the differential expression of genes in rice seedlings that had been inoculated with Trichoderma asperellum SL2 with the gene expression in seedlings that had no such inoculation. The study showed that many genes related to plant growth enhancement and physiological functioning are differentially expressed in seedlings which have been symbiotically colonized by T. asperellum SL2. In these seedlings, specific genes related to photosynthesis, RNA activity, stomatal activity, and root development were found to be up-regulated as others were down-regulated. Although the exact causal mechanisms at the molecular level remain to be identified, the presence of Trichoderma versus its absence was associated with almost ten times more significant up-regulations than down-regulations for specific genes that have been identified from previous genomic mapping. Such analysis at the molecular level can help to explain observed phenotypic effects at the organismic level, and it begins to illuminate the observed beneficial relationships expressed phenotypically between crop plants and certain symbiotic microbes.


Gene expression Rice Transcriptomic analysis Trichoderma 



We express appreciation for helpful feedback and suggestions from Dr. Gary Harman, Professor Emeritus, Cornell University, Geneva, NY, USA.

Compliance with Ethical Standards

Conflict of interest

The authors declare no conflicts of interest.


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Authors and Affiliations

  1. 1.Institute of Biological Sciences, Faculty of ScienceUniversity of MalayaKuala LumpurMalaysia
  2. 2.Department of Agrotechnology, Faculty of AgricultureUniversitas Islam RiauPekanbaruIndonesia
  3. 3.Centre for Research in Biotechnology for AgricultureUniversity of MalayaKuala LumpurMalaysia
  4. 4.School of Biosciences and Biotechnology, Faculty of Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  5. 5.SRI International Network and Resources CenterCornell UniversityIthacaUSA

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