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Shu-Yi Yang Assistant Professor

Ph.D., University of Lausanne, Switzerland

Specialty: Plant Molecular Biology, Plant-Microbe Interactions


Office: Life Science Building R1047

Telephone: 886-2-3366-2533​

Current Research Interests


Discovery of the transcriptional regulation mechanism of symbiosis-related genesRevealing the molecular mechanism essential for symbiosis-related stress tolerance.

Research Introduction

  • Arbuscular mycorrhizal (AM) symbiosis is the name given to the endosymbiotic association of a plant root and a fungus from the phylum Glomeromycota. More than 80% of vascular plants can be colonized by AM fungi. Inside root inner cortex cells, the fungal hyphae develops highly branched tree-like structures called arbuscule, which is the major site for nutrient exchange between fungi and plant. From my past research, I found that 70% of the overall Pi acquired by the rice cultivar Nipponbare is delivered via the symbiotic route. Surprisingly, mutations in PT11 or PT13, two symbiosis-specific rice Pi transporters, both affected fungal colonization and arbuscule formation, so each gene is essential for AM symbiosis. However, for symbiotic Pi uptake, only PT11 is necessary and sufficient. Besides, so far the transcriptional regulation mechanism of PT11 and PT13 is still mysterious and worth for further investigation. Like PT11 and PT13, a set of genes which was exclusively expressed in mycorrhizal roots might be essential for the cellular reprogramming during AM symbiosis. However, so far the transcriptional regulation mechanism of these genes was not fully understood. Transcription factors which expression is up-regulated by AM symbiosis are often important for AM symbiosis. By comparing the transcriptomes between non-mycorrhizal and mycorrhizal rice using RNA-Seq technology, AM-specific or induced transcription factors in rice can be identified. The expression of these candidate genes can be confirmed in tomato to see if the conservation exists between monocot and dicot. The function and target genes regulated by these transcription factors can be further analyzed. Even though the benefits of AM symbiosis on host plant stress tolerance are widely reported, the molecular mechanisms behind is still unclear. In order to find the possible plant-AM combination for improving plant stress tolerance, several combinations between the host plant, tomato and rice, and the AM fungi, will be tested under drought and salt stress conditions. During this process, different stress responses resulted from diverse combination between plants and AM fungi will be acquired for further analysis to identify the molecular mechanisms. To identify which pathways might be essential for symbiosis-related stress tolerance, the transcriptome and metabolomics approach will be applied on plants with different treatments, including non-mycorrhizal and mycorrhizal plants grown with or without stress. These analyses could help us to find the candidate genes or metabolites highly correlated with symbiosis-involved stress tolerance.​

Well-developed arbuscule inside rice cortical cells indicated by white arrowhead (A). WGA-Alexafluor 488 cell wall staining of Rhizophagus irregularis structures of wild type (B), pt11 RNAi line (C) and pt13 RNAi line (D) roots. Bars = 20 µm. Histochemical GUS staining of a proportion of a R. irregularis colonized rice root expressing empty vector (E), pPT11-GUS (F) and pPT13-GUS (G) constructs. Arrowheads represent cortical cells containing arbuscules. Bars = 20 µm.

Selected Publications

  1. Hsieh, YH, Wei, YH, Lo, JC, Pan, HY and Yang, SY* (2022), Arbuscular mycorrhizal symbiosis enhances tomato lateral root formation by modulating CEP2 peptide expression. New Phytologist. DOI:

  2. Yang SY*, Lu WC, Ko SS, Sun CM, Hung JC and Chiou TJ. (2019). uORF and phosphate-regulated expression of rice OsNLA1 controls phosphate transport and reproduction. Plant Physiology. DOI:

  3. Roth R, Chiapello M, Montero H, Gehrig P, Grossmann J, O'Holleran K, Hartken D, Walters F, Yang SY, Hillmer S, Schumacher K, Bowden S, Craze M, Wallington EJ, Miyao A, Sawers R, Martinoia E, Paszkowski U. (2018). A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal 
    symbiosis at the peri-arbuscular membrane.
    Nature Communications. 9(1):4677

  4. Yang SY*, Huang TK*, Kuo HF and Chiou TJ. (2017). Role of vacuoles in phosphorus storage and remobilization. Journal of Experimental Botany Journal of Experimental Botany. 68 (12): 3045–55

  5. Liu TY*, Huang TK*, Yang SY*, Hong YT, Huang SM, Wang FN, Chiang SF, Tsai SY, Lu WC and Chiou TJ (2016) Identification of plant vacuolar transporters mediating phosphate storage. Nature Communications. 31 (7): 11095

  6. Gutjahr C*, Gobbato E*, Choi JM, Riemann M, Johnston MG, Summers W, Carbonnel S, Mansfield C, Yang SY, Nadal M, Acosta I, Takano M, Jiao WB, Schneeberger K, Kelly KA and Paszkowski U (2015) Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex. Science. 350 (6267): 1521-24

  7. Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A, Szweykowska-Kulinska Z, Echeverria M and Karlowski WM (2015) Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. BMC Genomics. 16(1):1009

  8. Gutjahr C, Sawers RJ, Marti G, Andrés-Hernández L, Yang SY, Casieri L, Angliker H, Oakeley EJ, Wolfender JL, Abreu-Goodger C, Paszkowski U (2015) Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi. PNAS. 112(21):6754-59.

  9. Yang SY, Grønlund M, Jakobsen I, Grotemeyer MS, Rentsch D, Miyao A, Hirochika H, Kumar CS, Sundaresan V, Salamin N, Catausan S, Mattes N, Heuer S, Paszkowski U (2012) Nonredundant Regulation of Rice Arbuscular Mycorrhizal Symbiosis by Two Members of the PHOSPHATE TRANSPORTER1 Gene Family. The Plant Cell. 24(10):4236-51

  10. Yang SY and Paszkowski U (2011) Phosphate import at the arbuscule: just a nutrient? Mol Plant Microbe Interact. 24(11):1296-99.

  11. Yang SY, Shih MD, Lin TP, Hsing YIC (2011) Two soybean (Glycine maxL.) GmPM proteins reduce liposome leakage during desiccation. Botanical Studies. 52 (4): 465-70

  12. Lin YF, Liang HM, Yang SY, Boch A, Clemens S, Chen CC, Wu JF, Huang JL, Yeh KC. (2009). Arabidopsis IRT3 is a zinc-regulated and plasma membrane localized zinc/iron transporter. New Phytologist. 182(2):392-404

  13. Sawers RJH, Yang SY, Gutjahr C, Paszkowski U (2008) The molecular components of nutrient exchange in arbuscular mycorrhizal interactions. In: Z.A. Siddiqui et al., (eds.), Mycorrhizae: Sustainable Agriculture and Forestry, pp. 37-59   ©2008 Springer, Dordrecht, The Netherlands.

Courses Taught

  • Plant physiology

  • ​Seminar

  • General Biology

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