Main Goal

植物病毒病害防治 Management of viral disease

Plants face numerous challenges from the natural environment during their growth, such as pathogen infections, insect attacks, and extreme climate. The interactions among plant hosts, pathogens, and environmental factors directly affect plant health. To survive and thrive, plants have evolved a powerful biological defense system over millions of years, enabling them to recognize and respond to external threats. However, the long-term co-evolution between plants and pathogens has led pathogens to develop various strategies to overcome plant immune responses, while environmental factors further influence these interactions.Thus, the dynamic interactions among plants, pathogens, and environmental factors create a complex, multi-layered biological network. Understanding the interactions among the three not only helps us explore the mysteries of life but also contributes to the development of plant health management strategies. In our laboratory, we use genomics, proteomics, and metabolomics technologies to explore the interaction mechanisms among plant viruses, host crops, and environmental factors. Since plant viruses often cause significant economic losses in global agriculture, we aim to develop innovative control strategies by thoroughly studying these triadic biological mechanisms to ensure the sustainable health and stability of global agriculture.

Research topics

• Potato virus Y (PVY) 與寄主之交互作用機制 Interaction mechanism between potato virus Y (PVY) and Its host

植物病毒所編碼的蛋白通常具有多功能性，不僅能夠劫持寄主蛋白以促進自身的複製、移動等感染過程，還能透過與寄主蛋白的相互作用抑制植物的抗病毒免疫反應。相對地，植物蛋白也能夠辨識病毒蛋白，進而啟動抗病毒免疫反應。深入了解病毒與寄主之間的交互作用，對於開發有效的抗病毒策略具有重要價值。馬鈴薯Y病毒（ PVY）是影響全球茄科作物產量的主要病毒之一。然而，目前PVY與寄主蛋白之間的相互作用仍存在許多未解之謎。為了更全面解析PVY與寄主蛋白的交互作用，我們將採用TurboID鄰近標定技術，此技術可克服傳統方法難以偵測較弱或短暫蛋白質交互作用的限制，有助於更全面地找尋PVY與寄主的相互作用蛋白，並進一步深化對PVY感染機制的理解。

The proteins encoded by plant viruses are often multifunctional, not only capable of hijacking host proteins to facilitate their replication, movement, and other infection processes but also interacting with host proteins to suppress the plant antiviral immune response. Conversely, plant proteins can recognize viral proteins and activate antiviral immune responses. A deeper understanding of the interactions between viruses and host plants is crucial for developing effective antiviral strategies. PVY is one of the most significant viruses affecting the yield of Solanaceous crops worldwide. However, many aspects of the interactions between PVY and host proteins remain unresolved. To achieve a more comprehensive analysis of these interactions, we will employ the TurboID proximity labeling technique, which overcomes the limitations of conventional methods that struggle to detect weak or transient protein-protein interactions. This approach will help us identify a broader spectrum of PVY-host interacting proteins, contributing to a deeper understanding of PVY infection mechanisms.

• 探討Tomato yellow leaf curl Thailand virus（TYLCTHV）新蛋白在致病力中之角色 Investigating the Role of a Novel Protein in the Pathogenicity of Tomato yellow leaf curl Thailand virus (TYLCTHV)

病毒的基因組相較於原核與真核生物小得多，為了最大化其編碼蛋白的能力，常使用非典型的轉譯策略 。雖然大部分病毒編碼的蛋白質已被鑑定，但越來越多證據顯示，植物與動物病毒中仍存在未被發現的隱藏開放閱讀框 (Open reading frames, ORFs)，這些ORFs可能編碼具有未知功能的病毒蛋白，顯示我們對病毒的了解仍然有限。近期透過核糖體分析技術 (Ribosome profiling) 在番茄黃化捲葉病毒泰國株 (Tomato yellow leaf curl Thailand virus, TYLCTHV)基因組（DNA-A 及 DNA-B）中鑑定出17個全新隱藏ORFs。然而，這些ORFs對TYLCTHV的複製、細胞間移動、系統性移動及致病力的具體功能仍不清楚。因此，我們計劃逐一探討這些隱藏ORFs的生物功能，以更全面理解TYLCTHV的感染週期，並為病毒致病機制的研究提供更深入的見解。

The genome of viruses is significantly smaller compared to prokaryotic and eukaryotic organisms. To maximize their protein-coding capacity, viruses often utilize non-canonical translation strategies. While most viral proteins have been identified, increasing evidence suggests the presence of previously unreported hidden open reading frames (ORFs) in both plant and animal viruses. These ORFs may encode viral proteins with unknown functions, indicating that our understanding of viruses remains incomplete. Recently, using ribosome profiling, 17 novel hidden ORFs were identified in tomato yellow leaf curl Thailand virus (TYLCTHV) genome (DNA-A and DNA-B). However, the specific roles of these ORFs in viral replication, cell-to-cell movement, systemic movement, and pathogenicity remain unclear. Therefore, we plan to systematically investigate the biological functions of these hidden ORFs to gain a more comprehensive understanding of the TYLCTHV infection cycle and provide deeper insights into viral pathogenic mechanisms

• 抗病毒機制探討 Investigation of antiviral immunity mechanisms

植物面對病毒威脅時，已演化出多種抗病毒機制。然而，植物究竟如何透過不同的免疫機制來對抗病毒入侵，仍有待進一步研究。內質網已知在細胞內的蛋白質合成與折疊調控中扮演關鍵角色。然而，病毒可進入ER並形成病毒複製複合體，並破壞細胞內蛋白質平衡，導致ER逆境。為了緩解ER逆境，植物會活化多種ER逆境感測蛋白，並啟動未折疊蛋白反應（unfolded protein response, UPR）。先前研究已顯示，某些UPR基因與病毒抗性有密切關聯，例如類熱逆境轉錄因子（heat stress transcription factor, HSF-like transcription factor），TBF1。然而，UPR基因在病毒抗性中的具體功能與其調控機制仍未被完全揭示。為此，我們將探討UPR相關基因在病毒抗性中的具體角色及其分子調控機制。

Plants have evolved various antiviral mechanisms to defend against virus infection. However, how plants utilize different immune strategies to counter virus invasion remains to be further explored. The endoplasmic reticulum (ER) plays a crucial role in protein synthesis and folding regulation within the cell. Viruses are known to enter the ER, forming virus replication complexes (VRCs) that disrupt cellular protein homeostasis, leading to ER stress. To alleviate ER stress, plants activate multiple ER stress-sensing proteins and initiate the unfolded protein response (UPR). Previous studies have shown that certain UPR genes are closely associated with antiviral resistance, such as the heat stress transcription factor (HSF-like transcription factor), TBF1. However, the precise roles and regulatory mechanisms of UPR genes in antiviral resistance remain largely unknown. Therefore, we aim to investigate the specific roles and molecular regulatory mechanisms of UPR-related genes in antiviral resistance.

Viral diseases have long been a major threat to the potato industry. With climate change driving global temperature increases, high temperatures may exacerbate the severity of viral infections and could even compromise the resistance of previously resistant cultivars. Consequently, heat stress poses a significant risk to the occurrence and severity of potato viral diseases. Currently, there is a lack of comprehensive studies domestically examining the effects of high temperatures on viral infections across different potato cultivars. We will continue to investigate the impact of heat stress on viral infections in various potato cultivars and explore the underlying molecular mechanisms, aiming to provide more effective disease management strategies for the potato industry.

Topic 2

病害之健康管理 Disease Health Management

1. 了解田間病害發生狀況以及病原菌之特性 Understanding the occurrence of diseases and characteristics of pathogens in the field

2. 建立檢測技術 Establishment of detection method 

3. 建立防治策略 Development of control strategies

• 馬鈴薯病毒病害發生調查、生物性與分子特性研究與防治 Investigation, biological and molecular characterization, and management of potato viral diseases

馬鈴薯為台灣重要的茄科作物，也是全球第四大糧食作物。台灣的主要馬鈴薯產區集中於台中、雲林及嘉義地區，栽培品種以克尼伯（Kennebec）與大西洋（Atlantic）等外來品種為主，但多年來也育成了適合當地栽培的新品種。馬鈴薯產業長期受到病毒病害的威脅。在台灣已被報導的馬鈴薯病毒包括potato leafroll virus (PLRV)，以及potato virus A、S、X、M和Y (PVA, PVS, PVX, PVM, PVY) 等。然而，目前國內對於馬鈴薯病毒的發生情況及其生物與分子特性的研究仍相對不足。因此，釐清田間病害發生的原因與嚴重程度，並鑑定台灣馬鈴薯病毒的系統，進一步探討其生物與分子特性，將有助於發展更適切的抗病毒策略。此外，開發有效的病毒檢測技術，能夠協助進行更精準的病害發生調查，為馬鈴薯產業的健康管理提供顯著幫助。

Potato is a crucial Solanaceous crop in Taiwan and the fourth most important food crop globally. The primary potato-growing regions in Taiwan are Taichung, Yunlin, and Chiayi, where the dominant cultivars are the imported Kennebec and Atlantic cultivars. However, over the years, new cultivars better suited to local growing conditions have also been developed. The potato industry has long been threatened by viral diseases. In Taiwan, reported potato viruses include potato leafroll virus (PLRV) and potato virus A, S, X, M, and Y (PVA, PVS, PVX, PVM, PVY). However, there remains a significant lack of research on the occurrence, and biological and molecular characteristics of potato viruses. Clarifying the causes and severity of viral diseases in the field, identifying the diversity of potato virus strains in Taiwan, and further exploring their biological and molecular characteristics will be essential for developing more effective antiviral strategies. Additionally, establishing reliable virus detection techniques will support more accurate disease monitoring and provide valuable tools for the sustainable health management of Taiwan's potato industry.

Topic 3

病毒載體之開發與應用 Development and Application of Viral Vectors

1. 開發不同病毒之病毒載體 Development of viral vectors from various viruses

• Potato virus Y (PVY)  雙表現載體之開發 Development of PVY-based dual expression vector

為了提升馬鈴薯的產量並增強其抗病與抗逆境能力，深入探討參與農藝性狀改良及抗逆境的關鍵基因至關重要。然而，由於常見的馬鈴薯品種為四倍體且具自交不親和的特性，傳統遺傳學技術在馬鈴薯基因功能分析上的應用受到限制。為克服這些挑戰，開發病毒載體作為基因功能性分析的替代工具是一種可行的策略。我們將開發potato virus Y（ PVY) 作為基因功能性分析的病毒載體，PVY可改造成雙重表達載體，能夠同時進行多目標基因的靜默（Virus-induced gene silencing, VIGS）或基因過表現（Virus-mediated protein overexpression, VOX）。此技術的發展將為馬鈴薯基因功能研究提供一種更靈活且高效的工具，有助於深入解析關鍵基因的生物學功能，並為未來的作物改良與逆境管理提供科良好的基礎。

To enhance potato yield and improve its resistance to biotic and abiotic stresses, it is crucial to explore key genes involved in agronomic trait improvement and stress tolerance. However, due to the tetraploid nature and self-incompatibility of common potato cultivars, the application of traditional genetic tools for gene functional analysis remains limited. To overcome these challenges, developing viral vectors as alternative tools for gene functional analysis offers a promising strategy. We aims to develop potato virus Y (PVY) as a viral vector for gene functional analysis. PVY can be engineered into a dual-expression vector capable of simultaneously inducing multi-target genes silencing (Virus-induced gene silencing, VIGS) or genes overexpression (Virus-mediated protein overexpression, VOX). The advancement of this technology will provide a more flexible and efficient tool for functional genomics research in potatoes, contributing to a deeper understanding of key gene functions and supporting future crop improvement and stress management strategies.