马铃薯是我国四大主粮作物之一，马铃薯产业的健康可持续发展对保障我国粮食安全、完成脱贫攻坚和实现乡村振兴具有关键性作用。马铃薯的生产安全受到各类病害的严重威胁，且病害日趋多样化、严重化和复杂化，因此病害检测是落实病害预防的先决条件。致病疫霉（Phytophthora infestans）引起的晚疫病，是马铃薯产业的头号病害。致病疫霉变异快，田间群体结构和毒性复杂。系统性解析我国致病疫霉群体遗传多样性、毒性多样性以及二者关联规律，对深入理解晚疫病的成灾机制至关重要，且能够为马铃薯病虫害绿色防控提供理论基础。为此，本研究首先明确了我国马铃薯四大产区的主流病原菌，进而深入揭示了我国致病疫霉群体的遗传和毒性多样性，并初步解析了致病疫霉利用效应子克服马铃薯抗性的毒性机制。具体研究内容如下：

         马铃薯主要病害病原菌集成检测体系的构建与田间样本检测。卵菌病原菌致病疫霉，真菌病原菌茄链格孢菌（Alternaria solani）、禾谷镰刀菌、茄丝核菌和粉痂菌，以及细菌病原菌茄科雷尔氏菌、黑腐果胶杆菌和链霉菌是8种造成马铃薯主要病害病原菌。快速精确检测这些病原菌是马铃薯病害科学防控的前提条件，然而现有病原菌检测方法不能满足同时快速精确检测的要求。为此，本研究优化了一套病原菌集成检测体系（integrated-LAMP assays, iLAMPs），该体系能够高效且特异地检测这8种造成马铃薯主要病害病原菌。本研究进一步利用iLAMPs调查了全国四大马铃薯作区共206份病叶和239份病薯的带菌率，发现72.81%的病叶和84.94%的病薯携带多种病原菌。不同病原菌在病叶和病薯中的检出率各不相同。致病疫霉和茄链格孢菌是主流病原菌，且二者在西南作区和南方作区中显著共存。综上所述，本研究优化了一个马铃薯主要病害病原菌集成检测体系，该体系可快速精确检测田间样品的带菌率，为我国马铃薯病害监测和病害防治提供了技术方法和理论支撑。

         我国致病疫霉群体遗传多样性和毒性多样性的研究。致病疫霉田间变异快，群体遗传和毒性的多样性是造成晚疫病常年爆发的主要原因。为揭示我国致病疫霉群体的遗传多样性、毒性多样性以及二者的关联规律，本研究首先建立了我国致病疫霉菌种资源库，共收集了1996–2022年来自于我国四大马铃薯产区的652株致病疫霉和284份gDNA样品。基因分型和进化分析结果表明，我国致病疫霉群体分为CN-1、CN-2和CN-3这3个类群，分别属于全球致病疫霉群体的EU、US和SIB谱系。同时，主流类群CN-1的优势基因型MLG24与欧洲致病疫霉群体优势基因型EU-13同源。基因流分析结果表明，CN-1和CN-3类群整体呈现由北向南扩散的规律，其中CN-1类群由北向西南地区扩散的规律尤为明显。本研究进一步以西南地区的致病疫霉群体为研究对象，发现西南地区致病疫霉群体同样包含EU、US和SIB这3个谱系，且EU谱系的MLG24为优势基因型。西南地区致病疫霉群体已克服R3a、R3b和Rpi-blb3的抗性，并且克服Rpi-blb2、R8、Rpi-blb1和Rpi-vnt1.1抗性的菌株比例从2019–2022年逐年上升。基因型和毒力型关联分析表明，MLG24基因型群体的毒性多样性最丰富，包括2株可克服7种抗病基因抗性的强毒性菌株CQ-22-16-1和CQ-22-20-1。这2株强毒性菌株可侵染30种主栽马铃薯，但可以被2种Solatium candolleanum野生马铃薯（PI 458379和PI 607884）和3种药剂（霜脲氰、烯酰吗啉和氟啶胺）有效防控。综上所述，本研究明确了我国致病疫霉的群体结构和扩散规律，揭示了西南地区致病疫霉群体的基因型和毒力型的多样性，提供了强毒性菌株的防控案例。

         致病疫霉利用胞外效应子克服马铃薯抗性的机制研究。基于西南地区致病疫霉群体毒性检测结果，本研究进一步检测了全国652株致病疫霉的毒性表型。相对于其它抗病基因，Rpi-vnt1.1的抗性表现最佳。然而，7株MLG24基因型菌株能够克服Rpi-vnt1.1的抗性，其中2株可通过沉默Avrvnt1克服抗性，另外5株克服抗性的机理暂不清楚。本研究进一步以MLG24基因型群体为研究对象，利用GWAS定位了致病疫霉克服Rpi-vnt1.1抗性的遗传位点，挖掘到一个果胶裂解酶家族成员GOAT （Gwas Of AvrvnT1）。GOAT是一个胞外效应子，其可以抑制疫霉保守病原相关分子模式INF1以及效应子Avrvnt1引起的细胞坏死，促进烟草疫霉和致病疫霉侵染烟草。综上所述，本研究利用GWAS定位到克服Rpi-vnt1.1抗性的候选蛋白GOAT，初步明确了胞外效应子GOAT抑制植物免疫，促进疫霉侵染的生物学功能。

         综上所述，本研究优化了一个马铃薯主要病害病原菌集成检测体系，明确了致病疫霉和茄链格孢菌是我国四大马铃薯产区的主流病原菌。本研究进一步以我国致病疫霉群体为研究对象，发现该群体分为3个类群，其中主流类群CN-1的优势基因型MLG24中出现了克服7种抗病基因抗性的强毒性菌株，并提供了防控案例。最后，本研究通过GWAS定位到克服Rpi-vnt1.1抗性的候选效应子GOAT，初步明确了胞外效应子GOAT抑制植物免疫促进疫霉侵染的生物学功能。本研究的成果有助于理解晚疫病的成灾机制，最终为我国马铃薯晚疫病精准防控提供理论支持和材料基础。

Potato is one of the four major crops in China and the healthy and sustainable development of the potato industry plays a key role in ensuring the food security of China, completing poverty alleviation and achieving rural revitalization. Since potato production is severely threatened by various diseases, which are becoming increasingly diversified, severe and complex, the rapid and accurate detection of pathogens ranks first in disease monitoring. The oomycete pathogen Phytophthora infestans causes late blight, which is the most destructive potato disease and seriously threatens the development of potato industry in China. P. infestans evolves rapidly, leading to complex field populations and the continuous emergence of high virulence isolates. Systematically analyzing the genotypic and virulence dynamics of P. infestans populations in China and elucidating the relationship between them will deepen the comprehensive understanding of pathogenic mechanisms of late blight, which ultimately provides theoretical and material foundations for the resistance improvement of potatoes to achieve green pest and disease control. To this end, this study has identified the main pathogens in the four major potato-growing regions, revealed the diversity of the late blight population in China and preliminarily elucidated the biological roles of P. infestans effectors in overcoming potato resistance. Research details are followed:

Development and application of the integrated pathogen detection system for common potato diseases. The oomycete pathogen P. infestans, the fungal pathogens Alternaria solani, Fusarium graminearum, Rhizoctonia solani and Spongospora subterranea, and the bacterial pathogens Ralstonia solanacearum, Pectobacterium atrosepticum and Streptomyces scabies are the eight major pathogens causing significant diseases in potatoes. Rapid and accurate detection of these pathogens is a prerequisite for the scientific control of potato diseases. However, current detection methods for potato diseases do not meet the requirements for simultaneous, rapid and accurate detection of these important pathogens. To address this issue, this study has established an integrated detection system for potato diseases called iLAMPs, which can efficiently and specifically detect all eight major potato pathogens simultaneously. Furthermore, iLAMPs was applied to survey 206 diseased leaves and 239 diseased tubers collected from the four major potato-growing regions. 72.81% of the diseased leaves and 84.94% of the diseased tubers were found to carry multiple pathogens. In addition, the detection rate of different pathogens in diseased leaves and tubers significantly varies. Moreover, P. infestans and A. solani were the two prevalent pathogens, which significantly co-detected in the southwestern and southern potato-growing regions. In summary, this study has developed an iLAMPs detection system for major potato diseases, which can rapidly and accurately detect the presence of important potato pathogens in field samples. This system provides a technical method and case study for potato disease monitoring and control in China.

Genotypic and virulence dynamics of P. infestans populations in China. P. infestans is the causative agent of late blight and exhibits rapid field variation, which promotes genotypic and virulence dynamics of field populations and leads to the widespread epidemics of late blight. To monitor and control late blight, this study aims to reveal the genotypic and virulence dynamics of P. infestans populations in China and to analyze the correlation between them. To this end, this study first established a P. infestans collection, which includes 652 isolates and 284 gDNA samples from the four major potato-growing regions between 1996 to 2022. The P. infestans populations in China consist of three clusters namely CN-1, CN-2 and CN-3, which were belonged to the EU, US and SIB lineages of the global populations, respectively. The dominant genotype MLG24 in the main cluster CN-1 is homologous to the dominant genotype EU-13 in Europe. CN-1 and CN-3 clusters generally spread from north to south, with the CN-1 cluster significantly spreads from north to southwest. Therefore, this study further focused on the P. infestans populations in the southwestern region, and analyze the relationship between genotypes and pathotypes. Consistent with the national populations, the P. infestans populations in the southwestern region also comprise three lineages, with MLG24 in the US lineage being the dominant genotype. The P. infestans populations in the southwestern region have already overcome the resistance mediated by R3a, R3b and Rpi-blb3, and the number of highly virulent isolates overcoming resistance mediated by Rpi-blb2, R8, Rpi-blb1 and Rpi-vnt1.1 is increasing annually. Correlation analysis between genotypes and pathotypes showed that MLG24 isolates have the highest virulence dynamics and include two highly virulent isolates, CQ-22-16-1 and CQ-22-20-1, which have overcome the resistance of seven resistance genes. These two highly virulent isolates can infect 30 major potato cultivars but can be effectively controlled by two wild potato species and three chemicals. In summary, this study, for the first time, systematically revealed the population structure and spread patterns of P. infestans populations in China, revealed the genotypic and virulence dynamics of the P. infestans populations in the southwestern region and provided new strategies for the control of highly virulent P. infestans isolates.

Virulence mechanism study of P. infestans apoplastic effectors in overcoming the potato resistance. Based on the virulence detection results of the P. infestans populations in southwestern region, this study further examined the virulence dynamic of the P. infestans populations in China. Compared to other resistance genes, Rpi-vnt1.1 was the most effective one. However, Rpi-vnt1.1 resistance can be conquered by seven isolates from the MLG24 sub-population. Therefore, this study further focused on the MLG24 sub-population to identify P. infestans virulence factors by GWAS and ultimately identify a pectate lyase, which was named GOAT (Gwas Of AvrvnT1) in this study. GOAT is an apoplastic effector, inhibits the protein accumulation of the conserved P. infestans pathogen-associated molecular pattern INF1 and Avrvnt1, and suppresses immune responses activated by them. In addition, GOAT can promote the infection of Phytophthora. in Nicotiana benthamiana. In summary, this study uses GWAS to identify the candidate protein GOAT, and preliminarily revealed the biological function of the apoplastic effector GOAT in suppressing plant immunity and promoting Phytophthora infection.

Taken together, this study established an integrated pathogen detection system for common potato diseases and revealed that P. infestans and A. solani were the two prevalent pathogens in the four main potato-growing regions. Hence, this study further focused on studying the P. infestans populations in China. These populations consisted of three clusters while the dominant MLG24 genotype of the main CN-1 cluster contained two highly virulent isolates that could overcome the resistance mediated by seven resistance genes. In addition, this study also provided case studies to control late blight by these two highly virulent isolates. Furthermore, this study used GWAS to identify a candidate in overcoming Rpi-vnt1.1 resistance, and preliminarily revealed the biological function of this candidate. Results of this study can deepen current knowledge of the virulence mechanisms of P. infestans and ultimately provide theoretical and material supports for precise prevention and control of late blight in China.