Late blight is a disease that occurs in cultivated tomatoes (Solanum lycopersicum) and its close relative, the potato (Solanum tuberosum). This disease is caused by the oomycete Phytophthora infestans that was responsible for the Irish potato famine of the 1840s ^[1][2][1,2]. In Thailand, tomatoes and potatoes are usually grown in the north and northeast. The cultivation areas for these two crops have generally increased each year because of the increasing demand for fresh and processed food. In 2020, tomato and potato cultivation covered more than 6000 hectares in the north and northeast of Thailand [3]. Specifically, Chiang Mai and Tak provinces are the main areas where both tomatoes and potatoes are being grown. During the period between December and February, which is referred to as the winter season in Thailand, the conditions in the north and northeast of Thailand are high humidity (>90%) and low temperatures (on average 21 °C). Thus, these areas are suitable for the development of the late blight disease. As such, these crops face the risk of infection by this pathogen, which can cause serious damage and subsequently severe economic losses.

The first populations of P. infestans isolates were characterized in tomatoes in 1994 based on their phenotypes, mating type, metalaxyl sensitivity, and two allozyme genotypes, glucose-6-phosphate-isomerase (Gpi 86/100) and peptidase (Pep 92/100) ^[4][5]. Eighteen samples of late blight tomato isolates were collected from the regions of Mae-Rim, Mae-Tang, San Sai, Praow, Chai Prakran, and Fang, which are located in Chiang Mai. The results demonstrated that all tomato isolates were sensitive to metalaxyl and the A1 mating type. The dilocus allozyme genotype was found for 86/100 of the Gpi and 92/100 of Pep. Gotoh et al. ^[5][6] used the same P. infestans population as Nishimura et al. ^[4][5] to perform RFLP with an RG57 probe and mitochondrial DNA haplotype analysis. Late blight tomato isolates were found to be of the US-1 and US-1.3 clonal lineages according to the RFLP genotypes and of the Ib mtDNA haplotype according to the mitochondrial genotype.

Six years later, in 2000, the populations of P. infestans in tomatoes were characterized by Petchaboon et al. ^[6][11]. Late blight isolates were collected in Mae-rim during 2000–2002 from the same areas as the Nishimura collection in 1994. The study revealed that the populations of tomatoes were of the US-1, US-1.3, US-1.4, and TH-2 genotypes. All genotypes were the A1 mating type, showing sensitivity to moderate resistance to metalaxyl and Ib mtDNA. Thus, the analyses revealed that the P. infestans of the tomato populations in Thailand were from the same lineage that had caused epidemics from 1994 until 2002.

3. Populations of P. infestans in Potatoes Isolated in Chiang Mai and Tak Provinces

The population structure of late blight disease in Thailand for potatoes was first characterized by Gotoh et al. ^[5][6] using the collection of Nishimura et al. ^[4][5]. The results of the analysis of phenotypic and genotypic data by Gotoh et al. ^[5][6] demonstrated that the P. infestans in potatoes had equal proportions of both A1 and A2 mating types, Ia and Ib mitochondrial haplotypes, and US1 and TH1 genotypes. Petchaboon et al. ^[6][11] studied the population structure of P. infestans in potatoes from 2000 until 2002 at the same locations. During 2000–2002, only the A1 mating type and two common clonal lineages, RF006 and RF008, were found in both Tak and Chiang Mai provinces. These two genotypes were not reported for the collected isolates in 1994 by Gotoh et al. ^[5][6]. To conclude, for the period of 1994 to 2002, the data from the studies of P. infestans in potatoes in Thailand showed that the population of late blight has changed from the A1 and A2 to the A1 mating type. The genotype of the RG57 fingerprint showed that the US1 genotype in 1994 was replaced with the RF006 and RF008 genotypes in 2002. The latest data from 2000 to 2009 also showed that only the A1 mating type was lacking RG57 fingerprint data. 

4. Change in P. infestans Population Structure in Thailand

Gotoh et al. ^[5][6] and Petchaboon et al. ^[6][11] found that the P. infestans populations in tomatoes in Thailand were of the same lineage as US-1. The P. Infestans that infected potatoes in 1994 were also of the US-1 lineage. Importantly, Petchaboon et al. ^[6][11] demonstrated that the change in the population structure of P. infestans originated from potato isolates. In a study ranging from 2000 to 2002, the researchers found two common genotypes, RF006 and RF008, in the potato isolates. Two hypotheses may explain the changes that have occurred in the P. infestans isolates in potatoes.

• First, the variation could have occurred owing to recombination through sexual reproduction. P. infestans is a heterothallic oomycete composed of two mating types, assigned A1 and A2. The oomycete has a coenocytic diploid mycelium and can reproduce both sexually and asexually ^[7][14]. When two compatible strains of oomycete interact with two different mating types, for example, A1 and A2, sexual reproduction can occur. The result of this mating system was the formation of thick-walled, resistant oospores ^[8][15]. The appearance of self-fertile pathotypes permits the sexual reproduction of P. infestans worldwide ^[9][10][16,17].
• Second, another potential source of change in the population structure is through the migration of new genotypes. The global exacerbation of disease is caused by the migration of new strains ^[11][23]. The existing global population structure of P. infestans has been created via a series of migrations and displacements of clonal lineages ^{[12][13][14][15][16][17]}[24,25,26,27,28,29]. The evidence revealed that the appearance of the original population of P. infestans was first dominated by the HERB-1 ^[18][30] and later by the US-1 lineage. The P. infestans that caused the Irish potato famine was replaced by the US-1 clonal lineage ^[19][7].

When focusing solely on Thailand, the first hypothesis regarding sexual reproduction is less likely to be evident. This is because the mating of P. infestans requires the presence of both A1 and A2 mating types in the same area, the infection of the same leaf, and the formation of oospores for zygote formation ^[20][32]. The emergence of a new genotype occurs through the sexual process, resulting in the appearance of different clonal lineages of different mating types. Therefore, migration is the most likely explanation for the population change in potato isolates. Considering the historical potato production records in Thailand, two cultivars, ‘Spunta’ and ‘Kennebec’, were used for potato production in 1994. The population analysis of P. infestans at that time showed that potato isolates in Chiang-Mai had the TH-1, US-1, and US1.3 genotypes, with equal proportions of the A1 and A2 mating types, and sensitivity to metalaxyl ^[5][6]. The main reason for the P. infestans population in tomatoes not changing is due to the absence of factors affecting its life cycle, such as the lack of pressure, the absence of migration of new genotypes, and the disappearance of sexual reproduction. This is because tomatoes in Thailand during the 20th and 21st centuries were a minor crop that alternated with the main crop, which was rice. As a result, disease management in tomato crops did not extensively use fungicides, and this lack of intervention did not exert any force on the life cycle of pathogens.

5. Factors Affecting Different Responses to Metalaxyl in P. infestans Populations in Tomato and Potato Isolates

5.1. The Use of Metalaxyl for Disease Management

The overuse of chemical fungicides has led to an increased degree of pathogen resistance ^[21][36]. The management of late blight with the indiscriminate use of metalaxyl has led to the development of resistant strains of the oomycete, which have been found in many countries ^{[22][23][24][25]}[37,38,39,40]. Potato production in Thailand has rapidly expanded during the 20th and 21st centuries. Potato consumption has also changed from home cooking to potato chips and French fries on an industrial scale. As a result, domestic production changed, providing opportunities for foreign trade ^[26][41]. A production system based on contract farming started in 1988 by the United Food company, which used ‘Kennebec’ as the contract cultivar for production in the San Sai district in Chiang Mai province ^[27][42]. By 1990, potato production had rapidly expanded, leading to a nearly fivefold increase in production within only 20 years.

5.2. Host Preference of P. infestans

P. infestans shows host preference (or specificity), which is associated with a particular lineage ^{[28][29][30][31][32][33][34]}[45,46,47,48,49,50,51]. For example, US-8 is pathogenic mainly on potatoes, whereas US-7, US-11, and US-17 are pathogenic on both potatoes and tomatoes ^[14][35][26,52]. In addition, in Columbia, Uganda, and Kenya, similar data patterns revealed that adapted lineages rarely cause severe disease in other hosts, and the pathogens prefer hosts within a single lineage ^[34][36][51,53]. In Thailand, most clonal lineages in tomatoes are US1, which normally shows sensitivity to metalaxyl. So, US-1 preferentially infects tomato, which shows metalaxyl sensitivity. Conversely, most isolates from potatoes showed resistance to this fungicide.

5.3. Migration of New Genotypes from Infected Potato Seeds

Due to the popularity of potatoes in Thailand, the risk posed by the import of infected potato seeds is higher than that of the import of tomato seeds. Potato production increased by 673% in 2012 in comparison with the production in 1990; however, 353% more land in Northern Thailand was used for potato production at that time ^[26][41]. Between 2015 and 2019, the rate of imported potatoes, including both processing and seed potatoes, increased by 15.43% [3]. More specifically, for seed potatoes, the total import of 7099 tons in 2021 originated from the United Kingdom, Australia, the Netherlands, America, and Canada [3]. The two main cultivated potato varieties are ‘Spunta’ and ‘Atlantic’. The ‘Spunta’ variety is mainly imported from the Netherlands to support the fresh market, and the ‘Atlantic’ variety is imported from Scotland and Australia to support the production of potato chips and French fries ^[26][41].

6. The Importance of P. infestans Population Study

P. infestans is one of the most aggressive pathogens and has been classified as ‘high risk’, mainly because of its high adaptability to the host ^[37][55]. P. infestans has a vast genome (240 Mb), consisting of many structures that can develop variable strains and undergo rapid mutations, such as conserved gene sequences with a low number of repeats ^[38][39][56,57]. Currently, potato production in Asia has expanded dramatically and accounts for over 40% of the world’s production ^[40][58]. A late blight network for Asia, AsiaBlight, was established following the success of EuroBlight. It is an inclusive network of scientists, farmers, and other stakeholders working on potato late blight disease. The cooperation and data sharing among researchers from across Asia will contribute to the sustainable production of healthy potato crops, thereby improving nutrition and food security for billions of people in Asia. The study of P. infestans populations based on mating type, evaluating fungicide effectiveness, and assessing genotypic variation is necessary for understanding the aggressiveness and adaptability of the pathogen. This understanding is crucial for effective late blight disease management. P. infestans populations can be identified using standard methods such as metalaxyl sensitivity, allozyme analysis, RG 57 DNA fingerprinting, mtDNA haplotypes, SSRs, and 12-plex SSRs ^[41][35]. In Thailand, studies by Petchaboon et al. ^[6][11], Jaimasit and Prakob ^[42][12], and Sopee ^[43][13] have revealed that the majority of damages are attributed to the importation of infected potato seeds, as determined by these standard methods. Nowadays, Thailand has increased the amount of imported fresh and seed potatoes, mainly due to consumption demand. Thus, there is a high possibility of new genotypes being present, together with the existence of different mating types, which can promote genotypic variability by sexual reproduction. Thus, the study of P. infestans populations should always be monitored and be ongoing research. In conclusion, the P. infestans from the tomato population in Thailand is the same lineage that was endemic from 1994 until 2002. Additionally, the clonal lineage that was found in the potato population changed from US-1 in 1994 to RF006 and RF008 in 2002. This change in P. infestans in the potato population was possibly caused by potato seeds imported into Thailand. The P. infestans population in potatoes shows resistance to metalaxyl, whereas tomato isolates show sensitivity to the fungicide. The three possible causes of this are (i) the use of metalaxyl, (ii) the host preference of P. infestans, and (iii) the migration of new genotypes from infected potato seeds.