Population genetics of Phytophthora species based on short sequence repeat (SSR) marker: a review of its importance and recent studies

Phytophthora is a genus of oomycete (water molds) whose member species mostly live as plant pathogens and have been reported to cause enormous economic losses on crops worldwide. In recent years, population genetics of Phytophthora pathogens have been broadly studied to evaluate their adaptive evolution. Population genetic studies focus on analyzing the level of genetic diversity and the structure of the pathogen population. A population’s genetic diversity is proportional to its evolutionary potential. The generation and maintenance of genetic variation in pathogen populations are influenced by the biology of the pathogen and its host, environments, agricultural practices, and human activities. Understanding the population genetics of plant pathogens allows us to track the dynamic of the pathogen population and their adaptive ability, assisting the development of sustainable disease management strategies. This review presents the importance of population genetics, short sequence repeat (SSR) marker utilization in population genetic studies, and recent population genetics studies of Phytophthora pathogens related to agricultural practices.


Introduction
Phytophthora is a genus of filamentous fungus-like oomycote, with most of its species living as plant pathogens.Around 181 species of this genus have been reported as plant pathogens and the cumulative number of disease reports caused by Phytophthora spp.reached 12.413 reports from 136 countries over the past 142 years [1].Several Phytophthora species have wide host ranges [2][3][4] and are highly invasive, making it one of the world's most destructive genera of plant pathogens [5,6].Pathogens from this genus commonly cause stem cankers, damping off, collar rots, root rots, tuber rots, fruit rots, leaf blights, and fruit blights [7].Phytophthora diseases are major threats to various ecosystems, including agriculture, forestry, and conservation worldwide [8,9].
The ability of Phytophthora spp. to produce asexual (zoospores and chlamydospores) and sexual spores (oospores) is one of determining factors in their successful invasion and survival [10].Phytophthora spp.also demonstrated the interspecies universality of mating hormones within the genus Phytophthora [11], permitting crossbreeding.Crossbreeding is important in arms races between plants and parasites [12].The occurrence of sexual and asexual reproduction in a pathogen population 1230 (2023) 012102 IOP Publishing doi:10.1088/1755-1315/1230/1/012102 2 promotes a greater evolutionary potential.In sexual reproduction, new genotypes can be generated by reshuffling genes or rearranging the intragenic site mechanism [13].The beneficial genotype formed through recombination that undergoes selection can be passed down through asexual reproduction to their progenies, increasing their frequency in the population [14].Besides recombination by sexual reproduction, mitotic recombination has also been documented in Phytophthora species.P. ramorum is an asexual species reported to undergo mitotic recombination and form homozygous allele combinations, increasing its evolutionary potential and supporting its establishment as an invasive species [15].Overall, recombination increases genetic and genotypic diversity in pathogen populations.The genetic variation level in a population aligns with its evolutionary potential, determining the pathogen's adaptability to fluctuating environmental conditions [16,17].
In a natural ecosystem, plants and pathogens are engaged in continuous co-evolution, in which the pathogen evolves to plant resistance traits, and the plant evolves in response to pathogen virulence traits.Co-evolution has reciprocity; the resistance gene's contribution to the host's fitness is determined by the frequency of the virulence gene and vice versa.However, in modified ecosystems such as agroecosystems, pathogens are advantaged as the grower controls the choices of plant genotype grown in the field, disrupting the coevolutionary dynamics of the plant-pathogen interactions [18].Pathogen evolution in agroecosystems occurs faster than natural ecosystems due to large-scale monoculture cultivation, agrochemical applications, and international trade in agricultural products [19,20].Furthermore, there is a rising concern that disease management practices become selection pressure that enhances the evolution of the targeted pathogen population.The deployment of indiscriminate agrochemicals and quantitative resistance of a resistant cultivar may become selection agents for enhanced pathogen aggressiveness.Targeted selection of a specific character is the cause of the rapid breakdown of resistant plants and the emergence of resistance to certain pesticides [16].Such selection will increase the pathogen population's virulence and lead to plant resistance breakdown [21].Targeted selection and reduced genetic diversity in populations have been reported to cause P. infestans resistance to metalaxyl fungicides in Mexico [22].Knowledge about the factors that influence the genetics of a population can help to predict the dynamics of the pathogen population and its evolutionary trajectory.Therefore, understanding the fundamental factors affecting pathogen population genetics is essential to assist the formulation of sustainable disease management strategies that minimize disease epidemics while simultaneously reducing selection pressure on pathogens to evolve increased adaptability and infectivity [19].
Population genetics is the study of genetic composition in a population and how the frequencies of alleles and genotypes change over time within and between populations.Population genetic study is important to understand the dynamic and evolutionary potential of the plant pathogen population.The development of molecular markers in recent years has greatly contributed to population genetics study.This literature review presents the importance of population genetics, the advantages of short sequence repeat (SSR) markers in population genetic studies, and recent population genetics studies of Phytophthora pathogens, focusing on factors affecting the population's genetic diversity and structure.

Importance of population genetics study in plant pathogens
Population genetics is the study of the genetic variation within and among populations and the factors that influence that variation over time.Population genetics study in plant pathogens is important to understand how genetic diversity is generated and maintained within populations, how populations evolve and adapt to changing environments, and how genetic variation can lead to speciation.Population genetics study in plant pathogens is important for several reasons: 1) Understanding the genetic diversity and structure of pathogen populations can help to identify the source of the introduction and spread of the pathogen [12,23].This information can be used to develop effective disease management and control strategies.2) Population genetics studies can provide insights into the evolutionary processes that drive the emergence and spread of new pathogen strains.This information can help to predict the potential impact of emerging pathogen strains on crops and ecosystems [24][25][26].It can also help identify areas of high genetic diversity within the pathogen population, which can be targeted for surveillance and monitoring to prevent the emergence of new virulent strains.3) Population genetics studies can help identify pathogen adaptation mechanisms to different host plants and environments.This information can be used to develop sustainable disease management strategies [20,27] 4) Population genetics studies can provide information on the genetic basis of pathogen virulence and resistance, which can be used to develop new approaches for breeding crops resistant to plant pathogens [28,29].
Overall, population genetics studies in plant pathogens provide important information that can be used to develop more effective and sustainable strategies for managing plant diseases and protecting global food security.

SSR marker
Microsatellites are nucleotide sequences with repetitive motifs of 5 to 50 repeats, and each repeat motif consists of tandemly arranged units of 1-6 bp [30,31].Microsatellites can be short tandem repeats (STR), simple sequence repeats (SSR), or simple sequence length polymorphism (SSLP).Microsatellites have been reported to have a higher mutation rate than other parts of DNA.The generation of mutation in SSRs occurs primarily due to slip-strand mispairing (SSM), unequal crossing over, and recombination error [32][33][34].
Microsatellite markers are widely used in genetics-based research, including population genetics.Microsatellite markers are polymorphic; their high informativeness and capability to distinguish between genotypes make this marker widely used in the population genetics study of Phytophthora species [35][36][37][38][39][40][41][42][43].The following are the important properties of SSR markers: 1) SSR is widely distributed in the genome -SSRs are ubiquitously distributed throughout the genome, in the coding and non-coding regions, especially in the euchromatin of eukaryotes and coding and non-coding nuclear and organellar DNA [44] 2) SSR markers are polymorphic -SSR has a higher mutation rate than other parts of DNA, resulting in increased genetic variation.The microsatellite is part of VNTR with a mutation rate between 10 3 -10 6 per cell generation.This mutation rate is ten times greater than the point mutation and is very evolutionarily stable [45].3) SSR markers are locus-specific and PCR-based -SSR markers represent a specific location on the genome and can be developed as primers to amplify microsatellite regions at loci.SSR markers are PCR-based and require a small amount of DNA template for amplification [46] 4) SSR markers are co-dominant markers that can distinguish heterozygous alleles; these markers amplify genes on homologous chromosomes.Microsatellite loci can detect more than one allele and thus has high informativeness [46] 4. Factors affecting the population genetics of Phytophthora species All population that exists in nature has evolutionary potential.Evolution occurs in two steps; the first is increased genetic variation in the population of a species, then followed by the changed frequency of alleles in the population by selection or genetic drift.Genetic diversity is important for the long-term survival of a population, as it allows for the possibility of adaptation to new environmental conditions or the emergence of new strains that are better adapted to prevailing conditions.In contrast, a lack of genetic diversity can lead to reduced fitness.In this section, we present factors affecting the genetic diversity and population structure of phytophthora spp.from recent studies (table 1), including mode of reproduction, dispersal mechanism, and agricultural practices.

Mode of reproduction
Phytophthora species have a complex life cycle that involves asexual and sexual reproduction-both mode of reproduction affect the overall genetic diversity of the Phytophthora population [47].Genetic recombination, which occurs during sexual reproduction, plays an important role in the population genetics of Phytophthora species.During sexual reproduction, different strains of phytophthora can exchange genetic material, creating new genetic combinations and genetic diversity within the population.The population of P. infestans from Latvia and Lithuania suggest the occurrence of sexual recombination, evidenced by the high frequency of oospore and genetic diversity in the population [40].
The presence of sexual and asexual reproduction of P. infestans was also reported in central Mexico [39].The high number of unique MLGs in P. capsici population from China also suggests the occurrence of outcrossing and sexual recombination in the population [38].These reports are also in line with another study that revealed a low population genetic diversity of P. parasitica in Chongqing resulting from clonality, as there is only MT A2 reported in the population.The limited population variation in this population is most likely from random mutation [48].The occurrence of sexual reproduction in a population does not always result in genetic recombination.P. infestans population in Poland showed moderately high genetic diversity.However, despite the nearly equal ratio of mating types A1 and A2 in the populations, there is a lack of evidence supporting genetic recombination in this study, as genetic variation is not necessarily generated from recombination [49].The co-occurrence of both MTs can coexist without sexual recombination, possibly due to the availability of susceptible hosts in a large scale and favorable environment, fostering low selection pressure that favors a limited range of genotypes [42].

Dispersal mechanism
The dispersal capacity of a pathogen narrates the gene flow between populations.Gene flow refers to the movement of genetic material from one population to another through various mechanisms, including active and passive dispersal [50].Gene flow can significantly affect pathogen population genetics, introducing new genetic variation into populations and influencing their genetic diversity [16,23].It can also alter the genetic structure of populations, which may affect the distribution and frequency of different alleles or genotypes [51].The rate of gene flow between different populations is influenced by several factors, such as pathogen mobility and mode of distribution, size, and distance between population habitats [52].The different rates of gene flow also determine variable levels of genetic variation across the population.High gene flow rates between two populations increase their genetic homogeneity and prevent genetic differentiation.In contrast, low rates of gene flow prevent a population from diverging.The relation between gene flow and population genetics of Phytophthora species has been reported in several studies.The lack of geographic structuring due to the occurrence of gene flow has been documented in several Phytophthora populations, including P. nicotianae [53], P. infestans [40], and P. palmivora [41,42].One-way gene flow also may account for the gradient genetic structure of P. infestans in Mexico [39] and the change in P. sojae population structure over years and geographies [37].The dispersal ability in microbes varies greatly and is determined by their dispersal traits, such as motility and chemotaxis, spore formation, and dormancy [50].For Phytophthora species, its spore trait is a primary determinant in their migration.Phytophthora produces sexual (oospores) and asexual spores (chlamydospores, sporangia, and zoospores) that can effectively incite Phytophthora diseases [10].In most cases, sporangium and zoospore have a limited dispersal distance as they are prone to unfavorable conditions.On another side, oospores and chlamydospores are more resilient to adverse climatic conditions and survive in soil or plant material [54].The dispersal mechanisms of Phytophthora species include active and passive dispersal.Five potential mechanisms are inoculum dispersal within the soil, inoculum dispersal in surface water, splash dispersal from soil to plants aboveground, aerial dispersal from sporulating lesions to other aerial parts of plants, and dispersal by human or invertebrate activity [55].
The long-distance movement of Phytophthora inoculum is most likely mediated by human activities, especially the trade of infected plant material.A study documented that the imported soybean seeds planted in Fujian facilitate the introduction of infested soil, creating strong fluctuation in the source of P. sojae primary inoculum between years [37].A study on the population structure of P. palmivora in Indonesia also suggests long-distance movement mediated by cocoa seedling transportation between different areas in Indonesia [41].The lack of geographic isolation of P. nicotianae in Indonesia was reported to be caused by extensive migration of the isolates via plant material or host adaptation [56].Another study also documented the genetic similarity of P. infestans due to the lack of migration boundaries and the free spread of P. infestans isolates between populations [40].

Agricultural practices
Agricultural practices can significantly impact the population genetics of plant pathogens.Disease control using fungicides and other management strategies can select for resistant strains of the pathogen, leading to changes in the population structure and diversity [20].Other agricultural practices such as crop rotation, irrigation, and cropping system can also affect the overall pathogen population genetics.Crop rotation can affect the pathogen's ability to survive in the soil and may impact the population's genetic diversity.A study on population genetics of P. infestans revealed that short crop rotations between growing seasons facilitate oospore-driven epidemics, stimulating a genetically diverse P. infestans population.The diversity from the soil's oospore population was then maintained by low fungicide application rates, reducing the likelihood of selection pressure [40].Irrigation can also affect the population structure, as it is involved in the survival and dispersal of the pathogen.P. sojae dispersal mediated by connecting rivers and streams between different sub-regions and no-tillage system in the majority of soya beans fields in Argentina are thought as the reason for the lack of geographic structuring in the population [57].On the other hand, the genetic structure associated with host species has been documented in P. nicotianae population, indicating that the intensive cropping systems support the host specialization of the pathogen [43].

Conclusion
Population genetics study in plant pathogens is important to understand how genetic diversity is generated and maintained within populations, how populations evolve and adapt to changing environments, and how genetic variation can lead to speciation.The genetic variation of Phytophthora population results from their coevolutionary interaction with hosts, its biological traits related to their reproduction and dispersal ability, agricultural practices, and other ecological factors.Understanding factors affecting the population genetics of Phytophthora species can help to track their population dynamic and evolutionary trajectory, supporting to the development of an effective sustainable disease management.

Table 1 .
Population genetics studies of Phytophthora species using SSR markers