Res. Plant Dis > Volume 31(4); 2025 > Article
Mandal, Kang, and Kil: Genomic Evolution of Tomato Spotted Wilt Virus and Its Resistance-Breaking Ability

ABSTRACT

Tomato spotted wilt virus (TSWV) continues to cause major losses in a wide range of crops due to its broad host range, the efficiency of its thrips vectors, and its capacity for rapid genomic diversification. This combination has complicated long-term disease management and has contributed to the repeated emergence of resistance-breaking (RB) strains in tomato, pepper, and other susceptible crops. While TSWV biology has been extensively investigated, the complex interplay among host range, vector biology, plant resistance, and RB evolution is often examined individually, neglecting its role as an integrated process. In this review, we aim to integrate current knowledge across these areas. We first describe the broad botanical range of TSWV and how movement among diverse hosts exposes viral populations to heterogeneous selection pressures. We then summarize key features of thrips-mediated transmission, including viral replication within vector tissues and the roles of vector immunity and associated microbes. Major resistance loci used in breeding, such as Sw-5, Sw-7, and Tsw, are reviewed, highlighting their mechanisms and limitations. We also analyze documented RB isolates from different regions, discussing the factors that appear to drive resistance breakdown, including genome reassortment, mutations in viral effectors such as NSs and NSm, environmental influences, and shifts in host or vector populations. Together, these perspectives demonstrate how interactions among TSWV, its plant hosts, and thrips vectors shape viral evolution in agricultural ecosystems. A clearer understanding of these processes will be essential for improving surveillance efforts and guiding the development of more sustainable and durable management strategies.

Introduction

Tomato spotted wilt virus (TSWV) is a tripartite, negative-sense single-stranded RNA virus that threatens global food security by causing enormous yield losses (Zhang et al., 2021). It belongs to the genus Orthotospovirus (family Tospoviridae) and has a host range of more than 1,500 plant species across nearly 90 angiosperm families (Abudurexiti et al., 2019; Parrella et al., 2003). TSWV infection typically causes concentric yellow rings on leaves (Fig. 1A) and fruits, which later turn brown; necrosis and bronzing may also develop as infected tissues age (Rotenberg and Whitfield, 2018). Globally, TSWV is estimated to cause about 1 billion dollars in crop losses annually, underscoring its status as a devastating plant pathogen (Kabaş et al., 2021). It is considered the second most important plant virus in agriculture (Scholthof et al., 2011).
Fig. 1.
(A) Tomato spotted wilt virus (TSWV) symptoms on pepper leaves and (B) TSWV genome with three different segments of RNA. ORF, open reading frame; GN/GC, glycoproteins; RdRp, RNA dependent RNA polymerase.
RPD-2025-31-4-291f1.jpg
TSWV is an enveloped, spherical virion approximately 80-110 nm in diameter. Its genome consists of three single-stranded RNA segments—small (2.9 kb), medium (4.8 kb), and large (8.9 kb), which are individually encapsulated and encode five proteins (Adkins, 2000). Among them, three proteins including a nucleocapsid gene, a two-domain-containing glycoprotein (GN/GC), and an RNA-dependent RNA polymerase that replicates and transcribes the viral genome are present in all bunyaviruses (Oliver and Whitfield, 2016). Using its tripartite genome (Fig. 1B), TSWV can exchange entire genomic segments between co-infecting variants/isolates within the same host plant, generating new reassortant genotypes (Best, 1961). In addition to these features, TSWV also codes for two genes, providing a specific adaptation capacity to plants and insects: NSs is the silencing suppressor, which helps to prevent the silencing of host antiviral RNA, and NSm is the movement protein involved in both host cells and long-distance movement inside the host plant (Lewandowski and Adkins, 2005).

Wide Host Range of TSWV

Compromised fitness arising from host alteration limits the concurrent occurrence of RNA viruses in multiple hosts (Elena et al., 2009; García-Arenal and Fraile, 2013). Some evolutionary studies have predicted that viruses can pass between alternative hosts and vectors. This provides evidence of mutation-mediated fitness that may increase in one host but decrease in another, which is an antagonistic pleiotropy-mediated fitness trade-off between hosts (Duffy et al., 2006; Elena et al., 2011). However, high fitness across multiple hosts has often been reported in experimental evolution studies showing the passage of microbes through different host environments (Bedhomme et al., 2012). Therefore, the fitness trade-off of microbes remains unclear, particularly for pathogens such as TSWV, considering their past ecological success. TSWV can rapidly adapt to new hosts and expand its host range owing to its high level of genetic diversity and positive pleiotropic effects of mutations (Ruark-Seward et al., 2020).
TSWV occurrence has been reported in over 1,500 plant species in more than 90 families, including a large number of cultivated crop species, such as tomato (Solanum lycopersicum), pepper (Capsicum annuum), onion (Allium cepa), spinach (Spinacia oleracea), peanut (Arachis hypogaea), potato (Solanum tuberosum), tobacco (Nicotiana tabacum), eggplant (Solanum melongena L.), and others (Brittlebank, 1919; Cho et al., 1987; Costa, 1941; Kamberoglu et al., 2009; Mullis et al., 2004; Sakimura, 1940; Sherwood et al., 2003; Smith, 1931). Different weed species also serve as natural reservoirs of TSWV during the off-season, aiding its successive transmission to crops during cropping time (Chatzivassiliou et al., 2001; Cho et al., 1987; Parrella et al., 2003). TSWV infection in ornamental plants such as chrysanthemum (Dendranthema grandiflora L.) and snapdragon (Antirrhinum majus L) has also been reported (Renukadevi et al., 2015; Senthilraja et al., 2018).
The first report of TSWV in South Korea was in sweet pepper in 2004 (Kim et al., 2004), after which it has also been reported in pepper, tomato, potato, soybean (Glycine max), Brugmansia suaveolens, Hoya carnosa, Eustoma grandiflorum, Humulus japonicus, and Peperomia obtusifolia (Choi et al., 2014; Kim et al., 2018; Yoon et al., 2017, 2018). TSWV infection was reported in hot pepper (Capsicum annuum), bell pepper (C. annuum var. angulosum), and tomato (Solanum lycopersicum) in greenhouses as well as hot pepper in open fields in eight areas of Jeonnam Province in 2013 (Ko et al., 2013). Comprehensive information on the identification of 23 crop species (five from the Solanaceae family) as TSWV host plants was reported in South Korea in 2020, with 42 weed hosts with three lifespans as important reservoirs of the viruses for overwintering (Kil et al., 2020). This continuous expansion of its host range not only enhances the long-term persistence of TSWV in agricultural ecosystems but also creates a large reservoir of genetic diversity, fueling the heterogeneous selection pressures that drive viral evolution and complicate disease management.

Insect Vectors

Plant viruses depend extensively on insect vectors for transmission and multiplication (Hogenhout et al., 2008). Multiple concurrent biotic stresses caused by pathogens and insect herbivores affect plants in several ways. Insects and pathogens that share the same host must interact to produce negative, positive, or neutral consequences (Belliure et al., 2005, 2010; Eigenbrode et al., 2018; Pan et al., 2013; Thaler et al., 2010).
Therefore, TSWV evolutionarily modifies the vector behavior and performance in such a way that its acquisition by vectors and transmission to plant hosts are highly enhanced (Eigenbrode et al., 2018). Thrips are the only known vectors of TSWV. Only nine of the 1,000 species of thrips are known to transmit TSWV (Table 1), all of which belong to the suborder Terebrantia and the family Thripidae (Inoue et al., 2004; Riley et al., 2011). Thrips exhibit a unique interaction with TSWV, transmitting the virus in a persistent, circulative manner (Rotenberg and Whitfield, 2018). Only the first-instar larvae of thrips can acquire the virus inside their body, multiply it inside the midgut cells, and transfer it to the salivary glands of adults, from where the virus enters the plant hosts as the vector feeds on plants. TSWV must cross several membrane barriers during this process (De Assis Filho et al., 2002; Kritzman et al., 2002). Thus, compared with the direct effects, direct and indirect (plant-mediated) effects may be co-created by TSWV replicating inside both the vector body and the host plant (Belliure et al., 2005; Shrestha et al., 2012).
Table 1.
List of thrips vectors reported to transmit TSWV
Thrips vector Reference
Frankliniella occidentalis Medeiros et al. (2004),
Nagata et al. (2004)
Thrips tabaci Wijkamp et al. (1995)
Frankliniella schultzei Sakimura (1969),
Wijkamp et al. (1995)
Frankliniella fusca Naidu et al. (2001), Sakimura (1963)
Frankliniella intonsa Wijkamp et al. (1995)
Frankliniella bispinosa Avila et al. (2006)
Thrips setosus Tsuda et al. (1996)
Frankliniella gemina Borbón et al. (1999)
Frankliniella cephalica Ohnishi et al. (2006)

TSWV, tomato spotted wilt virus.

TSWV activates innate immunity in its important vector F. occidentalis by activating genes, including those encoding defensin, cecropin, lectin, Toll-3, and Jun N-terminal kinase. This occurs without harming the vector's life cycle or inducing any cytopathological changes, which may pave the way for understanding and developing novel control strategies against plant viruses transmitted by insect vectors (Medeiros et al., 2004). Regarding the complex transmission biology of TSWV, gene networks that regulate plant metabolism and defense responses increase the susceptibility of virus-infected plants to vector colonization, thus benefiting both the vector and virus (Nachappa et al., 2020).
Comparing vector and non-vector thrips species, Shrestha et al. (2019) found that only non-vector thrips contained viral replication inhibitors (radical S-adenosylmethionine), whereas vector and non-vector species contained viral replicator contigs but to some extent differed in immune signaling pathways. TSWV has been reported to affect different life stages of F. fusca when treated with it, showing different transcriptome-level responses (Shrestha et al., 2017). Recent mold-breaking studies have revealed the importance of insect microbes in virus biology as well as their vector competence. However, the mechanism of interaction between the virus and its insect vector remains complex.
Consequently, understanding the molecular mechanisms of viral replication and circulation within thrips, including the role of vector immunity and associated microbes, is crucial. This complex vector-virus relationship ensures the efficient long-distance spread of TSWV, linking its survival in the vector to its evolutionary success in the host plants.

Control through Host Resistance

Sound epidemiological principles and Integrated Disease Management approaches, including physical, cultural, chemical, and biological measures, are required to manage TSWV. Given the inevitable losses caused by TSWV in a wide range of crops, various resistant varieties have been developed, but are still insufficient to fully control this highly transmissible virus. The strong interaction among host, vector, and virus further complicates efforts to reduce disease severity. In addition, the remarkable capacity of the virus for genome reassortment represents a continuing threat to agriculture. Managing insect vectors for high-yielding cultivars and increasing the use of resistant cultivars are recommended for TSWV control in terms of qualitative damage reduction (Kim et al., 2021).

Gene-mediated natural resistance.

Ardent research directed toward the development of sustainable management strategies, such as genetically resistant plant varieties, has been successfully conducted. Finlay (1953) reported that five genes were inherited by four TSWV-resistant tomato varieties. Later, more intensification was added to this list of resistance genes to reduce the agricultural losses caused by this harmful disease agent (Table 2).
Table 2.
Compilation of TSWV-resistant genes reported and their source plants
Resistance gene Source plant Reference
Tsw Capsicum chinense, C. annuum De Ronde et al. (2019), Jahn et al. (2000)
Sw-1 Lycopersicon peruvianum Paterson et al. (1989)
Sw-1a L. pimpinellifolium, Finlay (1953), Roselló et al. (1998)
Sw-1b L. esculentum Finlay (1953), Holmes (1948), Roselló et al. (1998)
Sw-2 L. pimpinellifolium, L. esculentum Finlay (1953), Holmes (1948)
Sw-3 L. pimpinellifolium, L. esculentum Finlay (1953), Holmes (1948), Roselló et al. (1998)
Sw-4 L. pimpinellifolium, L. esculentum Finlay (1953), Holmes (1948), Roselló et al. (1998)
Sw-5 L. peruvianum (Solanum peruvianum), L. esculentum, S. chmielewski, S. sitiens Gardner and Panthee (2012), Giordano et al. (2000), Kabaş et al. (2021), Roselló et al. (2001)
Sw-5a L. peruvianum Brommonschenkel et al. (2000), Folkertsma et al. (1999), Spassova et al. (2001)
Sw-5b L. pimpinellifolium, L. peruvianum, L. esculentum, L. pennellii, L. neorickii, L. huaylasense, L. galapagense, L. corneliomuelleri, L. cheesmaniae, L. arcanum, L. chilense Brommonschenkel et al. (2000), Folkertsma et al. (1999), Kabaş et al. (2021), Spassova et al. (2001), Zhu et al. (2017)
Sw-5c L. peruvianum Brommonschenkel et al. (2000), Folkertsma et al. (1999), Spassova et al. (2001)
Sw-5d L. peruvianum Brommonschenkel et al. (2000), Folkertsma et al. (1999), Spassova et al. (2001)
Sw-5e L. peruvianum Brommonschenkel et al. (2000), Folkertsma et al. (1999), Spassova et al. (2001)
Sw-5f L. esculentum Rehman et al. (2009)
Sw-6 L. esculentum Roselló et al. (1998)
Sw-7 L. chilense Canady et al. (2001)

TSWV, tomato spotted wilt virus.

Natural resistance mechanism.

Plants use pathogen-associated molecular pattern-triggered immunity as the first line of defense against immune responses when invaded by pathogens (El-Sappah et al., 2019). Specific pathogen effectors are recognized by nucleotide-binding leucine-rich repeat receptors (NLRs) in tomatoes during viral invasion and activate effector-triggered immunity (Caplan et al., 2008; Muthamilarasan and Prasad, 2013; Ramirez-Prado et al., 2018; Tian et al., 2021). TSWV in plants activates salicylic acid-mediated defense, inducing rapid transcriptional activation of resistance (R) genes (Beris et al., 2018; Huang, 2021; Nachappa et al., 2020). TSWV-infected tomatoes and other plants use RNA interference as a conserved regulatory mechanism that supports gene regulation by providing a strong defense against invading viruses (Mitter et al., 2013; Ramesh et al., 2017).

Gene description.

Many natural resources of TSWV-resistant germplasm have been previously screened from both cultivated and wild tomatoes, as a result of which several TSWV-resistant genes have been identified (Qi et al., 2021). In total, eight resistance gene loci, Sw-1a, Sw-1b, Sw-2, Sw-3, Sw-4, Sw-5, Sw-6, and Sw-7, have been identified in tomatoes (Qi et al., 2021). In addition, the Tsw locus was identified in pepper and examined to determine its connection to the capacity of TSWV-A to overcome Sw-5 gene resistance. Distinct viral gene products control the outcome of infection in plants carrying Tsw and Sw-5, and these two loci share different evolutionary ancestors (Jahn et al., 2000). Sw-1a and Sw-1b are single dominant allele pairs of Sw-1 that have been reported to be present in L. pimpinellifolium and Lycopersicon esculentum, respectively (Finlay, 1953). Sw-2, Sw-3, and Sw-4 are recessive genes that are also present in tomatoes and are resistant to TSWV, although they are inherited independently (Finlay, 1953). These recessive characteristics give rise to specific resistance in homozygotes, which restricts commercial breeding of hybrids (Roselló et al., 2001).
Sw-5, a single dominant resistance gene, was developed to confer active vertical resistance to tomato plants (Stevens et al., 1991). Sw-5 has six homologous paralog genes (Sw-5a, Sw-5b, Sw-5c, Sw-5d, Sw-5e, and Sw-5f) that are loosely clustered within the same gene family (de Oliveira et al., 2018; Stevens et al., 1995). The extensively used Sw-5 gene cannot provide sustainable resistance at high concentrations of TSWV (Batuman et al., 2017). The Sw-6 gene has also been identified in tomatoes with very weak and partial resistance against TSWV and a narrower effect than that of Sw-5 (Roselló et al., 1998, 2001). The most recent major advance in Sw gene discovery was the identification of Sw-7, a single dominant gene that confers resistance against various TSWV isolates from Florida, Georgia, Hawaii, and South Africa (Canady et al., 2001; Scott et al., 2005; Stevens et al., 2006, 2007).

Molecular marker.

Marker-assisted selection targets desired genes that determine target traits using molecular markers. This reduces breeding costs and improves selection accuracy without environmental effects (Qi et al., 2021). The use of multiple molecular markers (e.g., RAPD, SCAR, AFLP, CAPS, In-Del, SNP, and KASP) associated with the Sw-5 gene has improved the efficiency and accuracy of TSWV resistance breeding in tomato and pepper (Panthee and Ibrahem, 2013; Qi et al., 2021; Śmiech et al., 2000). In search of new resistance against TSWV, Sw-7 gene-related markers (e.g., RFLP, SSR, and SCAR) have been identified for further analysis (Dockter et al., 2009; Stevens et al., 2007; Tanksley et al., 1992).

Alternative resistance strategies.

An alternative strategy involving host resistance to thrips has been developed for pepper and potato, which correlates with restricted TSWV spread (Jericho and Wilson, 2003; Maris et al., 2003). Genetically modified tobacco, tomato, and peanut plants with the NSm or nucleocapsid genes have been reported to be TSWV resistant (Culbreath et al., 2003; Gubba et al., 2002; Herrero et al., 2000; Jan et al., 2003). A study by Srinivasan et al. (2017) on peanut cultivation suggested that host resistance should not be considered the only option for TSWV management but should be combined with other control techniques. Because newly developed resistant cultivars show better control efficiency than older cultivars, resistance may break easily under high thrips and TSWV pressure (Srinivasan et al., 2017).
While Sw-5 and other major resistance loci have provided effective control, the mechanisms of these R genes inherently place strong selection pressure on the viral population. This pressure, combined with the inherent genetic plasticity of TSWV, creates the perfect evolutionary pathway for the emergence of resistance-breaking (RB) variants, a challenge that necessitates integrated management strategies.

Resistance-Breaking

Globally, TSWV is the second most economically important plant virus owing to its catastrophic nature (Scholthof et al., 2011). The combination of strong virulence, wide host range, and efficient transmission by thrips makes TSWV difficult to control. These same features also complicate efforts to unravel the molecular mechanisms underlying RB and evolutionary emergence of new RB isolates. The development of a sturdy and efficient resistance against TSWV would lead to a substantially positive economic impact on agricultural production (López et al., 2011).

Mechanism of RB.

The three ssRNA segments (L, M, and S) in the TSWV genome allow the exchange of genome segments between variants that co-infect the same plant. This process gives rise to a new term, ‘reassortment’ (different from recombination) (Tentchev et al., 2011). The evocative representation of the ‘boom and bust’ cycle of resistance genes is used to protect the crops from TSWV, where resistant cultivars are grown on large geographical scales (the boom part), which is then subjected to resistance breakdowns (the bust part). The sustainability of plant resistance to viruses has been reported to be related to two major issues: (1) the ability of the virus to yield RB properties, which depends on the number of mutations required for such properties and (2) the impact of these mutations on virus rivalries (Ayme et al., 2006, 2007; Desbiez et al., 2003; Fabre et al., 2009; Harrison, 2002; Janzac et al., 2010; Jenner et al., 2002).

Reassortment reports.

The extensive occurrence of TSWV reassortment events in isolates from Turkey, Spain, France, and Italy has revealed that the reassortment mechanism is actively responsible for TSWV emergence and epidemics worldwide (Tentchev et al., 2011). Within a very short time of evolving resistant host plants, TSWV routinely breaks resistance in different commercial crops, such as pepper (Hobbs et al., 1994; Moury et al., 1997) and tomato (Cho et al., 1996; Latham and Jones, 1998).
In recent years, RB strains of TSWV have been reported in Capsicum species carrying the Tsw gene in Italy (Roggero et al., 2002) and in tomato species carrying the Sw-5 gene in Spain (Aramburu and Marti, 2003). The first report of TSWV strains breaking the resistance induced by the Tsw gene under field conditions was from Spain in 2004 (Margaria et al., 2004), followed by Australia (Thomas-Carroll and Jones, 2003) and Spain in 2011 (Debreczeni et al., 2011). In 2012, RB TSWV isolates were recovered to overcome resistance in different pepper hybrids from different locations in southern Italy (Crescenzi et al., 2013). Similarly, TSWV infection has been reported in genetically resistant pepper plants in Sam-sun, Turkey, and Argentina (Borbón et al., 1999; Deligoz et al., 2014; Ferrand et al., 2015). Tomato varieties with resistance genes were reported to be severely infected with TSWV in Turkey in 2016 because of changes in the genetic structure of TSWV isolates (Fidan, 2016).
Tomato cultivars carrying the Sw-5 gene became susceptible to TSWV in the Central Valley of California, USA, in 2016 (Batuman et al., 2017). In Italy, virulent TSWV mutants were reported to break Sw-5-mediated resistance in tomatoes in 2018 (Di Rienzo et al., 2018). In 2019, the first detection of Sw-5b RB by RB TSWV isolates in Serbia was observed in protected crops of a tomato (Sw-5b+) cultivar at two separate locations (Petrović et al., 2021). In South Korea, the first report of RB TSWV isolates in C. annuum carrying the Tsw gene was published in August 2021. Temperature-mediated RB was also reported in a single dominant resistance gene Tsw from Capsicum chinense, where the resistance failed to function at above 28°C (De Ronde et al., 2019). The occurrence of RB TSWV strains C118Y and D122G in tomato plants harboring the Sw-5 resistance gene was reported as the first RB variant in North Carolina (Lahre et al., 2023). In addition, the first report of TSWV occurrence in C. annuum plants carrying the Tsw resistance gene was reported in Texas for Bushland TSWV RB isolates (Gautam et al., 2023).

Natural reassortment.

The tripartite genome of TSWV can easily exchange entire genomic segments among different isolates within the same plant in nature giving rise to new TSWV variants. In the Tsw gene, the avirulence factor is the NSs protein translated from S RNA segment (de Ronde et al., 2013; Margaria et al., 2007). NSs protein is multifunctional and exhibits RNA silencing suppressor activity, and RB is not linked to the alteration of any universal specific amino acid of this protein. The expansion and simultaneous occurrence of different TSWV strains infecting pepper plants reported in the Mediterranean Basin indicates an increased diversity of RB TSWV strains through the substitution of amino acid positions in nature (Almasi et al., 2020).
It is well known that TSWV exists in nature as heterogeneous populations of stable isolates that may serve as genetic reservoirs for adaptation. A new reassortment strain may develop through the exchange of resistant strains from two separate regions. Such exchanges have been predicted between European and Asian TSWV populations (Tentchev et al., 2011) as well as among isolates from New Zealand (Timmerman-Vaughan et al., 2014) and Korea (Lian et al., 2013), and one of the two TSWV lineages has also been reported in Italy (Margaria et al., 2014). A brief study in Italy revealed that TSWV isolates from two distinct subpopulation clusters, named TSWV-A and TSWV-D, similar to those in the USA (TSWV-A) and the Netherlands (TSWV-D), could attack resistant cultivars of host plants (Finetti-Sialer et al., 2002). Another phylogenetic analysis based on the nucleocapsid gene of Mediterranean isolates also showed clustering of two distinct Italian subpopulations, in contrast to other countries (e.g., France, Spain, and Bulgaria) with two groups of TSWV isolates (Turina et al., 2012). TSWV-p331 in northern Italy was also found to originate from two evolutionary TSWV strains through natural reassortment. Similar to p331, NSs protein carries a high number of amino acid substitutions and is a potent silencing suppressor (Thomas-Carroll and Jones, 2003). However, the reassortment process in TSWV remains poorly understood.

In-lab genome reassortment.

Genome organization is the key to distinguishing different genera as well as the translational polarity of the genome segments, which may be either negative-sense or a combination of negative-sense and ambisense. The tripartite viral genomes of closely related viruses from the Bunyaviridae family offer the potential to exchange genetic information through reassortment as a mechanism for generating diversity (Qiu et al., 1998). The serial passage of two suppressed isolates, TSWV-10 and TSWV-D, to TSWV nucleocapsid transgene-mediated resistant tobacco indicated the use of genome reassortment in TSWV for adaptation to new host genotypes (Qiu and Moyer 1999). The NSs protein encoded by the S RNA segment of TSWV has been previously identified as a genetic determinant of Tsw-based RB (Margaria et al., 2007). Recent TSWV reassortment events in South Korea have been attributed to the emergence of the TSWV-YI strain, which carries the L and M RNA segments derived from the local South Korean TSWV population and the S RNA segment originating from a foreign population. Therefore, TSWV-YI is a new RB variant and a reassortant containing genetically distinct S RNA segment (Kwon et al., 2021).

Recent valuable studies.

Padmanabhan et al. (2019) studied the Sw-7 gene and identified its involvement in callose accumulation, lignin deposition, proteolysis, transcriptional activation, and phosphorylation. In addition, the potential involvement of PR-5 in Sw-7 resistance has been demonstrated, with PR-5 over-expressed plants conferring enhanced resistance, thereby delaying virus accumulation and symptom expression (Padmanabhan et al., 2019). New cultivars that can provide resistance against Sw-5 RB isolates have been identified through mechanical inoculation methods and SCAR markers in tomatoes as follows: S. penellii, S. chmielewski, S. habrochaites, L. peruvianum, and S. sitiens, LA0716, LA1028, LA1777, LA2744, and LA4110 (Kabaş et al., 2021). A multiplex reverse-transcription polymerase chain reaction assay for the detection of emergent Tsw RB variants in South Korea with high specificity and sensitivity was developed to manage the introgression of assortments (Kwon et al., 2022). RB strains from Korea mostly aligned with RB strains from Italy and Spain (Fig. 2A), and the RB region was between 1,200 and 1,500 bp in their sequences (Fig. 2B), which provides valuable information for understanding the genomic pattern of RB. Plants increase the transcription of genes that produce pathogenesis-related (PR) proteins during pathogen attacks or infections. Genome-wide identification of plants producing the PR protein, thus revealing the important role of PR-10 and Sw-5b genes in the defense response to the TSWV infection, has recently been realized. Transcription-level analysis of PR-10 family members showed that the PR-10 gene is highly expressed in some parts of tomato plants, and its association with Sw-5b gene transcription and activity in tomato leaves is strongly induced by TSWV infection (Islam et al., 2022). The development of Sw-5b-resistant tomato and Tsw-resistant pepper cultivars has led to the recent emergence of RB strains worldwide, facilitating the emergence of novel RB strains (Chinnaiah et al., 2023). The discovery of a novel TSWV-RB Mexican isolate encoding a non-canonical NSm C118F substitution associated with Sw-5 gene-mediated RB in tomato is a new viral adaptation that suggests further crop monitoring, considering the establishment of novel RB isolates (Rodríguez-Negrete et al., 2023).
Fig. 2.
Genomic characteristics and resistance-breaking (RB) patterns of tomato spotted wilt virus (TSWV) isolates. (A) Phylogenetic alignment of documented RB isolates and non-resistance-breaking (NRB) isolates of TSWV based on partial S RNA sequences. RB isolates from Korea cluster closely with RB groups previously reported from Italy and Spain, suggesting possible shared evolutionary origins or reassortment-driven convergence. (B) Schematic representation of the genomic region associated with RB mutations. The highlighted region (approximately 1,200-1,500 bp within the S RNA segment) corresponds to the NSs coding region and encompasses amino acid substitutions reported to be associated with loss of avirulence in pepper (Tsw gene) and tomato (Sw-5 gene). Mutations within this region affect the RNA silencing suppressor function of NSs, enabling RB isolates to evade host immunity. The diagram summarizes representative RB isolates and their known mutation sites to illustrate the conserved and variable amino acid positions implicated in resistance breaking.
RPD-2025-31-4-291f2.jpg
In summary, the emergence of RB strains is not attributable to a single factor, but rather to a complex, multi-layered evolutionary trajectory involving the co-occurrence of point mutations in key effectors and genome reassortment. This dynamic process fundamentally challenges the durability of monogenic resistance genes in agricultural settings.

Conclusion

This review has systematically integrated the intricate connections among TSWV host range, thrips vector biology, host resistance, and the mechanisms driving RB evolution. A critical takeaway from this synthesis is that TSWV's capacity to overcome resistance is fundamentally rooted in the ecological interplay among the virus, the plant, and the vector, rather than a simple mutation event. The high genetic diversity and rapid mutation rate of TSWV are major challenges for global agriculture. Its complex genomic structure facilitates the continual generation of novel variants. Diverse cultivated and wild plant species serve as reservoirs, while insect vectors enhance its spread and maintain a dynamic network of interactions among virus, host, and environment. Although new resistance genes have been introduced, TSWV has repeatedly overcome these barriers through mutation and reassortment. This situation calls for alternative and complementary management approaches, in addition to the improvement of gene-based resistance. Based on the application of new breeding techniques, the development of broad-spectrum resistance against TSWV is necessary for the accumulation of transgene proteins, RNA silencing, artificial NLR evolution, gene editing, production of new-generation antiviral compounds, and other vector-derived host resistance. Therefore, future research must shift from managing individual components to developing holistic, integrated strategies that address TSWV as a dynamic, evolving system, securing the long-term sustainability of crop production.

NOTES

Conflict of Interest

No potential conflict of interest relevant to this article was reported.

Acknowledgments

This research was supported by a grant (RS-2025-02273065) funded by the Rural Development Administration of Korea.

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