International Journal of Molecular Sciences Review Advances and Prospects of Virus-Resistant Breeding in Tomatoes Zolfaghar Shahriari 1,2,† , Xiaoxia Su 1,† , Kuanyu Zheng 1, * and Zhongkai Zhang 1, * 1 2 * † Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; shahriari225@gmail.com (Z.S.); sxx919@163.com (X.S.) Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz 617-71555, Iran Correspondence: zky@yaas.org.cn (K.Z.); zzk@yaas.org.cn (Z.Z.); Tel.: +86-871-6512-3133 (K.Z. & Z.Z.) These authors contributed equally to this work. Abstract: Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies. Citation: Shahriari, Z.; Su, X.; Zheng, K.; Zhang, Z. Advances and Keywords: virus resistance gene; RNAi; tomato breeding; CRISPR-Cas; genome editing Prospects of Virus-Resistant Breeding in Tomatoes. Int. J. Mol. Sci. 2023, 24, 15448. https://doi.org/10.3390/ ijms242015448 Academic Editors: Yong-Gu Cho and Yangyong Zhang Received: 1 August 2023 Revised: 15 October 2023 Accepted: 16 October 2023 Published: 22 October 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1. Introduction Tomato (Solanum lycopersicum L.) is one of the most economically valuable fruit or vegetable crops worldwide. According to the Food and Agriculture Organization of the United Nations (FAO) Statistical report, the total worldwide production of tomatoes was 189.23 million tons in 2021, with a value of over USD 30 billion. Viral diseases can significantly decrease the yield and quality of tomatoes [1]. According to the new classification system (2022) approved by the International Committee for the Classification of Viruses (ICTV), there are 181 viral species infecting tomato crops. The major tomato viral pathogens that have been emerging worldwide over the past 20 years include the following genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus [1–3]. Considering that most of these viruses are transmitted by insect vectors, the main agronomic and classic management of viral diseases involves controlling the vector with insecticides and uprooting symptomatic plants or those with sanitary voids to reduce the incidence of the virus [4,5]. However, these controlling methods only reduce the viral effects to some extent and cannot efficiently eliminate tomato virus disease [6]. Virus resistance breeding is the most promising method for controlling viral diseases [7,8]. Combining conventional hybrid breeding with marker-assisted selection (MAS) to introduce resistance genes from wild germplasm into cultivated cultivars has proven to Int. J. Mol. Sci. 2023, 24, 15448. https://doi.org/10.3390/ijms242015448 https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2023, 24, 15448 2 of 22 be effective for virus resistance breeding in tomatoes [8–10]. However, most of the virus resistance genes currently found in tomatoes are single-gene-mediated with qualitative resistance, and thus, virus mutation and mixed infection can easily lead to resistance breakdown [11–13]. In addition, some emerging tomato viruses, such as tomato chlorosis virus (ToCV), tomato brown rugose fruit virus (ToBRFV), and tomato mottle mosaic virus (ToMMV), still lack relevant natural resistance genes, making conventional virus resistance breeding in tomatoes challenging [14–16]. This review summarizes tomato viruses and their characteristics. According to the epidemic characteristics of tomato viruses, we propose that tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Based on this proposition, we summarize and analyze the advantages and characteristics of three tomato antiviral breeding strategies: MAS-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we discuss the challenges and provide suggestions for improving these three breeding strategies in the future. 2. Tomato Viruses and Their Epidemic Characteristics Currently, the main tomato epidemic viruses worldwide include begomoviruses, orthotospoviruses, tobamoviruses, potyviruses, and criniviruses. The classification and details of these viruses are listed in Table 1. These major epidemic viruses generally cause tomato plant leaf shrinkage, chlorosis, leaf and fruit necrosis, spotting, and other symptoms, which significantly impact tomato quality and yield (Figure 1). Figure 1. Symptoms of viral diseases in tomatoes. (A) Symptoms of TSWV on tomato fruits. (B) Symptoms of ToBRFV on tomato fruits. (C) Symptoms of TYLCV on tomato leaves. (D) Symptoms of ChiVMV on tomato leaves. (E) Symptoms of ToCV on tomato leaves. A typical characteristic of plant viruses is the rapid nucleotide mutation and genome recombination rates, which contribute to the emergence of novel viral strains or species, Int. J. Mol. Sci. 2023, 24, 15448 3 of 22 increase the virulence of the virus, and cause the breakdown of host resistance, resulting in severe symptoms in the host plant [17–19]. Another characteristic of plant viruses, as revealed by high-throughput sequencing or other means of detection, is the presence of high mixed-infection incidence in the field between viruses or between viruses and other pathogens [2,20,21]. Mixed infections usually increase synergies between pathogens and the breakdown of host resistance, which has been reported in many cases [13,22]. Therefore, developing a quick response against the resistance breakdown caused by virus mutation, recombination, and mixed infection to efficiently create broad-spectrum and persistent antiviral germplasm materials has become a major challenge and the primary objective in tomato antiviral breeding. Table 1. Classification and details of the major epidemic viruses of tomato. Genus Epidemic Species Worldwide Genome Transmission Symptoms References Whitefly, seed Yellowing, curling, and a significant loss in apical leaf. Early-infected plants are frequently infertile. Since most blooms (>90%) droop after infection, there is almost no or fewer small fruit. [23–26] [27–29] Tomato yellow leaf curl virus (TYLCV)) and tomato leaf curl virus (ToLCV) Single-stranded DNA (ssDNA) Orthotospovirus Tomato spotted wilt virus (TSWV) Negative-sense single-stranded ambisense (-ssRNA) RNA Thrips, seed Stunting, necrosis, bronzing, chlorosis, ring spots, and ring patterns on the leaves, stems, and fruits. Tobamovirus Tobacco mosaic virus (TMV), tomato mosaic virus (ToMV), and tomato brown rugose fruit virus (ToBRFV) Single-stranded positive-sense RNA (+ssRNA) Seed, mechanical transmission such as by hand, pruning tools, soil, etc. Yellow–green mottling on the leaves; stunted growth; flowers and leaflets may be curled, distorted, and smaller than normal in size. [15,30–34] Potyvirus Potato virus Y (PVY), and, chilli veinal mottle virus (ChiVMV) Single-stranded positive-sense RNA (+ssRNA) viruses Aphid, seed Leaf mosaic, mottle and crinkling, vein necrosis and necrotic spots, stem and petiole necrosis, leaf drop, and yield reduction. [2,21,35,36] Crinivirus Tomato chlorosis virus (ToCV) Single-stranded positive-sense RNA (+ssRNA) viruses Whitefly Leaf chlorosis, chlorotic flecking, and bronzing. Fruits are symptomless but with reduced yield. [37,38] Begomovirus 3. Strategies of Tomato Resistance Breeding against Viruses At present, there are three main strategies for tomato antiviral breeding: MAS-based hybrid breeding, RNAi-based transgenic breeding, and CRISPR/Cas-based gene editing. (1) MAS-based hybrid breeding. In this strategy, wild or domestic germplasm with resistance genes is hybridized with non-resistance germplasm materials, and F1 hybrid generation is further selfed for multiple generations. By serving as a resistance selection method for the selfed generations, MAS allows for the rapid creation of new resistance germplasm (Figure 2A) [39]. (2) RNAi-based transgenic breeding. In this strategy, a targeted virus gene/dsRNA/microRNA sequence is transferred into the non-resistant germplasm material by the Agrobacterium-mediated transformation method so as to induce the RNA silencing effect in the host plant to resist virus infection (Figure 2B) [40]. Int. J. Mol. Sci. 2023, 24, 15448 4 of 22 (3) CRISPR/Cas-based gene editing. In this strategy, a CRISPR/Cas vector is designed to target the DNA/RNA sequence of the virus or the host’s susceptible genes, thus interrupting the replication and assembly process of the virus in the host, ensuring resistance against the virus (Figure 2C) [41]. These three strategies are discussed in the following sections. Figure 2. Strategies of tomato resistance breeding against viruses. (A) Marker-assisted selection (MAS)-based hybrid breeding. (B) RNA interference (RNAi)-based transgenic breeding. (C) CRISPR/Cas-based gene editing. 4. Virus Resistance Gene and MAS-Based Hybrid Breeding in Tomatoes 4.1. The Tomato Ty Gene Family Encoding for Resistance against Begomoviruses At present, six begomoviruses resistance genes, all belonging to the Ty gene family, have been identified, namely, Ty-1, Ty-2, Ty-3, Ty-4, Ty-5, and Ty-6 (Table 2). Ty-1, Ty-3, Ty-4, and Ty-6 are derived from the wild tomato species S. chilense, while Ty-2 and Ty-5 are obtained from S. habrochaites and the commercial tomato cultivar Tyking, respectively [42,43]. Ty-1 is allelic with Ty-3, and the two genes are located on chromosome 6 of S. chilense [44]. Ty-1/3 increases the cytosine methylation of viral genomes and induces a hypersensitive response to viral infections, conferring plants with TYLCV resistance [45]. Although Ty-1 exhibits broad-spectrum begomoviruses resistance, recent studies have shown that resistance is compromised by the co-infection with a beta satellite [46]. Gene Ty-2 located on the long arm of S. habrochaites chromosome 11 has been identified as the nucleotidebinding domain and a leucine-rich repeat-containing (NB-LRR) gene [47]. Moreover, the Ty-4 gene maps to chromosome 3 of S. chilense and has been reported to increase virus resistance in combination with Ty-3 [42]. The recessive TYLCV resistance gene Ty-5 located on chromosome 4 of the commercial tomato cultivar Tyking encodes the mRNA surveillance factor Pelota [8,42]. A recent study showed that Ty-5 confers broad-spectrum resistance to two representative begomoviruses occurring in China [8]. Ty-6, located on chromosome 10 of S. chilense, effectively complements the resistance conferred by Ty-3 and Ty-5 [48]. It was reported that Ty-6 also confers resistance to tomato mottle virus (ToMoV), suggesting that the gene inhibits both mono- and bi-partite begomoviruses in tomatoes [48]. Although PCR-based markers have been identified and developed for Ty-1, Ty-2, Ty-3, and Ty-4 TYLCV-resistant loci, these markers are inconsistent, thus limiting their application in MAS [49,50]. Int. J. Mol. Sci. 2023, 24, 15448 5 of 22 Table 2. A brief review of virus resistance gene families in tomatoes. Resistance Gene Family Ty gene family (against begomoviruses) Sw gene family (against orthotospoviruses) Tm gene family (against tobamoviruses) Pot-1 gene (against potyviruses) Resistance Genes Source of Resistance Genes Location on Chromosome Gene Action Efficiency Resistance Mechanism Ty-1 Solanum chilense 6 Dominant Broad-spectrum begomoviruses resistance Ty-1 encodes an RNA-dependent RNA polymerase (RDR) involved in the RNA silencing pathway, increasing antiviral RNAi responses and the viral genome’s cytosine methylation. Ty-2 S. habrochaites 11 (Long arm) Dominant TYLCV resistance Ty-2 encodes a nucleotide-binding leucine-rich repeat (NLR) protein. The Ty-2 could recognize TYLCV Rep/C1 protein and induce hypersensitive responses (HR) in host plant. Ty-3 S. chilense 6 Dominant Complementary resistance Ty-3 encodes an RNA-dependent RNA polymerase (RDR) involved in the RNA silencing pathway. Ty-4 S. chilense 3 Dominant Increase virus resistance in combination with Ty-3 Not reported. Ty-5 Tyking 4 Recessive Broad-spectrum resistance Encodes messenger RNA (mRNA) surveillance factor Pelota. Silencing of Pelota in a susceptible line rendered the transgenic plants highly resistant. Ty-6 S. chilense 10 Dominant Complements the resistance conferred by Ty-3 and Ty-5 Not reported. Sw-1a Lycopersicum pimpinellifolium Not reported Dominant Some degree of resistance to specific TSWV Not reported. Sw-1b L. pimpinellifolium Not reported Dominant Some degree of resistance to specific TSWV Not reported. Sw-2 L. pimpinellifolium Not reported Recessive Some degree of resistance to specific TSWV Not reported. Sw-3 L. pimpinellifolium Not reported Recessive Some degree of resistance to specific TSWV Not reported. Sw-4 L. pimpinellifolium Not reported Recessive Some degree of resistance to specific TSWV Not reported. Sw-5 S. peruvianum 9 Dominant High level of resistance to a wide range of TSWV Sw-5 belongs to nucleotide-binding leucine-rich repeat (NB-LRR) type R gene. Sw-5 confers resistance by recognizing a 21-amino-acid peptide region of the viral movement protein NSm, triggering immunity response. Sw-6 L. pimpinellifolium Not reported Incompletely Dominant Some degree of resistance to specific TSWV Not reported Sw-7 L. chilense 12 Dominant Resistance to a wide range of TSWV Involved in pathogenesis-related (PR) proteins PR1 and PR5-related resistance process. Tm-1 S. habrochaites 2 Incompletely Dominant TMV partial resistance Tm-1 encodes a protein that binds ToMV replication proteins and inhibits the RNA-dependent RNA replication of ToMV. Tm-2 S. peruvianum 9 Dominant TMV partial resistance Tm-2 belongs to nucleotide-binding leucine-rich repeat (NB-LRR) type R gene, which can recognize movement proteins (MPs) of TMV and ToMV and activate a resistance response. References [8,42,44–47,51–54] [10,50,52–54] Tm-22 S. peruvianum 9 Dominant Confers a more effective TMV resistance Tm-2 belongs to nucleotide-binding leucine-rich repeat (NB-LRR) type R gene, which can recognize movement proteins (MPs) of TMV and ToMV and activate a resistance response. Pot-1 L. hirsutum 3 Recessive PVY resistance Tomato Pot-1 is the orthologue of the pepper pvr2-eIF4E gene, encoding the plant-susceptible eIF4E1 translation initiation factor protein. Duplicate recessive Pot-1 genes interrupt the interaction of the potyviruses VPg protein with the eIF4E1, suppressing virus replication. [14,55–60] 2 [61–63] Int. J. Mol. Sci. 2023, 24, 15448 6 of 22 4.2. The Tomato Sw Gene Family Conferring Resistance against Orthotospoviruses S. Peruvianum, reported as the first wild tomato with a broad-spectrum resistance to tomato spotted wilt virus (TSWV), has been widely crossed with commercial cultivars since the 1930s [7]. Studies on molecular genetics indicated that this resistance was conferred by a single dominant gene/locus named Sw-5, which was initially found to be effective against several TSWV isolates from the United States [64] and Brazil [65]. Sw-5 also exhibits a broad spectrum and high level of resistance to other orthotospoviruses, including tomato chlorotic spot virus (TCSV), chrysanthemum stem necrosis virus (CSNV), and groundnut ringspot virus (GRSV), and is widely used in tomato breeding [7,66]. Sw-5 was discovered near the telomeric area of chromosome 9 between the CT71 and CT220 restriction fragment length polymorphism (RFLP) markers [67]. The Sw-5 locus is part of a loosely clustered gene family containing six paralogous genes: Sw-5a, Sw-5b, Sw-5c, Sw-5d, Sw-5e, and Sw5f [7,10]. Among these genes, only Sw-5b has universal resistance to various TSWV isolates, although Sw-5a and Sw-5b are highly homologous (95%) [10,68]. In addition to the Sw-5 gene, seven other genes resistant to TSWV belonging to the Sw gene family have been currently identified in tomatoes, and they include Sw-1a, Sw-1b, Sw-2, Sw-3, Sw-4, Sw-6, and Sw-7 (Table 2). The introgression/incorporation of these resistance alleles in the commercial varieties could create materials with broad-spectrum resistance [69]. Molecular markers associated with TSWV resistance in tomatoes were summarized in a previous study that developed more than 20 molecular linkage markers for Sw-5 and Sw-7 TSWV resistance genes [10]. Some of these linkage markers included randomly amplified polymorphic DNA (RAPD), a sequence-characterized amplified region (SCAR), amplified fragment length polymorphisms (AFLP), cleaved amplified polymorphic sequence (CAPS), insertion– deletion (In-DEL), SNP, competitive allele-specific PCR (KASP), RFLP, and simple sequence repeats (SSR). However, the linkage molecular markers of Sw-1a, Sw-1b, Sw-2, Sw-3, Sw-4, and Sw-6 have not been reported yet [10]. 4.3. The Tomato Tm Gene Family Conferring Resistance against Tobamoviruses For more than five decades, three resistance genes, Tm-1, Tm-2, and Tm-22 , have been considered as the resistance factors against tobamoviruses in tomatoes (Table 2) [55,56,70]. Tm-1 is an incompletely dominant gene derived from the wild tomato S. habrochaites [14,55]. Conversely, Tm-2 and Tm22 are completely dominant genes introgressed from S. peruvianum and are considered allelic [14]. Tm-22 confers more effective resistance than Tm-1 or Tm-2 and has shown durable ToMV resistance for the last 60 years, explaining why it is the most currently and widely utilized in breeding tomato cultivars [71]. Reports showed that ToBRFV overcomes all the tobamoviruses resistance genes in tomatoes, including the durable Tm-22 resistance gene [57]. The PCR-based markers for Tm-1, Tm-2, and Tm-22 resistant genes have also been reportedly used for MAS [50,72,73]. Despite the many advantages and several reports on its application in studying virus resistance genes, MAS is still in the research stage of its utilization in breeding tomatoes for virus resistance [50]. 4.4. The Tomato Pot 1 Gene Conferring Resistance against Potyviruses The wild tomato relative Lycopersicon hirsutum PI247087 was identified as the source of resistance to potyviruses [61,62]. Analysis indicated that resistance is conferred by a single recessive gene, pot-1, mapped to the short arm of tomato chromosome 3 in the vicinity of the recessive py-1 locus for resistance to corky root rot [61]. Studies revealed that the recessive pot-1 gene is the orthologue of the pepper (Capsicum annuum) pvr2 gene [63]. 4.5. The Challenges in Breeding Tomato Hybrid Cultivars against Viruses Although using natural virus-resistant germplasm resources for hybrid breeding is the preferred and most effective way for obtaining resistant commercial varieties, only a few virus-resistant tomato germplasm resources are available, and the resistance is limited to a few viruses [74]. For example, virus resistance hybrid breeding cannot be applied Int. J. Mol. Sci. 2023, 24, 15448 7 of 22 against emerging viruses, such as ToCV, ToBRFV, ToMMV, etc., due to the lack of their corresponding natural resistance genes [14–16]. The other challenge is that most of the virus-resistance genes discovered so far exhibit single-gene-mediated qualitative resistance, which can be easily broken by virus mutations and mixed-infection, a phenomenon that has been commonly reported [12,13,75]. Improving multiple virus-resistant lines and cultivars by introducing several resistance genes targeting different viruses in a cultivar may play an important role in future tomato improvement projects [76–79]. Though promising, this process is complex and requires very long cycles of hybrid breeding. One example is a homozygous breeding line UMH 1203 carrying the Tm-2a , Ty-1, and Sw-5 genes, which took 10 years to successfully develop multiple resistance against ToMV, TSWV, and TYLCV from several tomato landraces [78,80]. Nevertheless, a yield reduction of 40–50% has been reported for this breeding line at lowvirus-incidence conditions [80]. Several reports indicated that the introgression of TYLCV resistance caused most of the yield reduction observed in fresh tomatoes due to the introgressed genes and/or linkage drag from the wild tomato species [80,81]. This reduction in agricultural yield would only be acceptable when cultivating under high levels of virus infection, and these new multi-resistance lines should only be used to develop cultivars for highly virus-infected areas [81]. 5. RNAi-Based Transgenic Breeding RNA silencing, also known as RNAi, is a conserved defense mechanism that suppresses the expression of viral nucleic acids, transposable elements, or host genes that need to be regulated [40,82]. The principle is based on the recognition and splicing of the doublestranded (ds) or hairpin (hp) RNA by Dicer-like (DCL) proteins into 21- to 24-nucleotide (nt) small RNAs (sRNAs). The subsequent steps involve a series of sRNA signal amplification and cleavage target mRNA processes with the participation of RNA-induced silencing complex (RISC) [83]. RNAi is an important pathway for plants resisting viral infections through the sequence-specific degradation of target viral RNA [40,74,84–86]. In the first-generation antiviral transgenic strategy, a single-stranded sequence of a viral gene, such as viral coat protein (CP) gene, RNA dependent RNA polymerase (RdRp) gene, etc., is transferred into the host plant genome, inducing the RNA silencing effect against the target virus by the host (Table 3). Subsequent studies found that transferring double-stranded RNA (dsRNA) or hairpin RNA (hpRNA) constructed based on viral sequences was more effective in inducing the RNA silencing effect than single-stranded viral sequences, making it a second-generation antiviral transgenic strategy (Table 3). With the recent depth of research on sRNAs, a new antiviral gene transfer strategy based on artificial sRNA engineering technology has been developed [87]. This third-generation antiviral transgenic strategy is based on artificial microRNAs (amiRNAs) or synthetic transacting small interfering RNAs (syn-tasiRNAs), which are 21 nt and artificially engineered to be highly specific to ensure a high sequence complementarity with target virus RNA and overcome the limited specificity of RNAi [88,89]. AmiRNAs and syn-tasiRNAs are functionally similar but are generated differently. AmiRNAs are derived from the DCL1 cleavage of miRNA precursors with foldback structures, while syn-tasiRNAs are produced in a multi-step RNAi process [90]. The biggest advantage of the third-generation antiviral transgenic strategy based on amiRNAs and syn-tasiRNAs is that it aggregates multiple-virus-targeting, which rapidly creates broad-spectrum resistance [91–93]. Many successful cases have been reported in this regard. For example, Arabidopsis miR159 was used as a backbone to express genes targeting P25, HC-Pro, and Brp1 of potato virus X (PVX), potato virus Y (PVY), and potato spindle tuber viroid (PSTVd) via the third-generation antiviral transgenic strategy, demonstrating resistance against PVX, PVY, and PSTVd co-infection simultaneously [92]. Another study showed that the Arabidopsis TAS3a gene was engineered to express syntasiRNAs targeting the genome of turnip mosaic virus (TuMV) and cucumber mosaic virus Int. J. Mol. Sci. 2023, 24, 15448 8 of 22 (CMV). The transgenic Arabidopsis thaliana plants expressing these syn-tasiRNAs showed high levels of resistance to both viruses [91]. In general, the third-generation antiviral transgenic strategy has shown high potential for virus resistance breeding. However, public concern and controversy over genetically modified (GM) crops and the strict regulation of policies have greatly inhibited the commercial development potential of GM crops. Therefore, some researchers opt to apply amiRNAs or dsRNA exogenously as crude extracts to prevent virus infection, which can also effectively induce the gene-silencing pathway in host plants against virus infection [94,95]. Table 3. RNAi-based transgenic virus breeding methods in plants. Strategy First-generation antiviral transgenic strategy Secondgeneration antiviral transgenic strategy Target Virus Genus RNAi Induction Method Targeted Region Precursor(s) Efficiency Reference TMV Tobamovirus ssRNA CP cDNA Delayed symptom development; 10 to 60 percent of the transgenic plants failed to develop symptoms. [96] TMV Tobamovirus ssRNA CP cDNA The resistance level of expression TMV CP from the pal2 promoter is less than that of the 35S promoter. [97] TSWV Orthotospovirus ssRNA N cDNA Lack of systemic symptoms and little or no systemic accumulation of virus. [98] ToLCV Begomovirus ssRNA Rep cDNA A high level of resistance and inheritability of the transgene was observed up to T2. [99] TLCV Begomovirus ssRNA CP cDNA T1-generation transgenic plants were showed variable degrees of disease resistance/tolerance compared to the untransformed control. [100] ToLCNDV Begomovirus ssRNA AV2 cDNA Transgenic plants showed symptomless, although viral DNA could be detected in some plants by PCR. [101] PRSV Potyvirus ssRNA CP cDNA PRSV infection was not observed on any of the transgenic resistance (TR) plants. TR plant yields were at least three times higher than the industry average. [102] TMV Tobamovirus dsRNA CP, p126 dsRNA The application of TMV p126 dsRNA onto tobacco plants induced greater resistance against TMV infection as compared to CP dsRNA (65 vs. 50%). [103] ToLCV Begomovirus hpRNA AC1, AC4 hpRNA Provides a promising approach to suppress a wide spectrum of ToLCV infection in the tomato. [104] ToLCV Begomovirus dsRNA AC4 dsRNA Absolute absence of leaf curl virus disease symptoms and reduction in nematode symptoms. [105] ToCMoV Begomovirus hpRNA AC1, AC4, AV1, AC5 hpRNA Most transgenic lines showed significant delays in symptom development, and two lines had immune plants. [106] PVY Potyvirus dsRNA CP dsRNA Highly resistant to three strains of PVY. [107] [108] [109] PVY Potyvirus CaCV GBNV CMV ChiVMV Orthotospovirus Cucumovirus Potyvirus hpRNA CP hpRNA Nine of the ten transgenic lines showed no infection by PVYO , and six of the nine showed no infection by PVYNTN . hpRNA viral silencing suppressors gene hpRNA Efficiently controls multiple viruses Int. J. Mol. Sci. 2023, 24, 15448 9 of 22 Table 3. Cont. Strategy Third-generation antiviral transgenic strategy Target Virus Genus RNAi Induction Method Targeted Region Precursor(s) Efficiency Reference ToLCNDV Begomovirus amiRNA AV1, AV1 + AV2 AthmiR319a High tolerance when targeting AV1 + AV2. Moderate tolerance when targeting AV1. [87] TYLCV Begomovirus amiRNA AC1+Rep AthmiR159a Confer resistance to TYLCV. [110] TSWV Orthotospovirus syn-tasiRNA TAS1c 100% of the plants were resistant. [111] TSWV Orthotospovirus syn-tasiRNA RdRP TAS1c Delay of viroid accumulation [112] amiRNA L, M, G TomiR6026 Bioinformatic assay showed successful results in controlling both viruses. [93] PhCMoV, ToBRFV Alphanucleorhabdovirus Tobamovirus NSm+RdRP PVY Potyvirus amiRNA CI, NIa, NIb, CP AthmiR319a Higher protection when targeting NIb or CP. [113] PVY, PVX, PSTVd Potyvirus Potexvirus Pospiviroid amiRNA P25, HC-Pro, Brp1 AthmiR159a Resistance against PVX, PVY, and PSTVd coinfection simultaneously, whereas the untransformed controls developed severe symptoms. [92] PRSV: papaya ringspot virus; ToLCV: tomato leaf curl virus; ToLCNDV: tomato leaf curl New Delhi virus; ToCMoV: tomato chlorotic mottle virus; CaCV: capsicum chlorosis virus; GBNV: groundnut bud necrosis virus; PhCMoV: physostegia chlorotic mottle virus; ToBRFV: tomato brown rugose fruit virus. 6. Virus Resistance Breeding Based on the CRISPR/Cas Genome Editing CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPRassociated) systems have recently emerged as efficient genome editing tools that provide a new breeding strategy for crop breeding against pathogens [114]. CRISPR/Cas has been successful in breeding some crops for pathogen resistance, such as wheat resistant to rust fungi [115], rice resistant to bacterial blight [116], and tomatoes resistant to viruses [114,117]. The CRISPR/Cas system comprises two key components: the guide RNA (gRNA) that complements the target editing sequence and the Cas endonuclease that cleaves the sequences targeted by the gRNA [118]. Cas endonuclease can be divided into two distinct classes (I and II) and six types (I to VI) based on their functional mechanisms [119]. Class I includes types I, III, and IV, which utilize a multi-protein effector complex, while Class II includes types II, V, and VI, which utilize a single effector protein, conferring it a wider adaptability than Class I [120,121]. The CRISPR/Cas system is utilized in two ways in virus resistance breeding: (1) targeting the viral genomic sequence for gene editing by cleaving or mutating the viral genome to inhibit viral replication in the host [41,122,123] and (2) knocking out or mutating the host susceptibility genes involved in virus infection and replication process to reduce the compatible interaction between host and the virus [124]. 6.1. CRISPR/Cas Genome Editing Targeting DNA Viruses CRISPR/Cas9, which is currently widely used in gene editing, belongs to Class II and Type II [121]. Since DNA viruses can form dsDNA intermediates during replication, the CRISPR/Cas system can be used to target viral DNA sequences for cleavage or mutation to inhibit viral replication. TYLCV was the first geminivirus to be edited by CRISPR/Cas9 for TYLCV-resistant tobacco breeding [125]. This method has been successfully used on tobacco, Arabidopsis, and tomato to generate multi-generational stable resistance against TYLCV, demonstrating the great potential of CRISPR/Cas in anti-geminivirus breeding (Table 4). For the CRISPR/Cas-mediated engineering of tomato against geminiviruses, the intergenic (IR), CP, and replication (Rep) regions of the geminiviruses were selected as target sites of gRNA (Table 4). The genus Geminivirus has a conserved sequence (5′ TAATATAC-3′ ) in the IR region. Therefore, an IR-gRNA targeting this conserved sequence could be used to develop a broad-spectrum resistant tomato that is resistant to various geminiviruses, including TYLCV, cotton leaf curl kokhran virus (CLCuKoV), and merremia mosaic virus (MeMV). This could significantly reduce the virus accumulation and alleviate disease symptoms in tomatoes [125,126]. Int. J. Mol. Sci. 2023, 24, 15448 10 of 22 6.2. CRISPR/Cas Genome Editing Targeting RNA Viruses The Cas endonucleases of the CRISPR/Cas system targeting plant RNA viruses mainly include FnCas9 (discovered from Francisella novicida) belonging to Type II of Class II of the Cas nuclease family [127] and CRISPR/Cas13 (formerly known as C2c2) belonging to Type VI of Class II [128]. Cas13 can be divided into several groups, including Cas13a, Cas13b, Cas13c, etc. [129–131]. Cas13a is the first direct homolog of the Cas13 family used to cleave single-stranded RNA (ssRNA) fragments in CRISPR/Cas-mediated gene editing [129]. So far, the CRISPR/FnCas9 and CRISPR/Cas13a systems have been successfully used to edit potatoes, tobacco, rice, sweet potato, and other crops for resistance against various RNA viruses. These viruses include PVY, TMV, CMV, southern rice black-streaked dwarf virus (SRBSDV), rice stripe mosaic virus (RSMV), etc. (Table 4). The gRNA target site in the RNA viruses is similar to that in DNA viruses, which is mainly located in the IR region and some key regions of the RNA virus coding protein (Table 4). Unfortunately, CRISPR/Cas-mediated editing against RNA viruses has not been reported in tomatoes. Int. J. Mol. Sci. 2023, 24, 15448 11 of 22 Table 4. CRISPR/Cas gene editing system used to create virus resistance in tomatoes and other crops. Target Virus Genus Plant Targeted Genome CRISPR/Cas TYLCV Begomovirus Tomato Viral DNA TYLCV Begomovirus Tomato Viral DNA TYLCV Begomovirus Tomato CLCuKoV Begomovirus MeMV Begomovirus CMV Targeted Region Efficiency Reference CRISPR/Cas9 CP, IR Significant reduction or delayed accumulation of viral DNA compared to the control plants. [132] CRISPR/Cas9 CP, Rep Low accumulation of the viral DNA genome compared to the control plants. [114] Viral DNA CRISPR/Cas9 IR, CP, RCRII Reduction or delayed accumulation of viral DNA, abolishing or significantly attenuating symptoms of infection. [125] Tomato Viral DNA CRISPR/Cas9 IR, CP, RCRII Tomato Viral DNA CRISPR/Cas9 IR, CP, RCRII Significantly limits CLCuKoV and MeMV replication and systemic infection. [126] Cucumovirus Arabidopsis Viral RNA CRISPR/FnCas9 ORF1a, ORF CP, 3′ UTR Tobamovirus Tobacco Viral RNA CRISPR/FnCas9 Significantly attenuated infection symptoms and reduced viral RNA accumulation. The resistance was inheritable, and the progenies showed significantly low virus accumulation. [133] TMV 3′ ORFs TuMV Potyvirus Tobacco Viral RNA CRISPR/LshCas13a HC-Pro, CP Targeting the HC-Pro rather than those targeting the coat protein (CP) sequence significantly inhibits TuMV-GFP accumulation and systematic movement. [134] TuMV Viral RNA CRISPR/LshCas13a HC-Pro, CP Significant inhibition of TuMV-GFP accumulation level and systematic movement in T1 and T2 plants. [135] [136] Potyvirus Arabidopsis PVY Potyvirus Potato Viral RNA CRISPR/LshCas13a P3, CI, NIb, CP Specifically resistant to multiple PVY strains while having no effect on unrelated viruses such as PVA or Potato virus S. TMV Tobamovirus Tobacco Viral RNA CRISPR/LshCas13a RdRp, MP, CP Significant reduction or delayed accumulation of viral RNA compared to the control plants. [137] SRBSDV Fijivirus Rice Viral RNA CRISPR/LshCas13a ORF Abolishing or significantly attenuating symptoms of infection. T3 transgenic plants we tested showed stable resistance to SRBSDV. [137] RSMV Cytorhabdovirus Rice Viral RNA CRISPR/LshCas13a ORF Abolishing or significantly attenuating symptoms of infection. T3 transgenic plants we tested showed stable resistance to RSMV. [137] SPCSV Crinivirus Sweet potato Viral RNA CRISPR/LwaCas13a CRISPR/13d RNase3 Transgenic plants and their grafted plants showed a significant reduction in virus accumulation and were asymptomatic. [138] TYLCV Begomovirus Tomato Tomato genome CRISPR/Cas9 SlPelo Knocking out the bialleles of SlPelo proved to suppress systematic infection of TYLCV. [117] PVY Potyvirus Tomato Tomato genome CRISPR/Cas9 eIF4E1 Significant reduction in susceptibility to the N strain (PVY-N) but not to the ordinary strain (PVY-O). [139] CMV Cucumovirus Tomato Tomato genome CRISPR/Cas9 eIF4E1 Viral aphid transmission from an infected susceptible plant to gene-edited plants was reduced compared with the parental control. [139] TEV Potyvirus Tomato Tomato genome CRISPR/Cas9 eIF4E1 A combination of mutations in regions I and II of eIF4E1 associates with resistance to several isolates of potyviruses. [140] [140] PVY Potyvirus Tomato Tomato genome CRISPR/Cas9 eIF4E1 Differences in silent targets showed differences in resistance levels. PepMoV Potyvirus Tomato Tomato genome CRISPR/Cas9 eIF4E1 Knocking out eIF4E1 exhibited a significant reduction accumulation of PepMoV but not TEV. [141] PVMV Potyvirus Tomato Tomato genome CRISPR/Cas9 4E2 (eIF4E2) Knocking out eIF4E2 exhibited resistance to six of the eight PVMV isolates but not to other potyviruses. [142] TuMV Potyvirus Tomato Tomato genome CRISPR/Cas9 eIF(iso)4E Homozygous mutations and transgene-free T2 and T3 generation in self-pollinating species showed no differences in dry weights and flowering times with wild-type plants under standard growth conditions. [143] ToBRFV Tobamovirus Tomato Tomato genome CRISPR/Cas9 SlTOM1a-e Quadruple-mutant plants did not show detectable ToBRFV CP accumulation or obvious defects in growth or fruit production. The quadruple-mutant plants also showed resistance to three other tobamoviruses. [31] ToBRFV Tobamovirus Tomato Tomato genome CRISPR/Cas9 SlTOM1 SlTOM3 SlTOM1a and SlTOM3 are essential for the replication of ToBRFV but not for ToMV and TMV. [144] Int. J. Mol. Sci. 2023, 24, 15448 12 of 22 6.3. CRISPR/Cas Genome Editing Targeting Host Susceptible Genes Since plant viruses are highly dependent on the host to complete their replication cycle, the replication, assembly, and movement of viruses in plant cells require interaction with host–plant-specific factors, often referred to as susceptibility genes (S genes), for successful infection [145]. Editing these susceptible genes via CRISPR/Cas to break compatible interactions between the virus and host can help develop resistance in the host plants [146]. A well-known S gene that confers resistance to potyviruses is the eukaryotic translation initiation factor 4E (eIF4E). eIF4E is a mRNA cap-binding protein that plays a critical role in initiating mRNA translation and regulating protein synthesis [124]. Studies have shown that eIF4E can interact with the viral protein genome-link (VPg) of PVY to promote the translation, replication, and intercellular movement of the PVY [124,147]. In recent years, there have been many reports of using CRISPR/Cas to knock out or mutate the eIF4E homologous gene in tomatoes to obtain tomato lines with complete resistance to potyviruses (Table 4). Tobamoviruses, especially TBoRFV, which emerged recently, are another important group of viruses that threaten tomato production. The TOBAMOVIRUS MULTIPLICATION1 (TOM1) gene encoded by Arabidopsis is required for the replication of TMV [148]. When TOM1 was mutated in Arabidopsis, the accumulation of TMV was significantly inhibited [148]. The CRISPR/Cas9-mediated knockout of TOM1 homologs, including SlTOM1a-e and SlTOM3, in tomatoes resulted in ToBRFV resistance in tomato plants [31,144]. In addition, SlPelo, a TYLCV susceptibility gene in tomatoes [149], has been successfully used for CRISPR/Cas-mediated antiviral breeding [117]. Tomatoes with SlPelo knockout showed significant inhibition and limited spread of TYLCV [117]. These results show great potential for CRISPR/Cas antiviral breeding targeting host-susceptible genes, but only if the molecular interactions between viruses and hosts are well-understood. 7. Future Prospects 7.1. CRISPR/Cas-Mediated Tomato Breeding for Resistance against Orthotospoviruses Orthotospoviruses cause significant yield and quality reduction in tomatoes [150]; however, there are limited technologies to control these viruses at present. Some progress has been made in the study of TSWV resistance genes, particularly the Sw-5 gene and its homologs, which have been identified in tomatoes and are widely used in tomato hybrid breeding. However, many TSWV strains have been reported to break the Sw-5-mediated resistance in tomatoes worldwide [12,151]. In addition, some orthotospoviruses, such as capsicum ring spot virus (CYRSV), have been reported to break down the Sw-5-mediated resistance in tomatoes [152]. These results indicate that it is urgent to develop new methods for tomato resistance breeding against orthotospoviruses. So far, gene editing-mediated tomato breeding has achieved great success in developing resistance against geminiviruses, tobamoviruses, and potyviruses. However, there are no reports on gene editing-mediated breeding for resistance against orthotospoviruses. The gRNA targeting some critical genes of orthotospoviruses, such as nuclear protein N and RNA silencing suppressor NSs, may be a good strategy to create tomato lines resistant against orthotospoviruses. Targeting host-susceptible genes via the gene-editing method is also a viable strategy for tomato breeding against orthotospoviruses. Several host factors interacting with TSWV have been identified, one such factor being the eukaryotic translation elongation factor 1A (eEF1A). eEF1A interacts with the RNP of TSWV, and silencing eEF1A via virus-induced gene silencing (VIGS) significantly inhibits TSWV replication in tobacco [153,154]. Ribosomal protein S6 (RPS6) is a host factor that is part of the 40S ribosomal subunit. Silencing RPS6 showed high resistance to TSWV in tobacco [155]. The suppressor of the G2 allele of skp1 (SGT1) is a co-chaperone that interacts with Hsp70 [156]. Tobacco SGT (NbSGT1) interacts with TSWV NSm to promote intercellular and systemic motility of the virus [157]. Int. J. Mol. Sci. 2023, 24, 15448 13 of 22 Thus, the homologs of these susceptibility factors in tomatoes could be a potential target for gene editing against orthotospoviruses. 7.2. Challenges of the CRISPR/Cas-Mediated Antiviral Breeding in Tomato CRISPR/Cas genome editing technology has great advantages compared with conventional breeding techniques. These advantages include shortening breeding cycles and saving breeding costs. However, at present, CRISPR/Cas mainly relies on the Agrobacterium-mediated transgene method to integrate exogenetic DNA segments into the plant genome, making its application controversial and as strictly regulated as that of GM crops. This also restricts the future commercial application of CRISPR/Cas in resistance breeding. Therefore, the development of DNA-free genome editing methods can help to avoid the abovementioned problems. The current DNA-free genome editing techniques include four main methods. (1) Selecting mutant plants without CRISPR/Cas elements from the gene-edited selfed or hybrid progenies. The selection process usually takes a lot of time and effort; therefore, new rapid selection techniques have been developed, such as inserting visible fluorescent markers into CRISPR/Cas vectors to improve selection efficiency [158]. (2) Polyethylene glycol (PEG)-mediated transient expression of CRISPR/Cas system in plant protoplast. The biggest challenge of this method is the difficulty of plant regeneration from protoplasts. Fortunately, gene editing in wild tomatoes has been successful with the PEG-mediated protoplast method [159]. (3) Modifying the plant virus as the vector to deliver the CRISPR/Cas system. So far, various plant viruses have been modified to deliver gRNA, including DNA viruses such as TYLCV, Bean yellow dwarf virus (BeYDV) [160,161], and wheat dwarf virus (WDV) [162]; RNA viruses such as TSWV [163], barley stripe mosaic virus (BSMV) [164], tobacco rattle virus (TRV) [165], and sonchus yellow net rhabdovirus (SYNV) [166] have also been used for gRNA delivery. Plant viruses have many advantages as delivery vectors, including their ease of manipulation, high accumulation levels (including gRNA and repair templates), and systemic movement across host plants, leading to high expression levels of the gRNA in specific tissues, such as flowers, fruits, buds, etc. However, as gRNA carriers, the carrying capacity of plant viruses is greatly limited (typically < 1 kb) [167]. For these reasons, the future development direction of a plant-virus-based CRISPR/Cas delivery system for tomatoes would be to expand the delivery capacity by modifying more potential viruses that can carry large DNA/RNA sequences. (4) Utilizing endogenous mobile mRNA from plants as carriers for gRNA delivery. Some plant endogenous mRNAs can be used for long-distance transport through the phloem. Studies found that a key motif of mRNA, tRNA-like sequence (TLS), is critical for the long-distance transport of mRNA in the phloem [168]. The studies constructed TLS into the Cas9 vector and expressed Cas9/gRNA-TLS construct in the rootstock through transgenic methods. Thus, the gRNA could also be delivered from rootstock to the scion with the assistance of TLS sequences, and the DNA-free genome editing seeds can be selected from the scion plants [169]. This method utilizes the plant endogenous delivery system, making it much more effective than the exogenic delivery system. In addition, this method does not require additional removal of transgenes or regeneration of plants from the transfected protoplasts, meaning that the breeding cycle is greatly shortened and the efficiency of gene editing is improved. Tomato is also a very suitable crop for grafting, and grafting is conducive to the polymerization of multiple resistances in commercial tomato production [169]. However, the current research on mobile mRNA has mainly focused on model plants such as Arabidopsis and tobacco, and little is known about the tomato’s mobile mRNA. Therefore, more research needs to be carried out in the future to explore the potential of the mobile mRNA of tomatoes as a gRNA delivery vector. A potential risk of CRISPR/Cas-mediated antiviral breeding is that targeting the viral genetic sequence could potentially accelerate virus evolution and the breakdown of the host’s resistance. For example, the gene-edited cassava materials targeting the AC2 and AC3 sequences of the African cassava mosaic virus (ACMV) did not show significant resistance compared with the control group. Further sequencing studies found that 33% to 48% of the Int. J. Mol. Sci. 2023, 24, 15448 14 of 22 edited viruses evolved a conserved single-nucleotide mutation at the target recognition site to evade the gRNA recognition and avoid CRISPR/Cas9 cleavage [170]. Therefore, simultaneously targeting multiple sites of the viral genome may be a better way to reduce the risk of viruses evading recognition by gRNA due to single-site mutations [171]. In addition, there is another practical issue that needs to be considered; that is, the possible negative effects of antiviral gene editing on plants need to be evaluated. Balancing the yield, quality, and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits [172,173]. Genome editing in dealing with viruses for virus resistance may also affect other important agricultural traits and agronomic traits of crops, such as yield, biotic and abiotic resistance, etc. [174,175]. Unfortunately, no detailed data on antiviral gene-edited field crops in the field have been reported so far. 7.3. Suggestions for Improving Tomato Antiviral Breeding in the Future We summarized the advantages, challenges, and prospects of three different antiviral breeding strategies, including MAS-based hybrid breeding, RNAi-based transgenic breeding, and CRISPR/Cas-based gene editing, as presented in Table 5. Table 5. Suggestions for improving tomato antiviral breeding in the future. Methods Characteristics Challenges Suggestions and Future Prospects i. i. ii. i. MAS-based hybrid breeding ii. Relay on conventional breeding method. Widely used in commercial breeding. iii. iv. v. i. RNAi-based transgenic breeding ii. Genetic engineering method. Rapidly and efficiently creates broad-spectrum resistance against multiple viruses. i. ii. Long breeding cycles compared with genetic engineering breeding. Lack of natural resistance genes. Single-gene-mediated resistance is easily broken down by viruses. Difficulty in developing broad-spectrum resistance against multiple viruses. Needs appropriate and reliable DNA markers. Public controversy and strict regulation of policies on GM crops. Homology-dependent gene silencing and unwanted recombination, non-target effects and off-target effects. ii. iii. iv. i. ii. i. i. i. ii. CRISPR/Cas-based gene editing iii. Genetic engineering method. Relies on Agrobacteriummediated transgene technology. Shows great potential in antiviral breeding. ii. iii. iv. Controversial and strictly regulated like GM crops. The technology needs to be improved to meet the needs of commercial breeding. Has the potential risk of accelerating virus mutation and evolution. Inefficient targeting of the S gene for editing. ii. iii. iv. Reinforce integration of ecological, biogeographical, and genetic discipline of tomato and tomato viruses, which will help to identify tomato local adaption and source of resistance against emerging virus species or strains. Utilizing selection and breeding methods, such as genomic prediction (GP), genome-wide association studies (GWAS), and major QTL mapping to identify potential new resistance genes. Finding closed, reliable, and effective new molecular markers for virus resistance genes. Using the gene pyramiding method to polymerize multiple resistances in the shortest possible time. The third-generation antiviral transgenic technology (amiRNAs and syntasiRNAs) has improvements, including more specialized in-targets, to overcome the unwanted recombination and off-target effect. Exogenous application of RNAi. research and development. Developing DNA-free gene editing technology, including DNAfree selection techniques, and a PEG/virus/endogenous mRNA mediated delivery system. Improving the efficiency of gene editing and reducing the off-target rate by utilizing endogenous promoter and optimized delivery system. Developing gene editing techniques targeting multiple viruses simultaneously or targeting multiple sites of a virus simultaneously. Developing the S gene editing targets based on the molecular interaction mechanism between viruses and hosts. Int. J. Mol. Sci. 2023, 24, 15448 15 of 22 For future MAS-based hybrid breeding against tomato viruses, the biggest challenge is how to identify novel antiviral genes in tomatoes to address emerging viruses or strains. Based on the arms race pathogen–host model of concerted evolution, we suggest a reinforced integration of ecological, biogeographical, and genetic discipline of tomato and tomato viruses, which will help us identify tomato’s local adaption and source of resistance [176]. Gene regulatory networks via monogenetic methods will help to explain the heritability of antiviral traits [176]. Selection of breeding methods, such as genomic prediction (GP), genome-wide association studies (GWAS), and major QTL mapping, should also be utilized to identify potential new resistance genes. These techniques have already been successful in identifying new virus resistance genes [176–179]. To overcome the challenges of developing broad-spectrum resistance against multiple viruses, we suggest utilizing the gene pyramiding method through MAS to integrate multiple resistance genes into a single plant in the shortest possible time [79]. For RNAi-based transgenic breeding against tomato viruses, public controversy and strict regulation of policies on GM crops is the biggest challenge. How to improve transgenic technology from the technical level to eliminate public concerns becomes the key focus of future research. Although CRISPR/Cas-based gene editing has great potential for breeding tomatoes against viruses, several challenges need to be addressed to ensure its application in future antiviral breeding. These include developing DNA-free gene editing technology, improving the efficiency of gene editing and reducing the off-target rate, and developing multiple targets gene editing technology and the S gene editing targets. 8. Conclusions Despite many years of agricultural research, there is still a lack of effective chemical control or agronomic management measures to curb viral diseases. The most effective and suitable method is utilizing natural genetic resistance resources or genetic tools to obtain cultivars resistant to viruses. However, identifying the resistance sources/genes for all plant viruses is difficult, and natural sources/genes could be broken by viral mutation. RNAi transgenic research presents a new, useful way to control viral diseases, but the technique is faced with concerns about GM crops, off-target results, and unwanted recombination. A technology that could provide a viable alternative for virus resistance breeding in the future is CRISPR/Cas-mediated gene editing. The CRISPR/Cas gene-editing technology allows for the removal of the exogenous DNA via technical means, thus ensuring DNA-free editing and avoiding the controversy and policy restriction associated with GM crops. However, there is still a need to further explore the virus–plant molecular interactions, develop the endogenous delivery system based on DNA-free genome editing technology, and evaluate how the technology affects other important crop traits such as yield and tolerance to other biotic and abiotic stresses to optimize the efficiency of gene editing for tomatoes. Author Contributions: Z.Z. conceived and designed the manuscript; K.Z. wrote Sections 5–8 of the manuscript; Z.S. wrote Sections 3 and 4 of the manuscript, Figure 2, Tables 2 and 3; X.S. wrote Sections 1 and 2 of the manuscript and generated the data shown in Tables 1, 4 and 5. All authors have read and agreed to the published version of the manuscript. Funding: This research was funded by the Yunnan Seed Laboratory (grant number 202205AR070001), the Major Science and Technology Program of Yunnan Province (grant number 202202AE090022), the National Natural Science Foundation of China (grant number 32160620 and 31660508), and the Fund for Reserve Talents of Young and Middle-aged Academic and Technical Leaders of Yunnan Province (grant number 202305AC160026). Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: Not applicable. Int. J. Mol. Sci. 2023, 24, 15448 16 of 22 Conflicts of Interest: We declare that we have no conflict of interest nor any commercial or associative interest that represents a conflict of interest in connection with the work submitted. References 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. Hanssen, I.M.; Lapidot, M.; Thomma, B.P. Emerging viral diseases of tomato crops. Mol. Plant-Microbe Interact. 2010, 23, 539–548. [CrossRef] [PubMed] Xu, C.X.; Sun, X.P.; Taylor, A.; Jiao, C.; Xu, Y.M.; Cai, X.F.; Wang, X.L.; Ge, C.H.; Pan, G.H.; Wang, Q.X.; et al. Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing. J. Virol. 2017, 91, e00173–17. [CrossRef] [PubMed] De Almeida, G.Q.; Silva, J.O.; Copati, M.G.F.; Dias, F.O.; Santos, M.C. Tomato breeding for disease resistance. Multi-Sci. J. 2020, 3, 8–16. [CrossRef] García-Estrada, R.S.; Diaz-Lara, A.; Aguilar-Molina, V.H.; Tovar-Pedraza, J.M. Viruses of Economic Impact on Tomato Crops in Mexico: From Diagnosis to Management-A Review. Viruses 2022, 14, 1251. [CrossRef] Rodríguez, E.; Téllez, M.M.; Janssen, D. Whitefly Control Strategies against Tomato Leaf Curl New Delhi Virus in Greenhouse Zucchini. Int. J. Environ. Res. Public Health 2019, 16, 2673. [CrossRef] [PubMed] Tatineni, S.; Hein, G.L. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. Phytopathology 2023, 113, 117–141. [CrossRef] De Oliveira, A.S.; Boiteux, L.S.; Kormelink, R.; Resende, R.O. The Sw-5 gene cluster: Tomato breeding and research toward Orthotospovirus disease control. Front. Plant Sci. 2018, 9, 1055. [CrossRef] [PubMed] Ren, Y.X.; Tao, X.R.; Li, D.W.; Yang, X.L.; Zhou, X.P. ty-5 Confers Broad-Spectrum Resistance to Geminiviruses. Viruses 2022, 14, 1804. [CrossRef] Nevame, A.Y.M.; Xia, L.; Nchongboh, C.G.; Hasan, M.M.; Alam, M.A.; Yongbo, L.; Wenting, Z.; Yafei, H.; Emon, R.M.; Ismail, M.R.; et al. Development of a New Molecular Marker for the Resistance to Tomato Yellow Leaf Curl Virus. BioMed Res. Int. 2018, 8120281. [CrossRef] Qi, S.M.; Zhang, S.J.; Islam, M.M.; El-Sappah, A.H.; Zhang, F.; Liang, Y. Natural Resources Resistance to Tomato Spotted Wilt Virus (TSWV) in Tomato (Solanum lycopersicum). Int. J. Mol. Sci. 2021, 22, 10978. [CrossRef] Gautam, S.; Chinnaiah, S.; Workneh, F.; Crosby, K.; Rush, C.; Gadhave, K.R. First report of a resistance-breaking strain of tomato spotted wilt orthotospovirus infecting Capsicum annuum with the Tsw resistance gene in Texas. Plant Dis. 2022, 107, PDIS-09. [CrossRef] [PubMed] Lahre, K.A.; Shekasteband, R.; Meadows, I.; Whitfield, A.E.; Rotenberg, D. First Report of Resistance-Breaking Variants of Tomato Spotted Wilt Virus (TSWV) Infecting Tomatoes with the Sw-5 Tospovirus-Resistance Gene in North Carolina. Plant Dis. 2023, 107. [CrossRef] García-Cano, E.; Resende, R.O.; Fernández-Muñoz, R.; Moriones, E. Synergistic Interaction Between Tomato chlorosis virus and Tomato spotted wilt virus Results in Breakdown of Resistance in Tomato. Phytopathology 2006, 96, 1263–1269. [CrossRef] Jewehan, A.; Kiemo, F.W.; Salem, N.; Tóth, Z.; Salamon, P.; Szabó, Z. Isolation and molecular characterization of a tomato brown rugose fruit virus mutant breaking the tobamovirus resistance found in wild Solanum species. Arch. Virol. 2022, 167, 1559–1563. [CrossRef] Tettey, C.K.; Yan, Z.Y.; Ma, H.Y.; Zhao, M.S.; Geng, C.; Tian, Y.P.; Li, X.D. Tomato mottle mosaic virus: Characterization, resistance gene effectiveness, and quintuplex RT-PCR detection system. J. Integr. Agric. 2022, 21, 2641–2651. [CrossRef] Fiallo-Olivé, E.; Navas-Castillo, J. Tomato chlorosis virus, an emergent plant virus still expanding its geographical and host ranges. Mol. Plant Pathol. 2019, 20, 1307–1320. [CrossRef] Sanjuán, R.; Domingo-Calap, P. Mechanisms of viral mutation. Cell. Mol. Life Sci. 2016, 73, 4433–4448. [CrossRef] Elena, S.F.; García-Arenal, F. Plant Virus Adaptation to New Hosts: A Multi-scale Approach. Curr. Top. Microbiol. Immunol. 2023, 439, 167–196. [PubMed] Díaz-Pendón, J.A.; Sánchez-Campos, S.; Fortes, I.M.; Moriones, E. Tomato Yellow Leaf Curl Sardinia Virus, a Begomovirus Species Evolving by Mutation and Recombination: A Challenge for Virus Control. Viruses 2019, 11, 45. [CrossRef] Rivarez, M.P.S.; Vučurović, A.; Mehle, N.; Ravnikar, M.; Kutnjak, D. Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front. Microbiol. 2021, 12, 671925. [CrossRef] Choi, H.; Jo, Y.; Cho, W.K.; Yu, J.; Tran, P.T.; Salaipeth, L.; Kwak, H.R.; Choi, H.S.; Kim, K.H. Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics. Int. J. Mol. Sci. 2020, 21, 7565. [CrossRef] Ontiveros, I.; López-Moya, J.J.; Díaz-Pendón, J.A. Coinfection of Tomato Plants with Tomato yellow leaf curl virus and Tomato chlorosis virus Affects the Interaction with Host and Whiteflies. Phytopathology 2022, 112, 944–952. [CrossRef] [PubMed] Fiallo-Olivé, E.; Lett, J.M.; Martin, D.P.; Roumagnac, P.; Varsani, A.; Zerbini, F.M.; Navas-Castillo, J. ICTV Virus Taxonomy Profile: Geminiviridae 2021. J. Gen. Virol. 2021, 102, 001696. [CrossRef] [PubMed] Kenyon, L.; Tsai, W.S.; Shih, S.L.; Lee, L.M. Emergence and diversity of begomoviruses infecting solanaceous crops in East and Southeast Asia. Virus Res. 2014, 186, 104–113. [CrossRef] [PubMed] Prasad, A.; Sharma, N.; Hari-Gowthem, G.; Muthamilarasan, M.; Prasad, M. Tomato Yellow Leaf Curl Virus: Impact, Challenges, and Management. Trends Plant Sci. 2020, 25, 897–911. [CrossRef] Int. J. Mol. Sci. 2023, 24, 15448 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. 39. 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 17 of 22 Kil, E.J.; Kim, S.; Lee, Y.J.; Byun, H.S.; Park, J.; Seo, H.; Kim, C.S.; Shim, J.K.; Lee, J.H.; Kim, J.K.; et al. Tomato yellow leaf curl virus (TYLCV-IL): A seed-transmissible geminivirus in tomatoes. Sci. Rep. 2016, 6, 19013. [CrossRef] Abudurexiti, A.; Adkins, S.; Alioto, D.; Alkhovsky, S.V.; Avšič-Županc, T.; Ballinger, M.J.; Bente, D.A.; Beer, M.; Bergeron, É.; Blair, C.D.; et al. Taxonomy of the order Bunyavirales: Update 2019. Arch. Virol. 2019, 164, 1949–1965. [CrossRef] Zhang, Z.K.; Zheng, K.Y.; Zhao, L.H.; Su, X.X.; Zheng, X.; Wang, T.T. Occurrence, Distribution, Evolutionary Relationships, Epidemiology, and Management of Orthotospoviruses in China. Front. Microbiol. 2021, 12, 686025. [CrossRef] Wang, H.; Wu, X.; Huang, X.; Wei, S.; Lu, Z.; Ye, J. Seed Transmission of Tomato Spotted Wilt Orthotospovirus in Peppers. Viruses 2022, 14, 1873. [CrossRef] Adams, M.J.; Adkins, S.; Bragard, C.; Gilmer, D.; Li, D.; MacFarlane, S.A.; Wong, S.M.; Melcher, U.; Ratti, C.; Ryu, K.H.; et al. ICTV Virus Taxonomy Profile: Virgaviridae. J. Gen. Virol. 2017, 98, 1999–2000. [CrossRef] Ishikawa, M.; Yoshida, T.; Matsuyama, M.; Kouzai, Y.; Kano, A.; Ishibashi, K. Tomato brown rugose fruit virus resistance generated by quadruple knockout of homologs of TOBAMOVIRUS MULTIPLICATION1 in tomato. Plant Physiol. 2022, 189, 679–686. [CrossRef] [PubMed] Zhang, S.K.; Griffiths, J.S.; Marchand, G.; Bernards, M.A.; Wang, A.M. Tomato brown rugose fruit virus: An emerging and rapidly spreading plant RNA virus that threatens tomato production worldwide. Mol. Plant Pathol. 2022, 23, 1262–1277. [CrossRef] [PubMed] Sakem, N.; Mansour, A.; Ciuffo, M.; Falk, B.W.; Turina, M. A new tobamovirus infecting tomato crops in Jordan. Arch. Virol. 2016, 161, 503–506. Xu, Y.T.; Zhang, S.L.; Shen, J.G.; Wu, Z.J.; Du, Z.G.; Gao, F.L. The phylogeographic history of tomato mosaic virus in Eurasia. Virology 2021, 554, 42–47. [CrossRef] Inoue-Nagata, A.K.; Jordan, R.; Kreuze, J.; Li, F.; López-Moya, J.J.; Mäkinen, K.; Ohshima, K.; Wylie, S.J.; ICTV Report Consortium. ICTV Virus Taxonomy Profile: Potyviridae 2022. J. Gen. Virol. 2022, 103, 001738. [CrossRef] Quenouille, J.; Vassilakos, N.; Moury, B. Potato virus Y: A major crop pathogen that has provided major insights into the evolution of viral pathogenicity. Mol. Plant Pathol. 2013, 14, 439–452. [CrossRef] Orfanidou, C.G.; Pappi, P.G.; Efthimiou, K.E.; Katis, N.I.; Maliogka, V.I. Transmission of Tomato chlorosis virus (ToCV) by Bemisia tabaci Biotype Q and Evaluation of Four Weed Species as Viral Sources. Plant Dis. 2016, 100, 2043–2049. [CrossRef] Moodley, V.; Gubba, A.; Mafongoya, P.L. Prevalence, epidemiology and molecular studies of Tomato chlorosis virus (ToCV) in South Africa. PLoS ONE 2019, 14, e0220298. [CrossRef] Maurya, D.; Mukherjee, A.; Bhagyashree; Sangam, S.; Kumar, R.; Akhtar, S.; Chattopadhyay, T. Marker assisted stacking of Ty3, Mi1.2 and Ph3 resistance alleles for leaf curl, root knot and late blight diseases in tomato. Physiol. Mol. Biol. Plants 2023, 29, 121–129. [CrossRef] Akbar, S.; Wei, Y.; Zhang, M.Q. RNA Interference: Promising Approach to Combat Plant Viruses. Int. J. Mol. Sci. 2022, 23, 5312. [CrossRef] Baltes, N.J.; Hummel, A.W.; Konecna, E.; Cegan, R.; Bruns, A.N.; Bisaro, D.M.; Voytas, D.F. Conferring resistance to geminiviruses with the CRISPR-Cas prokaryotic immune system. Nat. Plants 2015, 1, 15145. [CrossRef] HEl-Sappah, A.H.; Qi, S.M.; A Soaud, S.; Huang, Q.L.; M Saleh, A.; A S Abourehab, M.; Wan, L.Y.; Cheng, G.T.; Liu, J.Y.; Ihtisham, M.; et al. Natural resistance of tomato plants to Tomato yellow leaf curl virus. Front. Plant Sci. 2022, 13, 1081549. [CrossRef] Mangal, M.; Srivastava, A.; Sharma, R.; Kalia, P. Conservation and Dispersion of Genes Conferring Resistance to Tomato Begomoviruses between Tomato and Pepper Genomes. Front. Plant Sci. 2017, 8, 1803. [CrossRef] [PubMed] Verlaan, M.G.; Hutton, S.F.; Ibrahem, R.M.; Kormelink, R.; Visser, R.G.; Scott, J.W.; D Edwards, J.; Bai, Y.L. The tomato yellow leaf curl virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA–dependent RNA polymerases. PLoS Genet. 2013, 9, e1003399. [CrossRef] [PubMed] Butterbach, P.; Verlaan, M.G.; Dullemans, A.; Lohuis, D.; Visser, R.G.; Bai, Y.L.; Kormelink, R. Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection. Proc. Natl. Acad. Sci. USA 2014, 111, 12942–12947. [CrossRef] [PubMed] Voorburg, C.M.; Yan, Z.; Bergua-Vidal, M.; Wolters, A.M.A.; Bai, Y.; Kormelink, R. Ty-1, a universal resistance gene against geminiviruses that is compromised by co-replication of a betasatellite. Mol. Plant Pathol. 2020, 21, 160–172. [CrossRef] Yamaguchi, H.; Ohnishi, J.; Saito, A.; Ohyama, A.; Nunome, T.; Miyatake, K.; Fukuoka, H. An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato. Theor. Appl. Genet. 2018, 131, 1345–1362. [CrossRef] [PubMed] Gill, U.; Scott, J.W.; Shekasteband, R.; Ogundiwin, E.; Schuit, C.; Francis, D.M.; Sim, S.C.; Smith, H.; Hutton, S.F. Ty-6, a major begomovirus resistance gene on chromosome 10, is effective against Tomato yellow leaf curl virus and Tomato mottle virus. TAG. Theor. Appl. Genet. 2019, 132, 1543–1554. [CrossRef] Arens, P.; Mansilla, C.; Deinum, D.; Cavellini, L.; Moretti, A.; Rolland, S.; van der Schoot, H.; Calvache, D.; Ponz, F.; Collonnier, C. Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing. Theor. Appl. Genet. 2010, 120, 655–664. [CrossRef] [PubMed] Osei, M.K.; Prempeh, R.; Adjebeng-Danquah, J.; Opoku, J.A.; Danquah, A.; Danquah, A.; Danquah, E.Y.; Blay, E.; Dapaah, H.A. Marker-Assisted Selection (MAS): A Fast-Track Tool in Tomato Breeding. In Recent Advances in Tomato Breeding and Production; IntechOpen: London, UK, 2018; pp. 93–113. Int. J. Mol. Sci. 2023, 24, 15448 51. 52. 53. 54. 55. 56. 57. 58. 59. 60. 61. 62. 63. 64. 65. 66. 67. 68. 69. 70. 71. 72. 73. 74. 75. 76. 18 of 22 Shen, X.; Yan, Z.; Wang, X.; Wang, Y.; Arens, M.; Du, Y.; Visser, R.G.F.; Kormelink, R.; Bai, Y.; Wolters, A.A. The NLR Protein Encoded by the Resistance Gene Ty-2 Is Triggered by the Replication-Associated Protein Rep/C1 of Tomato Yellow Leaf Curl Virus. Front. Plant Sci. 2020, 11, 545306. [CrossRef] Hallwass, M.; de Oliveira, A.S.; de Campos Dianese, E.; Lohuis, D.; Boiteux, L.S.; Inoue-Nagata, A.K.; Resende, R.O.; Kormel-ink, R. The Tomato spotted wilt virus cell-to-cell movement protein (NSM) triggers a hypersensitive response in Sw-5-containing resistant tomato lines and in Nicotiana benthamiana transformed with the functional Sw-5b resistance gene copy. Mol. Plant Pathol. 2014, 15, 871–880. [CrossRef] [PubMed] Padmanabhan, C.; Ma, Q.; Shekasteband, R.; Stewart, K.S.; Hutton, S.F.; Scott, J.W.; Fei, Z.; Ling, K.S. Comprehensive transcriptome analysis and functional characterization of PR-5 for its involvement in tomato Sw-7 resistance to tomato spotted wilt tospovirus. Sci. Rep. 2019, 9, 7673. [CrossRef] Loon, L.C.V.; Strien, E.A.V. The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins. Physiol. Mol. Plant Pathology 1999, 55, 85–97. [CrossRef] Lanfermeijer, F.C.; Dijkhuis, J.; Sturre, M.J.; Haan, P.; Hille, J. Cloning and characterization of the durable tomato mosaic virus resistance gene Tm-22 from Lycopersicon esculentum. Plant Mol. Biol. 2003, 52, 1039. [CrossRef] Ishibashi, K.; Kezuka, Y.; Kobayashi, C.; Kato, M.; Inoue, T.; Nonaka, T.; Ishikawa, M.; Matsumura, H.; Katoh, E. Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1. Proc. Natl. Acad. Sci. USA 2014, 111, E3486–E3495. [CrossRef] Hak, H.; Spiegelman, Z. The Tomato Brown Rugose Fruit Virus Movement Protein Overcomes Tm-22 Resistance in Tomato While Attenuating Viral Transport. Mol. Plant-Microbe Interact. 2021, 34, 1024–1032. [CrossRef] Ishibashi, K.; Ishikawa, M. Mechanisms of tomato mosaic virus RNA replication and its inhibition by the host resistance factor Tm-1. Curr. Opin. Virol. 2014, 9, 8–13. [CrossRef] [PubMed] Hak, H.; Raanan, H.; Schwarz, S.; Sherman, Y.; Dinesh-Kumar, S.P.; Spiegelman, Z. Activation of Tm-22 resistance is mediated by a conserved cysteine essential for tobacco mosaic virus movement. Mol. Plant Pathol. 2023, 24, 838–848. [CrossRef] Weber, H.; Schultze, S.; Pfitzner, A.J. Two amino acid substitutions in the tomato mosaic virus 30-kilodalton movement protein confer the ability to overcome the Tm-2(2) resistance gene in the tomato. J. Virol. 1993, 67, 6432–6438. [CrossRef] Parrella, G.; Ruffel, S.; Moretti, A.; Morel, C.; Palloix, A.; Caranta, C. Recessive resistance genes against potyviruses are localized in colinear genomic regions of the tomato (Lycopersicon spp.) and pepper (Capsicum spp.) Genomes. Theor. Appl. Genet. 2002, 105, 855–861. [CrossRef] Diaz-Pendon, J.A.; Truniger, V.; Nieto, C.; Garcia-Mas, J.; Bendahmane, A.; Aranda, M.A. Advances in understanding recessive resistance to plant viruses. Mol. Plant Pathol. 2004, 5, 223–233. [CrossRef] [PubMed] Ruffel, S.; Gallois, J.L.; Lesage, M.L.; Caranta, C. The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Mol. Genet. Genom. 2005, 274, 346–353. [CrossRef] [PubMed] Stevens, M.; Scott, S.; Gergerich, R. Inheritance of a gene for resistance to Tomato spotted wilt virus (TSWV) from Lycopersicon peruvianum Mill. Euphytica 1992, 59, 9–17. [CrossRef] Boiteux, L.S.; Giordano, L.D. Genetic basis of resistance against two Tospovirus species in tomato (Lycopersicon-esculentum). Euphytica 1993, 71, 151–154. [CrossRef] Dianese, E.C.; Fonseca, M.E.N.; Inoue-Nagata, A.K.; Resende, R.O.; Boiteux, L.S. Search in Solanum (section Lycopersicon) germplasm for sources of broad-spectrum resistance to four Tospovirus species. Euphytica 2011, 180, 307–319. [CrossRef] Stevens, M.R.; Lamb, E.M.; Rhoads, D.D. Mapping the Sw-5 locus for Tomato spotted wilt virus resistance in tomatoes using RAPD and RFLP analyses. Theor. Appl. Genet. 1995, 90, 451–456. [CrossRef] Spassova, M.I.; Prins, T.W.; Folkertsma, R.T.; Klein-Lankhorst, R.M.; Hille, J.; Goldbach, R.W.; Prins, M. The tomato gene Sw5 is a member of the coiled coil, nucleotide binding, leucine-rich repeat class of plant resistance genes and confers resistance to TSWV in tobacco. Mol. Breed. 2001, 7, 151–161. [CrossRef] Hanson, F.S. Viral Diseases of Tomato—Origins, Impact, and Future Prospects with a Focus on Tomato Spotted Wilt Virus and Tomato Yellow Leaf Curl Virus; IntechOpen: London, UK, 2022. Laterrot, H.; Pecaut, P. Gene Tm-2: New source. Rep. Tomato Genet. Coop. 1969, 19, 13–14. Lanfermeijer, F.C.; Jiang, G.Y.; Ferwerda, M.A.; Dijkhuis, J.; Haan, P.D.; Yang, R.; Hille, J. The durable resistance gene Tm-22 from tomato confers resistance against ToMV in tobacco and preserves its viral specificity. Plant Sci. 2004, 167, 687–692. [CrossRef] Ohmori, T.; Murata, M.; Motoyoshi, F. Molecular characterization of RAPD and SCAR markers linked to the Tm-1 locus in tomato. Theor. Appl. Genet. 1996, 92, 151–156. [CrossRef] Ohmori, T.; Murata, M.; Motoyoshi, F. Identification of RAPD markers linked to the Tm-2 locus in tomato. Theor. Appl. Genet. 1995, 90, 307–311. [CrossRef] Kuo, Y.W.; Falk, B.W. RNA interference approaches for plant disease control. BioTechniques 2020, 69, 469–477. [CrossRef] [PubMed] Moreno-Pérez, M.G.; García-Luque, I.; Fraile, A.; García-Arenal, F. Mutations That Determine Resistance Breaking in a Plant RNA Virus Have Pleiotropic Effects on Its Fitness That Depend on the Host Environment and on the Type, Single or Mixed, of Infection. J. Virol. 2016, 90, 9128–9137. [CrossRef] Kumar, A.; Tiwari, K.L.; Datta, D.; Singh, M. Marker assisted gene pyramiding for enhanced Tomato leaf curl virus disease resistance in tomato cultivars. Biol. Plant 2014, 58, 792–797. [CrossRef] Int. J. Mol. Sci. 2023, 24, 15448 77. 78. 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. 91. 92. 93. 94. 95. 96. 97. 98. 99. 100. 101. 102. 103. 19 of 22 Kumar, A.; Jindal, S.K.; Dhaliwal, M.S.; Sharma, A.; Kaur, S.; Jain, S. Gene pyramiding for elite tomato genotypes against ToLCV (Begomovirus spp.), late blight (Phytophthora infestans) and RKN (Meloidogyne spp.) for northern India farmers. Physiol. Mol. Biol. Plants 2019, 25, 1197–1209. [CrossRef] [PubMed] García-Martínez, S.; Grau, A.; Alonso, A.; Rubio, F.; Valero, M.; Ruiz, J.J. UMH 1422 and UMH 1415: Two Fresh-market Tomato Breeding Lines Resistant to Tomato Mosaic Virus and Tomato Spotted Wilt Virus. Hortscience A Publ. Am. Soc. Hortic. Sci. 2014, 49, 1465–1466. [CrossRef] Dormatey, R.; Sun, C.; Ali, K.; Coulter, J.A.; Bai, J. Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. Agronomy 2020, 10, 1255. [CrossRef] García-Martínez, S.; Grau, A.; Alonso, A.; Rubio, F.; Valero, M.; Ruiz, J.J. UMH 1200, a breeding line within the Muchamiel tomato type resistant to three viruses. HortScience 2011, 46, 1054–1055. [CrossRef] Rubio, F.; García-Martínez, S.; Alonso, A.; Grau, A.; Valero, M.; Ruiz, J.J. Introgressing resistance genes into traditional tomato varie-ties: Effects on yield and quality. Acta Hortic. 2012, 935, 29–33. [CrossRef] Baulcombe, D. RNA silencing in plants. Nature 2004, 431, 356–363. [CrossRef] Svoboda, P. Key Mechanistic Principles and Considerations Concerning RNA Interference. Front. Plant Sci. 2020, 11, 1237. [CrossRef] [PubMed] Sharma, N.; Prasad, M. Silencing AC1 of Tomato leaf curl virus using artificial microRNA confers resistance to leaf curl disease in transgenic tomato. Plant Cell Rep. 2020, 39, 1565–1579. [CrossRef] Singh, A.; Mohorianu, I.; Green, D.; Dalmay, T.; Dasgupta, I.; Mukherjee, S.K. Artificially induced phased siRNAs promote virus resistance in transgenic plants. Virology 2019, 537, 208–215. [CrossRef] [PubMed] Vu, T.V.; Choudhury, N.R.; Mukherjee, S.K. Transgenic tomato plants expressing artificial microRNAs for silencing the pre-coat and coat proteins of a begomovirus, Tomato leaf curl New Delhi virus, show tolerance to virus infection. Virus Res. 2013, 172, 35–45. [CrossRef] Cisneros, A.E.; Carbonell, A. Artificial Small RNA-Based Silencing Tools for Antiviral Resistance in Plants. Plants 2020, 9, 669. [CrossRef] [PubMed] Carbonell, A. Secondary Small Interfering RNA-Based Silencing Tools in Plants: An Update. Front. Plant Sci. 2019, 10, 687. [CrossRef] [PubMed] Carbonell, A.; Lison, P.; Daros, J.A. Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance. Plant J. 2019, 100, 720–737. [CrossRef] [PubMed] Carbonell, A.; Daròs, J.A. Artificial microRNAs and synthetic trans-acting small interfering RNAs interfere with viroid infection. Mol. Plant Pathol. 2017, 18, 746–753. [CrossRef] Chen, L.; Cheng, X.; Cai, J.; Zhan, L.; Wu, X.; Liu, Q.; Wu, X. Multiple virus resistance using artificial trans-acting siRNAs. J. Virol. Methods 2016, 228, 16–20. [CrossRef] Jiang, L.; Mu, R.; Wang, Z.; Liu, S.; Lu, D. Silencing P25, HC-Pro and Brp1 of Potato Virus (Viroid) Using Artificial microRNA Confers Resistance to PVX, PVY and PSTVd in Transgenic Potato. Potato Res. 2023, 66, 231–244. [CrossRef] Gaafar, Y.Z.A.; Ziebell, H. Novel Targets for Engineering Physostegia Chlorotic Mottle and Tomato Brown Rugose Fruit Virusresistant Tomatoes: In Silico Prediction of Tomato microRNA Targets. PeerJ 2020, 8, e10096. Cisneros, A.E.; Martín-García, T.; Primc, A.; Kuziuta, W.; Sánchez-Vicente, J.; Aragonés, V.; Daròs, J.A.; Carbonell, A. Transgenefree, virus-based gene silencing in plants by artificial microRNAs derived from minimal precursors. Nucleic Acids Res. 2023, gkad747. [CrossRef] Halder, K.; Chaudhuri, A.; Abdin, M.Z.; Majee, M.; Datta, A. RNA Interference for Improving Disease Resistance in Plants and Its Relevance in This Clustered Regularly Interspaced Short Palindromic Repeats-Dominated Era in Terms of dsRNA-Based Biopesticides. Front. Plant Sci. 2022, 13, 885128. [CrossRef] Abel, P.P.; Nelson, R.S.; De, B.; Hoffmann, N.; Rogers, S.G.; Fraley, R.T.; Beachy, R.N. Delay of Disease Development in Transgenic Plants that Express the Tobacco Mosaic Virus Coat Protein Gene. Science 1986, 232, 738–743. [CrossRef] [PubMed] Reimann-Philipp, U.; Beachy, R.N. Coat protein-mediated resistance in transgenic tobacco expressing the tobacco mosaic virus coat protein from tissue-specific promoters. Mol. Plant-Microbe Interact. 1993, 6, 323–330. [CrossRef] [PubMed] MacKenzie, D.J.; Ellis, P.J. Resistance to tomato spotted wilt virus infection in transgenic tobacco expressing the viral nucleocapsid gene. Mol. Plant-Microbe Interact. 1992, 5, 34–40. [CrossRef] Praveen, S.; Mishra, A.K.; Dasgupta, A. Antisense Suppression of Replicase Gene Expression Recovers Tomato Plants from Leaf Curl Infection. Plant Sci. 2005, 168, 1011–1014. [CrossRef] Raj, S.K.; Singh, R.; Pandey, S.K.; Singh, B.P. Agrobacterium-mediated Tomato Transformation and Regeneration of Transgenic Lines Expressing Tomato Leaf Curl Virus Coat Protein Gene for Resistance Against TLCV Infection. Curr. Sci. 2005, 88, 1674–1679. Mubin, M.; Mansoor, S.; Hussain, M.; Zafar, Y. Silencing of the AV2 Gene by Antisense RNA Protects Transgenic Plants Against a Bipartite Begomovirus. Virol. J. 2007, 4, 10. [CrossRef] Ferreira, S.A.; Pitz, K.Y.; Manshardt, R.; Zee, F.; Fitch, M.; Gonsalves, D. Virus Coat Protein Transgenic Papaya Provides Practical Control of Papaya Ringspot Virus in Hawaii. Plant Dis. 2002, 86, 101–105. [CrossRef] Konakalla, N.C.; Kaldis, A.; Berbati, M.; Masarapu, H.; Voloudakis, A.E. Exogenous application of double-stranded RNA molecules from TMV p126 and CP genes confers resistance against TMV in tobacco. Planta 2016, 244, 961–969. [CrossRef] Int. J. Mol. Sci. 2023, 24, 15448 20 of 22 104. Ramesh, S.V.; Mishra, A.K.; Praveen, S. Hairpin RNA-mediated Strategies for Silencing of Tomato Leaf Curl Virus AC1 and AC4 Genes for Effective Resistance in Plants. Oligonucleotide 2007, 17, 251–257. [CrossRef] [PubMed] 105. Koulagi, R.; Banerjee, S.; Gawade, B.H.; Singh, A.K.; Jain, P.K.; Praveen, S.; Subramaniam, K.; Sirohi, A. Host-delivered RNA Interference in Tomato for Mediating Resistance Against Meloidogyne Incognita and Tomato Leaf Curl Virus. Plant Cell Tiss. Organ Cult. 2020, 143, 345–361. [CrossRef] 106. Ribeiro, S.G.; Lohuis, H.; Goldbach, R.; Prins, M. Tomato Chlorotic Mottle Virus is a Target of RNA Silencing but the Presence of Specific Short Interfering RNAs does not Guarantee Resistance in Transgenic Plants. J. Virol. 2007, 81, 1563–1573. [CrossRef] 107. Missiou, A.; Kalantidis, K.; Boutla, A.; Tzortzakaki, S.; Tabler, M.; Tsagris, M. Generation of Transgenic Potato Plants Highly Resistant to Potato Virus Y (PVY) through RNA Silencing. Mol. Breed. 2004, 14, 185–197. [CrossRef] 108. McCue, K.F.; Ponciano, G.; Rockhold, D.R.; Whitworth, J.L.; Gray, S.M.; Fofanov, Y.; Belknap, W.R. Generation of PVY Coat Protein siRNAs in Transgenic Potatoes Resistant to PVY. Am. J. Pot. Res. 2012, 89, 374–383. [CrossRef] 109. Prasad Babu, K.; Maligeppagol, M.; Asokan, R.; Krishna Reddy, M. Screening of a Multi-virus Resistant RNAi Construct in Cowpea through Transient Vacuum Infiltration Method. Virus Dis. 2019, 30, 269–278. [CrossRef] 110. Al-Roshdi, M.R.; Ammara, U.; Khan, J.; Al-Sadi, A.M.; Shahid, M.S. Artificial microRNA-mediated Resistance Against Oman strain of Tomato Yellow Leaf Curl Virus. Front. Plant Sci. 2023, 30, 14:1164921. [CrossRef] 111. Carbonell, A.; Lopez, C.; Daròs, J.-A. Fast-Forward Identification of Highly Effective Artificial Small RNAs Against Different Tomato spotted wilt virus Isolates. Mol. Plant Microbe Interact. 2019, 32, 142–156. [CrossRef] [PubMed] 112. López-Dolz, L.; Spada, M.; Daròs, J.-A.; Carbonell, A. Fine-Tune Control of Targeted RNAi Efficacy by Plant Artificial Small RNAs. Nucleic Acids Res. 2020, in press. [CrossRef] 113. Song, Y.Z.; Han, Q.J.; Jiang, F.; Sun, R.Z.; Fan, Z.H.; Zhu, C.X.; Wen, F.J. Effects of the Sequence Characteristics of miRNAs on Multi-viral Resistance Mediated by Single amiRNAs in Transgenic Tobacco. Plant Physiol. Biochem. 2014, 77, 90–98. [CrossRef] 114. Tashkandi, M.; Ali, Z.; Aljedaani, F.; Shami, A.; Mahfouz, M.M. Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato. Plant Signal. Behav. 2018, 13, e1525996. [CrossRef] 115. Wang, N.; Tang, C.L.; Fan, X.; He, M.Y.; Gan, P.F.; Zhang, S.; Hu, Z.Y.; Wang, X.D.; Yan, T.; Shu, W.X.; et al. Inactivation of a wheat protein kinase gene confers broad-spectrum resistance to rsust fungi. Cell 2022, 185, 2961–2974. [CrossRef] 116. Oliva, R.; Ji, C.; Atienza-Grande, G.; Huguet-Tapia, J.C.; Perez-Quintero, A.; Li, T.; Eom, J.S.; Li, C.; Nguyen, H.; Liu, B.; et al. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat. Biotechnol. 2019, 37, 1344–1350. [CrossRef] [PubMed] 117. Pramanik, D.; Shelake, R.M.; Park, J.; Kim, M.J.; Hwang, I.; Park, Y.; Kim, J.-Y. CRISPR/Cas9-mediated generation of pathogen resistant tomato against tomato yellow leaf curl virus and powdery mildew. Int. J. Mol. Sci. 2021, 22, 1878. [CrossRef] 118. Pramanik, D.; Shelake, R.M.; Kim, M.J.; Kim, J.-Y. CRISPR-mediated engineering across the central dogma in plant biology for basic research and crop improvement. Mol. Plant. 2021, 14, 127–150. [CrossRef] 119. Shmakov, S.; Smargon, A.; Scott, D.; Cox, D.; Pyzocha, N.; Yan, W.; Abudayyeh, O.O.; Gootenberg, J.S.; Makarova, K.S.; Wolf, Y.I.; et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat. Rev. Microbiol. 2017, 15, 169–182. [CrossRef] [PubMed] 120. Makarova, K.S.; Zhang, F.; Koonin, E.V. SnapShot: Class 1 CRISPRCas systems. Cell 2017, 168, 946–946.e1. [CrossRef] [PubMed] 121. Makarova, K.S.; Zhang, F.; Koonin, E.V. SnapShot: Class 2 CRISPRCas systems. Cell 2017, 168, 328–328.e1. [CrossRef] 122. Ji, X.; Zhang, H.W.; Zhang, Y.; Wang, Y.P.; Gao, C.X. Establishing a CRISPR-Cas-like immune system conferring DNA virus resistance in plants. Nat. Plants 2015, 1, 15144. [CrossRef] 123. van Beljouw, S.P.B.; Sanders, J.; Rodríguez-Molina, A.; Brouns, S.J.J. RNA-targeting CRISPR-Cas systems. Nat. Rev. Microbiol. 2023, 21, 21–34. [CrossRef] 124. Lebedeva, M.V.; Nikonova, E.Y.; Terentiev, A.A.; Taranov, V.V.; Babakov, A.V.; Nikonov, O.S. VPg of Potato Virus Y and Potato Cap-Binding eIF4E Factors: Selective Interaction and Its Supposed Mechanism. Biochem 2021, 86, 1128–1138. [CrossRef] 125. Ali, Z.; Abulfaraj, A.; Idris, A.; Shakila, A.; Tashkandi, M.; Mahfouz, M.M. CRISPR/Cas9-mediated viral interference in plants. Genome Biol. 2015, 16, 238. [CrossRef] 126. Ali, Z.; Shakila, A.; Tashkandi, M.; Zaidi, S.S.; Mahfouz, M.M. CRISPR/Cas9-mediated immunity to geminiviruses: Differential interference and evasion. Sci. Rep. 2016, 6, 26912. [CrossRef] [PubMed] 127. Hirano, H.; Gootenberg, J.S.; Horii, T.; Abudayyeh, O.O.; Kimura, M.; Hsu, P.D.; Nakane, T.; Ishitani, R.; Hatada, I.; Zhang, F.; et al. Structure and engineering of Francisella novicida Cas9. Cell 2016, 164, 950–961. [CrossRef] [PubMed] 128. Abudayyeh, O.A.; Essletzbichler, P.; Shmakov, S.; Makarova, K.S. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessoryproteins Csx27 and Csx28. Mol. Cell 2017, 65, 618–630. 129. Abudayyeh, O.O.; Gootenberg, J.S.; Konermann, S.; Joung, J.; Slaymaker, I.M.; Cox, D.B.; Shmakov, S.; Makarova, K.S.; Semenova, E.; Minakhin, L.; et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 2016, 353, aaf5573. [CrossRef] [PubMed] 130. Smargon, A.A.; Cox, D.B.; Pyzocha, N.K.; Zheng, K.; Slaymaker, I.M.; Gootenberg, J.S.; Yan, W.X.; Chong, S.; Zhang, H.; Makarova, K.S.; et al. Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol. Cell 2018, 70, 327–339. 131. Yan, Z.; Pérez-de-Castro, A.; Díez, M.J.; Hutton, S.F.; Visser, R.G.F.; Wolters, A.-M.A.; Bai, Y.L.; Li, J.M. Resistance to Tomato Yellow Leaf Curl Virus in Tomato Germplasm. Front. Plant Sci. 2018, 9, 1198. [CrossRef] Int. J. Mol. Sci. 2023, 24, 15448 21 of 22 132. Ghorbani Faal, P.; Farsi, M.; Seifi, A.; Mirshamsi Kakhki, A. Virus-induced CRISPR-Cas9 system improved resistance against tomato yellow leaf curl virus. Mol. Biol. Rep. 2020, 47, 3369–3376. [CrossRef] 133. Zhang, T.; Zheng, Q.F.; Yi, X.; An, H.; Zhao, Y.L.; Ma, S.Q.; Zhou, G.H. Establishing RNA virus resistance in plants by harnessing CRISPR immune system. Plant Biotechnol. J. 2018, 16, 1415–1423. [CrossRef] [PubMed] 134. Aman, R.; Ali, Z.; Butt, H.; Mahas, A.; Aljedaani, F.; Khan, M.Z.; Ding, S.; Mahfouz, M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 2018, 19, 1. [CrossRef] [PubMed] 135. Aman, R.; Mahas, A.; Butt, H.; Aljedaani, F.; Mahfouz, M. Engineering RNA virus interference via the CRISPR/Cas13 machinery in Arabidopsis. Viruses 2018, 10, 732. [CrossRef] 136. Zhan, X.H.; Zhang, F.J.; Zhong, Z.Y.; Chen, R.H.; Wang, Y.; Chang, L.; Bock, R.; Nie, B.H.; Zhang, J. Generation of virus-resistant potato plants by RNA genome targeting. Plant Biotechnol. J. 2019, 17, 1814–1822. [CrossRef] 137. Zhang, T.; Zhao, Y.L.; Ye, J.J.; Cao, X.; Xu, C.H.; Chen, B.; An, H.; Jiao, Y.T.; Zhang, F.S.; Yang, X.; et al. Establishing CRISPR/Cas13a immune system conferring RNA virus resistance in both dicot and monocot plants. Plant Biotechnol. J. 2019, 17, 1185–1187. [CrossRef] [PubMed] 138. Yu, Y.C.; Pan, Z.Y.; Wang, X.; Bian, X.F.; Wang, W.C.; Liang, Q.; Kou, M.; Ji, H.T.; Li, Y.J.; Ma, D.F.; et al. Targeting of SPCSV-RNase3 via CRISPR-Cas13 confers resistance against sweet potato virus disease. Mol. Plant Pathol. 2022, 23, 104–117. [CrossRef] 139. Atarashi, H.; Jayasinghe, W.H.; Kwon, J.; Kim, H.; Taninaka, Y.; Igarashi, M.; Ito, K.; Yamada, T.; Masuta, C.; Nakahara, K.S. Artificially edited alleles of the eukaryotic translation initiation factor 4E1 gene differentially reduce susceptibility to cucumber mosaicvirus and potato virus Y in tomato. Front. Microbiol. 2020, 11, 564310. [CrossRef] 140. Kuroiwa, K.; Danilo, B.; Perrot, L.; Thenault, C.; Veillet, F.; Delacote, F.; Duchateau, P.; Nogué, F.; Mazier, M.; Gallois, J.L. An iterative gene-editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to multiple potyvirus isolates. Plant Biotechnol. J. 2023, 21, 918–930. [CrossRef] 141. Yoon, Y.J.; Venkatesh, J.; Lee, J.H.; Kim, J.; Lee, H.E.; Kim, D.S.; Kang, B.C. Genome editing of eIF4E1 in tomato confers resistance to pepper mottle virus. Front. Plant Sci. 2020, 11, 1098. [CrossRef] 142. Moury, B.; Lebaron, C.; Szadkowski, M.; Ben Khalifa, M.; Girardot, G.; Bolou Bi, B.A.; Koné, D.; Nitiema, L.W.; Fakhfakh, H.; Gallois, J.L. Knock-out mutation of eukaryotic initiation factor 4E2 (eIF4E2) confers resistance to pepper veinal mottle virus in tomato. Virology 2020, 539, 11–17. [CrossRef] 143. Pyott, D.E.; Sheehan, E.; Molnar, A. Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants. Mol. Plant Pathol. 2016, 17, 1276–1288. [CrossRef] 144. Kravchik, M.; Shnaider, Y.; Abebie, B.; Shtarkman, M.; Kumari, R.; Kumar, S.; Leibman, D.; Spiegelman, Z.; Gal-On, A. Knockout of SlTOM1 and SlTOM3 results in differential resistance to tobamovirus in tomato. Mol. Plant Pathol. 2022, 23, 1278–1289. [CrossRef] 145. Garcia-Ruiz, H. Susceptibility Genes to Plant Viruses. Viruses 2018, 10, 484. [CrossRef] 146. Kan, J.; Cai, Y.; Cheng, C.; Jiang, C.; Jin, Y.; Yang, P. Simultaneous editing of host factor gene TaPDIL5-1 homoeoalleles confers wheat yellow mosaic virus resistance in hexaploid wheat. New Phytol. 2022, 234, 340–344. [CrossRef] [PubMed] 147. Ivanov, K.I.; Eskelin, K.; Lohmus, A.; Makinen, K. Molecular and cellular mechanisms underlying potyvirus infection. J. Gen. Virol. 2014, 95, 1415–1429. [CrossRef] 148. Yamanaka, T.; Ohta, T.; Takahashi, M.; Meshi, T.; Schmidt, R.; Dean, C.; Naito, S.; Ishikawa, M. TOM1, an Arabidopsis gene required for efficient multiplication of a tobamovirus, encodes a putative transmembrane protein. Proc. Natl. Acad. Sci. USA 2000, 97, 10107–10112. [CrossRef] [PubMed] 149. Lapidot, M.; Karniel, U.; Gelbart, D.; Fogel, D.; Evenor, D.; Kutsher, Y.; Makhbash, Z.; Nahon, S.; Shlomo, H.; Chen, L.; et al. A Novel Route Controlling Begomovirus Resistance by the Messenger RNA Surveillance Factor Pelota. PLoS Genet. 2015, 11, e1005538. [CrossRef] [PubMed] 150. Turina, M.; Kormelink, R.; Resende, R.O. Resistance to Tospoviruses in Vegetable Crops: Epidemiological and Molecular Aspects. Annu. Rev. Phytopathol. 2016, 54, 347–371. [CrossRef] 151. Chinnaiah, S.; Gautam, S.; Workneh, F.; Crosby, K.; Rush, C.; Gadhave, K.R. First report of Sw-5 resistance-breaking strain of tomato spotted wilt orthotospovirus infecting tomato in Texas. Plant Dis. 2023, 107. [CrossRef] 152. Zheng, K.Y.; Chen, T.C.; Wu, K.; Kang, Y.C.; Yeh, S.D.; Zhang, Z.K.; Dong, J.H. Characterization of a New Orthotospovirus from Chilli Pepper in Yunnan Province, China. Plant Dis. 2020, 104, 1175–1182. [CrossRef] [PubMed] 153. Helderman, T.A.; Deurhof, L.; Bertran, A.; Boeren, S.; Fokkens, L.; Kormelink, R.; Joosten, M.H.A.J.; Prins, M.; van den Burg, H.A. An Isoform of the Eukaryotic Translation Elongation Factor 1A (eEF1a) Acts as a Pro-Viral Factor Required for Tomato Spotted Wilt Virus Disease in Nicotiana benthamiana. Viruses 2021, 13, 2190. [CrossRef] 154. Komoda, K.; Ishibashi, K.; Kawamura-Nagaya, K.; Ishikawa, M. Possible involvement of eEF1A in Tomato spotted wilt virus RNA synthesis. Virology 2014, 468–470, 81–87. [CrossRef] 155. Helderman, T.A.; Deurhof, L.; Bertran, A.; Richard, M.M.S.; Kormelink, R.; Prins, M.; Joosten, M.H.A.J.; van den Burg, H.A. Members of the ribosomal protein S6 (RPS6) family act as pro-viral factor for tomato spotted wilt orthotospovirus infectivity in Nicotiana benthamiana. Mol. Plant Pathol. 2022, 23, 431–446. [CrossRef] 156. Spiechowicz, M.; Zylicz, A.; Bieganowski, P.; Kuznicki, J.; Filipek, A. Hsp70 is a new target of Sgt1--an interaction modulated by S100A6. Biochem. Biophys. Res. Commun. 2007, 357, 1148–1153. [CrossRef] 157. Qian, X.; Xiang, Q.; Yang, T.Q.; Ma, H.Y.; Ding, X.S.; Tao, X.R. Molecular Co-Chaperone SGT1 Is Critical for Cell-to-Cell Movement and Systemic Infection of Tomato Spotted Wild Virus in Nicotiana benthamiana. Viruses 2018, 10, 647. [CrossRef] Int. J. Mol. Sci. 2023, 24, 15448 22 of 22 158. Gao, X.H.; Chen, J.L.; Dai, X.H.; Zhang, D.D.; Zha, Y.D. An effective strategy for reliably isolating heritable and Cas9-free arabidopsis mutants generated by CRISPR/Cas9 mediated genome editing. Plant Physiol. 2016, 171, 1794–1800. [CrossRef] 159. Lin, C.S.; Hsu, C.T.; Yuan, Y.H.; Zheng, P.X.; Wu, F.H.; Cheng, Q.W.; Wu, Y.L.; Wu, T.L.; Lin, S.; Yue, J.J.; et al. DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. Plant Physiol. 2022, 188, 1917–1930. [CrossRef] 160. Č ermák, T.; Baltes, N.J.; Č egan, R.; Zhang, Y.; Voytas, D.F. High-frequency, precise modification of the tomato genome. Genome Biol. 2015, 16, 232. 161. Yin, K.; Han, T.; Liu, G.; Chen, T.; Wang, Y.; Yu, A.Y.L.; Liu, Y. A geminivirus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing. Sci. Rep. 2015, 5, 14926. [CrossRef] 162. Gil-Humanes, J.; Wang, Y.; Liang, Z.; Shan, Q.; Ozuna, C.V.; Sánchez-León, S.; Baltes, N.J.; Starker, C.; Barro, F.; Gao, C.; et al. High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant J. 2017, 89, 1251–1262. [CrossRef] 163. Liu, Q.; Zhao, C.L.; Sun, K.; Deng, Y.L.; Li, Z.H. Engineered biocontainable RNA virus vectors for non-transgenic genome editing across crop species and genotypes. Mol. Plant 2023, 16, 616–631. [CrossRef] 164. Li, T.D.; Hu, J.C.; Sun, Y.; Li, B.S.; Zhang, D.L.; Li, W.L.; Liu, J.X.; Li, D.W.; Gao, C.X.; Zhang, Y.L.; et al. Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture. Mol. Plant 2021, 14, 1787–1798. [CrossRef] 165. Ali, Z.; Abul-faraj, A.; Li, L.; Ghosh, N.; Piatek, M.; Mahjoub, A.; Aouida, M.; Piatek, A.; Baltes, N.J.; Voytas, D.F.; et al. Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Mol. Plant 2015, 8, 1288–1291. [CrossRef] 166. Ma, X.N.; Zhang, X.Y.; Liu, H.M.; Li, Z.H. Highly efficient DNA-free plant genome editing using virally delivered CRISPR-Cas9. Nat. Plants 2020, 6, 773–779. [CrossRef] 167. Varanda, C.M.; Félix, M.D.R.; Campos, M.D.; Patanita, M.; Materatski, P. Plant Viruses: From Targets to Tools for CRISPR. Viruses 2021, 13, 141. [CrossRef] 168. Zhang, W.N.; Thieme, C.J.; Kollwig, G.; Apelt, F.; Yang, L.; Winter, N.; Andresen, N.; Walther, D.; Kragler, F. tRNA-Related Sequences Trigger Systemic mRNA Transport in Plants. Plant Cell 2016, 28, 1237–1249. [CrossRef] 169. Yang, L.; Machin, F.; Wang, S.F.; Saplaoura, E.; Kragler, F. Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks. Nat. Biotechnol. 2023, 41, 958–967. [CrossRef] 170. Mehta, D.; Stürchler, A.; Anjanappa, R.B.; Zaidi, S.S.E.A.; Hirsch-Hoffmann, M.; Gruissem, W.; Vanderschuren, H. Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses. Genome Biol. 2019, 20, 80. [CrossRef] 171. Mubarik, M.S.; Wang, X.; Khan, S.H.; Ahmad, A.; Khan, Z.; Amjid, M.W.; Razzaq, M.K.; Ali, Z.; Azhar, M.T. Engineering broad-spectrum resistance to cotton leaf curl disease by CRISPR-Cas9 based multiplex editing in plants. GM Crops Food 2021, 12, 647–658. [CrossRef] 172. Xiao, N.; Pan, C.; Li, Y.; Wu, Y.; Cai, Y.; Lu, Y.; Wang, R.; Yu, L.; Shi, W.; Kang, H.; et al. Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice. Genome Biol. 2021, 22, 283. [CrossRef] 173. Khera, P.; Pandey, M.K.; Mallikarjuna, N.; Sriswathi, M.; Roorkiwal, M.; Janila, P.; Sharma, S.; Shilpa, K.; Sudini, H.; Guo, B.; et al. Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hy-pogaea L.). Mol. Genet. Genom. 2019, 294, 365–378. [CrossRef] 174. Hua, K.; Zhang, J.; Botella, J.R.; Ma, C.; Kong, F.; Liu, B.; Zhu, J.K. Perspectives on the application of genome-editing technologies in crop breeding. Mol. Plant. 2019, 12, 1047–1059. [CrossRef] [PubMed] 175. Salava, H.; Thula, S.; Mohan, V.; Kumar, R.; Maghuly, F. Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects. Int. J. Mol. Sci. 2021, 22, 682. [CrossRef] [PubMed] 176. Guevara-Escudero, M.; Osorio, A.N.; Cortés, A.J. Integrative Pre-Breeding for Biotic Resistance in Forest Trees. Plants 2021, 10, 2022. [CrossRef] 177. Qi, S.; Shen, Y.; Wang, X.; Zhang, S.; Li, Y.; Islam, M.M.; Wang, J.; Zhao, P.; Zhan, X.; Zhang, F.; et al. A new NLR gene for resistance to Tomato spotted wilt virus in tomato (Solanum lycopersicum). Theor. Appl. Genet. 2022, 135, 1493–1509. [CrossRef] [PubMed] 178. Lv, J.; Deng, M.; Jiang, S.; Zhu, H.; Li, Z.; Wang, Z.; Li, J.; Yang, Z.; Yue, Y.; Xu, J.; et al. Mapping and functional characterization of the tomato spotted wilt virus resistance gene SlCHS3 in Solanum lycopersicum. Mol. Breed. 2022, 42, 55. [CrossRef] [PubMed] 179. Sáez, C.; Martínez, C.; Montero-Pau, J.; Esteras, C.; Sifres, A.; Blanca, J.; Ferriol, M.; López, C.; Picó, B. A Major QTL Located in Chromosome 8 of Cucurbita moschata Is Responsible for Resistance to Tomato Leaf Curl New Delhi Virus. Front. Plant Sci. 2020, 11, 207. [CrossRef] Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.