Tomato (Solanum lycopersicum L.) is an economically important crop worldwide, and it has been estimated that 5 million hectares of tomatoes are grown annually worldwide, producing more than 160 million tons of tomatoes (Food and Agriculture Organization 2013). Tomato also serves as an excellent academic model system for plant genetics and biology, especially for studying fruit biology, abiotic stress tolerance, and plant-microbe interactions. Development and practical use of molecular markers have been actively pursued in molecular breeding programs for tomato (Martin et al. 1993; Tanksley et al. 1995). Marker-assisted selection (MAS) and marker-assisted breeding (MAB) has been widely and successfully deployed in tomato breeding programs, especially for disease resistance, which allows selection of a single resistance gene and combination of multiple resistance genes (Foolad and Sharma 2005; Arens et al. 2010).

Various technological advancements have accelerated the investigation of the whole genome and genetic loci of interest. Single nucleotide polymorphisms (SNPs) are among the most common types of genetic variation and have been widely utilized in genomics for genome mapping, phylogenetic analysis, association studies, and tagging genes of interest (Jehan and Lakhanpaul 2006; Caicedo et al. 2007). Numerous verified SNPs have been successfully used to develop tomato cultivars for public and commercial use (Yang et al. 2004; Labate and Baldo 2005). Practical DNA markers can be applied in multiple types of breeding programs such as cultivar identification, parental line selection, and selection of progenies in segregating populations (Yeam et al. 2005; Lagudah et al. 2009). The release of the tomato genome sequence has expedited characterization of SNPs, allowing SNPs to be the most effective and useful genetic markers in modern tomato breeding programs (Tomato genome consortium 2012). Use of gene-based markers, which have increased due to the emergence of high-quality genome sequence information, is clearly advantageous for increasing the accuracy of MAS compared with utilization of markers generated based on DNA polymorphisms located adjacent to the gene of interest (Salgotra et al. 2014).

Despite decades of intensive efforts in disease resistance tomato breeding programs, a large number of diseases still threaten tomato production industries. Major diseases that challenge tomato production include Tomato yellow leaf curl virus (TYLCV), Tomato spotted wilt virus (TSWV), Tomato mosaic virus (ToMV), verticillium wilt caused by Verticillium spp., fusarium wilt caused by Fusarium oxysporum, late blight caused by Phytophthora infestans, leaf mold caused by Cladosporium fulvum, root-knot caused by Meloidogyne spp., bacterial spot caused by Xanthomonas spp., and bacterial speck caused by Pseudomonas syringae. Due to the intensive breeding efforts aimed at improving economically valuable traits, cultivated tomatoes have little variation in their gene pool. Hence, various wild relatives, including S. pimpinellifolium, S. pennellii, S. habrochaites, S. peruvianum, and S. chilense, have been investigated for use as disease resistance sources (Peirce 1971; Stevens et al. 1991; Zamir et al. 1994; Diwan et al. 1999). To pursue the resistance provided by these wild relatives in developing new tomato varieties, molecular markers have been developed and utilized in tomato breeding programs. In this review, we summarize the currently available molecular markers that confer resistance against each of the indicated diseases.

Tomato yellow leaf curl virus (TYLCV) resistance

Tomato yellow leaf curl virus (TYLCV), which is transmitted by the whitefly (Bemisia tabaci), is one of the most serious threats to tomato production worldwide. In Korea, TYLCV incidence was first reported in Tong- Young, Gyoengsangnamdo in 2008 and has spread rapidly throughout the country (Lee et al. 2010). TYLCV, which is a member of the genus Begomovirus within the family Geminiviridae, is a DNA virus with a genome of approximately 2.7?2.8 kb (Cohen and Harpaz 1964; Delatte et al. 2005). Several sources of TYLCV disease resistance have been identified among wild tomato species. Two major resistance loci on chromosome 6 were originated from S. chilense: Ty1 from “LA1969” and Ty3 from “LA1932” and “LA2779” (Zamir et al. 1994; Agrama and Scott 2006; Ji et al. 2007). Recently, a gene responsible for Ty1 resistance was identified as a DFDGD-class RNA-dependent RNA polymerase and was demonstrated to be allelic with Ty3 resistance (Verlaan et al. 2013). Ty2 resistance originated from S. habrochaites “B6013” and was recently mapped to a 300-kb interval on chromosome 11 (Hanson et al. 2000; Ji et al. 2009a; Yang et al. 2014). Ty4 was identified on chromosome 3 as an additional resistance locus in Ty3-carrying S. chilense “LA1932” and “LA2779” (Ji et al. 2009b). A recessive resistance locus located on chromosome 4, termed ty5, was identified in S. peruvianum (Friedmann et al. 1998; Anbinder et al. 2009). Recently, a gene responsible for ty5 resistance has been identified as a Pelo gene, which is the messenger RNA surveillance factor Pelota implicated in the ribosome recycling phase of protein synthesis (Lapidot et al. 2015). Furthermore, Ty6 on chromosome 10 appears to be a recessive resistance gene and has been additionally identified in Ty3-carrying S. chilense “LA2779” (Scott et al. 2015).

DNA markers for these TYLCV resistance genes are listed in Table 1. Since Ty1 and Ty3 were independently identified from different tomato accessions, different DNA markers that were closely linked to Ty1 or Ty3 were used in tomato breeding programs. However, it was recently confirmed that these two are in allelic relationship at a single locus (Verlaan et al. 2013; Caro et al. 2015). Resistance spectra and levels conferred by Ty1 and Ty3 are currently under investigation. In the case of Ty2 resistance, a sequence characterized amplified regions (SCAR) marker, T0302, was used reliably for the selection. However, it was recently mapped to a 300-kb interval on chromosome 11, gene identification that would allow development of gene-based marker is in progress (Wolters et al. 2015). A gene-based derived-cleaved amplified polymorphic sequences (dCAPS) marker for ty5 (Table 1) was developed based on the information given by Lapidot et al. (2015).

Tomato spotted wilt virus (TSWV) resistance

TSWV is a negative RNA virus belonging to the genus Tospovirus within the family Bunyaviridae. TSWV is effectively transmitted by thrips, and disease symptoms include bronzing, curling, necrotic spots and streaks, and stunting of stems and leaves (German et al. 1992). The wide host range of TSWV covers several hundred species in both monocotyledons and dicotyledons worldwide (Pappu et al. 2009). Tomato chlorotic spot virus (TCSV) and groundnut ringspot virus (GRSV), which are closely related to TSWV, also cause damage in the tomato production (Brommonschenkel et al. 2000).

Sources that are resistant to Tospoviruses have been found in diverse cultivars of S. lycopersicum (Saidi 2008). Some resistance genes for TSWV have also been identified in S. habrochaites (previously L. hirsutum “PI127826” and “LA1353”) and in S. habrochaites var. glabratum (“PI134417” and “LA1223”). To date, eight TSWV resistance genes (Sw1a, Sw1b, sw2, sw3, sw4, Sw-5, Sw-6, and Sw-7) have been reported (Finlay 1953; Price et al. 2007; Saidi and Warade 2008). Among these TSWV resistance genes, Sw-5 is the one that has been intensively studied and has been actively utilized in developing TSWV-resistant tomato varieties. Sw-5 resistance was characterized in S. peruvianum on chromosome 9 (Van Zijl et al. 1985; Stevens et al. 1991) and is known to confer a broad resistance against Tospoviruses, including TSWV, TCSV, and GRSV (Boiteux and Giordano 1993). The Sw-5 protein consists of a coiled-coil (CC) domain, a nucleotide-binding adapter (NB), and a leucine-rich repeat (LRR) domain (Spassova et al. 2001). Gene-based markers for Sw-5 are listed in Table 2. Markers for Sw-5 can be chosen and applied to the breeding programs, depending on the detection method of the user’s choice.

Tomato mosaic virus (ToMV) resistance

ToMV, which belongs to the genus Tobamovirus within the family Virgaviridae, has a positive sense RNA genome. Two resistance genes, Tm-1 and Tm-2, that confer resistance against ToMV have been introgressed to cultivated tomatoes. The Tm-1 gene, which displays semi-dominant inheritance, was originally identified from S. habrochites “PI126445” (Pelham 1966; Watanabe et al. 1987). Tm-1 protein does not share any functional domain with previously known resistance (R) proteins but physically binds to and functionally inhibits the replication proteins of ToMV (Ishibashi et al. 2007). The Tm-2 resistance gene was characterized in S. peruvianum and found to confer a higher level of resistance compared to that conferred by Tm-1. The Tm-2 and the Tm-22 resistance genes are considered to be allelic (Pelham 1966; Young and Tanksley 1989), and the Tm-22 resistance gene is more durable than the Tm-2 resistance gene (Fraser 1990). Consequently, Tm-22 is both practically and economically important and thus is employed as a ToMV resistance source in tomato breeding programs. Both Tm-2 and Tm-22 encode a member of the coiled-coil/nucleotide binding-ARC/LRR protein class of plant resistance (R) genes (Lanfermeijer et al. 2003). The Tm-22 and Tm-2 open reading frames only differ by seven nucleotides, resulting in four amino acid differences at the protein level. Two of these differences are located in the nucleotide-binding site, and two are located in the LRR domain (Lanfermeijer et al. 2005). ToMV allele-specific DNA markers derived from these above mentioned gene sequences are listed in Table 3.

Verticillium wilt resistance

Tomato verticillium wilt, which is also called vascular wilt disease, is a soil-born fungal disease caused by Verticillium dahliae and V. alboatrum, which are also responsible for the vascular wilt disease in over 200 dicotyledonous species (Fradin and Thomma 2006). A single dominant gene on chromosome 9, Ve, was reported to confer effective resistance against V. alboatrum race 1 (Schaible et al. 1951; Diwan et al. 1999). The Ve locus contains two closely linked, inversely oriented genes, Ve1 and Ve2, and the resistance spectrums of these resistance genes have been determined (Kawchuk et al. 2001; Fradin et al. 2009). Ve1 resistance is conferred by the extracellular LRR receptor-like protein class of disease resistance proteins (Kawchuk et al. 2001), which appear critical for switching on effector-triggered immunity in the host plant. Various allele-specific molecular markers for Ve1 and Ve2 have been reported (Table 4; Acciarri et al. 2007; Kuklev et al. 2009; Jung et al. 2015). Among the DNA variations between the Ve1 resistance allele and the ve1 susceptibility allele, a single-bp deletion, TCA/T-A at nucleotide position 1,220, results in a premature stop codon in the ve1 susceptibility allele, which is subsequently linked with loss of function and disease resistance (Kawchuk et al. 2001; Jung et al. 2015). Therefore, the gene-based CAPS marker derived from the single-bp deletion listed in Table 4 can be considered as a functional marker for the Ve1 resistance locus.

Fusarium wilt resistance

The fungus Fusarium oxysporum causes devastating wilt diseases in many important crops, and specifically, F. oxysporum f. sp. Lycopersici (Fol) causes fusarium wilt of tomato. Three races of Fol, race 1, 2, and 3, have been identified (Bohn and Tucker 1939; Grattidge and O’Brien 1982). Resistance against Fol has been characterized in multiple wild species of tomato. The I gene was identified in the wild tomato S. pimpinellifolium accession “PI79532” and confers resistance against Fol race 1 (Bohn and Tucker 1939). The I-2 gene, which confers resistance to Fol race 2, was identified in an S. lycopersicum × S. pimpinellifolium hybrid “PI126915”, and this gene encodes a coiled coil, nucleotide-binding (CC-NB)-LRR resistance protein (Stall and Walter 1965; Simons et al. 1998). I-3 resistance to Fol race 3 was identified in S. pennellii “LA716” (Scott and Jones 1989) and encodes an S-receptor-like kinase (SRLK) protein (Lim et al. 2008; Catanzariti et al. 2015). Furthermore, the I-7 resistance gene, which confers resistance to Fol race 1, 2, and 3, was identified in S. pennellii “PI414773” and encodes typical extracellular LRR receptor-like protein (LRR-RLP) (Lim et al. 2006; Gonzalez-Cendales et al. 2015). DNA markers for these resistance genes are listed in Table 5, and most of these markers are gene-based markers.

Late blight resistance

Late blight (LB) in tomato is caused by Phytophthora infestans, which also causes devastating LB in the potato. Although LB resistance in the potato has been extensively studied and more than 60 resistance genes have been characterized and/or located on the genetic map (Rodewald and Trognitz 2013), a few race-specific LB resistance loci have been characterized in the tomato. Two race-specific resistance genes, Ph1 and Ph2, from S. pimpinellifolium were mapped to chromosome 7 and 10, respectively (Peirce 1971; Moreau et al. 1998; Foolad et al. 2008). Another resistance gene from S. pimpinellifolium “L3708”, Ph3, which is the most effective LB resistance gene among the known genetic sources, confers incomplete resistance against a wide range of P. infestans isolates (Black et al. 1996; Kim and Mutschler 2006; Zhang et al. 2013). The Ph3 gene on chromosome 9 encodes a coiled-coil nucleotide-binding (NBS)-LRR (Zhang et al. 2014). Ph4 on chromosome 2 was discovered in S. habrochaites LA1033 (Kole et al. 2006), and Ph5-1 and Ph5-2, which were discovered from a novel resistance source S. pimpinellifolium “PSLP153”, are located on chromosome 1 and 10, respectively (Merk et al. 2012; Merk and Foolad 2012). DNA markers for the major LB resistance genes, Ph2 and Ph3, are listed in Table 6. In case of Ph3, a gene-based SCAR marker was developed based on two 11 bp deletions separated by 56 bp that generate a premature stop codon in the ph3 susceptible genotype. Therefore, the gene-based SCAR marker can be considered as a functional marker for the Ph3 resistance locus. In addition to these single dominant resistance genes, quantitative trait loci (QTL) that confer resistance to LB have also been identified in S. habrochaites and S. penellii (Brouwer and St Clair 2004; Smart et al. 2007; Li et al. 2011; Cai et al. 2012).

Leaf mold resistance

Leaf mold of tomato, which is caused by the fungus Cladosporium fulvum, is a worldwide problem in greenhouse conditions, particularly in areas with high humidity and moderate temperatures (Rivas and Thomas 2005). The genes conferring resistance against C. fulvum, the Cf genes, have been introduced into commercially grown tomato cultivars (Rivas and Thomas 2005). Among the multiple Cf resistance genes that originate from wild species, Cf-2, Cf-4, Cf-4E, Cf-5, and Cf-9 genes have been most intensively studied (Jones et al. 1994; Dixon et al. 1996; Thomas et al. 1997; Dixon et al. 1998; Takken et al. 1999). The Cf genes encode membrane-anchored proteins that are largely composed of extracellular LRRs (Rivas and Thomas 2005). Although the Cf genes share a high degree of homology, each Cf gene differs in its specificity for recognizing distinct fungal effectors. The Cf genes, Cf-2, Cf-4, Cf-4E, Cf-5, and Cf-9, trigger a race-specific hypersensitive response (HR) upon plant invasion by C. fulvum that secrets the avirulence factors Avr2, Avr4, Avr4E, Avr5, and Avr9, respectively (Jones et al. 1994; Dixon et al. 1996; Thomas et al. 1997; Dixon et al. 1998; Takken et al. 1999). Both Cf-4 from S. habrochaites and Cf-9 from S. pimpinellifolium are located at the same locus on chromosome 1 in an array of five paralogs (Parniske et al. 1997). Cf-2 from S. pimpinellifolium and Cf-5 from the landrace of S. lycopersicum (formerly L. esculentum var. cerasiforme) are located in a complex locus on chromosome 6 and consist of seven Cf-2/Cf-5 gene family homologs, which vary in LRR copy number from 25 to 38 (Dixon et al. 1998). A DNA marker for Cf-9 resistance gene is listed in Table 7. Although the genes that encode Cf-2, Cf-4, Cf-4E, Cf-5, and Cf-9 have been cloned and characterized decades ago, precise MAS in differentiating each Cf gene has been plagued by technical difficulties, due to the existence of the gene families and complex chimeric sequences.

Root-knot nematode (RKN) resistance

RKNs of the genus Meloidogyne cause major economic damage to crops around the world (Williamson and Hussey 1996). These nematodes penetrate the roots and migrate to the vascular cylinder, resulting in the formation of root-knots, which affect nutrient partitioning and water uptake in the plant (Roberts and May 1986). A single, dominant gene, Mi-1, which originated in S. peruvianum “PI128657”, was introgressed into modern tomato varieties (Castagnone-Sereno et al. 1994). Mi-1 encodes a CC-NBS-LRR with a nucleotide-binding site and a LRR region and confers resistance to three of the most damaging species of RKN: M. incognita, M. arenaria, and M. javanica. Moreover, this gene also confers resistance to potato aphid and whitefly (Milligan et al. 1998; Rossi et al. 1998; Vos et al. 1998). The Mi-1 locus consists of two clusters with three and four copies of Mi gene homologs (Seah et al. 2007). Mi-1.2, but not the other homologs, has been suggested to be a functional resistance gene (Milligan et al. 1998). Other genetic determinants of RKN resistance that have been identified in S. peruvianum accessions include major/minor QTLs: Mi-4 linked with Mi-1 on chromosome 6, Mi-3 and Mi-5 on chromosome 12, Mi-9 on chromosome 6, Mi-2 linked to Mi-8, and Mi-6 linked to Mi-7 (Veremis et al. 2000; Ammiraju et al. 2003). The practical use of these resistance loci, however, has not yet been investigated thoroughly. Allele specific markers for Mi-1 resistance are listed in Table 8.

Bacterial spot resistance

Bacterial spot of tomato, which is caused by a gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv), is one of the most destructive diseases both in the greenhouse and in the field, particularly in warm and humid environments (Jones et al. 1998). Recently, Xcv has been re-classified and divided into four distinct species (X. euvesicatoria, X. vesicatoria, X. gardneri, and X. perforans), which differ in their distribution, metabolic properties, and effector repertoires (Potnis et al. 2011). Five races (T1 to T5) of Xcv are recognized by different host genotypes. Xcv, which causes bacterial spot disease in both pepper and tomato, has been extensively studied. Effector-triggered immunity conferred by single dominant loci, including Xv3 and Xv4 (also known as RXopJ4), are mechanisms of HR resistance. Xv3 found in S. lycopersicum “H7981” and S. pimpinellifolium (accessions “PI126932” and “PI128216”) triggers HR resistance to T3 strains via recognition of the effector avrXv3 (Wang et al. 2011). A single locus Rx-4 on chromosome 11 (accession “PI128216”) also confers HR resistance to T3 strains; however, the degree of resistance is significantly affected by the genetic background (Robbins et al. 2009). Studies on Xv3 and Rx-4 indicated that these two genes are closely linked genes that react to the same bacterial effector or alleles of the same locus (Wang et al. 2011). Xv4 (RXopJ4) on chromosome 3 is a dominant resistance locus that originated from S. pennellii “LA716”, and Xv4 recognizes the Xcv effector XopJ4 of T4 strains (Astua-Monge et al. 2000). Rx-1 (chromosome 1), Rx-2 (chromosome 1), and Rx-3 (chromosome 5) that are responsible for HR-inducing resistance against Xcv T1 strains were identified in S. lycopersicum (accession “H7998”; Scott and Jones 1989); however, only Rx-3 appears to be effective in conferring field resistance. Bs4 on chromosome 5, which encodes a NB-LRR protein, recognizes the Xcv effector AvrBs4 (Schornack et al. 2004). A number of DNA markers for each Xcv resistance gene are summarized in Table 9. QTL that contribute Xcv resistance have been identified in S. lycopersicum “PI114490” (Hutton et al. 2010). In addition, the Bs2 resistance gene identified in a pepper species is very effective against bacterial spot in transgenic tomato plants (Tai et al. 1999).

Bacterial speck resistance

Bacterial speck disease in tomato is caused by Pseudomonas syringae pv. tomato. The resistance gene, Pto, which is a member of a small gene family encoding cytoplasmic serine/threonine protein kinases, is the first disease resistance gene characterized in plants (Martin et al. 1993). The molecular mechanisms of Pto resistance have been intensively studied. Indeed, the Pto kinase recognizes and physically interacts with the bacterial effectors AvrPto and AvrPtoB (Tang et al. 1996; Shan et al. 2000; Kim et al. 2002). Prf, an NBS?LRR gene located within a cluster of five Pto homologs, is also required for resistance to P. syringae pv. tomato (Salmeron et al. 1996). Among the five Pto homologs that are tightly clustered and exhibit different functions, PtoE is the gene responsible for conferring resistance to bacterial speck in tomato (Kim et al. 2002; Abramovitch et al. 2006). A gene-based CAPS marker for Pto resistance is summarized in Table 10. A recent study revealed that several QTLs in S. habrochites “LA1777” are involved in bacterial speck resistance; bsRr1-1 on chromosome 1, bsRr1-2 on chromosome 2, bsRr1-12a and bsRr1-12b on chromosome 12 (Thapa et al. 2015).

Due to the economic and academic importance of tomato, the genetics and molecular mechanisms of disease resistance to a variety of diseases have been intensively investigated, and the results have contributed to MAS in tomato breeding programs. In addition, extensive use of wild relatives of tomato rather than cultivated tomatoes as resistance sources required the use of molecular markers in order to track the resistance provided by these wild relatives and transfer such resistance to developing new tomato varieties. In this review, we summarized the currently available molecular markers that confer resistance to the major tomato diseases, including TYLCV, TSWV, ToMV, verticillium wilt, fusarium wilt, late blight, leaf mold, root-knot disease, bacterial spot, and bacterial speck. The provided marker information is expected to contribute to advancing MAS for disease resistance and to exploration of novel genetic sources for tomato breeding programs.