Skip to main content
Log in

Marker-assisted development and characterization of near-isogenic lines carrying the Rx4 gene for hypersensitive resistance to Xanthomonas euvesicatoria pv. perforans race T3 in tomato

  • Published:
Molecular Breeding Aims and scope Submit manuscript


Bacterial spot caused by several species of Xanthomonas is a devastating disease resulting in severe fruit yield loss and quality decline in tomato production areas worldwide. Lack of resistant commercial varieties is among the most critical factors limiting the application of integrated management to control the disease. Although sources for resistance to all species and races have been discovered over years, breeding for resistance to the disease is slow because the resistance is quantitatively inherited and sometimes linked to poor horticultural traits. Development of near-isogenic lines (NILs) by introgressing the shortest DNA fragment of the resistance gene region from the donor into elite cultivars is a promising approach to eliminating the negative effect on horticultural traits. In the current study, a strategy of combining traditional backcross with molecular marker-assisted foreground and background selection was adopted to generate NILs carrying the Rx4 gene for resistance to Xanthomonas euvesicatoria pv. perforans race T3 strain. The donor parent is a wild species Solanum pimpinellifolium accession PI 128216, and the recurrent parent is an elite processing tomato breeding line OH88119. Disease evaluation was performed in F1, BC4F1, BC6F1, BC6F2, BC6F3, and BC6F4 generations by infiltration of race T3 strain Xv829 to leaves of plants. Meanwhile, fruit traits including fruit weight, fruit color parameters, soluble solid content, pH, and firmness were collected from replicated field trials in BC6F4 and BC6F5. Five NILs with 159–1901 kb DNA fragments in the Rx4 gene region were obtained. They all showed high level of hypersensitive resistance to race T3, and their fruit traits were not significantly different from the recurrent parent OH88119. However, fruit weight of one NIL Rx4–1812 carrying the largest DNA fragment of 1901 kb in the Rx4 gene region was 9.5–11.8% lower than OH8819 though the difference was not statistically significant. This might be due to the linkage drag of FW11.2, a QTL for fruit weight in the same region. Overall, the NILs created here can be used as sources for developing resistant varieties and deciphering the mechanism of resistance to bacterial spot in tomato.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others


  • Berry SZ, Aldrich TS, Wiese KL, Bash WD (1995) ‘Ohio OX38’ hybrid processing tomato. HortScience 30:159

    Article  Google Scholar 

  • Coaker GL, Francis DM (2004) Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum. Theor Appl Genet108:1047–1055

  • Constantin EC, Cleenwerck I, Maes M, Baeyena S, Van Malderghema C, De Vosbc P, Cottyna B (2016) Genetic characterization of strains named as Xanthomonas axonopodis pv. dieffenbachiae leads to a taxonomic revision of the X. axonopodis species complex. Plant Pathol 65:792–806

    Article  CAS  Google Scholar 

  • Deng Y, Zhai K, Xie Z, Yang D, Zhu X, Liu J, Wang X, Qin P, Yang Y, Zhang G, Li Q, Zhang J, Wu S, Milazzo J, Mao B, Wang E, Xie H, Tharreau D, He Z (2017) Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science 355:962–965

    Article  CAS  Google Scholar 

  • EPPO (2013) PM 7/110 (1) Xanthomonas spp. (Xanthomonas euvesicatoria, Xanthomonas gardneri, Xanthomonas perforans, Xanthomonas vesicatoria) causing bacterial spot of tomato and sweet pepper. EPPO Bulletin 43:7–20

    Article  Google Scholar 

  • Francis DM, Berry SZ, Aldrich TS, Scaife KL, Bash WD (2002) ‘Ohio OX 150’ processing tomato. Rep Tomato Genet Coop 52:36–37

    Google Scholar 

  • Francis DM, Miller S (2005) Ohio 9834 and Ohio 9816: processing tomato breeding lines with partial resistance to race T1 of bacterial spot. HortScience 40:1566–1568

    Article  Google Scholar 

  • Fukuoka S, Saka N, Koga H, Ono K, Shimizu T, Ebana K, Hayashi N, Takahashi A, Hirochika H, Okuno K, Yano M (2009) Loss of function of a proline-containing protein confers durable disease resistance in rice. Science 325:998–1001

    Article  CAS  Google Scholar 

  • Gao DL, Huibers RP, Loonen AEHM, Visser RGF, Wolters AMA, Bai YL (2014) Down-regulation of acetolactate synthase compromises Ol-1-mediated resistance to powdery mildew in tomato. BMC Plant Biol 14:32

    Article  Google Scholar 

  • Gao LH, Qu M, Ren HZ, Sui XL, Chen QY, Zhang ZX (2010) Structure, function, application and ecological benefit of single slope energy efficient solar greenhouse in China. HortTechnology 20:626–631

    Article  Google Scholar 

  • Haggard JE, Johnson EB, St Clair DA (2013) Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites. G3-genes Genom genet 3:2131-2146

  • Haggard JE, St Clair DA (2015) Combining ability for Phytophthora infestans quantitative resistance from wild tomato. Crop Sci 55:240–254

    Article  CAS  Google Scholar 

  • Hallwass M, De Oliveira AS, Dianese ED, Lohuis D, Boiteux LS, Inoue-Nagata AK, Resende RO, Kormelink R (2014) 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 15:871–880

    Article  CAS  Google Scholar 

  • Horvath DM, Stall RE, Jones JB, Pauly MH, Vallad GE, Dahlbeck D, Staskawicz BJ, Scott JW (2012) Transgenic resistance confers effective field level control of bacterial spot disease in tomato. PLoS One 7(8):e42036

    Article  CAS  Google Scholar 

  • Hutton SF, Scott JW, Yang W, Sim SC, Francis DM, Jones JB (2010) Identification of QTL associated with resistance to bacterial spot race T4 in tomato. Theor Appl Genet 121:1275–1287

    Article  CAS  Google Scholar 

  • Hutton SF, Scott JW (2017) Fla. 7907C: a Fla. 7907 near-isogenic tomato inbred line containing the Begomovirus resistance gene, Ty-1. Hortscience 52:658–660

    Article  CAS  Google Scholar 

  • Illa-Berenguer E, Van Houten J, Huang ZJ, van der Knaap E (2015) Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet 128:1329–1342

    Article  Google Scholar 

  • Jones JB, Lacy GH, Bouzar H, Stall RE, Schaad NW (2004) Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst Appl Microbiol 27:755–762

    Article  CAS  Google Scholar 

  • Jones JB, Zitter TA, Momol TM, Miller SA (eds) (2014) Compendium of tomato diseases and pests, Second edn. USA, APS Press, Minnesota

  • Kabelka E, Franchino B, Francis DM (2002) Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp. michiganensis. Phytopathology 92:504–510

    Article  CAS  Google Scholar 

  • Liabeuf D, Sim SC, Francis DM (2018) Comparison of marker-based genomic estimated breeding values and phenotypic evaluation for selection of bacterial spot resistance in tomato. Phytopathology 108:392–401

    Article  Google Scholar 

  • Pei C, Wang H, Zhang J, Wang Y, Francis DM, Yang W (2012) Fine mapping and analysis of a candidate gene in tomato accession PI128216 conferring hypersensitive resistance to bacterial spot race T3. Theor Appl Genet 124:533–542

    Article  CAS  Google Scholar 

  • Potnis N, Timilsina S, Strayer A, Shantharaj D, Barak JD, Paret ML, Vallad GE, Jones JB (2015) Bacterial spot of tomato and pepper: diverse Xanthomonas species with a wide variety of virulence factors posing a worldwide challenge. Mol Plant Pathol 16:907–920

    Article  Google Scholar 

  • Robbins MD, Darrigues A, Sim S-C, Masud MAT, Francis DM (2009) Characterization of hypersensitive resistance to bacterial spot race T3 (Xanthomonas perforans) from tomato accession PI 128216. Phytopathology 99:1037–1044

    Article  Google Scholar 

  • Rossouw LT, Madala NE, Tugizimana F, Steenkamp PA, Esterhuizen LL, Dubery IA (2019) Deciphering the resistance mechanism of tomato plants against whitefly-mediated tomato curly stunt virus infection through ultra-high-performance liquid chromatography coupled to mass spectrometry (UHPLC-MS)-based metabolomics approaches. Metabolites 9:60

    Article  CAS  Google Scholar 

  • Rubio F, Alonso A, Garcia-Martinez S, Ruiz JJ (2016) Introgression of virus-resistance genes into traditional Spanish tomato cultivars (Solanum lycopersicum L.): effects on yield and quality. Sci Hortic 198:183–190

    Article  Google Scholar 

  • Scott JW, Francis DM, Miller SA, Somodi GC, Jones JB (2003) Tomato bacterial spot resistance derived from PI 114490, inheritance of resistance to race T2 and relationship across three pathogen races. J Am Soc Hortic Sci 128:698–703

    Article  Google Scholar 

  • Scott JW, Jones JB, Somodi GC, Stall RE (1995) Screening tomato accessions for resistance to Xanthomonas campestris pv. vesicatoria, race T3. HortScience 30:579–581

    Article  Google Scholar 

  • Scott JW, Hutton SF, Jones JB, Francis DM, Miller SA (2006) Resistance to bacterial spot race T4 and breeding for durable, broad-spectrum resistance to other races. Rpt Tomato Genet Coop 56:33–36

    Google Scholar 

  • Scott JW, Hutton SF, Shekasteband R, Sim SC, Francis DM (2015) Identification of tomato bacterial spot race T1, T2, T3, T4, and Xanthomonas gardneri resistance QTLs derived from PI 114490 populations selected for race T4. Acta Hortic 1069:53–58

    Article  Google Scholar 

  • Scott JW, Jones JB, Somodi GC (2001) Inheritance of resistance in tomato to race T3 of the bacterial spot pathogen. J Am Soc Hortic Sci 126:436–441

    Article  Google Scholar 

  • Sim SC, Robbins MD, Wijeratne S, Wang H, Yang WC, Francis DM (2015) Association analysis for bacterial spot resistance in a directionally selected complex breeding population of tomato. Phytopathology 105:1437–1445

    Article  CAS  Google Scholar 

  • Sun HJ, Zhang JY, Wang YY, Scott JW, Francis DM, Yang WC (2011) QTL analysis of resistance to bacterial spot race T3 in tomato. Acta Hortic Sin 38:2297–2308

    CAS  Google Scholar 

  • Timilsina S, Kara S, Jacques MA, Potnis N, Minsavage GV, Vallad GE, Jones JB, Fischer-Le Saux M (2019) Reclassification of Xanthomonas gardneri (ex Šutič 1957) Jones et al. 2006 as a later heterotypic synonym of Xanthomonas cynarae Trébaol et al. 2000 and description of X. cynarae pv. cynarae and X. cynarae pv. gardneri based on whole genome analyses. Int J Syst Evol Microbiol 69:343–349

    Article  CAS  Google Scholar 

  • Timilsina S, Jibrin MO, Potnis N, Minsavage GV, Kebede M, Schwartz A, Bart R, Staskawicz B, Boyer C, Vallad GE, Pruvost O, Jones JB, Gossa EM (2015) Multilocus sequence analysis of Xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri. Appl Environ Microbiol 81:1520–1529

    Article  Google Scholar 

  • Wang YQ, Zhang YX, Gao ZP, Yang WC (2018) Breeding for resistance to tomato bacterial diseases in China: challenges and prospects. Hortic Plant J 4:193–207

    Article  Google Scholar 

  • Wu Y, Che Y, Pan C, Xiao N, Yu L, Li Y, Zhang X, Pan X, Chen X, Liang C, Dai Z, Li A (2017) Development and evaluation of near-isogenic lines with different blast resistance alleles at the Piz locus in Japonica rice from the lower region of the Yangtze River, China. Plant Dis 101:1283–1291

    Article  CAS  Google Scholar 

  • Yang JJ, Wang YY, Shen HL, Yang WC (2014) In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome. DNA Res 21:429–438

    Article  Google Scholar 

  • Yang WC, Bai XD, Kabelka E, Eaton C, Kamoun S, van der Knaap E, Francis D (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol Breeding 14:21–34

    Article  CAS  Google Scholar 

  • Yang WC, Chen J, Zhang XM, Francis DM (2007) Recent advances in classification of tomato bacterial spot pathogen, genetics of resistance, and marker-assisted selection. Sci Agric Sin 40:283–290

    CAS  Google Scholar 

  • Yang WC, Sacks EJ, Ivey MLL, Miller SA, Francis DM (2005) Resistance in Lycopersicon esculentum intraspecific crosses to race T1 strains of Xanthomonas campestris pv. vesicatoria causing bacterial spot of tomato. Phytopathology 95:519–527

    Article  CAS  Google Scholar 

  • Zhao BM, Cao HP, Duan JJ, Yang WC (2015) Allelic tests and sequence analysis of three genes for resistance to Xanthomonas perforans race T3 in tomato. Hortic Plant J 1:41–47

    Google Scholar 

Download references


The authors would like to thank Dr. David M. Francis at the Ohio State University for providing tomato seeds of OH88119 and Dr. Jeffery B. Jones at the University of Florida for providing us the X. euvesicatoria pv. perforans race T3 strain.


The work was partially supported by the National Key Research and Development Program (2016YFD0101007), the National Natural Science Foundation of China (31572123), and the Construction of Beijing Science and Technology Innovation and Service Capacity in Top Subjects (CEFF-PXM2019_014207_000032).

Author information

Authors and Affiliations



The experiment was conceived and designed by NL and WY and was performed by NL and XZ. NL and WY analyzed data. NL, XZ, and WY wrote the manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to Wencai Yang.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material


(PDF 209 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, N., Zhang, X. & Yang, W. Marker-assisted development and characterization of near-isogenic lines carrying the Rx4 gene for hypersensitive resistance to Xanthomonas euvesicatoria pv. perforans race T3 in tomato. Mol Breeding 39, 172 (2019).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: