Association of the tomato co-chaperone gene Sldnaj harboring a promoter deletion with susceptibility to Tomato spotted wilt virus (TSWV)

Abstract

Tomato spotted wilt virus (TSWV) poses a significant threat as a devastating pathogen to the global production and quality of tomato (Solanum lycopersicum). Mining novel resistance genes within the tomato germplasm is an effective and environmentally friendly approach to combat TSWV. In this study, we investigated the mechanisms underlying high TSWV resistance in a specific tomato line after experimental inoculation, despite not possessing any known TSWV resistance genes. The candidate causal genes of disease resistance traits were finely mapped by constructing different genetic populations and performing bulk segregant analysis sequencing. This approach identified SlDnaJ (Solyc10g081220) as a key locus potentially regulating TSWV resistance. We determined a structural variant of SlDnaJ (designated Sldnaj) containing a 61-bp promoter sequence deletion that was specifically present in the germplasm of the susceptible M82 tomato plant lines. Sldnaj-knockout transgenic plants were significantly more resistant to TSWV than wild-type plants. Up-regulated expression of Sldnaj affected the salicylic acid/jasmonic acid signaling pathway, which induced and promoted the systemic infection of TSWV in M82 susceptible plants. In summary, this study identified a new candidate TSWV susceptibility gene with a natural deletion variation in tomato. These findings provide insights into the molecular mechanism underlying pathogen resistance while offering a target for breeding strategies of tomato with TSWV resistance.

Acknowledgements

This work was supported by the National Key Research and Development Program of China (2016YFD0101703), the Key Research and Development Program of Shaanxi Province (2019ZDLNY03-05), the Key Technology Research and Development Projects for Priority Agricultural Industry Chains in Xi’an City (24NYGG0006), the Scientific Research Starting Foundation for Doctoral of Hexi University (KYQD2023004).

Author contributions

Y.L. and S.Q. designed and performed the experiments. S.Q., L.M., Q.L., Y.L., Y.S., S.Z., and X.W. performed some experiments. L.M., P.Z., J.W., and B.W. helped analyze the data. L.M., Q.L., and Y.S. contributed research materials. X.C., C.Z., and X.Z. provided help and advice. Y.L. designed the experiment and supervised the study. S.Q., L.Y., Y.D., and J.Z. wrote and revised the manuscript. All the authors reviewed the final manuscript.

Data availability

All the relevant data can be found within this manuscript and its supporting information files.

Conflict of interest statement

The authors have no conflict of interest to declare.

Supplementary Data

Supplementary data is available at Horticulture Research online.

References

[1] Lefkowitz EJ, Dempsey DM, Hendrickson RC. et al.Virus taxon-omy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res. 2018; 46:D708-17

[2] Oliver JE, Whitfield AE. The Genus Tospovirus: emerging Bun-yaviruses that threaten food security. Annu Rev Virol. 2016; 3: 101-24

[3] Qi S, Zhang S, Islam MM. et al. Natural resources resistance to Tomato spotted wilt virus (TSWV) in tomato (Solanum lycoper-sicum). Int J Mol Sci. 2021; 22:10978

[4] Turina M, Kormelink R, Resende RO. Resistance to tospoviruses in vegetable crops: epidemiological and molecular aspects. Annu Rev Phytopathol. 2016; 54:347-71

[5] Huang H, Huang S, Li J. et al. Stepwise artificial evolution of an Sw-5b immune receptor extends its resistance spectrum against resistance-breaking isolates of tomato spotted wilt virus. Plant Biotechnol J. 2021; 19:2164-76

[6] Boiteux LS, Giordano LD. Genetic basis of resistance against two tospovirus species in tomato (lycopersicon-esculentum). Euphytica. 1993; 71:151-4

[7] Rosello S, Ricarte B, Diez MJ. et al. Resistance to tomato spotted wilt virus introgressed from Lycopersicon peruvianum in line UPV 1 may be allelic to Sw-5 and can be used to enhance the resistance of hybrids cultivars. Euphytica. 2001; 119: 357-67

[8] Padmanabhan C, Ma Q, Shekasteband R. et al. 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

[9] Spassova MI, Prins TW, Folkertsma RT. et al. 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; 7:151-61

[10] de Oliveira AS, Boiteux LS, Kormelink R. et al. The Sw-5 gene cluster: tomato breeding and research toward orthotospovirus disease control. Front Plant Sci. 2018; 9:1-7

[11] Lopez C, Aramburu J, Galipienso L. et al. Evolutionary analysis of tomato Sw-5 resistance-breaking isolates of tomato spotted wilt virus. J Gen Virol. 2011; 92:210-5

[12] Qi S, Shen Y, Wang X. et al. AnewNLR gene for resistance to Tomato spotted wilt virus in tomato (Solanum lycopersicum). Theor Appl Genet. 2022; 135:1493-509

[13] Chen H, Qian X, Chen X. et al. Cytoplasmic and nuclear Sw-5b NLR act both independently and synergistically to confer full host defense against tospovirus infection. New Phytol. 2021; 231: 2262-81

[14] Li J, Huang HN, Zhu M. et al. A plant immune receptor adopts a two-step recognition mechanism to enhance viral effector perception. Mol Plant. 2019; 12:248-62

[15] Sharma N, Sahu PP, Prasad A. et al. The Sw5a gene con-fers resistance to ToLCNDV and triggers an HR response after direct AC4 effector recognition. Proc Natl Acad Sci USA. 2021;

[16]

[17] Zhai Y, Gnanasekaran P, Pappu HR. Identification and character-ization of plant-interacting targets of tomato spotted wilt virus silencing suppressor. Pathogens. 2021; 10:1-14

[18] Kumar M, Torrance T, McAvoy T. et al. Natural occurrence of tomato chlorosis virus on tomatillo (Physalis philadelphica)inthe United States. Plant Dis. 2024; 108:1119

[19] Ontiveros I, Fernández-Pozo N, Esteve-Codina A. et al. Enhanced susceptibility to tomato chlorosis virus (ToCV) in Hsp90- and Sgt1-silenced plants: insights from gene expression dynamics. Viruses. 2023; 15:2370

[20] Künstler A, Füzék K, Schwarczinger I. et al. Heat shock-induced enhanced susceptibility of barley to Bipolaris sorokiniana is asso-ciated with elevated ROS production and plant defence-related gene expression. Plant Biol. 2023; 25:803-12

[21] Pulido P, Leister D. Novel DNAJ-related proteins in Arabidopsis thaliana. New Phytol. 2018; 217:480-90

[22] Muthusamy SK, Dalal M, Chinnusamy V. et al. Genome-wide identification and analysis of biotic and abiotic stress regulation of small heat shock protein (HSP20) family genes in bread wheat. J Plant Physiol. 2017; 211:100-13

[23] Lee K, Ziegelhoffer T, Delewski W. et al. Pathway of Hsp70 interactions at the ribosome. Nat Commun. 2021; 12:5666

[24] Rowarth NM, Dauphinee AN, Denbigh GL. et al. Hsp70 plays a role in programmed cell death during the remodelling of leaves of the lace plant (Aponogeton madagascariensis). JExp Bot. 2019; 71: 907-18

[25] Faust O, Abayev-Avraham M, Wentink AS. et al. HSP40 proteins use class-specific regulation to drive HSP70 functional diversity. Nature. 2020; 587:489-94

[26] Verma AK, Tamadaddi C, Tak Y. et al. The expanding world of plant J-domain proteins. CRC Crit Rev Plant Sci. 2019; 38: 382-400

[27] Wang G, Cai G, Kong F. et al. Overexpression of tomato chloroplast-targeted DnaJ protein enhances tolerance to drought stress and resistance to Pseudomonas solanacearum in transgenic tobacco. Plant Physiol Biochem. 2014; 82:95-104

[28] Lu M, Hellmann HA, Liu Y. et al. Editorial: protein quality con-trolling systems in plant responses to environmental stresses. Front Plant Sci. 2018; 9:1-3

[29] Jiang L, Huang Y, Sun L. et al. Occurrence and diversity of tomato spotted wilt virus isolates breaking the Tsw resistance gene of Capsicum chinense in Yunnan, Southwest China. Plant Pathol. 2017; 66:980-9

[30] Li S, Lin D, Zhang Y. et al. Genome-edited powdery mildew resistance in wheat without growth penalties. Nature. 2022; 602: 455-60

[31] Wang N, Tang C, Fan X. et al. Inactivation of a wheat protein kinase gene confers broad-spectrum resistance to rust fungi. Cell. 2022; 185:2961-2974.e19

[32] Agarwal G, Clevenger J, Kale SM. et al. A recombination bin-map identified a major QTL for resistance to tomato spotted wilt virus in peanut (Arachis hypogaea). Sci Rep. 2019; 9:18246

[33] Liao N, Hu Z, Li Y. et al. Ethylene-responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resis-tance in fresh fruits of watermelon. Plant Biotechnol J. 2020; 18: 1066-77

[34] Du Y, Zhao J, Chen T. et al. Type I J-domain NbMIP 1 proteins are required for both tobacco mosaic virus infection and plant innate immunity. PLoS Pathog. 2013; 9:e1003659

[35] Li C, Xu Y, Fu S. et al. The unfolded protein response plays dual roles in rice stripe virus infection through fine-tuning the movement protein accumulation. PLoS Pathog. 2021; 17:e1009370

[36] Chandran D, Rickert J, Huang Y. et al. Atypical E2F transcrip-tional repressor DEL1 acts at the intersection of plant growth and immunity by controlling the hormone salicylic acid. Cell Host Microbe. 2014; 15:506-13

[37] Xu Z, Xu X, Gong Q. et al. Engineering broad-spectrum bacterial blight resistance by simultaneously disrupting variable TALE-binding elements of multiple susceptibility genes in rice. Mol Plant. 2019; 12:1434-46

[38] Oliva R, Ji C, Atienza-Grande G. et al. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol. 2019; 37:1344-50

[39] Yuan T, Li X, Xiao J. et al. Characterization of xanthomonas oryzae-responsive cis-acting element in the promoter of rice race-specific susceptibility gene Xa13. Mol Plant. 2011; 4:300-9

[40] Wang X, Ju Y, Wu T. et al. The clade III subfamily of OsSWEETs directly suppresses rice immunity by interacting with OsHMGB1 and OsHsp20L. Plant Biotechnol J. 2024; 22:2186-200

[41] Wang C, Zhang X, Fan Y. et al. XA23 is an executor R protein and confers broad-spectrum disease resistance in rice. Mol Plant. 2014; 8:290-302

[42] Hofius D, Maier AT, Dietrich C. et al. Capsid protein-mediated recruitment of host DnaJ-like proteins is required for potato virus Y infection in tobacco plants. JVirol. 2007; 81:11870-80

[43] Soellick T-R, Uhrig JF, Bucher GL. et al. The movement protein NSm of tomato spotted wilt tospovirus (TSWV): RNA binding, interaction with the TSWV N protein, and identification of interacting plant proteins. Proc Natl Acad Sci USA. 2000; 97:2373-8

[44] von Bargen S, Salchert K, Paape M. et al. Interactions between the tomato spotted wilt virus movement protein and plant proteins showing homologies to myosin, kinesin and DnaJ-like chaperones. Plant Physiol Biochem. 2001; 39:1083-93

[45] Qian X, Xiang Q, Yang T. et al. Molecular co-chaperone SGT1 is critical for cell-to-cell movement and systemic infection of tomato spotted wilt virus in Nicotiana benthamiana. Viruses. 2018; 10:647-61

[46] Mansfeld BN, Grumet R. QTLseqr: an R package for bulk seg-regant analysis with next-generation sequencing. Plant Genome. 2018; 11:1-5

[47] Yang S, Tang X, Ma N. et al. Heterology expression of the sweet pepper CBF3 gene confers elevated tolerance to chilling stress in transgenic tobacco. J Plant Physiol. 2011; 168:1804-12

[48] Choi DS, Hwang IS, Hwang BK. Requirement of the cytosolic interaction between PATHOGENESIS-RELATED PROTEIN10 and LEUCINE-RICH REPEAT PROTEIN1 for cell death and defense signaling in pepper. Plant Cell. 2012; 24:1675-90

[49] Andolfo G, Sanseverino W, Aversano R. et al. Genome-wide iden-tification and analysis of candidate genes for disease resistance in tomato. Mol Breed. 2014; 33:227-33

[50] Wang J, Liu K, Li D. et al. A novel peroxidase CanPOD gene of pepper is involved in defense responses to phytophtora capsici infection as well as abiotic stress tolerance. Int J Mol Sci. 2013; 14: 3158-77

[51] Gao XZ, Yan P, Shen WT. et al. Modular construction of plasmids by parallel assembly of linear vector components. Anal Biochem. 2013; 437:172-7

[52] Qin SS, Chen XY, Jiang C. et al. Pruning induced yield and quality variations and the correlated gene expression and phy-tohormone changes in Lonicera japonica. Ind Crop Prod. 2019; 132: 386-95