Scientists identify Sldnaj as a genetic weak point making tomatoes prone to viral attack
image: The characteristics of CRISPR/Cas9-edited Sldnaj lines after TSWV inoculation. (A) Diagrammatic sketch of SlDnaJ targeting the two single-guide RNAs (sgRNAs). (B) Sequences of the edited regions of the CRISPR/Cas9-edited Sldnaj mutants (Sldnaj-cr1–5 and Sldnaj-cr17–3) and wild-type (WT). The two sgRNA target sites are indicated in Target 1 and Target 2 and the altered sequences in the edited line are indicated in blue. The Sldnaj-cr alleles were confirmed by sequencing of the PCR products from two T1 plants in the M82 background. (C) The leaf symptom phenotypes of the WT, Sldnaj-cr1–5, and Sldnaj-cr17–3 lines at 0, 14, 28, and 35 days postinoculation (dpi). (D) DAB and NBT staining of Sldnaj-cr lines at 7 dpi. (E) RT-qPCR detection of the expression of TSWV-cp in Sldnaj-cr lines at 0, 7, 14, 28, and 35 dpi. (F) RT-qPCR detection of the Sldnaj transcription levels in the Sldnaj-cr lines at 0, 7, 14, 28, and 35 dpi. (G) The ratio of DAB and NBT staining areas of the Sldnaj-cr lines. The error bars represent the standard deviations three biological replicates. Two asterisks and three asterisks indicate significant differences at P < 0.01 and P < 0.001, respectively. Image link: https://academic.oup.com/view-large/figure/508297153/uhaf019f6.tif
Credit: Horticulture Research
Tomato spotted wilt virus (TSWV) infects over 1,000 plant species and leads to billions of dollars in global agricultural losses annually. While several resistance genes (Sw-5, Sw-7, etc.) have been utilized in breeding, their effectiveness has gradually declined due to the emergence of resistance-breaking viral isolates. Moreover, most studies have focused on resistance genes, leaving susceptibility genes largely unexplored. Molecular chaperones, particularly heat shock protein (HSP) families such as DnaJ/HSP40, have been implicated in pathogen interactions. However, their specific roles in TSWV–tomato relationships remain poorly understood. Due to these challenges, there is a pressing need to explore novel genetic mechanisms underlying tomato susceptibility and resistance to TSWV.
Researchers from Northwest A&F University, Hexi University, and the Boyce Thompson Institute reported their findings (DOI: 10.1093/hr/uhaf019) in Horticulture Research on April 1, 2025. The team discovered that a co-chaperone gene, SlDnaJ (Solyc10g081220), plays a crucial role in tomato’s response to TSWV. A 61-bp deletion in its promoter—forming the variant Sldnaj—was identified specifically in the susceptible M82 tomato line. This natural deletion causes abnormal activation of Sldnaj, which interferes with defense signaling and promotes systemic viral infection.
Using bulk segregant analysis sequencing (BSA-seq) and quantitative trait locus (QTL) fine mapping, the researchers localized a dominant resistance locus on chromosome 10. Within this region, they identified SlDnaJ, a co-chaperone gene of the HSP40 family, as the candidate regulator of TSWV susceptibility. The Sldnaj variant harbors a 61-bp promoter deletion absent in resistant lines, leading to higher expression levels after infection. Transgenic assays showed that silencing or CRISPR/Cas9 knockout of Sldnaj in susceptible tomatoes significantly reduced viral symptoms and TSWV RNA accumulation, while overexpression of SlDnaJ enhanced resistance. Further analyses revealed that the promoter deletion alters cis-regulatory motifs related to salicylic acid (SA) and jasmonic acid (JA) responses. Overexpression or suppression experiments confirmed that Sldnaj regulates antioxidant enzyme activity and hormone balance, affecting systemic defense. The team concluded that up-regulated Sldnaj expression promotes TSWV infection by facilitating the interaction between host DnaJ proteins and viral movement proteins, thus increasing plant susceptibility.
"Our research reveals that tomato susceptibility to TSWV is not merely due to the loss of resistance genes, but also involves the activation of hidden susceptibility factors," said Prof. Yan Liang, corresponding author of the study. "The discovery of Sldnaj shows how a small promoter deletion can significantly shift the plant's immune balance. By editing this gene, we can transform a susceptible cultivar into a resistant one, paving the way for more durable and environmentally friendly virus-resistance breeding strategies in tomato.”
The identification of Sldnaj as a susceptibility gene opens a new avenue for developing tomato varieties with durable viral resistance. By editing or silencing this gene, breeders can enhance resistance without introducing foreign DNA, aligning with sustainable agricultural practices. Moreover, understanding the molecular link between co-chaperone function and hormone signaling provides a framework for designing cross-species resistance strategies. This study also establishes a foundation for exploring similar susceptibility genes in other crops such as pepper, peanut, and soybean, potentially contributing to global efforts in securing vegetable production against viral threats.
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References
DOI
Original URL
https://doi.org/10.1093/hr/uhaf019
Funding information
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).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2024. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.