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Background  The degradation of intracellular proteins plays an essential role in plant responses to stressful environments. ClpS1 and E3 ubiquitin ligase function as adaptors for selecting target substrates in caseinolytic peptidase (Clp) proteases pathways and the 26S proteasome system, respectively. Currently, the role of E3 ubiquitin ligase in the plant immune response to pathogens is well defined. However, the role of ClpS1 in the plant immune response to pathogens remains unknown.    Results  Here, wheat ( Triticum aestivum ) ClpS1 (TaClpS1) was studied and resulted to encode 161 amino acids, containing a conserved ClpS domain and a chloroplast transit peptide (1–32 aa). TaClpS1 was found to be specifically localized in the chloroplast when expressed transiently in wheat protoplasts. The transcript level of  TaClpS1  in wheat was significantly induced during infection by  Puccinia striiformis  f. sp.  tritici  ( Pst ). Knockdown of  TaClpS1  via virus-induced gene silencing (VIGS) resulted in an increase in wheat resistance against  Pst , accompanied by an increase in the hypersensitive response (HR), accumulation of reactive oxygen species (ROS) and expression of  TaPR1  and  TaPR2 , and a reduction in the number of haustoria, length of infection hypha and infection area of  Pst . Furthermore, heterologous expression of  TaClpS1  in  Nicotiana benthamiana  enhanced the infection by  Phytophthora parasitica .    Conclusions  These results suggest that TaClpS1 negatively regulates the resistance of wheat to  Pst .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02762-0.

TaClpS1, negatively regulates wheat resistance against Puccinia striiformis f. sp. tritici