The mutation of the gene encoding a stearoyl-acyl carrier protein fatty acid desaturase (ssi2) has been proved to enhance pathogen resistance in several plants, while it’s potential to regulate biotic and abiotic stresses in wheat is still unclear.  In this study, we cloned TaSSI2 gene in wheat and provided several evidences of its involvement in multiple biological functions.  By using barley stripe mosaic virus (BSMV)-induced gene silencing (VIGS) in wheat, it was found that TaSSI2 negatively regulated both powdery mildew and Fusarium head blight (FHB) resistance, which was consistent with the phenotype observed in knock-out mutants of Kronos.  The expression of TaSSI2 was down-regulated by in vitro treatments of methyl jasmonate (MeJA), but positively regulated by salicylic acid (SA) and abscisic acid (ABA), implying the cross-talk between different hormone signaling pathways involved in wheat to regulate biotic stresses is still to be elucidated.  Furthermore, the up-regulated expression of PR4 and PR5 indicated that TaSSI2 probably regulated FHB resistance by depressing the SA signaling pathway in wheat.  In addition, the over-expression of TaSSI2 increased the content of linolenic acid (18:3) and subsequently enhanced drought tolerance of transgenic Brachypodium.  This phenomenon might be associated with its subcellular localization in the whole cytosol, partly overlapping with Golgi apparatus and the secreted vesicles.  As a stearoyl-acyl carrier protein fatty acid desaturase, TaSSI2 was proposed to be involved in cell lipid metabolism and carried targets out of the cell from membrane or wax synthesis, resulting in enhanced drought tolerance in plant.