show Abstracthide AbstractThe yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation. Overall design: In order to delineate the major TF regulatory circuitry to abiotic stresses in Triticum Urartu, we performed DAP-seq to obtain a genome-wide binding profile of stress response TFs, ChIP-seq for three well-studied histone modifications (including H3K9ac, H3K4me3 and H3K27me3), DNase-seq, Bisulphite-seq and RNA-seq in 5 stresses.