Wheat-RegNet: An encyclopedia of common wheat hierarchical regulatory networks

Common wheat (Triticum aestivum, 2n = 6× = 42, AABBDD) is the staple crop worldwide. Elucidating the gene regulatory network provides essential information for mechanism studies and targeted manipulation of gene activity for breeding. However, it is a challenging task given the extremely large (16 Gb) and complicated allohexaploid genome of common wheat. Integrating multi-omics data is a compelling approach to construct the hierarchical regulatory network. Here, we collected 189 transcription factor (TF) binding profiles, 90 epigenomic datasets, 2356 transcriptomes, and genome-wide association study (GWAS) for 144 agronomic traits in common wheat, which were further integrated using machine learning approach to infer direct target genes and the hierarchical regulatory network. Wheat-RegNet, a web-based platform, is further developed providing four major functions: (i) to identify regulatory elements regulating input gene(s), and to infer the tissue and environmental response specificities; (ii) to identify the TFs responsible for regulating input gene(s) or locus/loci, as well as the associated GWAS traits; (iii) to construct the hierarchical regulatory network regulating input gene(s); and (iv) to browse hundreds of TF binding, epigenomic, and transcriptomic profiles of input region or gene. Well-organized results and multiple tools for interactive visualization are available through a user-friendly web interface. Wheat-RegNet is a highly useful resource for exploring gene regulatory information and for targeted manipulation, facilitating both hypothesis-driven research and breeding research in common wheat. Wheat-RegNet is freely available at http://bioinfo.sibs.ac.cn/Wheat-RegNet.