Plant genome assemblies and resequencing data have been dramatically accumulated. Demands for methodological innovations have increased in the post-genomic and pangenomic era for wheat research. We present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows improved performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. A refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat were proposed. We built Triticeae-GeneTribe database (TGT, http://wheat.cau.edu.cn/TGT/), by integrating 67 Triticeae genomes and 5 outgroup model genomes in networks of homolog genes and collinearity blocks. We de novo assembled the Tibetan semiwild wheat Zang1817 (http://wheat.cau.edu.cn/Zang1817genome/), and conducted population genomic study to trace the origin and adaption of Tibetan wheat. To explore large-scale genomic data, an easy-to-set-up web server fram-ework, SnpHub (http://guoweilong.github.io/SnpHub/), is developed and is applied to construct the portal of SnpHub servers for Triticum (Wheat-SnpHub-Portal, http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/). Especially, the WheatUnion (http://wheat.cau.edu.cn/WheatUnion/?language=en) database covering all published resequencing data in wheat were constructed collaboratively.

A genomic strategy ggComp (https://zack-young.github.io/ggComp/) is proposed, which utilized resequencing data to enable unsupervised identification of pairwise germplasm resource-based Identity-By-Descent (gIBD) blocks. A multi-scale genomic-based germplasm network was constructed database, and a corresponding database Wheat CompDB (http://wheat.cau.edu.cn/WheatCompDB/) was developed. The whole-genome level network helps to clarify pedigree relationship, demonstrate genetic flow, and identify key founder lines. At the single block level, the dissected germplasm-based haplotypes nicely matched with previously identified alleles of “Green Revolution” genes and can guide mining beneficial alleles in wheat breeding.