Email: guoweilong@cau.edu.cn

Wheat provides about one-fifth of the calories consumed by humans worldwide. However, with a huge genome size of ~16G bp and complex structural variations, progress in studying on wheat genomics is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade.

With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading a paradigm shift in wheat research. In the past several years, we have invented a panel of novel methods for decoding the complex genomes and evolutionary histories of wheat.

Based on an observed trimodal distribution of the genetic variant densities across the genomic windows, we developed two algorithms, IntroBlocker and ggComp, for dissecting the wheat germplasm resources with haplotypes at two levels, ancestral haplotype group (AHG) and the germplasm-based haplotypes (gHap), respectively. We constructed a pan-ancestry haploblock map across tetraploid and hexaploid wheats, and revealed the ancestral mosaics foundations of A&B genomes that emerged from the admixture of six founder wild emmer lineages.

We further build an evolution model of polyploid wheat highlighting the key roles of wild-to-crop and interploidy introgressions in shaping the reticulate evolutionary trajectory of wheat. We also build a multiscale germplasm network of wheat, that is efficient in clarifying pedigree relationships, demonstrating genetic flow during breeding, identifying key founder lines, and also provide a framework for mining beneficial gene alleles.

We also build a wheat integrative gene regulatory network, wGRN, by integrating gene expression, chromatin accessibility, TF binding, and TF motif information to guide trait-associated gene discovery for wheat improvement.

In summary, the utilization of efficient tools and multi-omics data will drive a transformation in wheat breeding technologies, thereby enhancing the development of superior wheat varieties to meet the increasing food demand of the growing population under ever-changing climatic conditions.