Zhang Lab

Plant Bioinformatics and Functional Epigenomics Group

Research Content

We are particularly interested in applying high-throughput technology to explore interesting and fundamental biological questions. Our current research has two major foci.

1. The genomic and epigenomic mechanisms underlying the benefits of polyploidy in wheat.

Both polyploidization and domestication are the major forces shaping current crop genomes. We are generating multi-omics data to characterize the major genomic and epigenomic changes during wheat polyploidization and domestication, and the ultimate goal is to reveal the mechanism underlying the benefits of polyploidy.

2. Development of methods, tools and platforms for high-throughput sequencing-aided gene mapping in wheat.

We are developing tools and platforms to address two issues essential for successful gene mapping. First, the accurate identification of genetic markers. The central idea of high-throughput sequencing-aided gene mapping is to detect a high density of molecular markers from a population with high confidence. However, given the high levels of polymorphisms in plants, such as the pan-genome of 62 rice cultivars having > 10,000 genes, there is a high probability of missing important genes and polymorphic loci. Additionally, for unsequenced organisms with large genome sizes, whole-genome sequencing and resequencing is costly. To address these issues, we developed an epigenome-guided de novo assembly of the core genome for divergent populations with large genomes, which is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes. Second, among the large numbers of polymorphic loci associated with a given trait, identifying functional polymorphisms is not trivial. We are developing platforms for the comprehensive annotation of the functional regulatory elements using information from the integration of plant multi-omics data. The ultimate goal is to facilitate the high-throughput data-aided mapping and cloning of loci controlling central agronomic traits.