The primary goal that motivates basic/applied research at the Zhiyong Liu's Laboratory is wheat improvement. We approach this goal from several different directions, studying individual genes and processes as well as comprehensive genomics projects. The disease resistant genes and yield associated loci are identified through map-based gene cloning and mutagenesis from wheat cultivars, landraces and wild relatives, like wild emmer and Aegilops tauschii. The elite and core wheat germplasm are genotyped using high-density SNP chips and NGS tools to dissect the genomic regions' contributions to various traits. These important genes/QTLs/regions aid genome selection in wheat breeding program. The model grass, Brachypodium distachyon, is adopted as a platform to mature the new technologies in wheat. Aegilops tauschii, the wheat D genome donor, is used to investigate the evolution of wheat D genome. What we are doing include:

        1. Mapping and cloning of wheat powdery mildew resistance genes.

        2. Mapping and cloning of wheat rust (stripe rust, leaf rust) resistance genes.

        3. Mapping and cloning of wheat spot blotch resistance genes.

        4. Mapping and cloning of wheat yield traits associated genes/QTLs.

        5. Wheat breeding.

        6. Cloning of Brachypodium distachyon BSMV resistance genes and understanding of host-virus interactions mechanism.

        7. Variants identifications in wheat D genome since separating from Aegilops tauschii.

Many kinds of foliar disease such as powdery mildew (caused by Blumeria graminis f. sp. tritici), stripe rust (caused by Puccinia striiformis Westend. f. sp. tritici), leaf rust (caused by Puccinia triticina), spot blotch (caused by Bipolaris sorokiniana), etc. are major threats for wheat production and food security. In addition to fungicides and biological control, breeding and using resistant cultivars is urgently needed to reduce the prevalence of these diseases. Our lab is focused on genetics analysis, molecular mapping, and map-based cloning of wheat genes conferring resistance to powdery mildew, stripe rust, leaf rust, spot blotch and other diseases from wheat cultivars, landraces, and wild relatives (such as Triticum dicoccoides, the tetraploid progenitor of cultivated wheat). We are performing comparative genomics analysis to develop high-density genetic linkage maps of the target genes and isolating the candidate disease resistance genes from wheat genome using forward genetics approach. In combining traditional bulked segregant analysis (BSA) and next generation sequencing technique (RNA-seq), we developed high efficient BSR-Seq pipeline for gene mapping in wheat and used in fine mapping and map-based cloning our target genes. Allelic variations of the isolated disease resistance genes were characterized and used for evolution analysis and functional marker development in wheat breeding program. Meanwhile, our works provide useful information for further dissecting host-pathogen interaction in wheat.

Yield components and plant architecture are key factors for developing high-yielding new cultivars in wheat breeding program. However, many traits related to yields and plant architecture are controlled by quantitative trait loci (QTL). By applying Infinium iSelect SNP assay, we constructed a high-density genetic linkage map using recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6 for mapping grain shape, size, weight, flag leaf size, plant height, pre-harvesting sprouting resistance, salt tolerance and root traits. A number of QTL were mapped and selected for developing advanced backcrossing near isogenic lines in a final goal of gene isolation. The identified QTL and linked markers also provide useful information for marker-assisted selection (MAS) in breeding program.

Our lab worked on developing breeder friendly new germplasm with advanced agronomic traits and yield performance by introgression of known disease resistance genes into elite commercial cultivars through advanced backcrossing and MAS. We are also developing new wheat lines with high yield potential and biotic and abiotic stress tolerance for commercial breeding program adaptable to major wheat-growing area in the Yellow & Huai River Valley Facultative Winter Wheat Region combining MAS and traditional breeding approaches.

We are also working on host-viral interaction research using Brachypodium as a model system. We cloned a Barley Stripe Mosaic Virus (BSMV) resistance gene Bsr1 from Brachypodium distachyon accession Bd3-1 and characterized its function and allelic variations in B. distachyonB. stacei and B. hybridum. In collaborations with Prof. Andrew Jackson from the University of California Berkeley and Prof. Dawei Li from China Agricultural University, we are studying the molecular interaction between Bsr1 and TGB1, the avirulence protein of Bsr1 from BSMV.