The research of this group focuses on different aspects of genomics, including structural, comparative and functional genomics. Below are summarized our current research activities:

1. Development of Resources for Enhanced Genome Research and Gene discovery - Large-insert BAC and BIBAC libraries are essential for modern genomics research. We helped pioneer the BAC and BIBAC technology (BAC Protocols), developed about 90 large-insert BAC and BIBAC libraries for a variety of plant, animal, insect and microbial species (BAC & EST Unigene Resources) and established the GENEfinder Genomic Resources at the Texas A&M University. This Resources has now become one of the largest genomic resource centers and a major resource for advanced research of structural, functional and comparative genomics in the world.

2. Structural Genomics – Research of structural genomics promises to provide a readily usable platform and a “freeway” for effective research of functional and comparative genomics. 

Whole-genome physical mapping of agricultural genomes - Genome physical mapping is the centerpiece of genomics research. We helped pioneer the physical mapping technology and strategy (Physical Mapping Tools) with BACs by fingerprint analysis, and developed the whole-genome BAC-based physical maps of several species, including indica rice, Arabidopsis thaliana, soybean, chicken and japonica rice. Recently, we have fully automated the procedure of whole-genome physical mapping with BACs. We are now developing a whole-genome, integrated physical/genetic map of cotton. 

DNA marker development, genetic map construction and gene/QTL mapping in crop plants: chickpea and cotton (Genetic Mapping) - Studies have shown that SSRs are desirable, readily usable DNA markers for marker-assisted selection and germplasm analysis. To facilitate use of DNA markers in marker-assisted breeding, integration of physical maps with genetic maps, high-resolution gene and QTL mapping, and gene cloning and characterization, we developed strategies and techniques to rapidly develop SSR markers from large-insert BACs. We are now developing an SSR map for chickpea and generating SSR markers for cotton. 

Isolation and characterization of chromosome centromeres in crop plants – Centromeres are vital to chromosome behavior and genetic material transmission. Extensive studies have been conducted in the centromeres of the plant model species, Arabidopsis thaliana, however, little has been done in the centromeres of crop plants. We are isolating and characterizing centromeric sequences of several plant genomes. 

Genomics of plant disease resistance gene – Disease is a common constraint to crop production. To better understand the molecular basis of disease resistance, we are working in the structural, functional and comparative genomics of disease resistance genes in several plant species using integrated DNA microarray, fingerprinting and genome sequencing techniques.  

3. Functional Genomics: gene position, function, expression, organization, and network - The development of whole-genome integrated physical/genetic maps has allowed us to initiate advanced research of functional genomics and determine the position, function, expression, organization and interaction of every gene. Using these maps, we are developing high-density, high-resolution transcript maps of several species.  

4. Comparative genomics: genome organization and evolution - Development of genome-wide integrated physical/genetic maps, availability of the large collection of BAC and BIBAC libraries, and development of advanced technologies have allowed us to study genome organization and evolution at the genome-wide level. We have studied the genome organization and evolution of plants using Arabidopsis and Oryza as the model systems. 

5. Bioinfomatics - To facilitate data analysis, manipulation and utilization, we established a core facility for bioinformatics of agricultural genomics and developed a web-based, integrated Genomic Information System (GIS) for genome research of agricultural species. Based on this system, we have created database for the integrated physical maps of Arabidopsis thaliana, indica rice, soybean, chicken, and japonica rice. 

6.  Mapping and Cloning of Genes and QTLs Important to Agriculture - Most genes of agronomic importance in crop plants are known only by their phenotypes. Map-based cloning has been proven an efficient approach to isolate such genes. Using this approach, we are working forward to cloning of several genes in crop plants (Gene Mapping & Cloning).