Research Programs
Bovine Genome Project
We will make significant contributions to the recently announced Bovine Genome Project. Consortium members include: USDA-ARS, TIGR, the University of Illinois Urbana-Champaign, Texas A&M University, researchers from Canada, France, New Zealand, Australia, Japan and The Human Genome Sequencing Center of the Baylor College of Medicine. We have contributed a cattle (Angus) bacterial artificial chromosome (BAC) library to the fingerprinting and BAC end sequencing effort in preparation for genome sequencing. The BAC library consists of 106,560 HindIII clones and represents 4x genome coverage. In addition to the library, we will provide the mapping data we have generated using these BACs. Over 2000 BACs have been isolated from the library by PCR-based screening with primers for markers or genes and we have mapping information on over 1000 of these loci. Furthermore, we have just completed a shotgun sequencing project that anchored 359 mapped BACs to the draft human genome sequence.
The Bovine Chromosome 5 Comparative Map is an example of the kind of anchored map we have generated and contributed to this project.
Another example is catte ESTs BLASTed against the Human Genome.
Positional Cloning
We are fine-mapping regions affecting carcass quality such as tenderness and marbling. We are also focusing on the horned and scurred loci. We are using these well-characterized regions to test some new methodologies that incorporate functional genomics into gene mapping strategies.
Functional Genomics
Most of the genes identified as part of the Human Genome Project do not have a function assigned. In order to determine the functions of the genes we identify in cattle and horses, functional and or gene expression assays will be required. Gene expression arrays will allow us to determine time and place of expression. We will need to develop appropriate functional assays to assign function in cases where the human or mouse genome cannot be used as a reference.
Nutritional Genomics
Nutritional genomics has been defined either as engineering agricultural organisms to improve human nutrition or as the study of nutrients and their effects on human health via genome scale experiments. Both of these definitions revolve around improvements to human health. In production livestock, nutritional genomics needs to be squarely aimed at improvements in animal production and health. In order to accomplish this, both short and long term goals need to be considered. The short-term goal is to optimize cattle feeding on the basis of genetic background. The long-term goal is to understand the pathways that control appetite, nutrient utilization and animal growth in order to optimize these pathways for particular purposes.
NCBA Carcass Merit Project
The Carcass Merit Project is a collaboration between Texas A&M University,
Kansas State University, Cornell, Colorado State University, MMI Genomics Inc.,
14 Breed Associations and is coordinated by the National Cattlemen's Beef
Association and funded with Beef Check off dollars. This project is an
industry-wide effort to characterize bulls in U.S. beef breeds for carcass
traits. The Carcass Merit Project is an outgrowth of the Texas A&M
University Angleton Project that was sponsored in part by the Beef Check off
dollar. The Angleton project identified several regions of the genome
associated with meat quality traits, such as marbling and tenderness, using a cross
between Angus and Brahman. These genomic regions are known as quantitative
trait loci or QTL. One objective of the Carcass Merit Project is to validate
segregation of QTL for selected carcass characteristics within each breed
participating in the study. Eleven QTL are under investigation in the Carcass
Merit Project: six for Warner Bratzler shear force tenderness, one for
tenderness as assessed by a sensory panel, three for marbling and one for rib
eye area. Each participating Breed Association has identified ten bulls and
fifty progeny for each bull for the QTL validation study. The validation
component of this project consists of scoring a bull and his progeny for DNA
markers in the QTL regions. Texas A&M University performs quality control
genotyping to verify the parentage and identity of all project animals. We are
also responsible for statistical analyses to validate segregation of the QTL in
each bull tested.
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