Phase 3 (2007 Deadline)
Discovery of Genetic Variation that Enhances Improvement of
Dairy Production and Health in Cattle and Buffalos
Tad S. Sonstegard, USDA Agricultural Research Service, Beltsville, MD
Masroor Ellahi Babar, University of Veterinary and Animal Sciences (UVAS), Lahore
Pakistani Funding (HEC): $ 351,000
US Funding (USAID): $ 183,700
Project Dates on US Side: April 1, 2008 - March 31, 2011
The hypothesis underlying this project was that genome-wide information on genetic variation will increase accuracy of predictions of genetic merit; will enhance heritability and reliability of these predictions through improved pedigree information; and will improve detection of most quantitative trait loci underlying a trait when analyzed using linkage disequilibrium mapping. Therefore, the central aim of this project was to develop genomic tools to aid characterization of the structure and function of both the bovine and water buffalo genomes, and then apply these tools using novel statistical methodology to accelerate genetic improvement for traits of economic importance in both species.
- Developed commercial, high-density SNP assay applicable to temperate and tropically adapted cattle and generated more than 150 billion base pairs of sequence data from water buffalos for SNP discovery and genome assembly
- Provided training to 304 undergraduate students, 121 graduate students, and 200 researchers
- Created and improved research infrastructure at UVAS, including renovation of undergraduate lab, upgrading of postgraduate lab, and development of hi-tech lab, bioinformatics lab, and forensic facility
- Created three new degree programs at UVAS, including BS in biotechnology and informatics, M. Phil/PhD in molecular biology and biotechnology, and M.Phil/PhD in bioinformatics
- Obtained trust funding from International Water Buffalo Genome Analysis Consortium to generate a de novo genome sequence assembly of water buffalo and discover polymorphism applicable to selection in all breeds of buffalo
- Established linkages with the Livestock and Dairy Development Department of the Government of Punjab
This project was completed on the US side as of March 31, 3011. Some of the data gathered and analyzed has been contributed to the ongoing International Water Buffalo Genome Project being led by Dr. John Williams of Parco Tecnologico Padano, Italy. Additional Pakistani students from UVAS may also be sent to USDA for training in the future. Dr. Babar is also working to strengthen linkages with the Livestock and Dairy Development Department of the Government of Punjab in order to bring the benefits of his research results to Pakistani dairy producers. He reports that the project allowed his lab to acquire the latest equipment for genetic analysis and bioinformatics, which has not only facilitated ongoing research efforts but also made it possible to organize relevant training workshops and new graduate-level courses at UVAS.
Progress Report Summaries
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2010 Show summary || Hide summary
By February 2010 this research team had completed a map showing shared genetic variation between U.S. and Pakistani dairy breeds. Some of the materials used for genotyping and sequencing in the process of creating the map belong to a new DNA repository at UVAS. This collection currently includes samples from more than 200 cattle and nearly 400 water buffalos and will be expanded in the future. The three researchers were among the co-authors on a paper entitled “Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics," which was published in Proceedings of the National Academy of Sciences in November 2009. Beyond its research aspects, this project has also facilitated the renovation of undergraduate and graduate student labs, the creation of a new genomics lab, and the upgrading of a bioinformatics lab at UVAS. This improved lab infrastructure has helped students in a new four-year degree program in biotechnology and informatics created at UVAS in 2008.
2009 Show summary || Hide summary
Genotyping work was carried out at USDA and the results were provided to Dr. Babar at UVAS, as well as to another U.S. collaborator on the project, Dr. Jerry Taylor at the University of Missouri. Further linkages have been established with researchers at the University of Maryland, the University of Iowa, and the Università della Tuscia in Italy to broaden the array of genomic data included in the project. Dr. Sonstegard had planned to host Dr. Babar for a research visit at USDA in the summer of 2009 (being entirely funded by the Pakistani side of the grant). However, the necessary security clearances and issuance of visa documentation took much longer than expected and Dr. Babar had other schedule commitments in the meantime, but ultimately he arrived on December 15, 2009, for a two-month stay at the USDA lab.
2008 Show summary || Hide summary
This project began on the U.S. side in April 2008, and by the end of the year the participants had already collected blood samples from various species of cattle and water buffalos and a first set of DNA samples had been shipped to Dr. Sonstegard’s lab at USDA. Further shipments followed in 2009.