In much of the developing world, goats are essential for survival and are highly valued for their meat, milk and hides. So it should come as no surprise that Agricultural Research Service (ARS) scientists and academic and industry colleagues, working with DNA from a domestic goat, used new technologies to develop a vastly improved and relatively inexpensive reference goat genome. This information will serve as a kind of instruction manual for scientists showing them how to use the same technologies to lower the cost of developing improved livestock genomes.
Similar genomes can now be assembled in less than one year for about $100,000--a fraction of the time and cost of earlier efforts. The previous contender for the best livestock genome assembly, the cattle genome, cost well over $50 million and required years of labor.
A reference genome serves as a road map for scientists for deciphering an animal’s genetic make-up and identifying genes associated with traits like disease resistance, heat stress tolerance or drought tolerance. An initial goat genome was sequenced in 2013, but huge sequencing gaps existed. The gaps represented “information black holes” or areas where information about important biological processes remained unknown.
For the new goat reference genome, researchers with ARS and the National Human Genome Research Institute (NHGRI) analyzed the DNA of 96 goats before choosing one representative breed, San Clemente. It is thought that Spanish explorers originally brought these goats centuries ago to the island off California that gave the breed its name. The goats faced no natural enemies and flourished, foraging freely across the island. By the mid-1980s, the U.S. Navy decided that the goats had to be removed from the island because they were destroying indigenous plants. Many were relocated, and the DNA used in this study was from a San Clemente goat in Virginia.
This work will have a major impact on efforts to improve livestock breeding and diagnosis of diseases in goats and eventually other livestock. Microarray chips with DNA markers are a key tool for swine, sheep, beef and dairy cattle breeders interested in improving traits like meat and milk production, reproductive success and disease diagnosis. In Africa, where livestock production is critical to sustaining growing populations, farmers and ranchers will now be able to use enhanced chips to link genes to key traits.
This work was funded by the U.S. Agency for International Development through the U.S. Government's Feed the Future initiative and the Agriculture and Food Research Initiative from the USDA’s National Institute of Food and Agriculture, with cooperation from the National Institutes of Health’s Human Genome Research Institute, Bionano Genomics and Phase Genomics.
Research findings on this new technology are published in Nature Genetics.