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Dairy Genetics East Africa Project Using SNP Chips to Improve Cattle Breeding in Kenya, Uganda

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Using array technology to improve agriculture in the developing world may not be as challenging as some might imagine. A project called Dairy Genetics East Africa has been relying on SNP chips to select the best-performing cattle breeds at sites in Kenya and Uganda, and is close to making recommendations on those breeds, according to John Gibson, the effort's principal investigator.

"The point of our study is that the technology only needs to be used during the research phase," Gibson told BioArray News this week. "Once we know what genotypes fit best to which systems then technology is not required in order to produce and deliver those animals to farmers."

Gibson is the director of the Center for Genetic Analysis and Applications at the University of New England in Armidale, Australia. In addition to UNE, other organizations taking part in DGEA include the International Livestock Research Institute, based in Nairobi, Kenya; and Picoteam, a multinational consultancy. The project commenced in 2011 and is founded by the Gates Foundation and other institutions and agencies.

The long-term objective of the project is to improve East African dairy production through breeding, a task complicated by a lack of pedigree information on cows, as well as the common practice of crossbreeding animals such that the smallholders who rely on the cows for milk production often know little about their genetic inheritance. Smallholders are farm owners who typically live on a few dollars a day and farm one or two acres of land.

Gibson and his fellow researchers are using Illumina's BovineHD BeadChip, a 770,000-marker array, to assess the breed composition of different animals. "This gives us the accuracy we need and allows us to explore a range of other genetic characteristics of these animals that would not be possible with the use of lower-density assays or other marker technologies," he said of DGEA's technology choice.

DGEA is also collecting field data on farmers' animals and practices, with the hope that they can correlate performance with breed and make recommendations on the most suitable breeds to use in different farming systems.

According to Gibson, most of the cattle used at the sites in Kenya and Uganda are crosses between European dairy breeds, such as Holsteins, Friesians, Ayrshire, Jersey, and Guernsey, and breeds indigenous to East Africa, such as Ankole, Nganda, and Zebu.

"In these systems there are no pedigree records and farmers do not know what proportion of different breeds are present in a given animal," Gibson said. "Having estimated the breed composition we can then determine what breed combinations work best for smallholders," he said.

To accomplish its goals, DGEA has needed to genotype a large number of animals, Gibson said, as a large amount of data is required to obtain estimates that have "sufficient accuracy that they are safe to develop recommendations to farmers." So far, DGEA has genotyped 2,120 cows in total using the BovineHD.

DGEA is now analyzing those data together with the collected field data to determine the best-performing breed combinations — work it expects to complete by the end of March, Gibson said. The project participants expect to make recommendations by May, but Gibson cautioned that they may need some additional data before they can make comprehensive recommendations.

Those recommendations may be useful for other farmers in the region, Gibson noted. "We believe our results will be applicable to a wide range of highland tropical dairy systems and we hope to extend our work to Ethiopia and Tanzania in the near future," he said.

Innovation Platform

Gibson discussed DGEA during a workshop at the Plant and Animal Genome conference in San Diego last week. In his talk, he made some more general comments about the process of translating the "experience, techniques, and practical solutions" gained through using genetics to inform breeding practices in the developed world to smallholders in the developing world.

According to Gibson, past initiatives that aimed to see genetics-based breeding implemented in regions like East Africa were unsuccessful because of the way they were managed. These programs, which he did not specify, were often "government run with no demand from farmers," Gibson said. Because of poor environments and infrastructure, programs were "never financially sustainable," he said, adding that they were also "overtaken by changing systems," often cross-breeding, which made decisions hard to implement from generation to generation. Altogether, Gibson characterized previous efforts as being "run by researchers who were not taking a holistic approach."

With these earlier failures in mind, Gibson said that DGEA has embarked on a parallel project — an "innovation platform" that "brings together all the players in smallholder dairy systems and dairy cattle genetics in particular" so that they can determine the issues facing them and develop "sustainable solutions to overcoming these bottlenecks to make their systems work better."

This is an extension of DGEA's philosophy of having the "local players develop the solutions, not us," Gibson said. "We just act as facilitators to the process and suppliers of information where required."

According to Gibson, DGEA's innovation platform has already generated new businesses and partnerships that aim to improve genetic delivery systems to smallholders in Kenya and Uganda, "with a much larger number in the pipeline." The next phase of DGEA's parallel project will be to help these emerging businesses and partnerships to scale up their activities "so that the whole smallholder dairy sector is serviced and all genetic service needs are met."

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