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Feed the Future Projects Turn to SNP Arrays to Support African Livestock Breeding Programs


Two projects are underway that will employ SNP array-based genotyping to inform African livestock breeding programs.

One will focus on breeding chickens that are less susceptible to Newcastle disease and resistant to heat, while the other aims to improve indigenous goat production for African smallholders. Both projects are funded through the US Agency for International Development as part of Feed the Future, the US government's global hunger and food security initiative, and may be the first of multiple projects to use state-of-the-art genomics research tools to benefit agriculture in the developing world.

According to a researcher involved in one of the projects, the ability to use tools such as SNP chips in such a setting stems from increased experience with the technology, as well as its declining cost, particularly for the lower-density arrays that will ultimately be used to guide breeding decisions.

"We now understand not only how to look efficiently at large-scale information, but also how to translate that into something that's more economical," said Susan Lamont, a professor of animal science at Iowa State University. "The technology and understanding of how to use that has now progressed to an appropriate stage where we can pursue such projects," she told BioArray News

Lamont and colleagues at the University of California, Davis, the University of Ghana, Sokoine University of Agriculture in Tanzania, and the University of Delaware received a five-year, $6 million grant in October to establish the Feed the Future Innovation Lab for Genomics to Improve Poultry. The effort aims to increase chicken production among Africa's rural households and small farms by identifying markers that can be used in breeding chickens that tolerate hot climates and resist infectious diseases, specifically Newcastle disease.

Huaijun Zhou, a former student of Lamont's and an associate professor of animal science in the College of Agricultural and Environmental Sciences at UC Davis is the principal investigator for the project.

Lamont discussed the project at the Plant and Animal Genome conference, held in January in San Diego. This week, she characterized it still as being in its "beginning stages," noting that participants had recently traveled to Ghana and Tanzania to coordinate the project, review the existing infrastructure, and better understand their African counterparts' capabilities for carrying out array-based research.

However, the first part of the project will be carried out in the US, not in Africa. Lamont said that the team will use a 600,000-marker Affymetrix array to genotype hundreds of unique chickens in order to narrow in on genetic locations that control traits of interest relative to Newcastle disease and heat resistance.

"We are starting out in the US because we can do it in well-controlled conditions," said Lamont. "The next stage is to go and work with the birds in Africa."

Lamont said that the project has identified six "ecotypes" – chickens that are local to certain regions within Ghana and Tanzania – that will also be genotyped using the Affymetrix 600K chip, so that they can be for the first time genetically characterized, and so that the data can be used in genome-wide association studies to identify variants linked to certain traits. She said that several thousand birds could be genotyped as part of this phase of the project.

Based on that information, the researchers will likely design a smaller-scale, focused array to validate their findings and to be sure they can reproduce generations of chickens that will carry beneficial SNP alleles. Beyond that phase of the project, the same arrays might be used to measure a variety of performance traits, in addition to viral and heat resistance. Ultimately, the researchers aim to make their findings available via local schools, setting up a "distribution and education program to distribute the improved local genotype," said Lamont.

"We are not importing birds into Africa," she added. "We are working with them to bring the power of genomics to accurately find the best breeding animals."

'The perfect goat'

The approach of Lamont and fellow investigators is similar to a number of projects underway that aim to translate SNP arrays to the developing world, one of which is Dairy Genetics East Africa, a three-year-old, Gates Foundation-supported project involving researchers from Australia, Uganda, and Kenya that aims to select for optimum cattle breeds for use in those countries.

But while Lamont's project and DGEA are focused on livestock that are also important in the US or Australia, another Feed the Future project is devoted to improving goats, an "orphan species," about which "previous existing literature is scant," in the words of Tad Sonstegard, a research geneticist at the US Department of Agriculture's Agricultural Research Service.

Sonstegard told BioArray News that while the "economic value of goat production in the US is not comparable to other livestock products like beef, dairy, or swine," it is an important animal in Southeast Asia and Africa, which are home to 90 percent of the world's goats.

Most of these animals have not been under intensive selection for production but have "adapted well to their current production environments through natural selection in the ages since domestication," Sonstegard said.

To better characterize the goats reared in the developing world, the USDA-ARS' lab in Beltsville, Md., and fellow researchers at the International Livestock Research Institute in Nairobi, Kenya, the Agricultural Research Council of South Africa, the African Union-backed Association for Strengthening Agricultural Research in Eastern and Central Africa, and other organizations and institutions have been using a 53,000-marker Illumina SNP chip to genotype goats indigenous to select countries across Africa in order to identify traits required for extensive production conditions.

This Feed the Future project commenced in 2012, and to date, participating researchers have genotyped 600 goats, and are considering adding goats from other continents into the study. "We are trying to look at breeds that are raised in similar environments but in different countries, in hopes of increasing our chances of finding signatures for selection for climate change, or disease resistance," said Sonstegard. "Those are the adaptive variants we need to keep in the population while we are doing genetic improvement."

While the data from the chips has been "useful and most of the markers are informative," Sonstegard said that the researchers may "need to go deeper with a genome resequencing survey of select animals from each population to better determine if there are regional differences between breeds and populations for other SNP not on the current Illumina product. ”Based on our preliminary unpublished findings," Sonstegard said, “it is seems like different East African goat breeds are highly similar across several countries.

Based on that resequencing, plus similar efforts undertaken by the International Goat Genome Consortium, Sonstegard and fellow researchers may work either with Affymetrix or Illumina to build a higher-density array for follow-on studies.

Still, he cautioned that translating those findings to goat breeding on the ground in Africa could be years away.

"Goat breeding is more long term," said Sonstegard, "but you could see some immediate improvement in just a couple years' turn-around time." Currently, little progress in breeding is made because the best performing young goats are sold for meat rather than being used as breeding stock. What Sonstegard and fellow researchers would eventually like to do is institute community-based breeding programs that will allow farmers to generate better-performing goats by practicing positive selection, he said.

"What community based breeding programs do is ask the farmer what type of goat they would prefer to produce – 'What is the perfect goat for their needs?' – and then based upon their criteria, set up a program where they are selecting for these needs and to make sure that those desirable goats are used as breeding stock in the next generation," said Sonstegard. "It is community-based, so that everybody has an opportunity to share in use of the best germplasm and in effect such exchange of animals can reduce inbreeding through herd isolation," he noted.

To support such community-based programs, Sonstegard and fellow researchers hope to incorporate a "very low-density DNA tool," that could be sequencing-based or use some sort of a low-cost DNA chip to follow participating smallholders' breeding programs to make sure future generations of goats retain a sustainable combination of adaptive variants for future generations of goats with improved production.

Still, he acknowledged that the researchers are still in the early stages of trying to identify what germplasm exists in Africa. "A short-term success would be finding adaptive variants or signatures within natural selection in African goats that are not in other populations and are related to survival," said Sonstegard. "Just knowing that information would be a big help."