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Genomics Takes on Agriculture in the Developing World

NEW YORK (GenomeWeb News) – Feed the Future. Dairy Genetics East Africa. Illumina's Agricultural Greater Good Initiative. These are just a few of the efforts underway, showcased at the Plant and Animal Genome Conference held in San Diego last week, to use genomics to advance agriculture in the developing world.

While talks narrowed in on a multitude of specific issues — reducing heat stress in chickens, assessing breed admixture in goats — presenters also touched upon common themes, such as the looming global food security crisis, why similar initiatives to improve agriculture in the developing world have failed in the past, and the way forward for current projects that aim to see next-generation sequencing and SNP genotyping chips adopted in places where the word "infrastructure" refers not to technology resources, but to traversable roads.

At PAG, Max Rothschild, director of the Center for Integrated Animal Genomics at Iowa State University, spoke about how livestock genomics could be used to address global food security issues. He noted that 75 years of genetic improvement, based on phenotypic selection, and a decade of genomics, based on sequencing and gene identification, have enabled the developed world's "success" in using new technologies to improve agricultural yield.

"Efficient agriculture gives more people in developed countries richer lives," Rothschild said.

"In the 1950s, 10 million cooked breakfasts required more than 15,000 acres of crops to feed animals. Today, 10 million cooked breakfasts requires 5,000 acres of crops to feed animals," he added. "With the right environment, genetic potential can be realized."

Some of the greatest changes in agricultural research have happened in the past decade. "Sequencing has changed things," Rothschild said. "Since 2001, all major species have been sequenced — chicken, pig, horse, goat, and sheep, though the sheep genome has not been published. Sequencing has been commoditized," he added, noting that there are SNP chips available now for "all major species."

Within his lab, research efforts range from studying reproduction and longevity in pigs to climate resistance in goats. But Rothschild said that his main objective is translating genomics-based discoveries to improve agriculture in developing countries.

"My interests lie in producing more food around the world," he said, "because we are not producing the food that we should with the resources we have."

A growing population

The main challenge is population growth. With the United Nations' Food and Agriculture Organization projecting that the world's population will climb by a third to 9 billion by 2050, and with most of that increase expected to occur in the developing world where hunger is already concentrated, food production needs to dramatically increase during the next four decades to meet the needs of that growing population. "Conservative estimates say we need to increase food production by 70 percent; others say we need to double it," Rothschild said.

He added that making improvements to food security in the developing world makes sense for reasons other than just malnutrition and hunger. "Hunger undermines the fight against HIV, malaria, and other global health threats," Rothschild said.

"Hunger robs countries of human potential; hunger can lead to the misuse of natural resources; hunger fuels social conflict and can contribute to political instability," he added. "Dealing with hunger is not only an issue of feeding people. It makes political sense, too, because it promotes stability around the globe."

But how exactly can the technologies at Rothschild's disposal be made available to breeders in regions like sub-Saharan Africa or Southeast Asia?

For the past five years, Rothschild said his lab has been working with partners in Uganda to improve livestock and development. It has also been taking part in Feed the Future, the US government's global hunger and food security initiative. Rothschild notes that "many other countries have similar programs," including the Australian Agency for International Development, the Danish International Development Agency, the Japan International Cooperation Agency, and Israel's Agency for International Development Cooperation.

The most acute issue, Rothschild said, concerns the development of institutional and human capacity in these countries, meaning "breeders, bioinformaticians, scientists, and so on."

During his presentation, Rothschild listed research priorities within these programs that include developing tools and reagents for breeding livestock, such as goats, that are important to underdeveloped areas; collecting DNA from breeds to understand current genetic distances and admixture; identifying populations for preservation and selection using high-density SNP chips and exome sequencing; and enhancing locally adapted breeds using combinations of crossbreeding and selection with low-density SNP chips.

Much of this work is still in its early stages in terms of implementation, he cautioned, with researchers using these technologies to conduct genome-wide association studies of animals in developing countries to identify desirable qualitative trait loci.

Roadblocks and Pipelines

One point that Rothschild made at PAG, which was echoed by several other researchers, is that scientists looking to make advancements in agriculture in developing countries need to take a broader approach to see those gains reach "smallholders," which Rothschild defines as farmers who live on between $1 a day and $2 a day and farm between one acre and two acres of land.

"We are not just trying to breed animals that are bigger or grow faster and are healthier," Rothschild said. "We need to rethink the whole chain — who is going to breed the livestock, develop feed for them, provide them with water?"

John Gibson, director of the Centre for Genetic Analysis and Applications at the University of New England in Australia, said that it was this lack of a wider perspective that doomed previous efforts to transfer genomics-informed breeding to developing countries.

"They were typically government run with no demand from farmers," said Gibson of past initiatives. "Because of poor environments, programs were never financially sustainable; they were overtaken by changing systems, often cross breeding, and they were run by researchers who were not taking a holistic approach," he said.

At PAG, Gibson discussed the Dairy Genetics East Africa project, a two-year-old partnership between his university, the International Livestock Research Institute, and Picoteam, a consultancy, to help smallholders in the region obtain the most appropriate cows for their farms in order to increase their milk yields and improve their livelihoods. Funded in part by the Bill and Melinda Gates Foundation, the project has been implemented at sites in Kenya and Uganda. Gibson, the project's principal investigator, has used SNP chips to understand breed compositions that, together with other data, will later be used to identify the most appropriate breeds for various dairy production systems and household circumstances.

While breeds are well established in most of the developed world, in the developing world changes are still occurring as different breeds are often crossbred with others. Moreover, breeders in these countries often do not keep track of breeding decisions, meaning that many cows are admixed, and it is unclear what portions of what breeds contribute to their genetic makeup, making it harder to correlate phenotypes with genotypes. Gibson, though, said that SNP chips should allow the project to tease out that information.

"It is not clear what the optimum genotype is, it is not clear what the optimum crossbreed is, but the new approach that high-density SNP chips make possible is to work with crossbred cattle, record their performance in situ, and use SNPs to determine breed composition," Gibson said.

"After we achieve this, we will do GWAS analyses, trying to separate breed versus inbred contributions," he said, noting that improving potential via selection is the next step after optimum breed composition has been achieved.

Despite the challenges inherent to such projects, Gibson said that changes in efficiency and productivity can be accomplished with relatively small changes to management and genotype.

"The optimal genotype depends on the environment," he said. "In this context, Iivestock function changes from a focus on survival to being a traded commodity as the production environment moves from very harsh to intensive production systems and genetic selection changes from focus on adaptation to focus on production."

As far as taking a "holistic" approach, Gibson said that technology application in developing countries needs to be "simple and cheap," if used widely. Cost issues are not only linked to the technologies, he added, but to how they are used.

"It can be feasible and valuable if used on a limited scale for a limited period of time where the required expertise, technical, and other capacities required can be brought in," Gibson said. He also said that private-public partnerships might be more successful than initiatives built using institutional funding. "For a limited time, you can find an agency that can help," he cautioned, "but that investment won't be there in 10 or 20 years."

Gibson also warned other researchers engaged in such efforts to pay attention to infrastructure. "Simple things like roads," he said, as an example. "Is there a road between the test provider and the farmer? If there isn't, how can the technology get to him?"

Gary Atlin, a maize breeder at the International Maize and Wheat Improvement Center, made a similar point during his talk at PAG about tackling these challenges systemically.

"Breeders in the developing world are not being trained to deliver crop improvement technology, and are not effectively supported by institutions," Atlin said. "It's important that breeders and their managers think in terms of pipelines — parent choice, quality-control genotyping, exchanging elite lines among breeders, evaluating and rewarding breeders for practice and success."

If initiatives can accomplish that, Atlin said, then "most of the gap between public and commercial breeding can be closed through breeding pipeline optimization."