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Genomic Approaches Help in Effort to Increase Food Security

SAN DIEGO (GenomeWeb Daily News) – The wild progenitors and relatives of domesticated plants and animals harbor genetic diversity that may be the key to developing crops and livestock that are more productive and can better survive in a changing world, according to speakers at the Plant and Animal Genome conference held here this week.

Some 7 billion people currently inhabit the Earth, and the human population is only set to grow. According to the US Agency for International Development, the planet's population will exceed 9 billion by 2050, requiring a 60 percent to 70 percent increase in agricultural production. At the same time, climate change and disease emphasize the need for more resilient crops and livestock.

The US government in 2010 launched an initiative dubbed Feed the Future to increase food security and end hunger, and it is now funding a number of projects aimed at increasing agricultural productivity.

At the PAG conference this week, researchers funded by the Feed the Future initiative described their work to study and ultimately tap the genetic diversity of wild relatives of crops and livestock like chickpea, sorghum, wheat, and chicken.

When chickpeas were domesticated, those lines only captured a portion of the plant's diversity. Douglas Cook, a professor at the University of California, Davis, and his colleagues are identifying and characterizing Cicer reticulatum and C. echinospermum, the wild progenitor and the sister species of chickpea, C. arietinum, at sites throughout Turkey.

At the same time, they have embedded microclimate sensors in the soil as part of a National Science Foundation-funded project to link the strains to differences in environmental conditions like rain abundance.

While this project is ongoing, Cook noted that RAD sequencing of 570 chickpea and chickpea relative genomes thus far identified some 53,000 segregating sites and that analysis with the tool STRUCTURE suggested that they uncovered three or four populations of the chickpea wild progenitor in their current sample set.

In the future, Cook said that he and his colleagues plan to develop panels of markers for certain traits like drought, frost, or heat tolerance, flowering time, and nitrogen fixation that they can use to identify a set of diverse wild plants to cross with elite plants to develop a quasi-domesticated set of wild plants.

Sorghum, on the other hand, has a rich genetic diversity within the cultivated species and has a measure of drought tolerance. Still, Andrew Paterson, director of the University of Georgia's Plant Genome Mapping Laboratory, and his colleagues are working to increase its ability to survive in drought conditions.

"While [sorghum] is drought resilient, it still has a long way to go to maximize its potential," Paterson said.

In addition, he and his colleagues hope to transform sorghum into a perennial crop from one that has to be planted each year. This could produce a higher yield from each planting and increase the economic viability of growing sorghum, as it "starts earlier and grows longer." A few lines of the plant have been shown to be perennials, and one of those has been shown to be able to survive in a broader geographic stretch and survive more stressors, traits that are of interest.

In addition to climate and environmental stressors, disease also threatens crops and livestock.

In wheat, one such disease threat currently comes from stem rust, a pathogen that the International Maize and Wheat Improvement Center's Rick Ward says is imperiling some 65 percent of world wheat, including small stakeholder farms.

Wheat and its relatives harbor genetic diversity, including some genes that confer resistance to the Ug99 strain of stem rust, though the pathogen is also adapting and showing resistance itself.

Race-specific and non-race-specific resistance within the wheat and related plant gene pools needs to be preserved and maintained, Ward said.

However, he noted that efforts toward resistant wheat would only be helpful when the resistant genes are included in competitive varieties of wheat. The future, he added, could include the development of cassettes with two or more resistance genes that could be introduced into certain wheat strains.

Such an approach of searching for already existing genetic diversity isn't limited to plant crops. Livestock, too, may benefit from drawing on reservoirs of genetic diversity.

Though chickens don't look particularly different from one another, Iowa State University's Susan Lamont said that they harbor genetic diversity that could be tapped. For instance, commercial entities have bred chickens for meat and egg production, but there are other traits like disease resistance, heat tolerance, and ability to survive on low-quality feed that are of more importance to small stakeholder farms in developing countries.

Chickens were among the first farm animals to be sequenced, Lamont noted, and a 600K high-density array is enabling genome-wide association studies to study a number of phenotypes like heat tolerance and resistance to Newcastle disease, and identify candidate genes.

This, she added, could lead to improved food security.