In the late 1980s thousands of chickens died from a cancer caused by a virus known as avian leukosis virus J because they were all descended from a few roosters susceptible to the disease.

This is just one example of how a lack of genetic diversity can imperil livestock and agriculture. Similar instances abound from the Irish potato famine of the 19th century to cattle raised for meat—one bull named Ivanhoe passed on his genetic susceptibility to an immune system disorder to roughly 15 percent of all the Holstein bulls in the U.S. today. Now a new study, published in Proceedings of the National Academy of Sciences USA, shows that the world's 40 billion commercial chickens—those raised for their meat and eggs—have half the genetic diversity possible in the chicken genome, rendering them susceptible to other crippling disease outbreaks.

Avian disease specialist Hans Cheng of the U.S. Department of Agriculture and his colleagues compared the variety of genes in more than 2,500 chickens, 1,440 of whom were from commercial farms in the U.S. Some of these industrial chickens had lost as much as 90 percent of the genes carried by their peers, such as the red jungle fowl of Asia, which gave rise to all chickens, as well as noncommercial breeds of chickens like the Chinese silkie. On average, commercial chickens lacked at least 50 percent of the genes present in the chicken genome.

"This lack of diversity in commercial stocks is most likely due to the use of a limited number of chicken breeds to form the commercial stocks," Cheng says. This "commercial stock may lack the genetic diversity necessary to combat new and emerging diseases."

All white egg-laying chickens in the U.S. are derived from the white Leghorn breed, whereas all chickens grown for meat, known as broilers, derive from the British Cornish, or Indian, game breed. Winnowing the genetic code has allowed farmers to meet the current global demand of 61 metric tons of meat and more than 55 million metric tons of eggs—an increase in production of 436 percent since 1970. But it has also allowed for the potential of a so-called "disease shock".

"Disease shocks have certainly been seen in the plant world and have had major impact, both human and economic: the famous Irish potato famine of the 19th century and more recently Dutch elm disease [a fungal infection]," says agricultural economist Carlos Seré, director general of the International Livestock Research Institute (ILRI). "Disease shocks in chicken populations could potentially occur, for example, with very transmissible and pathogenic avian flu viruses."

Without rare genes that, in essence, inoculate chickens against such bird flu, a virulent outbreak could shut down chicken farming. But it is hard to know which genes are missing, Cheng notes, because researchers have identified so few of the genes and their corresponding traits in the chicken genome.

"The poultry industry is clearly doing well for the selection of important agronomic traits," such as large breast muscles (more meat) and enhanced egg-laying, he says. "Until there is a necessity to add genetic diversity, they will continue to select within their existing populations."

He warns, however, that it may be too late by the time that necessity becomes apparent. To avert any mass deaths, he recommends that farmers breed commercial chickens with other types of chickens to preserve a reservoir of potentially useful genes. Of course, that may involve trade-offs in traits such as egg-laying that are now the goal.

Some researchers, including those at ILRI, have called for creating a "gene bank" for livestock similar to seed banks used for important crops that would contain a frozen record of livestock genetic diversity. "It would be interesting to do this for other livestock in which large-scale commercial breeding is important, such as dairy and pigs," Seré notes, to see how these domesticated animals have fared.

Such gene banks would require new technologies, however, since no one has successfully stored either rooster semen or the yolky egg over the long term. In the meantime, Cheng says research should continue to try to pinpoint genes that confer resistance to bird flu in other breeds of fowl to spare both humans and chickens. "If we could identify genetic resistance," Cheng says, "then this would greatly impact both the poultry industry and human health."