Starchy diet boosts gene copy number

Populations that eat more starch carry more copies of carb-digesting saliva gene

Sep 10, 2007
Charles Q. Choi
Diet can drive changes in genetic copy number, according to a study published online this week in Nature Genetics. The authors found that human populations with high starch diets have more copies of a gene that helps break down starch.The study is one of the first examples of natural selection favoring increases in gene copy number in humans, Hildegard Kehrer-Sawatzki at the University of Ulm in Germany, not a coauthor, told The Scientist. "The extra calories from roots and tubers that early human ancestors dug up could have fed a larger brain size," said Nathaniel Dominy at the University of California, Santa Cruz, lead coauthor on the study. Starch is metabolized in part by salivary amylase, which is encoded by AMY1. The number of copies of AMY1 found in people varies greatly across populations. Dominy and his colleagues investigated whether such copy number variation of AMY1 was linked to levels of salivary amylase in people and thus potentially with how much starch different populations consumed. Researchers studying genomic differences across populations have so far largely focused on single nucleotide polymorphisms, but copy number variation is increasingly considered a major source of genomic diversity.Using real-time quantitative PCR, the researchers analyzed AMY1in 50 European-American students and found that their levels of salivary amylase correlated with the number of copies of the gene, which ranged from two to 15. To see whether variations in AMY1 copy numbers were linked with diet, Dominy and his colleagues tracked the gene in populations that consume high starch versus low starch diets. High-starch populations included 50 European-Americans and 45 Japanese individuals, as well as 38 Hadza hunter-gatherers from east Africa, who rely highly on starchy roots and tubers. Low-starch populations included 36 Biaka and 15 Mbuti hunter-gatherers from the Congo rainforest in Africa, 17 Datog pastoralists from east Africa, and 25 Yakuts from Russia.On average, they found, the high-starch populations had more copies of AMY1. Twice as many individuals from high starch groups had six or more AMY1 copies than did those in the low-starch populations. The researchers speculate that higher salivary amylase levels may help derive more energy from starchy foods. In contrast to humans, 15 chimpanzees tested had just two copies of the gene. "We know chimps eat very little starch, and there's a growing movement among paleoanthropologists that suggests the dietary shift to more starch among humanity's earliest ancestors proved critical to our evolution," Dominy said.Dominy acknowledged the number of subjects they analyzed was relatively low, particularly for the low-starch groups, but noted that "the problem is there are very few populations on Earth today who have low-starch diets." Matthew Rockman at Princeton University, who did not participate in the study, said the number of subjects was "perfectly adequate." But Kehrer-Sawatzki noted that "the numbers are low and further studies are needed to confirm the trend."James Sikela at the University of Colorado Health Sciences Center in Aurora, also not a coathor, told The Scientist that this study suggested investigations of copy number variations "could allow us to track important events in human history."Sikela noted a recent study found that roughly 4,000 genes represent most of the copy number variation specific to primate lineages over the past 60 million years. He suggested future studies could investigate these genes to explore the importance of copy number variation in humans.Charles Q. Choi mail@the-scientist.comLinks within this article:George H. Perry et al., "Diet and the evolution of human amylase gene copy number variation," Nature Genetics, published online September 9, 2007. Travis, "Eat your way to better DNA," The Scientist, September 1, 2006. Dominy Ganguli, "Copy number a major source of variation," The Scientist, May 1, 2006. Spinney, "Getting started with SNPs," The Scientist, November 21, 2005. Roberts, "Looking at variation in numbers," The Scientist, March 14, 2005. Perkel, "Five questions on QPCR," The Scientist, December 1, 2006. Rockman Sikela Dumas et al., "Gene copy number variation spanning 60 million years of human and primate evolution," Genome Research, published online July 31, 2007.