ӳ����ý

The farm chicken was domesticated from the red jungle fowl (left) roughly 8,000 years ago.
Image courtesy of iStockphoto

In 1957, an animal science researcher at Virginia Tech named Paul Siegel began a decades-long study of White Plymouth Rock chickens, a breed favored by backyard farmers. From his original flock, he created two new flocks: one with the heaviest birds, and one with the lightest. Once a year, he bred the heaviest birds in the heavy flock with each other, and the lightest birds in the light flock with each other. Though they began as a single flock of similar-weight chickens, birds in Siegel’s heavy flock now grow to an average of 9 times the size of birds in the light flock.

Siegel’s feat demonstrates the power that human preference can have on the physical traits of animals — so-called “artificial selection.” But it also provides a unique model for exploring the molecular basis of traits like growth and reproduction, traits that helped mold the chicken from a wild creature into a farm animal. Researchers at Uppsala University in Sweden and the ӳ����ý of MIT and Harvard now reveal a key gene that controls weight in these chickens, just one of several findings in a new study aimed at uncovering what happened in the genome when the chicken was domesticated. The new work, led by senior author Leif Andersson at Uppsala, appears in the March 10 advance online publication of Nature.

Several thousand years ago, the chicken’s journey from wild creature to agricultural staple began. At first, humans simply selected the best red jungle fowl — the ancestor of the domestic chicken — to breed. More recently, 20th century farmers began breeding separate lines of those chickens into egg-laying birds (“layers”) or those raised for meat (“broilers”). Today, these two types, in addition to diverse breeds of each kind, provide scientists with ample resources to search for the genes that underlie traits of domesticated animals, and therefore, may provide insight for breeders. Domestic animals can also help reveal the genetic elements that control physiological traits, which may have bearing on the search for similar genes in other organisms, including humans.

Using older methods of searching for the genetic regions that control traits — known as quantitative trait loci (QTLs) — scientists were able to detect regions of the genome that might harbor genes controlling growth (i.e., amount of meat produced) or reproductive cycle (i.e., egg-laying capacity). But the technique of QTL mapping, which can only home in on a region several million letters of DNA and often hundreds of genes long, fell short of singling out the true trait-controlling genes. For that capability, researchers would have to wait for new tools stemming from the chicken’s genomic catalog.

In 2004, scientists completed sequencing of the 1 billion letters in the genome of the red jungle fowl, which is the same species as the domestic chicken. They also identified 3 million single-letter changes in the chicken genome, known as SNPs, which could be used as markers to search for trait genes. With the recent wide availability and lower cost of sequencing technology, the team at Uppsala and the ӳ����ý was able to launch a more thorough analysis of genetic variation in the chicken by sequencing the genomes of dozens of birds from four broiler breeds, four layer breeds, and the red jungle fowl. The team confirmed 2.5 million of the original SNPs and identified another 5 million more, giving researchers everywhere a fuller picture of chicken genetic variation and opening the door for new biological inquiries.

The team next wanted to use the new genome sequences and the broad catalog of genetic markers to search for genes with a role in domestication, explained co-first author Michael Zody of Uppsala and the ӳ����ý. The method stems from the role played by farmers in shaping the domestic chicken’s DNA. When a farmer chooses to breed chickens of a certain quality (e.g., breast size or number of eggs produced), he is artificially selecting the genes that control those traits to be passed on. By breeding the best chickens, he will eventually get a flock of chickens that all have the same version of the gene. That variant, whether it’s a single-letter substitution, a deletion, or other genetic change, is said to have “swept” through the population to a point that geneticists call “fixation.” The process is known as a “selective sweep,” and it leaves a telltale signature in the genome. Areas around the genetic variant are inherited along with it.

Because chickens were domesticated into diverse breeds relatively recently, the sweeps are large enough to find in the genome, given the right tools, yet small enough to narrow the search down to a few genes. “The selection mapping is a much finer-scale tool for trying to identify specific genes,” said Zody, who performed data analysis while earning his PhD under the advisement of study co-author and ӳ����ý researcher, Kerstin Lindblad-Toh. “Selection may point us to a gene that otherwise would have required an enormous amount of fine-scale mapping to refine the QTLs.”

The team scanned the genomes of the domestic breeds in the study, searching for areas that looked to be selective sweeps. They found many potential sweeps and chose to probe more deeply a sweep found at a gene that encodes the thyroid stimulating hormone receptor (TSHR) protein. TSHR is known to play a role in the regulation of metabolism and reproduction, suggesting that it could be a gene specific to domesticated animals. Wild chickens mate on an annual cycle, so birds that can produce eggs and offspring regardless of the season would have been more valuable to a farmer and they, and their genes, may have been bred preferentially.

Using the SNP markers identified earlier, the researchers confirmed that the domestic version of the TSHR gene occurs in the genomes of hundreds of chickens tested from diverse breeds. This strongly suggests that TSHR is, in fact, a domestication gene in chickens. With high-resolution data in hand, the team discovered that the substitution of a particular letter for another in the TSHR gene, which replaces one amino acid for another in the resulting protein, is likely a molecular source of altered reproductive traits in domestic chickens, compared to the red jungle fowl.

Although the TSHR finding requires more work to fully confirm the gene’s role in domestication, the finding would be significant. “It would be the first time someone identified a domestication mutation within animals,” explained Zody.

Because genes that function improperly are thought to play a role in rapid evolution, such as during domestication, the research team also searched for stretches of missing DNA in the domestic genome, identifying almost 1,300 that were “fixed,” or found in every single member of a single breed. One of these deletions, in a gene called SH3RF2, was found in all of Siegel’s high-growth birds, but few of the low-growth birds. At ten weeks old, broilers with a working version of the gene were 20% lighter than those missing the gene. Because appetite, rather than a dysfunction of metabolism, appears to direct the heavier birds’ weight gain, the gene could play a role in regulating appetite.

A breeding program by co-author Paul Siegel has produced two lines of White Plymouth Rock chickens with a 9-fold difference in weight: the low-growth line (left) and the high-growth line (right).Image courtesy of Paul Siegel.

Siegel, a co-author on the new study, continues to breed the high- and low-growth chickens, maintaining the lines as a powerful model for studying the genetic factors that influence weight. Although the chickens are extreme cases, they highlight a gene with a potentially large effect on appetite and weight, an elusive target in studies of humans, which have yielded weight genes with markedly smaller effects. “The 20% difference is interesting in terms of the power to detect this in a model system,” said Zody. “We wouldn’t necessarily see that difference, looking in a human population.” The study authors note that these heavy and light chickens provide the first animal model to explore the function of the SH3RF2 gene, knowledge that may have significance for many organisms, including humans.

The immediate findings of this study demonstrate the utility of this farm animal as a research tool for biomedical scientists searching for genes underlying traits and disease. The researchers plan to study many of the potential selective sweeps further, to explore the footprints of domestication left in the chicken genome. The many other breeds of chicken found across the globe provide fodder for future studies. Explained Zody, “We’re only sampling a very small fraction of the diversity of chicken breeds out there.”

The sequencing and analysis work in this study was performed at Uppsala University, with additional analysis performed at the ӳ����ý. Patents have been filed in Sweden on the genetic regions identified in the study, with authors listed as inventors. Other ӳ����ý researchers involved in the study include Ted Sharpe and Kerstin Lindblad-Toh.