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Sequencing Study Uncovers Selection Signals Behind Chicken Domestication

By Andrea Anderson

NEW YORK (GenomeWeb News) – By sequencing and comparing genomic DNA from wild red jungle fowl (Gallus gallus) and chickens (Gallus gallus domesticus) from several domestic populations, Swedish, French, and American researchers have been able to pinpoint parts of the chicken genome under selection during domestication.

The team re-sequenced genomic DNA from chickens belonging to eight domestic chicken populations as well as DNA from the red jungle fowl, the wild ancestor to domestic chickens. The research, which appears online today in Nature, indicates that chicken domestication has occurred relatively recently — within the past 6,000 to 8,000 years. It also points to particular genomic regions under selection in domestic birds, offering clues about the genetics behind some economically important chicken traits.

"We think that, in the long run, this is a very useful examination of the genome of the chicken," senior author Leif Andersson, an animal breeding and genetics researcher affiliated with Uppsala University and the Swedish University of Agricultural Sciences, told GenomeWeb Daily News.

During the last 8,000 or so years, Andersson explained, humans have spurred the evolution of chickens from wild ancestors to domesticated birds specialized for meat production (broilers) and egg laying (layers). "There have been dramatic changes in the phenotype," he said.

In an effort to understand what sorts of key genetic changes have occurred during this domestication process, Andersson and his co-workers used the Applied Biosystems SOLiD platform to do massively parallel sequencing of pooled DNA libraries generated for 37 chickens from four layer populations and 42 chickens from four broiler populations.

The team also sequenced pooled DNA from eight red jungle fowl from two zoo populations and re-sequenced genomic DNA from the female red jungle fowl line used in the original chicken genome sequence paper, published in Nature in 2004. After this screening stage of the project, they honed in on specific regions of the genome using Sanger sequencing, Andersson explained.

The researchers generated between four and five times genome coverage for each chicken population or roughly 44.5-fold coverage of the chicken genome overall, covering about 92 percent of the chicken reference genome.

By looking within and between each chicken population, the team identified 7,453,845 high confidence SNPs as well as nearly 1,300 deletions that seem to be fixed in one or more of the bird populations tested.

After using SNP data to discern relationships between the chicken populations tested, the researchers sifted through the genomic data to find parts of the genome showing signals of selection during chicken domestication, turning up 21 loci linked to potential selective sweeps in the domestic birds.

These signals of selection are very strong, Andersson noted, because this evolution has occurred so recently, leaving little time for neutral changes to spring up and blur signals of selection.

One of the most intriguing signals of selection fell on a chromosome 5 locus affecting TSHR, a gene coding for the thyroid stimulating hormone receptor, which is involved in reproduction and metabolic processes. When the researchers screened 271 chickens from 36 populations around the world, they consistently found selective sweeps affecting the TSHR region in the domestic birds.

In their subsequent experiments, the team looked at this TSHR locus in more detail, identifying specific mutations that may have contributed to selective sweeps.

They also identified parts of the genome that are specialized in certain types of domestic chickens. In broilers, for instance, the team found evidence of selective sweeps in parts of the genome containing genes related to muscle growth, metabolism, and appetite.

"I think that is really encouraging, that a lot of the hits that we found make sense," Andersson said.

And while they concluded that loss-of-function mutations don't seem to have been a major factor in chicken evolution and domestication overall, the researchers did find specific deletions affecting protein-coding sequences — including a deletion in the SH3RF2 gene that seems to differ between high- and low-growth chicken lines.

Based on such findings, those involved say the study "has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research."

For instance, Andersson noted, there may be local populations that are well adapted to a particular environment but do not produce as much as other chicken populations. By understanding which genetic features underlie productivity, he explained, it should be possible to combine the best traits from distinct populations.

Sequencing additional chicken lines in the future should also provide a better sense of the heterogeneity within chicken populations, Andersson said.

For their part, the team plans to do additional sequencing studies using mate pair read sequencing in an effort to find structural variation in the chicken genome, such as rearrangements and translocations. They also plan to do follow up functional studies aimed at understanding the mechanism behind some of the signals of selection identified so far.

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