The genome of rock pigeon reveals the origin of pigeons and the molecular traits

(Press-News.org) January 31, 2013, Shenzhen, China – In a study published today in Science, researchers from University of Utah, BGI, and other institutes have completed the genome sequencing of rock pigeon, Columba livia, among the most common and varied bird species on Earth. The work reveals the evolutionary secrets of pigeons and opens a new way for researchers to study the genetic traits controlling pigeons' splendid diversity. The findings also help to fill the genetic gaps in exploiting pigeon as a model for the molecular genetic basis of avian variation.

People are quite familiar with the homing pigeon that carried vital messages back and forth in the war period. These "war pigeons" which have been trained to carry messages are domesticated rock pigeons. Pigeons are common birds found in many parts of the world and have more than 350 breeds with different sizes, shapes, colors, color patterns, beaks, bone structure, vocalizations and arrangements of feathers on the feet and head–including head crests that come in shapes known as hoods, manes, shells and peaks.

To study the genetic basis of the diversity of pigeon, researchers sequenced a pigeon breed named Danish tumbler as the reference genome, and re-sequenced additional 36 domestic breeds and two feral pigeons by next-gen sequencing technology. It is learned that the pigeon is among the few bird genomes sequenced so far, along with those of the chicken, turkey, zebra finch and parrot, which will give researchers new insights into bird evolution.

Researchers could know more about the origin of pigeons with more available genomic resource. Previous studies provided limited evidence of pigeon's origin in the Middle East and some breeds' origin in India, and indicated kinship between common feral or free-living city pigeons and escaped racing pigeons. With additional genomic data in this study, the researchers found there are a lot of shared genetic heritage between the breeds from Iran and the breeds that are suspected from India, which is consistent with historical records of trade routes between those regions. These analyses indicate that major pigeon breed groups all originated in the Middle East.

They also analyzed partial genomes of two feral pigeons: one from a U.S. Interstate-15 overpass in the Salt Lake Valley, and the other from Lake Anna in Virginia. Despite being separated by 1,000 miles, the two pigeons are genetically very similar to each other and to the racing homer breed, supporting the idea that escaped racing homers are probably major contributors to feral populations.

Head crest is a common ornament and an important trait in mate selection in many bird species. With genome-wide population analysis, they found that the EphB2 (Ephrin receptor B2) gene acted like an on-off switch to create a head crest when mutated, and no head crest when normal.

In addition to obtain evidences from whole genome resequencing, they also confirmed the discovery by investigating the EphB2 locus in additional 61 crested birds from 22 breeds, and 69 uncrested birds from 57 breeds. Moreover, the researchers observed that the mutation and related changes in nearby DNA of EphB2 are shared by all crested pigeons, indicating the trait evolved just once and was spread to numerous pigeon breeds by breeders, but not evolved multiple times independently in different breeds.

Dr. Guojie Zhang, a major contributor from BGI, said, "I am so pleased to see this collaboration yields a significant achievement in tracking the origin of pigeons. This study provides new insights for researchers to better understand this lovely bird from the whole-genome level. Moreover, the pigeon genome will accelerate the studies of pigeons and other avian research, and provide a promising model for identifying the genetic basis of variation in traits of general interest."

### About BGI BGI was founded in Beijing, China, in 1999 with the mission to become a premier scientific partner for the global research community. The goal of BGI is to make leading-edge genomic science highly accessible, which it achieves through its investment in infrastructure, leveraging the best available technology, economies of scale, and expert bioinformatics resources. BGI, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications. BGI has a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research: research that has generated over 200 publications in top-tier journals such as Nature and Science. BGI's many accomplishments include: sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, more recently, have sequenced the human Gut Metagenome, and a significant proportion of the genomes for the1000 Genomes Project. For more information about BGI, please visit www.genomics.cn.

Contact information:

Bicheng Yang
Public Communication Officer
BGI
+86-755-82639701
yangbicheng@genomics.cn