Chicken genome analysis unlocks secrets of mammalian and bird evolution

12/07/04

U.SAn international consortium of researchers, including a geneticist at the University of California, Davis, uncovered a treasure trove of data when they analyzed the recently sequenced chicken genome, a development that will benefit research in basic biology and medicine for years to come.

Their analysis of the chicken genome -- the first genome of a livestock or bird species to be sequenced -- will appear in the Dec. 9 issue of the journal Nature.

"The draft sequence of the chicken genome and the findings provided in this first-level analysis truly revolutionize what research can be accomplished with this agriculturally and biomedically important species," said Mary Delany, a geneticist in UC Davis' Department of Animal Science and a co-author and a coordinator for the analysis.

"Before the genome was sequenced, we as researchers were essentially 'blind', but now we are able to 'see' the genome and more easily explore the mechanisms by which it operates," said Delany, an authority on the biology and genetics of the chicken. She noted that this new information will allow researchers to better understand the genetic and physical differences that occur in chickens and to develop genetically customized chicken strains that will serve as useful research models.

Detailed information about the chicken genome is considered particularly valuable to researchers because the chicken, in evolutionary terms, is a rather distant relative to humans and other mammals -- positioned between humans and fish. The sequencing of the chicken genome now equips researchers to explore how birds and mammals differ and how their chromosomal structure and protein content have evolved.

Some of the particularly interesting findings yielded by the analysis of the chicken genome include:

  • About 60 percent of the protein-coding genes in the chicken genome have counterparts in the human genome.

  • Several immune-related genes found in the chicken were previously thought to occur only in mammals.

  • In both bird and mammalian species, genes seem to perform similar roles in calcification.

  • The chicken genome lacks certain genes associated with casein milk proteins, salivary proteins and enamel proteins, mirroring the absence of teeth and milk-producing capabilities in birds.

  • Despite the evolutionary distance between chickens and humans, long blocks in the genomes of both species contain genes that share the same chromosomal position.

  • Expansion and contraction of gene families may be responsible for the independent evolution of mammals and birds.

  • The chicken seems to be the only vertebrate species whose genome has been sequenced that has lost more genes than it has gained in the evolutionary process.

The chicken that served as the DNA donor for the first draft sequencing project was a Red Jungle Fowl female from an inbred line that was developed in the 1950s at UC Davis by geneticist and breeder Hans Ablanalp, a professor emeritus of avian science. The Red Jungle Fowl is the ancestral species of all domestic chicken breeds. Delany notes that the hen, whose DNA was sequenced, lives at the poultry farm at Michigan State University and several different genomic research tools were created from her DNA.

The first draft of the chicken genome sequence, a $13 million project funded by the National Institutes of Health, was completed at the Washington University Genome Sequencing Center in St. Louis, Mo. in March 2004 and made available online to researchers. The draft sequencing project, along with a whole-genome sequencing conducted by the Beijing Genomics Institute in China using three different domestic chicken strains, revealed that the chicken genome is made up of about 1 billion DNA base pairs and is only about 40 percent the size of the human genome.

The genome of the chicken, which serves as a model for 9,600 other species of birds, provides insights that were unavailable from previous genome sequences. Delany noted that the chicken genome sequencing also underscores just how incomplete the current understanding of complex organisms is.

"Furthermore, the sequencing project illustrates how essential it is that we conserve avian stocks if we are to make further research advances," she said. "It's vital that we make sure that existing chicken lines are protected both as important agricultural species and as powerful research models."

Delany is a faculty member in UC Davis' renowned College of Agricultural and Environmental Sciences whose research programs range from production agriculture and nutrition to ecology and the environment.

Her contribution to the analysis of the chicken genome was supported by funds from the U.S. Department of Agriculture's National Research Initiative Competitive Grants Program, the University of California and the UC Davis Department of Animal Science.

Source: Eurekalert & others

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