ARS | Publication request: A GENETIC VARIATION MAP FOR CHICKEN WITH 2.8 MILLION SINGLE NUCLEOTIDE POLYMORPHISMS

Submitted to: Nature Magazine
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 4, 2004
Publication Date: December 9, 2004
Citation: Wong, G., Liu, B., Andersson, L., Groenen, M., Hunt, H.D., Cheng, H.H. 2004. A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms. Nature Magazine. 432:717-722.

Interpretive Summary: Sequence changes or polymorphisms in an organism are the basis for the variation in all inherited traits. Thus, it is critical that scientists identify where these sequence variations occur and how often they occur. In this paper, sequence variation in the chicken genome was identified by sampling three different domesticated chickens and comparing them to the complete genome from Red Jungle Fowl, the wild progenitor. It was determined that the chicken genome is highly variable compared to other organisms like human and mouse. Furthermore, the amount of sequence variation in and between chicken lines remained fairly the same indicating that there have been no severe restrictions on the chicken genome during domestication. This implies that there is an ample amount of genetic variation left to select in commercial populations. Finally, this information will greatly enhance the ability of scientists to identify agriculturally important genes and biological pathways.

Technical Abstract: We have constructed a polymorphism map for the chicken genome with 2.8 million SNPs based on comparisons of three domestic chickens (a broiler, a layer, and a Silkie) with the genome of red junglefowl, the wild ancestor of domestic chickens. Follow-up experiments indicated that over 90% are true SNPs, and over 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity was 5 SNP/kb in almost every possible comparison--between red junglefowl and domestic lines, between two different domestic lines, and within domestic lines --in contradiction of the notion that domestic animals are inbred relative to their wild ancestors. Domestication has not resulted in a significant loss of nucleotide diversity. Most of the observed SNPs originated prior to domestication, and few showed fixed differences between red junglefowl and domestic chickens. Potentially functional non-synonymous substitutions at highly conserved sites were identified and we present two examples from the RHAG and OTC genes.