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Title: Review of the initial validation and characterization of a 3K chicken SNP array

Author
item MUIR, W - PURDUE UNIVERSITY
item WONG, G - UNIVERSITY OF ALBERTA
item ZHANG, Y - CHINESE ACAD OF SCIENCES
item WANG, J - CHINESE ACAD OF SCIENCES
item GROENEN, M - WAGENINGEN UNIVERSITY
item CROOIJMANS, R - WAGENINGEN UNIVERSITY
item MEGENS, H - WAGENINGEN UNIVERSITY
item Zhang, Huanmin
item MCKAY, J - AVIAGEN
item MCLEOD, S - AVIAGEN
item OKIMOTO, R - COBB-VANTRESS
item FULTON, J - HY-LINE INTERNATIONAL
item SETTAR, P - HY-LINE INTERNATIONAL
item O'SULLIVAN, N - HY-LINE INTERNATIONAL
item VEREIJKEN, A - HENDRIX GENETICS
item JUNGERIUS-RATTINK, A - HENDRIX GENETICS
item ALBERS, G - HENDRIX GENETICS
item LAWLEY, C - ILLUMINA, INC.
item DELANY, M - UNIVERSITY OF CALIFORNIA
item Cheng, Hans

Submitted to: World Poultry Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/12/2007
Publication Date: 6/1/2008
Citation: Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A., Crooijmans, R.P., Megens, H.J., Zhang, H.M., McKay, J.C., McLeod, S., Okimoto, R., Fulton, J.E., Settar, P., O'Sullivan, N.P., Vereijken, A., Jungerius-Rattink, A., Albers, G.A., Lawley, C.T., Delany, M.E., Cheng, H.H. 2008. Review of the initial validation and characterization of a 3K chicken SNP array. World Poultry Science Journal. 64:219-225.

Interpretive Summary: 2004 was a historic year for biologists, especially poultry scientists, as the chicken genome sequence assembly was released. In addition, 2.8+ million in silico sequence variants were reported, which could provide a very large number of genetic markers for diagnostic tests, animal improvement, and traceability. In the first large-scale study, we find by surveying 2500+ chickens for 3000+ sequence variants that over 90% of these sequence variants are valid and can be used confidently. This knowledge has very significant impacts. For example, we can now generate very dense and accurate genetic maps that will aid in future improvements of the sequence assembly. We also show that commercial lines are missing a large fraction of the existing diversity in other chicken breeds, which suggests that the industry should look at non-traditional breeds for future genetic gains.

Technical Abstract: The year 2004 was a historic one for biologists and especially the chicken research community as the first draft of the chicken genome was published (International Chicken Genome Sequencing Consortium, 2004). The 6.6X coverage of a UCD001 female Red Jungle Fowl (RJF) genome was the first complete description of an avian species genetic blueprint. Simultaneously and equally important for chicken geneticists was the identification of 2.8+ million single nucleotide polymorphisms (SNPs) (International Chicken Polymorphism Map Consortium, 2004). This large dataset was generated by partial shotgun sequencing (1/4X genome coverage) of a Ross broiler male, an experimental White Leghorn female, and a Chinese Silkie female with comparisons of the reads to the RJF. This comparative dataset provided a major leap towards understanding how genetic variation contributes and explains phenotypic variation. Taking advantage of these achievements along with the introduction of high throughput and economical SNP typing platforms, a consortium submitted a USDA grant proposal in 2004 that was subsequently funded in the summer of 2005. This proceedings paper briefly documents the goals and current progress of this effort.