A world wide and genome wide assessment of biodiversity in commercial poultry populations

Authors: MUIR, WILLIAM - PURDUE UNIVERSITY; Cheng, Hans

Submitted to: National Breeders Roundtable Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 5/3/2007
Publication Date: 12/31/2007
Citation: Muir, W., Cheng, H.H. 2007. A World Wide and Genome Wide Assessment of Biodiversity in Commercial Poultry Populations. Proceedings of the 56th National Breeders Roundtable. p. 1-8.

Interpretive Summary:

Technical Abstract: Genetic diversity is the key to all genetic progress, past and future. Over the last 10,000 years, poultry was domesticated first from the wild jungle fowl, then in the last 1,000 years into standard breeds, such as game, meat, eggs, show, and dual purpose. In the last century, those breeds have been further reduced into a few commercially produced types, these include the broiler males, broiler female, white egg, and brown egg lines. These lines have since been strongly selected for both growth and egg production among other traits. During this process, genetic variability has been lost at each step. Important questions are, “How much variability has been lost” and “Is there adequate variability to meet future challenges, such as disease resistance?” Another important question is “Has the rate of loss been accelerated by modern commercial breeding practices?” With the advent of the chicken genome sequence and the identification of 2.8+ million single nucleotide polymorphisms (SNPs), it is possible to address biodiversity with respect to loss of alleles. To achieve this goal, a panel of 2551 informative SNPs spaced throughout the chicken genome were genotyped on 2580 unique individuals including 1440 commercial birds. Allele loss was assessed by determining the relationship with inbreeding, or through the use of SNP “weights” that corrects for ascertainment bias and avoids the need to extrapolate from the inbreeding coefficient. Results from both methods indicate that individual commercial breeding lines have lost 70% or more genetic diversity of which only 25% of this loss can be recovered by combining all stocks of commercial poultry. These results emphasize the need for concerted national and international efforts to preserve chicken biodiversity. This is the first report of a genetic diversity survey of virtually an entire agricultural commodity.