Title: "Missing Alleles as a Metric of Biodiversity: An Example Using Commercial Poultry Populations"
Speaker: Professor Bill Muir, PULSe Molecular Evolutionary Genetics Program and Department of Animal Sciences, Purdue University
Place: Mechanical Engineering (ME) 161; November 11, 2008, Tuesday, 4:30pm


Following decades of intense selection and competition that has reduced the poultry industry to relatively few multinational companies, the question arises as to whether sufficient genetic diversity exists as insurance to address future needs such as resistance to new or emerging diseases. With the chicken genome sequence and the identification of over 2.8 million single nucleotide polymorphisms (SNPs), it is now possible to address biodiversity with respect to loss of alleles. To achieve this goal, a panel of 2551 informative SNPs were genotyped on 2580 individuals including 1440 commercial birds. Allele loss was assessed was by (1) estimating the global SNP allele frequency distribution from a hypothetical ancestral population (HAP) as a reference, then determining the portion of the distribution lost, and (2) determining the relationship between allele loss and the inbreeding coefficient. Results indicate 50% or more of the genetic diversity in ancestral breeds is absent in commercial pure lines. SNP weights are shown to act as sentinels of biodiversity and provide an objective assessment of which strains are most valuable for preservation of genetic diversity. This is the first experimental analysis investigating extant genetic diversity of virtually an entire agricultural commodity. Furthermore, the concepts and analytical tools developed should prove useful for population analyses in other species.

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