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Commercial Chickens Low in Genetic Diversity, Study Finds

NEW YORK (GenomeWeb News) – The genetic diversity of commercial chickens is unexpectedly low, new research suggests.
In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, an international team of researchers looked at more than 2,500 SNPs in nearly 2,600 chickens from commercial, non-commercial, and other lines. Their results suggest that commercial chickens have far less genetic diversity than non-commercial lines — and roughly half that predicted in a hypothetical ancestral population.
“Just what is missing is hard to determine,” lead author William Muir, an animal sciences researcher at Purdue University, said in a statement. “But recent concerns over avian flu point to the need to ensure that even rare traits, such as those associated with disease resistance, are not totally missing in commercial flocks.”
Chickens have undergone intensive breeding efforts aimed at selecting specific traits over the past half a decade as modern chicken production has taken off. And although they noted that chicken breeders make efforts to avoid inbreeding in chicken lines, Muir and his team speculated that commercial chicken lines might still be missing alleles found in non-commercial and ancestral populations.
“Because these pure [commercial] lines have dramatically different agronomic traits than non-commercial standard breeds, gene flow does not occur between commercial and non-commercial poultry, resulting in essentially closed breeding structures,” the authors wrote, adding that “there is a realistic concern that genetic diversity for future needs may be compromised.”
In an effort to address this, Muir and his team looked at 2,551 informative SNPs in 2,580 birds — including more than 1,400 commercial birds, more than 1,100 chickens from experimental and standard breeds, and control birds such as the Red Jungle Fowl, a progenitor of domestic chickens, a Chinese Silkie, a commercial broiler, and a White Leghorn.
Collaborators at Illumina genotyped each bird based on a collection of SNPs selected by dividing the chicken genome into 3,072 bins and choosing three SNPs from each.
The researchers’ results suggested that commercial chickens have lower genetic diversity than their non-commercial counterparts — and only about half that of a hypothetical ancestral bird. Consequently, they added, commercial chickens may be missing rare alleles that contribute to disease resistance and offer other, yet unknown, advantages.
And, the authors argued, simply crossing commercial breeds would likely re-introduce just a fraction of potentially useful alleles. Instead, they suggested that breeders consider more wide-reaching strategies for increasing genetic diversity — for instance, inter-breeding commercial chickens with non-commercial and native birds.
“We suggest interbreeding some experimental commercial poultry lines with native or standard breeds as a backup plan, or ace in the hole, to help the industry meet future challenges, as traits such as disease resistance may be found among the rare alleles of other birds,” Muir said.
Muir is currently leading an international project to test the use of whole-genome selection in chicken breeding.

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