A gene bank’s collection of genetic diversity among minor chicken breeds

Authors: Blackburn, Harvey; KREHBIEL, B - Colorado State University

Submitted to: Poultry Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/26/2023
Publication Date: 6/1/2023
Citation: Blackburn, H.D., Krehbiel, B.C. 2023. A gene bank’s collection of genetic diversity among minor chicken breeds. Poultry Science. 102(8). Article e102827. https://doi.org/10.1016/j.psj.2023.102827.
DOI: https://doi.org/10.1016/j.psj.2023.102827

Interpretive Summary: To date, genetic diversity among and within fancier chicken breeds has not been quantified. This lack of information detracts from conservation efforts for live populations or collection of germplasm by gene banks. We sampled 10 fancier breeds from 8 small chicken hatcheries that sell chicks nationally. The European breeds (Crevecoeur and Buttercup) were genetically distinct from the other breeds evaluated. We found that among the breeds developed in the United States, Rhode Island Red and Plymouth Rock had substantial genetic diversity with effective population sizes that exceeded 100. The Aseel and Crevecoeur (originally from India and France, respectively) had effective populations of 47, below the suggested threshold suggested by the Food and Agriculture Organization. In general, populations owned by hatcheries selling these breeds have distinct populations, strengthening the genetic diversity among the live populations. The gene bank collections of these 10 breeds is genetically robust and suggests breeders can proceed with selecting their flock's without undue concern about the loss of genetic diversity and can call upon the gene bank to broaden genetic diversity within these breeds as needed.

Technical Abstract: Genetic differences among heritage or fancier breeds of chickens have not been quantified in the United States. Gene banks collecting germplasm for conserving these breeds need this information as do breeders and companies raising them. Our goal was to evaluate genetic diversity of 10 heritage/fancier chicken breeds that are a component of the national collection and to use this information to establish a baseline of their genetic diversity and future conservation efforts. Breeds could be broadly classified as European, Asian, Mediterranean, and United States (US) in origin. The US breeds were composite breeds developed between the 1849 and 1935. Animals (n = 24 to 31 per breed) were sampled for DNA analysis from two or three hatcheries per breed and a total of 8 hatcheries. The hatcheries were assumed to maintain and breed their own populations of the studied breeds. Effective population sizes ranged from 47 to 145 and used to estimate probabilities of extinction for a 50-generation timeline. It was determined that Crevecoeur and Aseel had a probability of extinction that exceeded 40%, the remaining eight breeds had probabilities that were < 28%. ADMIXTURE analysis indicated the minimal CV corresponded to nine populations. In that analysis New Hampshire and Rhode Island Red were classified as the same population, which was not unusual given that New Hampshire was developed as a subpopulation of Rhode Island Red. Crevecoeur and Buttercup were the two most genetically divergent breeds based upon pairwise Fst among the breeds and principal component analysis, which was supported by the ADMIXTURE results. Inbreeding coefficients computed from genomic information was lowest for Crevecoeur, Rhode Island Red, Buttercup and Andalusian (0.8 - 2.6%), while New Hampshire, Buckeye, and Aseel were highest (12.8 – 14.3%). Within breed Fst among hatcheries supplying animals for sampling generally indicated a genetic structure was present on a breed-by-breed basis. Genetic relationships within hatchery were also computed for each breed. Several of the hatcheries had sent samples that suggested genetic relationships as high as half-sibs while several other had genetic relationships closer to first cousins. We conclude that the chicken breeds evaluated have substantial genetic variability within the in-situ populations and the gene bank has captured this diversity for future use.