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

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 = 24-31 per breed) were sampled for DNA analysis from 2 or 3 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 8 breeds had probabilities of <28%. ADMIXTURE analysis indicated the minimal CV corresponded to 9 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 2 most genetically divergent breeds based on 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 others 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.

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford).

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events.