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Genetic Relationships and Inbreeding Coefficients of Swine Breeds
Genetic diversity allows adaptation to environmental changes and varied disease resistance. Without such diversity, a population could be decimated by disease or environmental fluctuations. Swine breeds facing extinction share characteristics such as small size, slow growth rate and high fat percentage which eliminate them from the high-input high-output business of commercial production. Small populations and lack of genetic information increases the chance that producers are breeding closely related individuals which ultimately eliminates genetic diversity by increasing levels of homozygosity in subsequent generations. By making genetic data available, producers can make more educated breeding decisions to preserve genetic diversity in future generations.
Hair samples were collected from Guinea, Ossabaw Island, Red Wattle, American Saddleback, and Mulefoot pigs and genotyped with the Porcine 60k SNP chip. Publicly available genotyping data were obtained for British Saddleback, Duroc, Landrace, Large White, Pietrain and Tamworth pigs. PLINK was used to construct a genomic relationship matrix and to calculate inbreeding coefficients. The following table summarizes average relationships (R) between individuals (n) within a breed, and average inbreeding coefficient (F) of individuals within a breed. American Saddleback and British Saddleback showed relatedness across the two breeds, so they were combined. The model was significant (P-value <0.0001) and significant differences across breeds are indicated by superscripts (α≤0.05).
Breed |
n |
R |
F |
Guinea |
14 |
0.16a |
0.26a |
Ossabaw Island |
10 |
0.37b |
0.47b |
Red Wattle |
5 |
0.49bc |
0.28a |
Saddleback |
22 |
0.14a |
0.15d |
Mulefoot |
4 |
0.69d |
0.39ab |
Duroc |
20 |
0.21a |
0.25a |
Landrace |
20 |
0.03e |
0.15c |
Large White |
20 |
0.05ef |
0.15c |
Pietrain |
20 |
0.07f |
0.12c |
Tamworth |
20 |
0.46c |
0.41b |
Popular breeds (Landrace, Large White, and Duroc) exhibit lower levels of R between individuals, on average as compared to R between individuals of endangered breeds, especially Ossabaw Island, Red Wattle, Mulefoot and Tamworth. Following a similar pattern, F is high for Ossabaw Island, Tamworth, and Mulefoot, and low for Large White and Landrace. While less common in the United States, Pietrain is a popular breed in Europe which likely accounts for low R and F values.
Having complete pedigrees and large populations allows commercial breeds to maintain low levels of R and F within a population. For heritage type breeds, lack of popularity means fewer individuals to select among, and, within a viable populous, even fewer have known pedigrees. This research is the first step toward preserving genetic diversity by providing producers with accurate genetic information.
Keywords: Swine Genetics