A Survey of Relationships Among Rare Breeds of Pigs

A Survey of Relationships Among Rare Breeds of Pigs

Summary

I have obtained samples from three rare breeds of swine (Guinea Hogs, Red Wattle, and Ossabaw Island) as stated in my grant proposal. I am in the process of collecting a few more samples from Red Wattle and analyzing the data.

From my preliminary findings, it appears there is a high level of inbreeding and relatedness present in each of the breeds. This indicates an increased level of homozygous alleles which would ultimately reduce the viability of each breed. This information will be helpful for producers who might be under the assumption certain animals are unrelated, when in fact they are closely related.

This study is close to being completed, but there are some different methods of estimating relationships that I would like to use to analyze the SNP data and see how the results vary. I will also work toward collecting additional Red Wattle samples.

A challenge of this study has been locating rare animals to sample and getting samples from producers in a timely manner because they are busy with many things. All the producers I have worked with have been amazing and excited about this project, and I appreciate the time they took to send samples.

I appreciated the opportunity to present my work at the SARE Farmers’ Forum and it was rewarding to see how interested the public and rare breed producers were in this project. I look forward to providing them with the final results of this project. Thank you for the chance to expand the information available to them and create interest in these fascinating breeds of pigs.

Objectives/Performance Targets

I obtained a partial pedigree for some of the Guinea hogs submitted for genotyping. I used this partial pedigree to compare relationships calculated from the pedigree to relationships calculated from the SNP data.

Setty’s MC Big Old Stiff Boar, Setty’s MC Wart Side Sow, Setty Lilly, Setty Rose, Setty Houdini, and DNC Seymour were all genotyped.
Table 1 shows the partial pedigree available for these animals.

Table 2 shows the relationship coefficients as calculated among individuals based on the partial pedigree (Table 1).

In table 2, I have highlighted the animals genotyped. Numbers between individuals indicate the level of relatedness. A relationship of 0.5 would be equivalent to a full-sibling or parent-offspring relationship. Relationships above 0.5 could indicate related individuals were mated at some point in the individual’s lineage or the individuals are actually full siblings and simply received many of the same genotypes from their parents. A full sibling or parent-offspring relationship could fall anywhere between approximately 0.35-0.65. SNPs give a better estimation of the relationship than a calculation based on pedigree alone. Cells lacking numbers, indicates there is no relationship or the pedigree was incomplete and a relationship could not be calculated.

The diagonal of table 2 indicates the animal’s relationship to itself. This should be “1”, in cases where this number is above 1, the numbers after the decimal indicate the inbreeding coefficient. For example, DNC Seymour has an inbreeding coefficient of .1875 indicating a mating between related individuals occurred at some point in this pig’s pedigree.

Next I calculated relationships among animals based off the SNP data. These relationship coefficients are shown in Table 3.

Lastly, I compared the SNP relationships to the pedigree relationships. This is shown in Table 4.

In table 4, only animals which had pedigree data can be compared to the SNP data. In some cases, there was still not enough pedigree information to calculate a relationship between two individuals (ex: Setty Rose and Setty Lily) however, using SNP information gives a more accurate representation of actual shared alleles. So for Setty Lily and Setty Rose, pedigree would indicate no relationship or simply not provide any information, but when they are compared using SNPs, they have a 0.45 level of relatedness. This is essentially a full-sibling level of relatedness. Other animals may be compared in a similar way to see the difference between pedigree calculations and SNP calculations.

I collected samples from 10 individuals. No pedigree data was available for most of these pigs so I did not use pedigrees to calculate relationships.

Table 5 shows the estimated relationships as calculated using SNP information. Table 5 can be read in the same way as the Guinea hog data. Each number shared between two individuals indicates the level of relatedness or essentially the percentage of shared alleles. A higher number indicates greater relatedness than a small number.

These pigs show similar levels of relatedness as compared to the Guinea Hogs. Considering samples came from multiple sources, lower levels of relatedness would have been expected. Such high relationship coefficients suggest previous generations have experienced matings between related individuals.

So far I have samples from five Red Wattle hogs. Hopefully, samples will be obtained from an additional five or six animals and included in this study. The same process was used to estimate relatedness between animals that was used for both the Guinea and Ossabaw Island Hogs. Table 6 shows the estimated relationships as calculated from SNP information.

Again, pedigree information was not available for all animals, but through talks with producers, it was expected that some animals would show an offspring/parent or sibling level of relatedness.

• Table 1. Guinea Hog Partial Pedigree
• Table 6. Red Wattle Hog SNP Relationship Coefficients
• Table 2. Guinea Hogs Pedigree Relationship Coefficients
• Table 4. Pedigree vs SNP Relationships (Pedigree relationship/SNP relationship)
• Table 5. Ossabaw Island Hog SNP Relationship Coefficients
• Table 3. Guinea Hog SNP Relationship Coefficients

Accomplishments/Milestones

I presented a portion of this research to producers at the NCR-SARE Farmer’s Forum in Columbia, Mo. I felt like this talk was a success and I had lots of questions from producers about this work. Everyone seemed excited about the outcomes of this project.

I have also submitted a report to the Guinea Hog association with the information I have so far about their animals. They were pleased with the results so far.

I look forward to finishing the analysis and creating handouts and reports for all the producers involved with this project as well as the public.

Impacts and Contributions/Outcomes

Collaborators: