Final Report for GNC10-145
Vertical integration of agriculture has dangerously reduced genetic variation among breeds used in commercial operations. Though benefits of biodiversity are often overlooked, there are farmers and organizations interested in preserving rare and endangered breeds for future generations. A constraint faced by many is the lack of pedigree data available for these breeds, which makes planning matings to avoid inbreeding difficult. Inbreeding increases homozygosity, therefore reducing genetic variation. Inbreeding often leads to the appearance of undesirable or deadly homozygous recessive traits which reduce a breed’s viability. This project focuses on increasing interest in rare pig breeds by expanding the genetic knowledge available to producers and the public. The main outcomes of this project are: 1) Establish relationships among animals without pedigree data; 2) Increase producer awareness of genetic variation in order to preserve rare breeds for future generations. Three viable, rare pig breeds with little or no pedigree data will be selected for evaluations. After collecting and genotyping DNA samples, relationships will be established for animals within these breeds of swine. Accurate relationship data will allow producers plan matings to maintain genetic diversity. Greater genetic variation will allow rare breeds to remain viable for future generations, providing farmers opportunities for niche marketing. A follow up with producers involved in this project will evaluate how the relationship data and genetic information has aided their reproductive management.
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.
Objectives for this project include calculating genetic relationships among rare breeds of swine, comparing rare and commercial breeds of swine, and providing producers with the information so they can make more informed breeding decisions.
Originally, only three rare breeds were going to be analyzed, but I was able to obtain samples from six rare breeds and an additional four commercial breeds.
Hair samples or SNP information was collected for ten breeds of swine with a range of four to twenty individuals per breed. Heritage breeds included Guinea, Ossabaw Island, Red Wattle, Saddleback, Mulefoot, and Tamworth. Commercial breeds included Duroc, Landrace, Large White, and Pietrain. Hair samples submitted by producers were genotyped by GeneSeek using the Porcine 60k SNP chip. Publicly available data was accessed online at http://datadryad.org/resource/doi:10.5061/dryad.v6f1g for Tamworth, Duroc, Landrace, Large White and Pietrain.
SNP data was converted to PED and MAP files for analysis in Plink. Plink was used to construct a genomic relationship matrix (GRM). Individuals or SNP’s not meeting the following criteria were removed: Minor allele frequency greater than 0.05 or call rate for individual greater than 0.90. To calculate inbreeding coefficient, the data set was first pruned to include SNP’s in approximate linkage equilibrium. The F value is the inbreeding coefficient estimate. Plink was also used to produce an MDS (multi-dimensional scaling) plot which is a good indicator of relationships between breeds.
SAS was then used to analyze Plink output. Differences between breeds were considered significant at α≤ 0.05.
Findings of this project show that commercial breeds exhibit lower levels of relatedness and inbreeding and endangered breeds have higher levels of relatedness and inbreeding. These results are summarized in Table 1.
Table 1 compares the average values for relatedness and inbreeding of individuals within each breed. R indicates the average level of relatedness between individuals within a breed. R is the percent of identical alleles two individuals share, indicating a greater level of similarity or relatedness. Mulefoot individuals showed the highest level of relatedness (0.69) while Landrace individuals had the lowest level of relatedness (0.03). These numbers indicate that, on average, two individuals selected at random from the Mulefoot breed are more likely to have some level of relatedness than two individuals selected from Landrace.
F is the inbreeding coefficient. This value indicates the level of homozygosity within an individual's genetic makeup. A higher value indicates more homozygosity, which is essentially a loss of genetic diversity within an individual. In the table, F is an average of inbreeding coefficients for all individuals within a breed. F is highest for heritage breeds and lower in commercial breeds. Ossabaw Island has the highest value (0.47) which is expected considering all Ossabaw Island hogs originate from the isolated herd on Ossabaw Island.
Table 2 is an MDS plot of the breeds in this study. This plot shows relationships between breeds. Breeds clustered more closely together (i.e. Landrace, Pietrain, and Large White) share a more similar genetic makeup than breeds plotted farther apart. Such a plot can be used to evaluate which breeds might possess unique traits as compared to commercial breeds. For example, outlying breeds such as Tamworth, Red Wattle and Duroc may carry unique genes not seen in breeds sharing similar genetic makeup.
In conclusion, this project indicates heritage breeds have many qualities worth preserving that are not seen in industry breeds and conservation efforts should continue. The results also show that loss of genetic diversity from high levels of inbreeding is a real threat to the conservation of heritage breeds.
Educational & Outreach Activities
2014 Midwest ASAS Meeting
This project was presented at the 2014 ASAS Midwest meeting in Des Moines, Iowa.
Genetic relationships and inbreeding coefficients of swine breeds. K. Roberts*, W. R. Lamberson, University of Missouri, Columbia.
2012 NCR-SARE Farmers Forum
This project was presented at the 2012 NCR-SARE Farmers Forum at the National Small Farm Trade Show and Conference in Columbia, MO. A video of this presentation can be viewed online through NCR-SARE's YouTube channel. Copy the following URL and paste it into your Internet browser to view it: https://youtu.be/b1kKYxaINNQ?list=PLQLK9r1ZBhhEGdL7uvTM8P0AzdBnksONr
Data is ready and can be made available to producers and the general public. Information from this project will help producers directly involved with the study by giving them detailed genetic information about their animals. It will also benefit other producers and those interested in preserving these breeds.
Details of this study were presented at the SARE Farmer's Forum in Columbia, Mo in 2012, at the University of Missouri Graduate Student Forum in 2013, and at the ASAS Midwest Conference in Des Moines, Iowa in March 2014.
Areas needing additional study
Additional research could be done by gathering genetic information from more breeds or more individuals within the breeds in this study. Creating a detailed map of all swine breeds could provide information benefiting both the small farmer and the industry.
Genes found only in heritage breeds could be of value to large scale operations, but without further research, such genes could be lost forever. Genes for disease resistance are of particular interest to farmers everywhere, but especially in large operations where swine live close together sharing food and water. In such operations, disease can spread quickly, and with increasing pressure from outside organizations to reduce or eliminate antibiotic use, having animals who are naturally disease resistant could prove vital to continued success of confined feeding operations.