 Welcome, Gisie Roberts. She's a graduate student with the University of Missouri. She's going to talk to you about a survey of relationships among rare breeds of swine. And I'll let you introduce yourself, at least briefly. Well, good morning. My name is Gisie Roberts. I am a graduate student here at the University of Missouri. Today, I'll be presenting part of my research, which was funded through a graduate student grant from SAIR. And we'll be looking at relationships among rare breeds of swine and also the importance of those relationships. So I'll start off with a little bit on breed diversity. Currently, there are over 70 different breeds of pigs around the world. However, in the US, with the advancement of vertical integration within the industry, the actual number of breeds that currently used on large scale production is very low. There's about seven that are very popular. And that's driven by consumer demand for a lean, uniform product. And so the Yorkshire or the Large White, Landrace, Chester White, Durrock, Berkshire, Hampshire, and Spot are the seven breeds currently used by most large scale operations. So the American Livestock Breed Conservancy recognizes that breed diversity is an important aspect of livestock production. And so they were founded to protect rare breeds of livestock and poultry. So they are working to protect approximately 180 different livestock and poultry breeds. So the main reason we're interested in breed diversity is to preserve genetic diversity. So industry breeds, since they're raised for a similar purpose, they share similar genetic makeup. They're bred to thrive in a specific environment, which is mainly a confined feeding operation. The less popular breeds and also the older heritage type breeds and some rare breeds that we're going to talk about are generally more genetically diverse. And therefore, they're able to tolerate varied living conditions, harsh environments. They are more disease-resistant and more self-sufficient, requiring less management in general. Also, many of these less popular breeds and older breeds have many unique traits that are not found in industry breeds. And so the ALBC lists seven critical swine breeds. They're defined as critical as having fewer than 200 registered each year in the US. And so from this list, we selected three that we felt we had the best ability to gain access to for DNA samples. So we selected the guinea hog, the Asaba Island, and the red wattle. And today, we'll actually be focusing on the research involving the guinea hog. So guinea hogs are characterized as small, hardy pigs. They're mature sizes around 100 pounds. They are excellent foragers. And they're also characterized by a high-fat content, which is one of the reasons maybe they're less popular because the industry looks for a lean pig today. They are good for subsistence farming due to their small size and their ability to thrive in harsh environments or where there's very rough forage. The Asaba Island hog comes from an isolated feral herd on Asaba Island. They are also a small, hardy pig, mature size about 100 pounds. And they are characterized by very large fat stores. And it is this reason that they're actually a good model for non-insolent, dependent diabetes in humans. Red wattle are actually very large pigs, 600 to 800 pounds. I believe I saw some out there. They're also very hardy. And they're characterized by a rapid growth rate in comparison to other rare breeds or heritage-type breeds. They have a lean, tender, flavorful meat and a mild temperament. So some challenges of conserving these breeds are that they aren't as popular and this is due to consumer demand for a lean, uniform product. And many of these breeds are characterized by a small carcass, high-fat content and a relatively slow growth rate. They also, the breed population is fairly small for most of these. So it's difficult for farmers to find the animals to purchase if they're wanting to raise them. Also, there aren't as many small pig farmers due to the more intensive management that pigs require as compared to, say, a small beef cattle farm. Also, the small herd size, so many of these farmers that are raising them have very small herds as compared to large confined feeding operations. So there can also be a lack of pedigree information on these pigs. Many of these are very old heritage-type breeds. When they were initially founded, there maybe wasn't a formal breed organization so we don't have a lot of that paperwork to trace their history back. And due to this lack of pedigree information, we get reduced genetic diversity because we're breeding very small populations. We get a lot of inbreeding. And so not knowing the relationships of the animals makes planning matings very difficult and ultimately reducing breed viability over time. So inbreeding is just defined as a high level of homozygosity, so there's more of the same kinds of alleles in the population. So this allows undesirable or lethal alleles to be expressed within a population and they can also become more concentrated within the population. And having more of similar alleles reduces genetic diversity and then ultimately in the long term reduces breed viability. So the objective of this research project is to determine relationships among rare breeds of pigs when the pedigree data is incomplete or unknown. To give farmers a better plan for mating in order to reduce inbreeding. And then ultimately we'd like to compare the rare breeds to each other and to industry breeds in order to see which are the more genetically diverse, which are more similar to industry breeds and how they all relate to each other. So the method of analysis consists of collecting DNA samples in the form of hair samples from each of the three breeds we've selected. We really only need 10 to 11 animals per breed to get a basic idea of the breed relations to each other. And then obviously if we wanted to look into more of how individuals are related to each other, well we'd need DNA samples from each of those individuals. And then the samples are then genotyped at gene seek and then when we get that data back we can then determine the relationships from the genotypes. So which is a quick little genetics review. So DNA is composed of four nucleotides, represented as A, T, G and C. And the sequence of these nucleotides and the DNA is important because the sequence is what codes for different genes. So in pigs we have 38 pairs of chromosomes. So there are two forms of the gene, one form of, so each chromosome has one form of the gene on it. And so those two forms could be the same or they could be different. So let's say we have a form A, which is allele A and a form B, allele B. And so then the animal's genotype is determined by which alleles it carries. So in this diagram we have, so each of these represents a chromosome. And so on this chromosome we have an allele for purple flowers and on this chromosome an allele for white flowers. And then we also get into dominance and recessive. So if purple flowers was dominant, then the flower would be purple. So in this case we have a heterozygous individual, right? Because it has one copy of each allele. Homozygous would mean that it has two forms of the same allele. So we would get A, A, or this would be purple, purple or white, white, or B, B. So therefore there are three possible genotypes. So how this relates to what we're doing is we're looking at single nucleotide polymorphisms. So the nucleotides again are the base pairs in the DNA. And so a SNP is what it's called is when a change occurs in a single nucleotide in the DNA. And so this then creates two different forms of an allele. So we'd have an A allele or a B allele. And in this picture you can see we have the sequence of DNA and then here we have a change. So this would be the SNP giving us one form of the allele that will have a T and the other form would have a C. So we would expect that related individuals would have a similar genetic makeup, meaning they would have more SNPs, more alleles in common. So we use the swine 60K SNP chip, which means that we're genotyping over 60,000 sites across three billion base pairs in the DNA. And so the genotypes come to us in a spreadsheet and they're coded as A for homozygous, H for heterozygous, and B for the other homozygous form. And so then with this in matrix form, we can, the SNP data can be used to measure levels of hetero or homozygosity in the animals. So this is an example of just a short, very small piece of a larger spreadsheet, right? So across the top, these are all different SNPs. And so this would extend for 60 plus thousand, right? It's a giant spreadsheet. And in this case we just have, these are all the animals though that we looked at. These are all guinea hogs. And so you can see in like that first column, they all have the same allele at that location. They're all homozygous for the B form of that gene. And then in the next column, we see that well all of them are alike, except for Samson, he's heterozygous. So you can see that just, I mean just looking at this, that he's less related to the rest of them than they are to each other. And then here we have Houdini, who's the odd one out with a heterozygous and the rest being homozygous. And then we have Houdini and Samson. In this case, both have a heterozygous genotype, whereas the rest are all homozygous. So this is what I'm looking at across all 60,000 SNPs, right? So through calculations, I don't go through each one individually like that would take forever. But we get a count of similar homozygous alleles, right? Because that's what we're interested in. We wanna know what the homozygosity is because that indicates a reduction in genetic diversity and indicates an increase in levels of inbreeding. So we're assuming that a higher number of similar alleles between two individuals would indicate a closer relationship. And so through some calculations, we can ultimately express this as a proportion or a percentage of shared alleles based on the total, out of the total number of SNPs. So we can see highlighted in yellow. So this is the diagonal of the matrix. And those numbers indicate the proportion of homozygosity within an individual animal. So like the first wort, Sidesau, he, or she maybe, has 74% homozygosity in the SNPs that we're looked at. So 74% of the alleles are homozygous. And then you can see that for Samson, he has a much lower level of homozygosity with only about half of his alleles being homozygous. So then if we look at some of these other numbers, so these all indicate, all of these numbers on the off diagonal indicate the percentage of similar alleles, homozygous alleles between individuals, right? So for the big old stiff bore and wort, Sidesau, they share 62% of their alleles are similar. Whereas if we look at Samson and wort, Sidesau, only just under 30%, just a pretty big difference. So based off this, our initial step was to just put them into families, kind of not very precise as far as the relationships between individuals, but just to get an idea of how these order out into some families. So we based this off of ones that had higher numbers of shared alleles. So again, this didn't give us precise levels of relatedness, but I could tell you that family two is much more closely related to each other than they are to the individuals in family four. So from this, just from those animals, we came up with five different families. But then the producer that we were working with, we wanted to be able to tell him, like, you know, Samson and family one actually is related to members of family four. Because from this, you might think that we have five completely unrelated families, and that's not necessarily the case. So in order to kind of calibrate our system and calculate more precise relationships, we took a sampling of pigs with known relationships. So I had full pedigrees on these pigs and they were actually industry breeds. And so we calculated both the relationships of the pigs based off of the pedigree and then also had them genotyped and calculated the relationships based off of what I showed you with the genotype, with the SNP data. And so from that, we were able to kind of create a formula and plug in the number of shared alleles from the guinea hogs into this formula and come up with more precise relationships. So in this case, now when we see a decimal place of like 0.5 or around 0.5, that indicates that the animals have a relationship, yes. Oh, thank you. Similar to a sibling or a parent offspring relationship. So here we can kind of see that we have fairly high levels of, you know, there are a lot of numbers over 0.5. So we have a lot, there's some levels of inbreeding, right, if we have animals that have a greater relationship than full siblings or parent offspring. But then we also see, we have some that aren't unrelated. Samson is unrelated to see more. So with some research, I was actually able to find a partial pedigree for these guinea hogs. So here's what I constructed from what I found and a little example, family tree. And just from this, you can already see there's some inbreeding present as DNC George and DNC Chunky are half siblings. So this is kind of an example of the calculations of the relationships based just off the pedigree using all the animals. And I've highlighted the animals that we actually have the SNP data for. So here in this table, we just did like the pedigree, the calculated relationship of the pedigree versus what we came up with with our SNP calculation. And in many cases, the actual relationship from the SNP is higher than what we expected based on the pedigree. And this is due to incomplete pedigrees, right? And our SNP information is very helpful for producers because based off a pedigree, we might think that Settie Lilly and the big boar are not very related at all. But then we look at our SNP relationship and it's 0.83. So you would, without expecting to, you would get a very high level of inbreeding within the offspring of that paring. So our future work will be to determine the relationships in the Asaba Island and the red waddle pigs and then how those relate to the guinea hogs and each other, comparing SNPs across breeds. And we'd also like to compare these to industry breeds to get a more complete picture of the origin of these breeds and see how maybe these heritage breeds way back have actually influenced industry breeds today. And then we'd like to provide this information to producers so that they can reduce possible matings that would increase inbreeding within the breed and others that are interested in the conservation of these breeds. So I'd like to thank Sarah for providing the funding for this research and the working with ALBC, Jeanette Merringer and Allison Martin and then my professor, Dr. Bill Lamberson, the producers who provided samples, Cheryl Fanning, Kevin Fahl and Robert Long and then some graduate students. And I'll take any questions. Yeah, Chester White, no, they're actually, yes, he's asking if the Tamworth, the Horford and the Chester White how they rank or considered rare breeds. Chester White is not, it's a very popular breed used extensively in the industry. Horford and Tamforth, I believe are considered rare. I don't know as far as like the level of rare, but yes, they're considered rare. Yes. How many years till the research is available or? Well, we've already had this information out to the producer that provided the samples. So he's been able to, yes, yeah, yes. Yes, we're actually, we're gonna work with extension and have the information available to anybody that wants it. I mean, if you wanted this, you could have it, but all we really have that's really ready is just these few animals from the guinea hogs. But yeah, if you wanted the information on the guinea hogs, you could, it would depend on money for it, or if you had money available to pay for the genotyping, then, I don't know, a few months you could have the information.