BY: Peter Hackett, MD
Q) What is genetic testing?
Genetic tests analyze segments of an animal’s DNA, usually genes. DNA comes in two types, nuclear DNA and mitochondrial DNA. Mitochondrial DNA consists of only a few genes, and only governs how cells convert nutrients into energy. When people talk about DNA they are almost always referring to nuclear DNA. Analysis of nuclear DNA (which is contained in the nucleus of every cell) is used to determine such things as parentage, ancestry, inbreeding, hybridization, and specific traits such as coat color, conformation, fiber type, milk and meat production, genetic defects or diseases, etc.
The entire nuclear DNA is called the genome.
Q) How is DNA used for testing? (See The Language of Genetics)
Like most animals, the yak has two copies of every gene, with one gene from each parent. These genes are carried in pairs of chromosomes, with one chromosome from each parent. The two copies of the paired genes are called alleles. These alleles can be exactly the same from each parent (homozygous alleles), or they can be different (heterozygous alleles). By analyzing these alleles in individuals and populations of animals, genetic testing very accurately identifies individuals, relationships, and traits such as those mentioned above. In fact, every animal has a unique genetic fingerprint based on the distribution and frequency of these alleles. In addition, these alleles can be used as “markers.” Within the alleles, a difference in a single base nucleotide, called a single nucleotide polymorphism (SNP) can be used as markers. For example, a certain SNP or allele of the gene determines coat color, and is therefore a “marker” for a certain coat color; another allele is a marker for absence of horns (polled animal). In addition, a SNP (or allele) that is found only in cattle is a marker for cattle DNA, while a SNP unique to yak is a marker for yak DNA.
Q) What are the steps in genetic testing?
DNA can be sourced from blood, hair follicles, saliva, tissue samples, etc.; any part of an animal. Tissue and blood samples consistently give the best results. After extracting the DNA, sequencing machines then determine the order (sequence) of the nucleotides in the DNA, allowing identification of DNA patterns, alleles, and SNPs specific to that animal. The determination of all DNA sequences in an individual is relatively slow and very costly, and has only been done on a few yaks: Queen Allante in North America, and, until only a couple of years ago one yak in China. However, recently the Chinese have sequenced a few dozen yaks. By comparing the DNA of sequenced yaks with known cattle DNA, which is very similar, Dr. Michael Heaton (USDA, Meat Animal Research Center) and Dr. Ted Kalbfleisch (University of Kentucky) discovered about 100 SNP markers that can be used to specifically study yak DNA, providing a practical option not requiring complete DNA sequencing. GeneSeek (Lincoln, Nebraska), a genetic testing company, has developed a test that uses these markers and provides useful information to yak breeders at a reasonable cost. USYAKS will be using GeneSeek for DNA testing.
Q) Why genetic testing? How will USYAKS use the results?
DNA testing has many purposes that are important to a breed association, such as parentage verification, degree of hybridization, genetic diversity, inbreeding, and various genetic traits. Many livestock breed associations use genetic testing in this way.
The USYAKS board, committees, and membership will decide how this test will be used.
Parentage. This new test using DNA sequencing is more accurate and reliable than older methods of parentage determination. This is critical for verifying pedigree accuracy, and in identifying parentage in multisire pasture matings.
Cattle introgression. In some ways, this is a test of species purity, since we can detect significant hybridization with cattle (Bos taurus or Bos indicus). One way is to check the DNA in the mitochondria, which is separate from the DNA on the 30 chromosomes, and is always passed down from the dam. Therefore, if the yak has a cattle maternal ancestor, the cattle mitochondria will be there, although the test cannot directly determine the timing of the original cattle maternal ancestor. However, if there has been recent introgression of cattle, then other cattle markers may be present, either sire or dam. For example, the original hybrid (referred to as an F1) will have half of the alleles from cattle and the other half from yak (assuming they are both “pure” animals). If an F1 female were bred back to a yak, the offspring (an F2) will have on average 1/4th of the alleles (28 of 110 tested alleles) from the cattle contribution and 3/4th of the markers from the yak contribution (82 of 110). If she were bred to a cattle bull, the markers would have the opposite proportions. And so on for 7/8th, 15/16th, etc. However, once the percentage of cattle or yak contribution is down to about 1-3%, this test may not be able to determine the exact contribution from the second species. That is, the test for cattle introgression is good to about the 5th or 6th cross, although the mitochondrial DNA will show a cattle dam ancestor. None of these tests are designed to detect bison introgression.
Genetic diversity. The North American (NA) yak population is extremely small, and likely represents only a tiny fraction of the complete yak genome. Most of the current NA yaks are believed to be descended from a small Canadian herd. Reduced genetic diversity can lead to reduced capability to withstand diseases and environmental conditions, and limit the potential of the species in many ways, such as in milk or meat production, fiber quality, etc. Genetic testing will enable USYAK to maintain what genetic diversity we currently have in our herd, and help determine the need for new germ plasm.
Inbreeding reduces genetic diversity, which can lead to multiple problems; such as yaks that are smaller, less robust, infertile, and with genetic diseases. The genetic test will allow us to determine a coefficient of inbreeding, or a heterozygosity index. Breeders can use this to manage their herds for optimal health. Some breed associations consider degree of inbreeding in their registration process.
With genetic testing, desirable traits can be identified and selected for breeding, and undesirable ones eliminated from breeding programs; for example, eliminating the cattle prion gene and its assumed susceptibility to prion disease (mad cow disease).
Q What are the goals of genetic testing?
1. To verify parentage, and to assist with registration of yaks.
2. To survey the genetics of our North American herd in order to understand the makeup of our animals. As a species association, we need to know the genome, genetic diversity, and inbreeding of our animals in order to preserve and protect the yak genome.
3. To prevent dilution of yak alleles by identifying those animals with a high percentage of introgression from other species.
4. To assist breeders with managing inbreeding.
5. To assist buyers by testing genetic characteristics of animals before purchase.
6. To promote the science of yak genetics, husbandry, and breeding.
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