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DNA provides the set of instructions that a cow needs in order to grow, produce milk, breed back, resist diseases, etc. Some parts of the DNA define what protein is made – an example of this is the genes that control red or black coat color. Other sections of DNA tell genes when to turn on or turn off.
Genes are the basic unit of inheritance and comprise DNA. For a small handful of traits like horned/polled and coat color (red/black), one or two genes determine the animal’s phenotype or performance. For most traits like production, reproduction, conformation, longevity, health, etc., many, many genes are involved and these genes interact with each other and with the environment in very complex ways to yield animals’ phenotypes.
SNP or Single Nucleotide Polymorphisms are base pairs sites in DNA where genotyping has identified that animals can differ. When a base pair differs for animals, it presents one of three scenarios: 1) there is no impact or association with performance differences, 2) there is an association with performance differences but this difference does not hold up over time with subsequent generations, and 3) there is an association with performance differences that does hold up across generations. Most base pair differences result in little or no perceptible difference in performance because in nature, large differences typically are undesirable for animals.
Accurate genetic evaluations require a blending of different pieces of information to compute a bull’s proof. In traditional evaluations, we combine pedigree contributions plus information from daughters. Genomic enhanced evaluations incorporate the same principles as traditional evaluations and so also require blending of different pieces of information to compute proofs. In the case of genomic enhanced evaluations, the pieces include genomic (DNA-based) information plus any remaining pedigree contributions plus information from daughters.
Chromosomes comprise two strands of the thread-like structure known as DNA. The
two individual strands of DNA are held together by base pair molecules of which there are four different types. For cattle, their 30 different chromosome pairs contain roughly 3 billion DNA base pairs. Technology has enabled us to obtain DNA from a blood, hair, tissue, or semen sample and from this DNA determine which of the four different bases are located at each of approximately 40,000 base pair sites. This process is referred to as genotyping. We would like to know the sequence of bases at each and every one of the 3 billion base pair sites because differences in bases found at these sites may influence characteristics of the animal, but determining all 3 billion base pairs is too costly today so instead we are looking at this subset of bases.
By genotyping a large number of sires which have highly accurate and reliable proofs, we can now begin to look for associations between the genotypes and the proofs of these bulls. These associations between progeny test proofs and sires’ genotypes at each of the 40,000 base pair sites are used to define the genomic information which contributes to bulls’ genomic proofs.
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