Genomics in Dairy Cattle

By: Carrie Urbanek

Overview

"Typically when we think about what traits are inherited from a dam or sire we believe it is all equal...offspring is expected to inherit approximately 50% from each parent, 25% from each grandparent and 12.5% from each great-grandparent" (Cowan 17). When observing an individual, such as a dairy cow, this isn't always the case. Genomics is allowing for this observation to better genetics in the Dairy Industry (Cowan 18).

What is Genomics?

Genotyping gives a picture of the dairy cow's genetic makeup (Weigel 3). Genomics is the study of a genome sequence in an animal in this, particular, case the dairy cow. Dictionary.com defines a genome as "...the complete genetic material of an organism, which is contained in the chromosomes. It is the full DNA sequence of the organism and is usually stated in base pairs"(Dictionary.com). In each dairy animal, there is 30 billion pairs of chromosomes, with 3 billion bases coming from each parent. The traits of animals are located in chromosomes. By studying DNA sequence patterns in dairy cattle, scientists have located health traits in the DNA (Weeks 7). Health traits include the immune system and the animal's resistance to disease. Genomics, therefore, takes the DNA information of the animal for the genetic value of the given animal (Hayes 2).

Methods

An Illumina BovineSNP50 Genotyping Chip is used to read the DNA of the animal. The chip takes a "picture" of the cow's DNA. People can see what traits the animal inherited from each parent. Genomic testing is based on the DNA sequence, to identify patterns in over 50,000 locations along the thirty pairs of chromosomes. These 50,000 locations can differentiate between two different animals. Single Nucleotide Polymorphisms, or SNPs, are found on this "picture", that the Genotyping Chip takes. SNPs are a variation at a single base pair in the chromosome.
The single base changes are represented by the letters A, T, C and G. When a genome copies, or new cells are made, sometimes a single base pair gets changed, left out, or substituted. This creates SNPs. For example, a sequence of ATC could change to GTC, in the chromosome, in just one generation. Therefore, genotyping is vitle to finding these genetic variations between generations (Weigel 1).

Cost/Economic Impact

Every animal that is genotyped using the Genotyping Chip, will cost about $225. Genomics in dairy cattle will have a larger economic impact on people, more so than they realize. The SNPs are being studied to find genotype-phenotype relations for simple and complex traits that could, potentially, have a huge impact on the future. According to Animal Frontiers, "The world population could reach 9 billion people by 2030. Meeting the growing food need using fewer resources is, therefore, one of the greatest challenges that contemporary agriculture is facing. It is critical to apply technical and scientific advancements systematically....of animal husbandry to fill the coming productivity gaps" (Eggen 3). By finding these genotype complex traits, people are able to manipulate genes of a dairy animal to suit them for the growing population. For example, many dairy breeds have been bred to insure they produce more milk. Over the years, dairy cattle have a higher milk production because dairy producers figured out the best method for their animals enabling them to produce more (Eggen 4).

History/Evolution

Genomics is a relatively new practice in the Dairy Industry. Official genomic evaluations were first introduced in the United States in 2009. Before the 1930's, there wasn't a unified or specific way to evaluate dairy cattle, thus, not much genetic progress was made. Since then, traits have been introduced, along with, new national programs, allowing for improvement in the dairy cow (Cowan 15). Since the 1930's, selective breeding came into play. Selective breeding allowed dairy producers to pick the best bulls to breed to their cows, for the best predicted outcome. This method tremendously improved genetics, but only to an extent. The problem with selective breeding is, breeders aren't exactly sure which genes are increasing, or decreasing, in population, in the genome sequence. This complication/problem led people to the idea of seeing and analyzing the genes in many different generations (Cowan 16). Many dairy producers, now, estimate the economic value of genotyping dairy animals to be, at least, $100 million in a little over a decade (Hayes 10).

Advantages

Genotyping dairy animals lead to many advantages for the industry. AI companies had to purchase bulls at a young age, based off of ancestral records. The bulls also had to be used, and sire approximately 100 daughters before they could have a reliable genetic source. This could take many years, and by the time the bull was old enough to be reliable, he could be 7 or 8 years old. Now with genomics, bulls, and even cows, are able to be genotyped at a very young age. Therefore, the generation interval is lessened, with a better chance of genetically superior animals. Genotyping, also, can lead to finding animals with recessive defects such as Limber Leg and CVM. CVM calves will be aborted or dead. By using genomics, genetics will continue to improve, which in turn, will improve people's idea of genetic superiority (Cowan 27).

10,000 Holstein Cow Genome Project

Australian dairy producers are using genomics for DNA calculations in value. "The project will substantially improve how well the DNA markers predict the value of bull and cow genetics for the 40 key dairy traits including;milk yield, protein, and resistance to mastitis" (Hayes 2). Dairy Producers, from Australia, selected 10,000 Holstein cows and collected DNA tail hair samples, from each. The cows used were required to have many ancestral records. The 10,000 cows aligned with the 50,000 DNA markers. By looking at these traits, dairy producers were able to compare the reliability. In Australia, following this project, farmers, and AI companies are beginning to use genomics in their herds (Hayes 3).

Works Cited

· "10000 Holstein Cow Genome Project." Agriculture. Department of Primary Industries, n.d. Web. 16 Oct. 2012. <http://www.dpi.vic.gov.au/agriculture/dairy/dairy-science-and-research/holstein-cow-genomes-project>.

· Cash Cow. Digital image. Getty Images, 2012. Web. 16 Oct. 2012. <http://www.photos.com/images-photo/cash-cow>.

· Collins, comp. "Genome." Def. 1. Dictionary.com. Dictionary.com, 2012. Web. 15 Oct. 2012. <http://dictionary.reference.com/browse/genome?s=t>.

· Cow Thumbs Up. Digital image. Istock Photos. Istock, n.d. Web. 16 Oct. 2012. <http://www.istockphoto.com/stock-illustration-21440369-cow-thumbs-up.php>.

· Cowan, Michael, and Kent Weigel. "The Genomics Revolution Is Upon Us." Genomics, Genomic Selection, Dairy Bull Genomics, Beef Bull Genomics, Bovine Genomics, Genomic Scanning, Benefit of Genomics, Future of Genomics. Accelerated Genetics, n.d. Web. 16 Oct. 2012. <http://www.accelgen.com/Genomics.aspx>.

· DNA Cow. Digital image. Istock Photos. Istock, n.d. Web. 16 Oct. 2012. <http://www.istockphoto.com/stock-photo-21223779-holstein-cow.php>.

· Eggen, Andre. "The Development and Application of Genomic Selection as a New Breeding Paradigm." The Development and Application of Genomic Selection as a New Breeding Paradigm. American Society of Animal Science, 2012. Web. 15 Oct. 2012. <http://animalfrontiers.org/content/2/1/10.full>.

· Eggen, Andre. "The Development and Application of Genomic Selection as a New Breeding Paradigm." The Development and Application of Genomic Selection as a New Breeding Paradigm. American Society of Animal Science, 2012. Web. 15 Oct. 2012. <http://animalfrontiers.org/content/2/1/10.full>.

· "Genetic Visions, Inc.®." Genetic Visions, Inc., Tests DNA from Cattle to Identify Genes Influencing Production Traits, Hair Color and Animal Health and Viability. Alterations in the Composition of DNA Provide "genetic Markers". A Genetic Marker Associated with a Trait of Interest Can Be Used in Cattle Breeding Programs as a Selection Tool. N.p., 2010. Web. 16 Oct. 2012. <http://www.geneticvisions.net/>.

· Holstein Cows. Digital image. Hazard Cow Photos. N.p., n.d. Web. 16 Oct. 2012. <http://www.nctc.net/hazard/photo/cows/>.

· Illumina BeadChip. Digital image. Kreatech. N.p., n.d. Web. 16 Oct. 2012. <http://www.kreatech.com/products/universal-linkage-systemtm-labeling-kits/gene-expression/illumina.html>.

· Weeks, W. A. "Genomics." Genomics. AAa, n.d. Web. 16 Oct. 2012. <http://aaa.senscia.com/contentPage.cfm?ID=539>.

· Weigel, Kent. "Genomic Selection in Dairy Cattle-Explanation and Impact." N.p., n.d. Web. 16 Oct. 2012. <http://dysci.wisc.edu/events/dairyday08/Weigel%20Genomics.pdf>.

· Weigel, Kent. "Genomics - A Practical Explanation." Genex Cooperative Inc - Genomics - A Practical Explanation. Genex, n.d. Web. 15 Oct. 2012. <http://genex.crinet.com/page2348/Genomics1>.