Research »   Genomics

Genomics

Genomics studies the structure, function, evolution and mapping of DNA and genomes. It deals with the complete set of genes and genetic material found in a cell or organism.

Genomic technologies draw both producer interest and research investment in the beef industry. Seedstock selection is one common application, but genomics has found widespread adoption in forage and feed grain breeding, diagnostic tests, vaccine development, source attribution for food safety recalls and other uses.


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Genetics 101

DNA is the genetic code that determines how an organism grows, what it looks like, and how it performs in a specific environment. Found in all living things, DNA gets passed from one generation to the next, allowing these organisms to maintain or improve their ability to survive and thrive.

DNA is a long chain, with each link of the chain containing a pair of four small molecules, known as base pairs. These molecules are abbreviated by the letters A, T, G, and C. This long chain is then coiled tightly into chromosomes. All cells in an organism contain a complete copy of that organism’s full genetic code.

Each cell has specialized machinery that reads the DNA code three letters at a time. These three-letter codes instruct the cellular machinery to start reading at a specific point. From that point, the base pairs code for specific amino acids, then finally a three-letter code instructs the cellular machinery to stop reading.

This segment - from start to stop - is referred to as a gene. The chain of amino acids the gene codes for is a protein. Some genes code for specific proteins in the body, such as hormones, enzymes, plant proteins and muscle proteins. Other genes influence when specific genes are turned on or off, or how actively they are expressed.

“Mutations” represent a slight change in the DNA sequence. They may result in early “stop reading” codes, changes where additional amino acids are inserted, no proteins are produced, or other adaptations.

These mutations may cause changes to physical traits, such as specific mutations in chromosome one that results in the polled gene in cattle. Mutations to the leptin gene, located on chromosome four, result in differences in backfat depth, lean yield, and days to market.

Other changes are called “silent mutations.” These occur when a change in the DNA sequence has no effect on the amino acids being produced. With 64 three-letter codes available and only 20 amino acids, each amino acid has more than one code.

Even though an animal’s genetics are determined at conception, many environmental factors can modify how genes are expressed.  For example, an animal may have a very high genetic potential for weight gain, but if there is a drought or feed is limited, the animal will obviously be unable to fulfill that genetic potential.

Click below to download our genomics fact sheet:

bovinnovation genomics fact sheet

The use of genomic tests in cattle

Most current genomic tests for cattle use SNP (Single Nucleotide Polymorphism) technology. These tests take advantages of mutations in a DNA sequence to identify the unique genetic makeup of the animal.

Although other methods are available to perform most genetic tests, SNP testing provides low genotype error rates, easy automation and the ability to easily standardize SNP tests across labs.

A SNP represents a single base pair mutation found at a specific location. Although SNP testing looks for specific changes in specific base pairs, the SNPs may not be tied to specific genes. Instead, SNP testing looks at areas that may be associated with, or located close to, a segment of DNA that codes for a specific protein.

SNP tests are easy to do from a producer standpoint as they can use a blood, tissue or tail hair sample.  SNP technology can be used for a variety of objectives, including: parentage determination; trait assessment; genetic abnormality testing; increasing accuracy of EPDs; and to sort cattle into management groups

DNA parentage testing

DNA parentage testing has been used in the purebred industry for many years and is now being adopted by commercial cow-calf producers as prices for the tests drop.

Producers might choose to adopt DNA parentage testing on their operations for many reasons. They may want to identify a ‘problem’ bull on their operation, such as a bull that sires high birth weight calves or low weaning weight calves. It may help identify superior sires - bulls siring high weaning weight calves or calves with a high ADG - to identify sires that are producing calves with specific traits, or sires that are not breeding many cows.

Parentage verification SNP tests take advantage of the fact that half a calf’s DNA is inherited from the sire and half from the dam. The tests look at specific SNPs on both the calf and possible sires. A process of elimination then determines the sire - if the calf carries SNPs not carried by a particular bull, that bull can be excluded as a potential sire. Therefore, it’s important to submit samples from all possible sires.

Trait assessment

 An animal that has inherited the same version of a particular gene from each parent is called homozygous.  If an animal receives a different form of the gene from each parent it’s called heterozygous. Heterozygous animals can pass on either form of the gene to their offspring,

SNP tests can be used to determine if animals are “carriers” for a specific trait. Recessive traits require that the offspring inherit a copy of the gene from each parent before it will display the recessive trait. Otherwise, the dominant copy from one parent (e.g. polled) will mask the recessive copy from the other parent. SNP tests can help to unmask carriers for some traits.

One example of a simply inherited dominant/recessive trait is horned and polled. Horned is the recessive form of the gene, so even if an animal doesn’t have horns, it may still carry the horned gene, and could pass the horned gene to its calves. If two carriers are bred to each other, there’s a one-in-four chance their offspring will express the recessive trait even though neither of the heterozygous parents do. Here’s an example showing what happens when mating a cow and bull that are both heterozygous polled:

Coat colour is another trait with a DNA test available. It’s most commonly used in black cattle to determine if they’re a “true black” or if they’re carrying the red gene.

Past research funded by the National Check-off validated that a mutation in the calpastatin gene was associated with differences in beef tenderness.

Genetic abnormality testing

Abnormalities in the skeleton, body formation, or the way the body functions can be present at birth., occasionally occur in beef cattle. They can be caused by the environment (e.g. crooked calf disease caused by lupine consumption), genetics, or both. If environment plays a factor, adjustments can be made to prevent the disease in the future. If the disease has a genetic component to it then genetic testing may be required to correct the problem.

Some examples of genetic abnormalities are: Condrodysplasia (dwarfism), Hypotrichosis (hairlessness), Arthrogryposis Multiplex (Curly Calf Syndrome) and Syndactyly (mulefoot).

Genetic abnormalities are often breed specific, only occur in a few breeds or only occur in specific bloodlines. Some breed associations are working to reduce the frequency of genetic defects within their breeds by using genetic testing to identify carriers.  Most genetic abnormalities follow a simple dominant/recessive inheritance pattern (like polled and horned in the example above), so you can avoid them by not mating two carriers.

Genetic abnormalities can result in abortion, or death shortly after birth.. If you suspect that you are seeing a genetic abnormality in your herd, talk your veterinarian to determine what’s causing the disease. If it’s genetic, test your bulls for carrier status. Avoid buying bulls that are carriers for the disease, or crossbreed to another breed that doesn’t have the disease. 

Genetic tests to sort animals into management groups

Genetic tests can be used to manage groups of cattle. Tests are available that give producers a better idea of how animals will perform in specific situations. These tests enable producers to sort animals accordingly. 

The leptin gene codes for a hormone that regulates appetite and fat deposition. Cattle have a base pair code of CC, TC or TT. The TT calves will typically deposit backfat faster and require fewer days on feed than TC or CC calves. By leptin testing, feedlot operators can sort calves into more uniform groups to feed and sell.

Genomically-Enhanced EPDs

Genomic tests can be used to increase the accuracy of EPDs. This does not guarantee that the EPD gets “better” - it just means it’s a more reliable selection tool.

Typically, as an animal has more offspring the accuracy of the EPD increases. A genomically-enhanced EPD allows that increase in accuracy to be seen before any progeny are produced.

When buying young bulls, this helps commercial producers have a better idea of how a bull will perform and what his offspring will look like. Genomically-enhancing the EPDs does not change how the EPD can be used, it just increases its accuracy. 

Cautions regarding the use of genomics

Genomics works very well for parentage testing, controlling inbreeding, and recessive allele testing for many genetic abnormalities. However, caution must be exercised when using genomics for selection or management. While genomics works very reliably in cases where the SNP is known to occur within an actual gene, in many cases the SNP may only located somewhere near the gene. In that case, how accurate GE-EPDs or MBVs are will depend on how closely related the animals tested are to the population in which the prediction equations used to generate the GE-EPDs or MBVs were developed.  GE-EPD/MBV prediction equations using SNPs that were discovered in one bloodline may not work as reliably in another, and GE-EPD/MPV prediction equations developed using SNPs that were discovered in one breed are unlikely to produce reliable results in a different breed.

Genomics in animal health

Diagnostic tests

Numerous diagnostic tests use genomics. Advancements in genomics have improved the ability to detect and understand many animal diseases.

Because researchers can now map the genome of a specific virus or bacteria, detecting them in a host animal becomes easier. Genomics has helped develop a test for trichomoniasis (trich) that can detect pathogenic trichominads and ignore harmless ones that may also be present.

Genomic tests have also been developed for bovine genital campylobacteriosis (vibrio). Traditional vibrio tests relied on sample cultures that took much longer. The organism also often died during sample shipment, resulting in a false negative culture test result. Using genomic technologies, more rapid, accurate and cost-effective tests are now available.

Researchers also use genomic technologies to improve current diagnostic tests. Research funded by the National Check-off is developing a single, rapid, cost-effective test that can detect a range of respiratory and enteric diseases. 

Vaccine development

Genomics plays a major role in developing more effective vaccines, discovering new infectious agents, and providing a better understanding of known vaccines and pathogens.

Vaccines encourage a cow’s immune system to develop antibodies against specific disease organisms. An important part of vaccine development is finding a unique protein on the bacteria or virus.

Genomics helps identify the best proteins to stimulate immunity and makes it much easier to multiply and produce these proteins in large quantities. This increases the effectiveness of the vaccine by making it more specific, with fewer side effects. It also decreases the cost of producing the vaccine.

Plant breeding

Plant breeders have been using genomics for years to help select valuable traits. Understanding a plant’s genetic sequence allows plant breeders to combine genomic tools with traditional breeding methods. That helps shorten the time it takes to develop new varieties and makes it easier to select for complex traits.

The use of genomic technology allows plant breeders to develop varieties with characteristics that are more robust, disease resistant, higher yielding, cold tolerant, winter hardy and so forth. Genomics allows plant breeders to identify superior lines more quickly and accurately, make more strategic selection and breeding decisions, resulting in more rapid genetic progress.

Current research funded by the National Check-off is using genomics as a tool to develop improved tame and native forages.

Food safety

Genomics has made major advancements in the area of traceability. In the event of a food safety recall, genetic tests can be used to link bacterial DNA to the originating facility and identify where along the production chain the contamination occurred.

Compared to bacterial culture, genomic testing increases both the accuracy and the speed in which food safety outbreaks can be traced.

To learn more on this topic, see the fact sheets posted on the right side of this page. External resources related to this topic are listed below.

Learn More

Designer Genes
Reynold Bergen
http://www.beefresearch.ca/blog/designer-genes/#more-3989 

Current state genomic selection tools for beef cattle
University of Nebraska-Lincoln
http://beef.unl.edu/cattleproduction/genomicselectiontools 

Genetics of Beef Cattle: Moving to the genomics era
Matt Spangler, Assistant Professor, Animal Science, University of Nebraska-Lincoln
http://www.gbcbiotech.com/bovinos/aplicaciones/general/Genomics%20of%20Beef%20Cattle%20Moving%20%20to%20the%20genomics%20era.pdf 

Genetic abnormalities in beef cattle
Ontario ministry of agriculture, food and rural affairs
http://www.omafra.gov.on.ca/english/livestock/beef/facts/93-007.htm

What do Genomic-enhanced EPDs Contribute?
The Beef Magazine
http://beefmagazine.com/genetics/0901-genomic-enhanced-epds

Delta Genomics SNP Project
Delta Genomics
https://www.youtube.com/watch?v=ONzWVIClIt0

Beef sire selection recommendations 
eBeef
http://articles.extension.org/pages/72946/beef-sire-selection-recommendations 

DNA sample collection 
eBeef
http://articles.extension.org/pages/73198/dna-sample-collection 

EPD basics and Definitions 
eBeef
http://articles.extension.org/pages/73314/epd-basics-and-definitions

The random shuffle of Genes: Putting the E in EPD
eBeef
http://articles.extension.org/pages/72650/the-random-shuffle-of-genes:-putting-the-e-in-epd 

Genetic Defects
eBeef
http://articles.extension.org/pages/72661/genetic-defects 

Genetic practices to improve beef cattle reproduction 
eBeef
http://articles.extension.org/pages/72667/genetic-practices-to-improve-beef-cattle-reproduction 

How DNA testing will affect the accuracy of EPD information 
eBeef
http://articles.extension.org/pages/72663/how-dna-testing-will-affect-the-accuracy-of-epd-information 

Value of collecting phenotypes
eBeef
http://articles.extension.org/pages/72640/value-of-collecting-phenotypes 

References

Berry D.R., Farcia J.F., Garrick D.J. 2016. Development and implementation of genomic predictions in beef cattle. Animal Frontiers. 6:1 32-38

Van Eenennaam A.L. 2015. How might DNA-based information generate value in the beef cattle sector? UC Davies extension.

Perez-de-Castro A.M., Vilanova S., Canizares J., Pascual L., Blanca J.M., Diez M.J., Prohens J., Pic. 2012. Application of genomic tools in plant breeding. Curr Genomics. 13:3 179-195

Raszek M.M., Guan L.L., Plastow G.S. 2016. Use of genomic tools to improve cattle health in the context of infectious diseases. Front. Genet. 07

Bergen R. 2012. Getting a grip on genomics. Canadian Cattlemen’s Magazine. July 2012 edition

Bergen R. 2012. More on genomics. Canadian Cattlemen’s Magazine. September 2012 edition 

 

 

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This topic was last revised on January 12, 2017 at 08:01 AM.

Fact Sheets

Canadian Cattlemen's Association Verified Beef Production Canada Beef
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