Red Charlie Test Now Publicly Available

GeneSeek launched the new red coat variant test, called Red Charlie.  Breeders interested in coat color testing on a red charlie suspect animal  need to order both the regular coat color test and the red charlie test to have a complete picture of the animal’s genotype for coat color.

The Red Charlie test will cost $7.00 in addition to the regular coat color test ($20.00).

Breeders can order Red Charlie through our usual DNA ordering process, either email the ASA at dna@simmgene.com or call 406-587-4531, ext. 3.

To read more about Red Charlie click here or read these FAQs.

Advertisements

Red Charlie – FAQs

In order to understand Red Charlie, a new red coat variant, breeders must first understand the inheritance and DNA testing for the main coat color gene. The following is a brief summary.

Coat Color inheritance: The main gene that controls the base coat color in cattle is called the extension gene. Historically, it was believed there were three alleles (variations) for this gene in cattle: black (ED), wild type (E+), or red (e). Black coat color is a dominant trait and will mask the presence of other coat color alleles. The wild type allele is dominant to red. Each animal will have two copies of the extension gene (one from each parent) and it can be any combination of the three alleles.

Since Black is dominant, a black animal could have three different pairing of the coat color alleles. A black animal can be homozygous black (ED/ED) or heterozygous black (ED/E+ or ED/e). An animal that is truly homozygous black should always pass a black gene to the progeny. Therefore, an animal that tests homozygous black should always have black progeny. Heterozygous black animals can pass on the wild type or red allele to the next generation and have wild type or red calves. Conversely, as red is a recessive trait, red animals are typically homozygous for the e allele (e/e) and would always pass the red allele to their calves. Sometimes red animals can carry the wild type allele so the example is a little over simplified.

DNA testing for coat color: The DNA marker for the red allele is a mutation in the extension gene that makes the gene unable to make a protein product. Without this protein, an animal will have a red coat. The DNA marker associated with the black allele makes the protein always active and the animal then has a black coat color. Wild type animals have the ability to either have black or red hair and are therefore can be affected by other genes for different coat color patterning (tiger striping or darker hair on the extremities).

There are an infinite number of possibilities that could result in the loss of function of the coat color gene, resulting in a new red coat variant. Red Charlie is a prime example.

FAQs

Q : What is Red Charlie?
A : Red Charlie is a newly discovered red coat color variant (allele). It works exactly like the existing red coat color allele except it wasn’t being detected by the DNA test for Coat Color. Like the red allele, Red Charlie causes a loss of function of the extension gene. Until recently, we did not know about this mutation so existing coat color test was unable to detect the Red Charlie mutation. Therefore, some animals were testing homozygous black but having red progeny.

Q : What does it mean if my animal is a Red Charlie carrier?
A : Being a Red Charlie carrier is equivalent to being a red carrier. Red Charlie carrier should be viewed just like an animal that tests heterozygous black (carries the red allele).

Q : How can I tell if an animal is a potential Red Charlie carrier?
A : Log-in to Herdbook Services, go to Data Search, Animal Search, enter in the ASA registration number, hit search. Click on TraitTrac.  Look under Genetic Traits, Red Charlie is abbreviated as RC.  Verify your animal’s status by using the legend key on the left and look to see if there are Red Charlie test results or carriers in the lineage.

Q : How can I order Red Charlie testing?
A : As of 5/12, Red Charlie is not available as a commercial test. However, GeneSeek is working on the final stages of making Red Charlie a publicly available test. Once available, tests can be ordered through the usual DNA test procedure – either call the office at 406-587-4531 or email the DNA department at DNA@simmgene.com.

Q : Will ASA be able to use the sample that was submitted for coat color testing to run Red Charlie?
A : Yes, the ASA can use any viable DNA sample to test for Red Charlie. Please contact ASA by emailing dna@simmgene.com or calling our office and providing us with the ASA registration number of the animal you would like to test. We will have the lab pull the sample and see if there is enough sample left to run the RC test.

Q : Does this mean all coat color testing done up to now is wrong?
A : No, animals without Red Charlie carriers in the lineage are likely okay (although this is not a guarantee).

Q : Should I be worried about the validity of my animals homozygous black coat color results?
A : Using TraitTrac will help identify animals that have the possibility of carrying Red Charlie. If an animal has coat color test results already and has a carrier in the lineage for Red Charlie, then there is a possibility that this animal carries Red Charlie as well. If there is no indication of Red Charlie in the TraitTrac system then the odds are low that the animal would carry this allele. However, there may be carriers that the ASA doesn’t know about so no known risk in the pedigree is not a guarantee of being free of Red Charlie.

Q : Is Red Charlie the same as Wild Type?
A : No, Red Charlie has nothing to do with the wild type coat color allele.

Q : Are red or wild type coat color test results affected by Red Charlie?
A : No, Red Charlie is linked only to the Black coat color allele so will only change black coat color test results.

Q : How do we know the Red Charlie coat color variant isn’t present in other pedigrees?
A : It isn’t likely to show up in other pedigrees but this is not a certainty.

Q : Will this affect animals that are tested heterozygous?
A : Animals that tested heterozygous black should be unaffected by Red Charlie. Red Charlie is only linked to the black allele and makes that black allele function like a red allele. So, if an animal tested heterozygous black and appears black, then this animals black allele must be functional and therefore does not carry the Red Charlie variant.

Q : What are the implications of breeding with a Red Charlie Carrier?
A : A Red Charlie carrier has a 50% chance of passing the Red Charlie allele to its progeny and a 50% chance of passing the black allele. See the punnett square below for a more detailed explanation. A Red Charlie carrier has a 50% chance of passing the Red Charlie allele to its progeny and a 50% chance of passing the black allele. See the punnett square below for a more detailed explanation.

Punnett Square showing the progeny outcomes when mating two heterozygous black animals

Screenshot from 2016-05-16 08:54:48e can represent either the traditional red coat color variant or the Red Charlie variant

  • ¼ of the calves will be homozygous black: These will appear black and always have black calves.
  • ½ of the calves will be heterozygous black: These will appear black and half of their calves will inherit the black allele.
  • ¼ of the calves will be homozygous red: These will appear red and always pass on the red allele.

To read more about Red Charlie and to view a list of tested Red Charlie carriers as of 5/12/16, click here.

If you have additional questions not answered above, please email dna@simmgene.com or call our office at 406.587.4531 and push number 3 for assistance.

 

 

DNA – What Testing Does ASA Offer and Which One Should You Request?

In this day and age with so many different DNA tests being offered, trying to figure out which one you should use or actually need on any given animal can be quite challenging. The following is an attempt to serve as an explanation of the various tests being offered and also suggestions for which groups of animals might best benefit from each test.

Genomic Tests – Genomic tests give a more accurate picture of what DNA markers an offspring inherited from its parents in the form of single nucleotide polymorphisms(SNPs). These DNA markers are associated with the genetic control of various traits.
GeneSeek Genomic Profiler HD(better known as GGP-HD) has up to 150,000 genetic markers and provides more extensive data than any other profile currently offered.  ASA REQUIRES all AI sires and Donor Dams to have a GGP-HD profile(including other breed sire and dams or commercial females). Additional add-on content is available, see DNA pricing sheet for more information.
GeneSeek Genomic Profiler LD(better known as GGP-LD) has around 47,000 genetic markers and provides you with an affordable option that offers high-accuracy genomic prediction. ASA recommends GGP-LD testing for herd sires and replacement heifers. Additional add-on content is available, see DNA pricing sheet for more information.
The GGP-HD and GGP-LD tests also include parent verification(if the parent animals have DNA on file for comparison) and diluter results.
GeneSeek Genomic Profiler uLD(better known as GGP-uLD) has around 9,000 genetic markers and provides you with an affordable option that offers high-accuracy genomic prediction. ASA recommends GGP-uLD testing for replacement heifers. Additional add-on content is NOT available on the uLD. If additional trait testing is needed on the animal, we recommend either the GGP-HD or GGP-LD.
The GGP-uLD test does include parent verification(if the parent animals have DNA on file for comparison).
The results of GGP-HD, GGP-LD and GGP-uLD testing are blended in to an animal’s EPDs, thus increasing the accuracy and resulting in the equivalent of an estimated 5-10 progeny already being recorded to that animal.  As you can imagine, genomic testing can have a large impact on maximizing your herd’s genetic potential, especially with regards to replacement heifers since most females would not achieve that level of accuracy until they are 8-10 years of age.
Genomic tests DO NOT automatically include trait testing such as horned/polled or coat color results.  If additional trait testing is desired it must be requested when you order the kit in addition to the genomic test and add-on pricing will apply.
Parent Verification(PV) is the minimum testing requirement for purchased embryos.  This testing simply confirms whether the animal qualifies or does not qualify to the sire/dam. Read more about parentage testing and how it works by clicking here.
Additional Trait Testing
Coat Color(CC) testing is utilized to confirm whether the animal is homozygous or heterozygous black.  A result confirming a homozygous black animal means these animal’s should always produce black calves when mated to non-diluted red or black cows. A heterozygous black result means these animal’s are black but carry one red gene.  When mated to non-diluted red cows, you can expect 50% of the calves to be black and 50% red. For more information on coat color, click here.
Red Charlie(RC) is a red coat color variant carried in certain pedigree lineages. To view whether your animal is a potential carrier of RC, check out the individual animal’s TraitTrac display.  To view more information on Red Charlie, click here.
Horned/Polled(HP) testing is utilized to confirm whether the animal is homozygous or heterozygous polled. A result confirming a homozygous polled animal means this animal’s calves will all be smooth polled.  A result confirming heterozygous polled means the animal has one horned gene and may have horned progeny if mated with another animal carrying a horn gene. There is no DNA test available for scurrs at present so these results do not include the scurr gene.  For more information on horned/polled, click here.
Diluter(DL) testing is used to see if an animal is a carrier of the dilution gene.  For more information on dilution, click here to be directed over to the Science Community Blog.
Oculocutaneous Hypopigmentation(OH) is a cosmetic genetic trait resulting in cattle having uniformly light colored irises coupled with an unusual chocolate coat color.  OH is a simple recessive trait meaning an animal must inherit two copies of the mutation to display the trait. For more information on OH, click here.
Genetic Defect TestingREQUIRED on any Sire or Donor Dam that are listed as having a  population risk(PR), documented carrier in the lineage(DL) or carrier in the lineage(CL) for any genetic defects under their TraitTrac.
Arthrogryposis Multiplex(AM)
Neuropathis Hydrocephalus(NH)
Contractural Arachnodactyly(CA)
Developmental Duplication(DD)
Osteopetrosis(OS)
Tibial Hemimelia(TH)
Pulmonary Hypoplasia with Anasarca(PHA)
For more information on these genetic conditions, click here.

Click here to view the ASA pricing for all the above mentioned tests. If you would like to request a kit, see How to Order a DNA kit.  For any other questions, concerns or to visit more about DNA testing either email dna@simmgene.com or call 406.587.4531.

Coat Color in SimGenetic Cattle

The following article is featured in the May/June issue of the Register magazine.  Dr. Jackie Atkins and Sally Buxkemper teamed up to provide you with a very informative, well written article on coat color that might answer most of the questions you have.  If you do have more questions, click over to the Science Forum, select DNA Testing, and then either Coat Color Dilution in Simmental Cattle or How do I know if my black cow/bull is homozygous black?, whichever topic your question would be best suited for.

Regarding the pictures below, if you click on them it will bring them up to full screen and you can continue to zoom in if needed.

Page 1

Page 1

Page 2

Page 2

Page 3

Page 3

New Red Coat Variant

This spring the American Simmental Association started investigating a possible new red coat color variant. Remington Lock N Load, 2503661, and some of his progeny, appear to carry a red coat color gene that is currently not recognized by the coat color test. In other words, the current coat color test is not able to detect the red coat color gene in animals in this lineage. As a result some animals were called homozygous black but have red progeny. The inheritance and functionality of this gene is likely the same as the existing red coat allele. Animals that are heterozygous for this new variant will pass the red allele to progeny 50% of the time. After mating two heterozygous animals, you can expect 25% homozygous black, 50% heterozygous, and 25% homozygous red calves. The only difference in this case is we are unable to detect this red variant in the current coat color test. The ASA is working with Dr. Clare Gill at Texas A&M to find a marker for the new red variant. If a new variant is discovered, this DNA sequence will be included on the commercially available coat color test. If you know of animals that may carry this red coat color variant, please contact Jackie Atkins at jatkins@simmgene.com with information. The more samples sent to Dr. Gill, the faster we can develop a test for the new variant.

Coat Color Testing – What is the Wild Type coat color allele?

By Dr. Jackie Atkins

Most of us have a good understanding of the two most common coat color alleles ~ the red and the black versions. Black is dominant to red so red cattle must have two red alleles and black cattle can either have two black alleles (homozygous) or can carry a red allele (heterozygous). Wild Type is a third option for the primary coat color gene (called the extension gene). The Wild Type allele is less common in our population of cattle and other genes can affect the coat color display. Because of its rarity and complexity with gene interactions, exactly how the Wild Type allele works is uncertain. Some report that the Wild Type allele is intermediate in dominance to the black and red alleles. Others report the wild type allele will be neutral to the red or the black alleles. This means, the coat color of a wild type carrier will be red if the second gene is red ~ or black if the second gene is black. A Simmental homozygous for the Wild Type allele will likely be brownish red or brownish black with darker areas around the muzzle, ear tufts, and tail switches.

To join in on the conversation or ask specific questions you may have about the wild type gene, visit the Science Forum, select DNA Testing, What is the Wild Type coat color allelle? If you haven’t checked out the Science Forum yet, hop on over and browse through it today. Here’s a list of the current DNA topics that have been posted so far.

Science Forum DNA Topics

A Punnett Square: A tool to help manage simple genetic traits

Written and prepared by Dr. Jackie Atkins, Director of Science and Education


A Punnett squares is a handy tool to predict expected progeny outcomes from a specific mating.  A Punnett square only works with simply inherited traits (where one or just a few genes control the phenotype i.e., coat color, horned/polled, or many genetic conditions).  To use a Punnett square, you should know the genes involved with the trait, the genotypes of the parents, and whether certain alleles (variations of the same gene) are dominant, recessive, or somewhere in between.

A few principles that will help you understand how to use a Punnett square:

  • All animals have two copies of each gene and pass along one copy to their offspring.

  • In a population, there can be several alleles for one gene; but, an individual can have at most two varieties per gene.

  • An individual with the same two alleles for a gene is homozygous.  An individual with two different alleles for a gene is heterozygous.

  • An animal has an equal chance of passing on each one of their alleles.

  • In traits with complete dominance (for example coat color), an animal needs only one of the dominant alleles to display the dominant phenotype.  An animal needs two recessive alleles to display the recessive phenotype.

  • To organize a Punnett square, assign the top of the square for one parent’s genotype and use the left side of the square for the other parent.  You will want one row or column per genotype option.  The genotype options depend on the potential alleles passed from the parents to the offspring.  For example, if a parent has a genotype of Aa, the parent will pass either an A or a to the next generation and these would be the genotype options.  If looking at two genes, then all combinations of the alleles for each gene need to be included (an individual that is Aa for gene  1 and Bb for gene 2 could pass AB, Ab, aB, or ab to the next generation).  Starting with the top parent, you can fill in the each column with the header genotype.  Similarly, each row can be filled in with the genotype option listed to the left for that row.  Each resulting cell will represent a potential genotype for the offspring (half from the sire and half from the dam) and has an equal chance of occurring.

  • If you mate two heterozygous parents for one trait and the trait is only controlled by one gene, you will have a Punnett square with four blocks (two options per parent).  If you have a trait controlled by two genes (or if you are looking at the frequency of offspring for two traits) and the parents are heterozygous, then you will have a Punnett square with 16 cells (two different genes and two alleles/gene = four options per parent).  See examples below.

  • Some of the cells in the Punnett square will have duplicate genotypes and these can be added together to find predicted frequency of the offspring.

  • Some of the cells within the Punnett square will have different genotypes but the same phenotype.  For instance, with a completely dominant trait, the heterozygotes will appear the same as the homozygote dominant animals.  

Given the above principles, here are examples of using Punnett squares to predict offspring from different matings.

Example 1: Coat Color, a simply inherited trait that exhibits complete dominance.

Alleles: E = black and dominant, e = red and recessive
Mating: A heterozygous black sire to a heterozygous black damPunnett_Sq_Ex1

Progeny outcome: In this example, 25% of the calves will be homozygous black (EE), 50% of the calves will be heterozygous (Ee), and 25% of the calves will be homozygous red (ee).  As the black allele is dominant and it only takes one black allele to display the black phenotype, 75% of the calves will have a black coat color (EE and Ee calves) and only the homozygous red calves will have red coat color (25%, ee).

 

Example 2: Two genes that affect the same phenotype: Dilution of Color.

This is an instance where a second gene affects the phenotype of the first gene (a phenomenon called epistasis, see the ASA Science forum post called “Coat Color Dilution in Simmental Cattle” at http://www.simmental.org/forum).  The dilution effect is a dominant trait where the dilution allele will cause genotypically black animals to have a grey coat color.  Red animals are typically unaffected by the dilutor gene (or possibly slightly lighter in color) but can pass the gene to their offspring.


Alleles:
Coat color: E = black and dominant, e = red and recessive

Dilution: D = coat color dilution (if black) and dominant, d = normal coat color and recessive

Mating:  The sire is heterozygous for coat color (Ee) and homozygous for the normal dilutor allele (dd).   The sire has two potential genotype combinations, Ed and ed.  The dam is homozygous red (ee) and carries the dilutor allele (Dd).  The dam also has two possible genotype pairings, eD or ed.

Punnett_Sq_Ex2

Progeny outcome: Each one of the resulting cells has an equal chance of occurring and each cell is genotypically unique; therefore, each genotype has a 25% chance of occurring (1/4). Phenotypically, we would expect 25% of the calves to be grey (and a carrier of the dilutor allele),

25% black, and 50% red (with half of these carriers of the dilution mutation).

 

Example 3:  Two separate genes with two independent traits, Coat Color and Horned/Polled.

 

In this example, we will use two heterozygous parents for each trait to display a more complicated Punnett square (16 cells). Neither gene affects the other so the traits are independent of one another.  Both traits are completely dominant (black coat color is dominant to red and polled is dominant to horned).  In reality, there are other genes that affect these traits (dilution, see above, or the scurred gene in polled cattle, but for this example, we will ignore these other genes).

 

Alleles: Coat color: E = black and dominant, e = red and recessive

Horned/polled: P = polled and dominant, p = horned and recessive

 

Mating: The sire and dam are both heterozygous parents for each trait.  As these are completely dominant traits, both parents will be black and polled, but carry the red and horned alleles.  Each parent will have 4 potential genotype pairings.

Punnett_Sq_Ex3

Progeny outcomes: Any calves with at least one E will be black (denoted as E_) and calves with at least one P will be polled (denoted as P_).  Out of 16 animals, there will be 9 black and polled offspring (E_/P_; only one homozygous for both traits), 3 black and horned (E_/pp), 3 red and polled (ee/P_), and 1 red and horned (ee/pp) for a ratio of 9:3:3:1.

These principles can be applied to understanding the frequency of passing along any simply inherited traits including most of the genetic conditions we screen.  Combine the information you gain from DNA test results with Punnett squares to help predict potential traits in calves from certain matings.  Punnett squares are a useful tool to help make mating decisions to optimize your herd.  If you have any questions or comments, please post on the ASA science forum post about Punnett squares (www.simmental.org/forum under Genetic Evaluation).