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has focused too much on their "exhaust emissions" - methane - and not nearly enough on their role as nature's "carbon-capturers and converters". From his base near Rockhampton in Central Queensland - Australia's beef capital - he's offered some food for thought for scientists and consumers alike.  Watch video

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Specific Conditions

Genetic Abnormality Reporting Form

  • Bovine Arthrogyrposis Multiplex Congenita (AM) aka curly calf

    There is Simmental-sourced literature discussing AM dating as far back as the mid-1980s; however, no documented cases have been established.  In 2008, the American Angus Association verified the presence of AM in two very popular sires.  These sires and their resulting generations of progeny, grand progeny, etc. have spread AM in many Angus pedigrees.  Consequently, Angus genetics entering into the ASA database, either commercial females bred to SimGenetic bulls, or registered Angus bulls and cows used to develop SimnAngus could carry AM.   Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, AM could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality-status (TraitTrac) for each animal in our database.
    Reporting Abnormal Calves: Call ASA immediately. ASA will reimburse all expenses. Take photos or video that best display the abnormality. We will need DNA (hair or tissue) from the calf, dam and sire. (We have DNA on all A.I. sires and donor dams.) If the calf is dead, chill the carcass until ASA has been contacted.
    "Curly Calf Syndrome" the Register, November 08, Dr. Wade Shafer, ASA Director of Performance Programs
    American Angus Association information on AM
    Useful Links:
    www.redangus.org
  • Bovine Mannosidosis

    A lethal autosomal recessive disorder associated with defective catabolism of glycoproteins due to the inherited deficiency of lysomal α-mannosidase (Burditt et al, 1978). Calves generally appear to be in poor condition and undersized. Many calves will have moderately enlarged lymph nodes throughout the body and may contain mild internal hydrocephalus. Calves seem to somewhat consistently have intracytoplasmic vacuolation lesions (Jolly et al., 1978). Two primary mutations exist, one responsible for the disorder in Galloway cattle and the other responsible for the disorder in Angus, Murray Grey, and Brangus from Australia. An additional mutation showed up in Red Angus embryos transported from Canada to Australia. These breed specific mutations may have originated in Scotland and been exported (via animals or germplasm) to America, New Zealand, and Australia. DNA testing is available and is based on the polymerase chain reaction (PCR) (Berg et al., 1997)

     

    References

    Burditt, L. J., N. C. Phillips, D. Robinson, B. G. Winchester. University of London. N. S. Van-de-Water, R. D. Jolly. Massey University. Characterization of the Mutant α-Mannosidase in Bovine Mannosidosis. 1978. www.ncbi.nim.gov. Accessed June 29, 2011.

  • Contractual Arachnodactyly (CA)

    CA, a genetic abnormality inherited as a simple recessive trait, has a negative impact on performance and productivity. Muscle development is reported consistently poor in the affected calves that survive. Severe cases have difficulty with locomotion and suckling and some die or get destroyed prematurely. 

    Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, Contractual Arachnodactyly could be a risk in certain cattle.  We strongly suggest using ASA's website Animal Search function to access the most up-to-date genetic abnormality-status (TraitTrac) for each animal in our database.

    Reporting Abnormal Calves: Call ASA immediately. ASA will reimburse all expenses. Take photos or video that best display the abnormality. We will need DNA (hair or tissue) from the calf, dam and sire. (We have DNA on all A.I. sires and donor dams.) If the calf is dead, chill the carcass until ASA has been contacted.

    For Dr. Steffen's notice and description on FCS, click here

    Useful Links

    Contractural Arachnodactyly (CA; Fawn calf syndrome) written in 2010 by Laurence Denholm.

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  • Development Duplication (DD)

    Recently the American Angus Association announced the discovery of another genetic condition called developmental duplication (DD). Most affected calves that survive to term are born with multiple limbs or polymelia. Polymelia occurs spontaneously in cattle of a variety of breeds as well as other species including sheep, horses, and humans. Other than an increased occurrence of mortality associated with calving difficulty, calves born with polymelia often thrive (especially following the removal of the limb[s]).

    During the last 4 years, the incidence of polymelia in purebred Australian Angus populations rose above expected sporadic levels. Drs. Laurence Denholm (NSW Department of Trade and Investment) and Jonathan Beever (Agrigenomics, Ltd. and the University of Illinois) found this condition was the result of a simple recessive mutated gene. After discovering a DNA variation that appears to directly cause the defect, Dr. Beever initially tested 1,099 high-use AI Angus bulls and found 72 carriers of the defective allele (a moderately high allele frequency of 3%). However, based on this allele frequency, the incidence of polymelia should be higher than is actually reported if all animals homozygous for the mutation demonstrated the defect (the defect would be called fully penetrant). Due to this discrepancy, Dr. Beever initially hypothesized a certain amount of embryonic loss during gestation in homozygous embryos. Upon further investigation, Dr. Beever found some homozygous animals with very minor phenotypes (e.g., a 2 inch long skin tag) and others that appear totally normal. Recently, a few dozen seemingly normal homozygous recessive animals have been discovered. When animals have the genotype and do not display the phenotype, this is referred to as incomplete penetrance. The cause of incomplete penetrance in DD is unknown but is being researched aggressively. Dr. Beever is examining the DNA of these normal homozygous recessive animals for a potential explanation (for instance, a second gene that interacts with the DD gene) and is planning breeding trials to understand the inheritance better.

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  • Dwarfism (Angus mutation, DW1)

    There are several forms (mutations) that result in conditions labeled as dwarfism.  Short-headed (snorter), long-headed, intermediate and compressed are all terms used to describe the various forms of dwarfism.  In 2002 and 2003 the American Angus Association identified calves determined to be dwarfs. Iowa State University (ISU) provided the research to identify a molecular marker (a SNP) that could indicate carriers of this form of the dwarfism gene.  In addition to the form of long head dwarfism, molecular markers are available for genotyping both Japanese Brown and Dexter cattle  (Bull dog) for certain strains of dwarfism. Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, Dwarfism could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality-status (TraitTrac) for each animal in our database. Reporting Abnormal Calves: Call ASA immediately. ASA will reimburse all expenses. Take photos or video that best display the abnormality. We will need DNA (hair or tissue) from the calf, dam and sire. (We have DNA on all A.I. sires and donor dams.) If the calf is dead, chill the carcass until ASA has been contacted.
    Useful Links
    www.angus.org
  • Hypotrichosis (HT)

    Obviously a recessive abnormality that displays a permanent absence and/or reduction of hair, hypotrichosis is apparent at birth.  This condition is often confused with premature birth.  Hair is thin either over the entire body or in distinct places.  For example, European Simmental brought “rat-tail” which resulted in greatly reduced hair at the tail switch.  Certain lines of Hereford are verified to carry hypotrichosis. Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, HT could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality status (TraitTrac) for each animal in our database. Reporting abnormal calves:  Call ASA immediately.  ASA will reimburse all expenses. Take photos or video that best display the abnormality.  We will need DNA (hair or tissue) from the calf, dam and sire (we have DNA on all A.I. sires and donor dams).  If the calf is dead, chill the carcass until ASA has been contacted. 
    Some useful links: http://hereford.org/node/25
    http://redangus.org/node/214
  • Idiopathic Epilepsy (IE)

    Like most other genetic abnormalities, a single pair of genes control this epilepsy.  First apparent in calves, environmental stresses such as thermal or physical e.g. stressful handling, etc. often bring out the seizures.  Hereford has made the most effort to identify carriers.  Since the 1960s and 70s featured very large numbers of Simmental bulls mated to Hereford cows in up breeding programs, IE is possible from pedigrees tracing to either Hereford or “commercial” cows. Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, IE could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality status (TraitTrac) for each animal in our database. Reporting abnormal calves:  Call ASA immediately.  ASA will reimburse all expenses. Take photos or video that best display the abnormality.  We will need DNA (hair or tissue) from the calf, dam and sire (we have DNA on all A.I. sires and donor dams).  If the calf is dead, chill the carcass until ASA has been contacted. 

    Useful Links: www.omia.angis.org.au/

    http://www.hereford.org/static/files/0408_Epilepsy.pdf
  • Neuropathic Hydrocephalus (NH)

    Hydrocephalus was first described by the ancient Greek physician Hippocrates. NH is documented in many mammal species including humans and cattle.  Typically apparent at birth and usually lethal in calves, large, fluid-filled, misshaped heads are the result of this mutation.  Hydrocephalus is mentioned as being observed in Simmental, but no cases are documented in our database.  Recently, the American Angus Association verified the presence of NH in a very popular genetic line. Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, NH could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality-status (TraitTrac) for each animal in our database.
    Reporting Abnormal Calves: Call ASA immediately. ASA will reimburse all expenses. Take photos or video that best display the abnormality. We will need DNA (hair or tissue) from the calf, dam and sire. (We have DNA on all A.I. sires and donor dams.) If the calf is dead, chill the carcass until ASA has been contacted.
     
    For Dr. Steffen's notice and description on hydrocephalus, click here .  
    Useful Links:
    www.angus.org
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  • Osteopetrosis (OS) aka marble bone

    Another of the simple recessive abnormalities, the affected calves are either born dead or die within 24 hours.  Often calves are born premature and with an obvious short lower jaw.  Bones are brittle.  OP has been verified in many species including humans.  Recently, some Red Angus pedigrees have been confirmed to carry osteopetrosis. Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, OP could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality status (TraitTrac) for each animal in our database. Reporting abnormal calves:  Call ASA immediately.  ASA will reimburse all expenses. Take photos or video that best display the abnormality.  We will need DNA (hair or tissue) from the calf, dam and sire (we have DNA on all A.I. sires and donor dams).  If the calf is dead, chill the carcass until ASA has been contacted. 
    Some useful links:   http://redangus.org/node/215
    http://www.osteopetrosis.org/
  • Oculocutaneous Hypopigmentation (OH)

    In the spring of 2012, the American Simmental Association (ASA) received an abnormality report indicating the occurrence of a newborn calf with "white-colored" eyes and a diluted hair coat (see picture at right). All the appropriate DNA samples were collected, used for the validation of parentage, and archived for future reference. Over the next two years, three additional calves were reported to the ASA with similar characteristics. Based on the recurrence of this trait, an investigation was initiated to establish whether the condition was genetic. DNA samples collected from the four affected calves were genotyped using the Neogen GGP-HD. The resulting genotypes were analyzed in contrast to the genotypes of ~80 Simmental sires. This analysis showed clear evidence that the condition is inherited as a recessive trait. Based on hese results, the DNA sequence for several genes was analyzed in each of the affected calves. Within one of these genes, a mutation was identified that is predicted to impair the function of the encoded protein. In fact, in mice, mutations within the same gene cause a very similar condition that is referred to as "chocolate", where black mice have a diluted coat color and beige-colored irises (or irides). Further investigation, including the genotyping of frequently used sires, indicates the mutation is present at a relatively low frequency in the Simmental population. This is consistent with the very low frequency of affected calves reported over the three year period. Examination of carrier pedigrees reveals the Simmental bull, PVF-BF BF26 BLACK JOKER (ASA #1930631), as the most popular recent ancestor with DNA available for testing. However, several of the genotyped carriers do not have this sire in their pedigrees indicating the mutation could be significantly older. Considering this information and the prior description of similar traits in other breeds, namely heterochromia irides (HI) in Angus cattle, the possible origin of this mutation was investigated by obtaining samples from known HI carriers. Although there are very few DNA samples available from these older animals, a sample was obtained for the Angus sire SIR WMS WARRANT (AAA #9196894). Indeed, WARRANT was found to be a carrier of this newly identified mutation. Therefore, it is most likely that the mutation was introduced into the Simmental population by the use of Angus cattle during the development of black purebreds. The subsequent screening of more than 1,200 Angus sires indicates the mutation has most likely been eliminated from the current Angus population via pedigree selection in the early 1980s. Based on these data, the scientific literature was reviewed in an effort to understand if there were documented features that clearly distinguish between the oculocutaneous hypopigmentation (OH) and heterochromia irides (HI) traits, both of which had been previously described. It is our opinion that the characteristics displayed by these affected Simmental calves is more representative of OH than it is of HI. Additionally, examination of the human and mouse literature also supports this designation. Thus, we suggest that if both phenotypes exist in the cattle population, WARRANT should be designated as an OH carrier. Further screening of current descendants of Angus HI carriers is being conducted but has not identified any additional carriers of this mutation within the Angus population. Information contained in reports and literature from the 70s and 80s, and in these current Simmental cases, indicate that this abnormal phenotype has little or no effect on the viability or performance of affected individuals. However, in some cases, a possible sensitivity to light has been reported. Thus, we suggest this mutation be monitored similarly to other non-lethal traits such as coat color or horned/polled. As with any recessive condition, breeders can avoid the appearance of affected calves by restricting matings between carrier animals.

    Reporting abnormal calves:  Call ASA immediately.  ASA will reimburse all expenses. Take photos or video that best display the abnormality.  We will need DNA (hair or tissue) from the calf, dam and sire (we have DNA on all A.I. sires and donor dams).  If the calf is dead, chill the carcass until ASA has been contacted. 

  • Pulmonary Hypoplasia with Anasarca (PHA)

    A new syndrome reported in Maine, Percentage Chi, and Shorthorn calves over the last few years, PHA is uniformly lethal. The dams also suffer from dystocia related to the large size of the calf. Anasarca refers to the collection of fluid in the skin and body cavities of the calf. In some cases the calves had been reported as "bulldogs" due to the facial appearance caused by this fluid collection. The term should not be applied as this syndrome is distinct from bulldog dwarfism and using the term could be misleading. The fluid markedly increases the size and weight of the fetus causing dystocia at time of delivery.  Small, under developed lungs are apparent in the dead calves. Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, PHA could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality-status (TraitTrac) for each animal in our database.

    Reporting Abnormal Calves: Call ASA immediately. ASA will reimburse all expenses. Take photos or video that best display the abnormality. We will need DNA (hair or tissue) from the calf, dam and sire. (We have DNA on all A.I. sires and donor dams.) If the calf is dead, chill the carcass until ASA has been contacted.

    Dr. Beever's Powerpoint Presentation on TH & PHA

    Cowboy Genetics" , Maine-Anjou Voice, May/June 2006, Dr. Lana Kaiser, Professor of Medicine at Michigan State University

    Useful Links:
    http://redangus.org/node/217
     
  • Tibial hemimelia (TH)

    This single autosomal recessive has been documented in cattle (early on in Galloway, more recently, in Shorthorn and percentage Maine and Chi) since the 1950s. TH is characterized by severe and lethal deformities in newborn calves. Affected calves are born with twisted rear legs with fused joints, have large abdominal hernias and/or a skull deformity. Should the calf survive the birthing process, they cannot stand to nurse and must be destroyed. Because the ASA has an open herdbook, allowing other breeds into our database and percentage pedigrees, TH could be a risk in certain cattle.  We strongly suggest using ASA’s website Animal Search function to access the most up-to-date genetic abnormality-status (TraitTrac) for each animal in our database.

    Reporting Abnormal Calves: Call ASA immediately. ASA will reimburse all expenses. Take photos or video that best display the abnormality. We will need DNA (hair or tissue) from the calf, dam and sire. (We have DNA on all A.I. sires and donor dams.) If the calf is dead, chill the carcass until ASA has been contacted.

    "Tibial Hemimelia Threatens SimGenetics" , the Register, Dr. Jerry Lipsey, ASA Executive Vice President

    Tibial Hemimelia, Meningocele, and Abdominal Hernia in Shorthorn Cattle

    Dr. Beever's Powerpoint Presentation on TH & PHA

    TH Information at www.maine-anjou.org

    Useful Links:

    www.redangus.org
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Genomics

Delivering Genomics Technology to the Beef Industry
Drs. Darrh Bullock, Matt Spangler, Alison Van Eenennaam, and Robert Weaber
This White paper summarizes the application of genomic information for beef cattle as of spring 2013

 

Basics of DNA Markers and Genotyping
Alison Van Eenennaam, Ph. D.
University of California – Davis
This two page article simply explains the fundamentals of DNA and how we use variations in DNA sequence for information about cattle (microsatellites, SNPs, etc.).

The Future Is Here
Wade Shafer, Ph. D.
American Simmental Association
This article explains how ASA uses genomic information in genetic evaluations and how adding this information can improve the accuracy of EPDs.

Marker Assisted EPDs
Matt Spangler, Ph. D.
University of Nebraska-Lincoln
This article summarizes the state of genomically enhanced EPDs for multiple breeds.

DNA Tests for Genetic Improvement in Beef Cattle
Matt Spangler, Ph. D.
University of Nebraska-Lincoln

 

Current State Genomic selection Tools for Beef Cattle

Dr. Matt Spangler
UNL Beef Genetics Specialist
University of Nebraska - Lincoln

Genomic technology and its application are rapidly evolving. Dr. Spangler discusses the current application of genomic tools including testing for genetic defects, paternity, genomic enhanced EPDs, and the potential for marker-assisted management. This webinar also focuses on the evolution of marker panels, and how they are being used to date including the numerous breeds that are including this information into their EPDs.

 

Predicting Genetic Merit of Beef Cattle
Dorian Garrick, Ph. D., Rohan Fernando, Ph. D., Kadir Kizilkaya, Ph. D., James Reecy, Ph. D.
Current selection strategies result in annual rates of genetic improvement less than one-quarter of the progress that is theoretically possible if merit could be accurately predicted by breeding age, suggests research—by Dorian Garrick, professor; Rohan Fernando, professor; Kadir Kizilkaya,postdoctoral fellow and James Reecy, associate professor—summarized in this Iowa State University Animal Industry Report.

ASA Experience with Incorporating Genomics into Genetic Evaluation
Lauren R. Hyde, Wade R. Shafer, Stephen C. McGuire, Mahdi Saatchi, and Dorian J. Garrick
At the annual meeting of the American Simmental Association (ASA) in January 2011, the Board of Trustees voted unanimously to fund and initiate the development of genomically enhanced expected progeny differences (GE-EPD). The project required a large number of DNA samples representing heavily used Simmental-influenced bulls.

 

Selection Indexes

 

Indexing Your Way To Genetic Improvement – Part I
Burt Rutherford
BEEF Magazine
This is the first part to a two part series on selection indices. This article introduces selection indices and how they can simplify bull selection including commentary by Drs. Bob Weaber (Kansas State University, Beef Extension Specialist) and Mike MacNeil (Delta G, Miles City, Montana).

Indexing Your Way To Genetic Improvement – Part II
Burt Rutherford
BEEF Magazine
Second part of a series of articles on selection indices describing which index to use for your operation. This again includes commentary from Drs. Bob Weaber (Kansas State University, Beef Extension Specialist) and Mike MacNeil (Delta G, Miles City, Montana).

Comparison of Selection Indices
Wade Shafer, Ph. D.
American Simmental Association
A highly qualified panel, representing beef, poultry, pork and diary industries, compare notes on selection. Coordinated by Wade Shafer, ASA Director of Performance Programs.

Genetic-Evaluation System -Part 1: Economically Relevant Traits
Wade Shafer, Ph. D.
American Simmental Association
There has been a dramatic increase in the number of traits quantified by EPDs since the early years of genetic evaluation. The ASA currently publishes EPDs on 15 traits and more are in the hopper. This wide array of EPDs provides seed for significant genetic improvement.

Genetic-Evaluation System -Part 2: Economically Relevant Traits
Wade Shafer, Ph. D.
American Simmental Association
We are on a mission to increase the effectiveness of our geneticevaluation system by decreasing its complexity. Discussion in the June/July issue focused on narrowing our array of EPDs to economically relevant traits (ERTs). Though this makes life simpler, we are still faced with a difficult task— putting appropriate selection pressure on the ERTs. This is where the economic selection index (ESI) comes in.

Constructing ASA Economic Indexes
Wade Shafer, Ph. D.
American Simmental Association
Some are of the impression that we use our intuition to construct our indexes, much like a chef would put together a gourmet meal—a dash of this and a pinch of that and voila! The truth is that it is not nearly that exciting. ASA’s indexes are constructed very similarly to the way an accountant would calculate projections on how the purchase of a piece of equipment will impact a firm’s bottom line.

Understanding the ASAs New Economic Selection Indexes
Wade Shafer, Ph. D.
American Simmental Association
Though we’ve had the benefit of EPDs in our tool chest for over twenty years, having EPDs without economic selection indexes is a bit like having superhighways without maps—you can drive fast but can’t be sure you’re traveling in the right direction. Indexes provide the maps. Our first indexes, the Terminal (TI) and All-Purpose (API), were published in the Spring ’05 Sire Summary. They are also available online for all animals that have EPDs on the traits the index is composed. These indexes provide the most powerful tools for genetic improvement our breed has ever seen.

Improving Profit via Genetics
Wade Shafer, Ph. D.
American Simmental Association

 

Multi-breed Evaluation

Multi-Breed Genetic Evaluation Part 1

PART 1 OF A SERIES

During the last two years, the American Simmental Association and Cornell University developed a genetic evaluation system to handle all performance records in the ASA data base regardless of breed composition. The ASA data base has a variety of crosses and breed combinations represented in it as a result of the upgrading policy for producing purebred Simmental and Simbrah. Also, the upgrading rules were changed to allow the registration of 12.5%, 25%, 37.5%, and 62.5% Simmental cattle. The ASA has two separate herdbooks, Simmental and Simbrah, which are connected by the Simmental genes sampled by Simbrah breeders to produce percentage and purebred Simbrah cattle. This genetic evaluation system will evaluate animals in the ASA data base regardless of their breed composition whether they are imported Simmentals from Europe, purebred Simmental, purebred Simbrah, or Angus cows bred to Simmental AI sires. The Multiple-Breed Evaluation System has been run for research purposes several times. The plans are to implement the system with the Fall 1997 Sire Summary in June, 1997.

Current Evaluation System

The current Simmental evaluation uses records of calves sired by purebred bulls. These records are analyzed using a multiple-trait animal model to produce EPDs for birth weight, weaning weight, yearling weight, maternal milk, maternal weaning weight along with predicted producing ability for cows. The contemporary group is defined as breeder, herd, management, sex of calf, and percent Simmental. Calves are split by percent Simmental so calves with the same heterosis potential are placed in the same contemporary group. The records are adjusted for age of dam using 12 age groups within percent Simmental by sex of calf groups. Different heritabilities are used to weight the individual records depending upon the percent Simmental and sex of calf.

The Simbrah evaluation uses only records from purebred Simbrah calves whose parents can range from 37.5% to 75% Simmental. First generation purebreds produced by mating Simmental parents to 1/4 3/4 parents are included in the evaluation once they are parents of purebred progeny. Any Simmental ancestors are treated as unknown so they contribute no information to their Simbrah descendants.

Multiple-Breed Evaluation (MBE) System
Across-Breed vs. Multiple-Breed
The MBE system is designed to compare animals with different backgrounds as long as they have been evaluated in the same system. The Simmental data base has sires from other breeds represented in it such as Angus, Brahman, Red Angus, Hereford, etc. The system will produce EPDs for those bulls comparable to EPDs for Simmental and Simbrah bulls. The term, Multiple-Breed, was chosen to describe that animals with different breed backgrounds are evaluated in the same program. The term, Across-Breed, describes an adjustment procedure developed by researchers at the USDA Meat Animal Research Center to convert EPDs from one breed to a comparable scale for another breed. The system developed by the ASA and Cornell is not an across-breed comparison and the EPDs cannot be compared to EPDs produced by other breeds' genetic evaluations.

Features of the Multiple-Breed System
The MBE system adds several new features compared to the current procedures used to produce Simmental and Simbrah EPDs. The features are a new contemporary group definition, continuous age of dam effects, breed of founder effect (direct and maternal), and heterosis (direct and maternal). The MBE is a multiple-trait animal model so it provide EPDs for birth weight, weaning weight, yearling weight, maternal milk, and maternal weaning weight. Also, predicted producing abilities will be calculated for cows evaluated in the system. The features of the MBE system handle breed differences and the effects of heterosis which results from crossing different breeds. By including these features, the MBE EPDs are comparable for all animals in the Simmental data base.

MBE Contemporary Groups-
In order to estimate breed differences and heterosis effects, the contemporary groups need to have animals with different breed backgrounds competing in the same environment. A contemporary group in the current Simmental evaluation is a group of calves from the same breeder, in the same herd, of the same sex, under the same management, and the same percent Simmental. For Simbrah, the percent Simmental requirement is dropped since all calves are purebred Simbrah. The contemporary group in the MBE system is a true management group. The requirement for percent Simmental is dropped from the definition of the contemporary group. All calves from a breeder's herd will be put in the same group as long as they are the same sex and managed alike. If a breeder has a purebred Simmental herd and a purebred Simbrah herd in different locations, the calves should be reported as different herds. The contemporary groups from the same herd should be larger by dropping percent Simmental from the contemporary group definition. The increased contemporary group size is important since it should lead to more reliable prediction of genetic differences among animals.

Age of Dam Effects -
The age of the calf's dam is a very important source of variation for birth weight and weaning weight. It is important to some degree for postweaning gain. For the current evaluation programs, age of dam is split into twelve classes and separate age of dam adjustments are used based on the dam's percent Simmental and the calf's sex. The twelve age of dam classes are less than two years of age, 2 to 2.5 years, 2.5 to 3 years, 3 to 3.5 years, 3.5 to 4 years, 4 to 4.5 years, 4.5 to 5 years, 5 to 9 years, 9 to 10 years, 10 to 11 years, and greater than 11 years. The calf records are adjusted for age of dam prior to calculating the EPDs.

The MBE age of dam effect is estimated by a continuous curve for each sex of calf by breed of dam combination. Breed of dam was grouped into seven biological types to avoid having to estimate 63 different age of dam curves. The biological types are Simmental, Angus, Hereford, Brahman, British, Continental, and Other. The age of dam effects will be estimated directly by the MBE system so no records will be adjusted for age of dam prior to the evaluation.

In figure 1, the age of dam adjustments for purebred Simmental bull calves at weaning are shown using the current adjustment factors (bars) and the MBE age of dam curve (line). The adjustments in the MBE are based on the actual age of the cow at time of calving where as in the current evaluation, cows are placed in age groups that vary from six months in length to four years. The mature cow base in the MBE system is a six year old Simmental cow. The current mature cow basis is defined as Simmental cows that are five to nine years of age at calving. A bull calf born to purebred Simmental cow calving at 2.7 years of age receives an adjustment of +52.6 lb. With the new age of dam adjustments, the calf's weaning weight is adjusted by +41.6 lb.

For crossbred cows, the age of dam effects will be weighted averages of the biological types represented in the dam. The age of dam curves for cows with different combinations of biological types are shown in table 1. The age of dam adjustment for purebred Simbrah dams will be a function of the Simmental and Brahman age effects weighted by the fraction of Simmental and Brahman genes.

Table 1. Age of Dam Curves for Cows of Varying Breed

Breed of Dam

Age of Dam Effect

Purebred Simmental (7/8 SM - 1/8 AN)

7/8 AODSM + 1/8 AODAN

F1 Simmental-Hereford

1/2 AODSM + 1/2 AODHH

Purebred Simbrah

5/8 AODSM + 3/8 AODBR

For birth weight and postweaning gain, maternal breed differences are not included in the evaluation. Realizing that maternal breed differences could be important for some traits, the age of dam effects for birth weight and postweaning gain are used to control maternal breed differences that could exist in the data. The Brahman breed is well known for a large negative maternal effect for birth weight. In a summary of crossbreeding studies, calves born to Brahman dams weighed about 14 lb. less at birth compared to calves born to Simmental dams. The birth weight age of dam curves for Simmental, Brahman, Angus, and Simbrah are shown in figure 2. For bull calves born to six year old Simmental, Angus, Brahman, and Simbrah cows, the age adjustment to a six year old Simmental base is zero, +.02, +13.0, and +4.8 lb., respectively.

In summary, the MBE system has several new features compared to the current evaluation programs used to evaluate Simmental and Simbrah cattle. The two features discussed in this article were a new contemporary group definition and a new method for adjusting for age of dam. The new contemporary group definition will group all calves of the same sex and management into one group regardless of their breed background. The new method of adjusting calves for age of dam uses a continuous curve. By treating age of dam as a continuous variable, the new age of dam adjustments will do a better job of adjusting records for calves from younger and older cows. Breeds are grouped into seven biological types and age of dam equations are fitted for each sex of calf-biological type combination. For birth weight and postweaning gain, the age of dam equations will account for maternal breed differences that could exist in the data such as the Brahman maternal effect for birth weight.

Multi-Breed Genetic Evaluation Part 2

Accounting for Breed Differences

PART 2 OF A SERIES

In the first installment of this series describing the Multiple-Breed Evaluation System developed by the ASA and Cornell University, the new contemporary group definition and age of dam effects were presented. For review, the new contemporary group places all calves in the same contemporary group as long as they are the same sex and have been managed alike in the same herd. The new age of dam effects treat the age of cow as a continuous variable instead placing cows into twelve distinct groups based on their age. Also, the age of dam adjustment will depend on the sex of the calf and the breed makeup of the cow.

Two important effects need to be adjusted for when using records from crossbred calves, breed differences and heterosis. The effects of heterosis are split further by looking at heterosis of the calf (direct) and heterosis of the dam (maternal). If the breed differences and heterosis effects are not accounted for properly, these differences could end up as part of the animal's EPDs.

Breed of Founder Effects

The breed differences in the Multiple-Breed Evaluation are accounted for determining the different breeds that exist in an animal's pedigree. All the pedigrees in the ASA data base are traced back to the most remote ancestor in each pedigree. These distant ancestors are called founders. The breed composition of a calf is determined by the breeds of all founders in the calf's pedigree and the number of generations between the calf and the founder animals. The expected genetic value of an animal is the weighted average of the breed of founder (BOF) effects as shown in table 1. If the calf was 75% Simmental, 25% Angus, its expected genetic merit would be the weighted average of the Simmental and Angus BOF effects. The BOF effect accounts for the genes from various breeds that contributed to the Simmental population through founder animals.

Table 1.

75% Simmental, 25% Angus
 3/4 BOF(SM) + 1/4 BOF(AN)
 

If breeders have been practicing selection, genetic trend will be present in the breed. A yearly BOF effect was created to account for the genetic trend that may be present in a breed. The yearly BOF effect adjusts the evaluation for the animal's breed composition along with the year(s) the genes were sampled from their respective breeds. There are sixty-three breeds represented in the ASA data base. Since only a handful of these breeds are represented in the ASA data to a significant degree, twelve breed groups were created for each year: Simmental, Angus, Hereford, Brahman, Gelbvieh, Charolais, Limousin, American, British, Continental, Dairy, and Mixed.

Given the nature of the ASA data base, it is very doubtful that these different BOF effects could be estimated from the data alone. A statistical procedure was used that combines information reported from the scientific literature (priors) and the information contained in the data. The prior information is very useful for those breeds that received very little sampling into the Simmental data base. For breeds like Angus, Hereford or Brahman, the prior values have very little influence since so many animals in the data have genes from those three breeds. The information from the literature was summarized to provide estimates of breed differences (Table 2). Based on roughly fifty published reports, these differences are our best estimates of the differences between the breeds represented in the ASA data. Also, the BOF solutions for 1991 are listed for each trait in table 2. The influence of the data on the BOF solutions can be seen by comparing the BOF solutions with the prior values for each breed group. For a few breed groups, the difference between the solutions and priors is very small indicating one of two things: 1) The prior values were very close to the differences seen in the Simmental data; or 2) There were very few animals with any genes from those breed groups in the Simmental data.
Table 2. Prior Values and 1991 Solutions for Breed of Founder Effects
(Scale: lb., 2xEPD, Simmental Base Breed)
         
 

BWT

WWT

PWG

MMK

 
  Prior  1991  Prior  1991  Prior  1991  Prior  1991
Simmental  0.0 -0.3 0.0  4.3 0.0  4.5  0.0  7.4 
Angus  -18.2 -11.9 -58.6 -43.1 -40.7  -30.3  -21.7 -8.4 
Hereford  -11.4 -9.6 -56.4  -49.7 -56.0 -50.7  -42.49 -29.8 
Brahman  1.8 0.2 -46.8 -49.8 -51.1 -50.9 -6.5 -10.2 
Charolais  3.7 -1.5 11.8 4.3 -14.6 -19.1    -9.1 -6.4 
Gelbvieh 3.3 1.9 22.1 22.2 -50.7 -49.6  11.4 11.7
Limousin  -4.3 -6.5 -19.1  -21.2 -46.7 -44.7  -8.1 -12.8 
American  -10.6 -9.8 -58.6  -57.5 -95.9 -90.9 7.2  8.2 
British -17.2 -12.1 -76.3  -66.8 -26.2 -23.9 -12.5 -2.5 
Continental  4.0 1.5 -6.7 -5.1 -25.8 -22.8 4.4 7.9
Dairy -5.1 -3.2 -24.2  -27.6 -32.1 -33.7  65.9 47.9 

 

These breed differences are expressed on a breeding value scale relative to Simmental. The important thing to consider is not the actual values for each breed group but the differences between breed groups. The difference between Angus and Simmental founders in 1991 for birth weight was -11.6 lb. Expressed on an EPD scale, the difference is -5.8. The contrasts between Brahman and Simmental for weaning weight and postweaning gain in 1991 were -54.1 and -55.4 lb., respectively.

The prior values are assumed to the same for each year. The data will provide the information to determine if a genetic trend exists in the genes sampled from the different breed groups represented in the Simmental data. If only a few animals from founder groups enter the population each year, the yearly BOF trends will fluctuate due to the limited sample of genes each year. Another statistical procedure was used to smooth the estimates of the BOF trends so the yearly estimates do not bounce wildly from year to year.

The BOF trend describes the average merit of the genes from a breed group entering the Simmental population in a given year. The founder animals may not be a random sample from their breed so the BOF effects are not true breed differences. The BOF trends for birth weight are shown in figure 1 for Simmental, Angus, Hereford, and Brahman. These trends are represented on a breeding value scale. From 1970 to 1994, the difference between founders from the Brahman and Simmental breeds increased from -1.6 lb. to +0.7 lb. The Angus trend indicated that breeders selected Angus cattle with higher birth weight genetics to enter the Simmental population. Compared to the prior difference between Angus and Simmental, -18.2 lb., the difference between Angus and Simmental founder genes was -12.0 lb. in 1994.

The BOF trends for maternal milk are shown in figure 2 for Simmental, Angus, Hereford, and Brahman. Breeders sampled genes for increased maternal ability from the Angus and Brahman breeds as shown by the increased trends from 1970 to 1994. The Hereford trend increased from 1970 to 1980 then stayed relative flat to 1994. From 1980 to 1994, compared to Angus and Brahman, there has been fewer Herefords entering the Simmental population as founder animals. Also, the Hereford genes present in the Simmental population have received very little selection for improved maternal performance.

Summary

The phrase, breed of founder, is used to indicate that a random sample of genes from a contributing breed is not needed to evaluate breed differences. The breed of founder effects are developed by tracing pedigrees and determining the breed(s) represented in the most distant animals (founder) in each pedigree. A time trend is included in the breed of founder effects to account the genetic trend that may be present in the genes sampled from other breeds. The MBE system uses two sources of information to estimate breed differences in the Simmental population: 1) Prior values estimated from the published crossbreeding studies in the scientific literature; and 2) the Simmental data base. The prior values provide a starting point which may be changed by the data in the MBE analysis. If the data contains a lot of animals with some Angus breeding, the prior difference between Angus and Simmental will have little impact on the final estimate. For other breeds that are not represented as well as Angus, Hereford, or Brahman, the prior values have a significant influence on the final estimates.
 

 

Multi-Breed Genetic Evalutation Part 3

Adjusting for Heterosis

Part 3 of a Series

In the current Simmental evaluation, heterosis is controlled by grouping calves according to percent Simmental. Calves from the same herd and management are split further by grouping 50%, 75%, and 87.5% and higher calves separately into different management groups. For the purebred Simbrah evaluation, records from purebred Simbrah calves are used only if their parents range from 3/8ths to 3/4ths Simmental. Only performance records of purebred Simbrah calves are used however, the expected heterosis of the calves can vary by the parents used to produce the purebred calves. By limiting the variation in percentage Simmental and Brahman of the parents, the range in expected heterosis is held under some control.

The Multiple-Breed Evaluation (MBE) system places all calves from the same herd in the same contemporary group as long as they have been managed alike and are the same sex. The restriction on percent Simmental is no longer a part of the contemporary group definition in the MBE analysis. By placing calves with different genetic backgrounds in the same contemporary group, the MBE system estimates breed differences and direct and maternal heterosis effects. For the traits included in the evaluation, heterosis provides an increase in performance that cannot be attibuted to the animal's breeding value.

The primary benefit from crossbreeding is the effect of heterosis on the performance of animals produced by crossing parents of different breeds. For beef cattle, two types of heterosis are important: heterosis expressed in the calfs performance (direct) and heterosis expressed in the crossbred dam (maternal). Heterosis results from the interaction of genes coming from parents of different breeds. The interaction among genes producing heterosis can be classified as dominance, the interaction of genes, or epistasis, the interaction of gene complexes. Studies at Montana State and the USDA indicate that heterosis in beef cattle traits is due mostly to the interaction of genes (dominance). The heterosis effects in the MBE system are proportional to the chance of getting genes from different breeds at a locus. In the MBE system, a direct heterosis effect is included for birth weight, weaning weight, and postweaning gain. A maternal heterosis effect is used for weaning weight.

With 63 different breeds, there are 1,953 different F1 combinations ignoring reciprocal crosses. For the vast majority of these combinations, there are very little if any data from which to estimate these different heterosis effects. To alleviate this problem, breeds were grouped into four classifications: British (B), Continental (C), Zebu (Z), and Other (O). This grouping provides ten combinations: B x B, B x C, ..., O x O. For example, the heterosis expressed by purebred Simbrahs would be represented in the C x Z group since purebred Simbrahs are 62.5% Simmental - 37.5% Brahman.

For each animal in the ASA data base, the fraction of expected heterozygosity is calculated as the product of the breed fractions represented in the parents. The percentage of heterozygosity is expressed relative to the fraction of heterozygosity expected in the F1 calf (100%). As an example, if a breeder mated a purebred Simmental bull that was 15/16ths Simmental and 1/16th Angus to a crossbred cow that was 3/4ths Angus and 1/4th Simmental, the heterozygousity of the calf is calculated as the product of gene fractions from different breeds. Because each parent has Simmental and Angus genes, the fraction of genes coming different breeds will be less than 100% since Simmental or Angus genes from each parent are considered the same for determining heterosis.


Table One:

Sire/Dam

75% AN (B)

25% SM (C)

93.75% SM (C)

70.3% B*C

6.25% AN (B)

1.6% B*C

In this example, the calf would retain 71.9% of the heterozygosity expressed in the F1 British x Continental cross calf. The expected heterosis of this calf would be .719*hBC where hBC is the pounds of heterosis in a F1 mating of British and Continental breeds. The combination of Simmental genes or Angus genes from both parents contributes nothing to the calfs heterosis since the genes are from the same breed.

A popular mating for producing 1st generation purebred Simbrah uses a 3/4 SM 1/4 BR sire and a F1 SM-BR dam. In this mating, the purebred Simbrah calf is 50% heterozygous for Simmental and Brahman genes. (Table 2):

Table Two: 

Sire/Dam

50% SM (C)

50% BR (Z)

75% SM (C)

37.5% C*Z

25% BR (Z)

12.5% C*Z

All the heterozygous gene pairs contain Continental and Zebu genes so the calf retains 50% of the expected Continental x Zebu heterosis.

How much heterosis is retained in a purebred Simbrah calf produced by mating purebred Simbrah parents? A purebred Simbrah calf will have some heterozygous gene pairs on its chromosomes since it is the product of mating parents with Simmental and Brahman genes. To determine the percent heterozygousity in the multi-generation purebred Simbrah calf, consider the example in table 3.

Table Three:

Sire/Dam

62.5% SM (C)

37.5% BR (Z)

62.5% SM (C)

23.4% C*Z

37.5% BR (Z)

23.4% C*Z

A purebred Simbrah calf retains 46.8% of the heterosis seen in a F1 Simmental-Brahman calf if the parents are purebred Simbrahs.

Just like the breed of founder effects, prior values are used to help estimate the direct and maternal heterosis effects in the MBE system. The prior values used in the MBE research run and the heterosis solutions are listed in table 4. The priors were estimated from a review of the literature in the same analysis that produced the breed of founder priors. For Birth Weight, Weaning Weight, and Postweaning Gain, you will notice very little difference between the priors and the solutions. The direct heterosis priors were given much more emphasis relative to the data since in previous research runs, negative estimates were obtained for the B x C direct heterosis effect for some traits. For maternal milk heterosis, the data were allowed to have some influence on the final solutions of maternal heterosis. As shown by the difference between the priors and solutions for MMK, the estimates for maternal heterosis were less than the literature values except for the C x Z group and the Z x Z group. The Z x Z group estimate was equal to its prior since there were not any cows that contributed to the Zebu x Zebu maternal heterosis group in the data.

Table 4. Prior Values and Solutions for Heterosis Effects1

 

     
       BWT      WWT      PWG       MMK  
  Prior  1991  Prior  1991  Prior  1991  Prior  1991
B*B 2.5 2.5 27.0 27.0 8.88  8.8  18.3  12.4 
B*C  1.3 1.3 14.7 14.6 7.0  7.0 25.7 19.6
B*Z  3.5 3.5 40.9 40.9 25.9 25.9 45.9 34.1
B*O 2.4 2.4 27.5 27.5 14.0 14.0 30.0 22.6 
C*C 1.0 1.0 0.7 0.7 26.8 26.8   32.7 17.3
C*Z 2.7 2.7 40.3 40.3 7.3 7.3  19.7 25.1
C*O 1.7 1.7 18.6  18.6 13.7 13.7  26.0 14.4
Z*Z 4.1 4.1 37.9 37.9 1.6 1.6 25.5 25.5
Z*O 3.4 3.4 39.7 39.7 34.8 34.8 30.4 28.4
O*O 2.5 2.5 27.4  27.4 15.4 15.4 25.4 47.9 

 

(1) B = British, C = Continental, Z = Zebu, O = Other
  

How much heterosis can a breeder expect by mating a purebred Simbrah sire to a F1 Simmental x Angus cow (Table 5)? From this mating, the calf would be 56.25% SM, 25% AN, and 18.75% BR. In the diagram below, the crossbred calf retained 68.9% of the heterozygousity of the F1 calf. The total heterozygousity of the calf is the sum of the three different heterosis combinations present when its parents are mated: 31.3% B*C + 18.8% C*Z + 18.8% B*Z.  

Tabel 4

Sire/Dam

50% SM (C)

50% AN (B)

62.5% SM (C)

31.25% B*C

37.5% BR (Z)

18.75% C*Z

18.75% B*Z

 

The expected direct heterosis for weaning weight from this mating would be .313*(14.6) + .188*(40.3) + .188*(40.9) or 19.8 lb. of added weaning weight due to heterosis. In the MBE, the calf's deviation is adjusted for direct heterosis by subtracting 19.8 lb. from the calf s record. If the adjustment was not made, the added weaning performance due to heterosis would be used to predict the EPDs of the calf and its parents thus biasing the EPDs.

Summary

When using records from crossbred calves, the differences in performance are due to differences among the breeds represented in the cross and the effects of heterosis. The calf's performance is influenced by heterosis in two ways: 1) heterosis expressed by the calf (direct) and 2) heterosis expressed by the dam (maternal). Heterosis results from the interaction of genes coming from different breeds represented in the calf's parents. If the calf was a product of mating a Hereford bull to an Angus cow, the calf would 100% heterozygous since every gene pair would have an Angus gene and a Hereford gene. If a calf was produced by mating a PB Simmental bull to a half-blood Simmental-Angus cow, 50% of the calf's gene pairs would be heterozygous for Simmental and Angus genes.

The MBE system calculates the heterozygousity of every calf and its dam in the Simmental data set. Since the data does not allow the expected heterosis to be determined for every F1 breed combination in the data, breeds are placed into four groups: British, Continental, Zebu and Other. Using these four biological types, ten groups are created to represent the combination of genes coming from different biological types.

As with the breed of founder effects, prior values are used to help estimate direct and maternal heterosis effects. For the direct heterosis effects for birth weight , weaning weight, and postweaning gain, the priors were given much greater emphasis compared to the data. The data were allowed to have greater influence on the estimates for maternal milk heterosis.

For calves of different genetic backgrounds in the same management groups, it is very important to adjust for heterosis differences. The added performance due to heterosis cannot be transmitted to the next generation since it results from the interaction of genes. Since heterosis is not part of the animals breeding value, the calf's record needs to be adjusted for the increased performance due to direct and maternal heterosis. The heterosis adjustment is analogous to the adjustment for age of dam. If differences due to heterosis remained part of the animal's own record, the animal and its parents would be given credit for superiority that would bias the EPDs.

 

Multiple-Breed Genetic Evaluation Part 4

Genetic and Gametic Trends
Part 4 of a Series

As a part of the Simmental and Simbrah National Cattle Evaluation, genetic trends are produced to describe the genetic change that has taken place over time. The genetic trends are the average EPDs for calves born in each year. For the current evaluations, genetic trends are calculated for purebred Simmental and purebred Simbrah. The Multiple-Breed Evaluation (MBE) will provide genetic trends for defined groups of animals such as purebred Simmental or purebred Simbrah. Also, the MBE system summarizes the genetic merit of genes coming from a breed group present in calves born in a given year. This yearly summary of genes coming from each breed group is called a gametic trend. This trend uses information from every animal born in a given year to measure the genes from the different breed of founder groups. Every animal with some fraction of Simmental breeding will contribute to the Simmental gametic trend. Likewise, every animal with some fraction of Angus breeding will contribute to the Angus gametic trends.

The genetic trends for purebred Simmental using the Fall 96 evaluation and the MBE Evaluation are shown in table 1. For both evaluations, the base is defined by setting the average EPD of purebred Simmentals born in 1986 to zero. The differences between the average EPDs from the F96 and the MBE analyses reflect differences between the two evaluations. The biggest difference between the F96 and MBE evaluations is the difference in the maternal milk genetic trends.

 

BWT

WWT

YWT

MMK

MWW

 

Fí96

MBE

Fí96

MBE

Fí96

MBE

Fí96

MBE

Fí96

MBE

1970

-0.5

-0.2

-7.1

-6.5

-11.2

-9.8

-0.4

2.8

-4.0

-0.5

1975

-0.5

-0.4

-6.5

-6.9

-10.7

-10.9

-0.8

1.7

-4.0

-1.8

1980

-0.5

-0.6

-4.8

-5.3

-7.5

-8.3

-0.1

0.9

-2.5

-1.7

1985

-0.1

-0.1

-0.8

-0.8

-1.3

-1.4

0.0

0.1

-0.4

-0.3

1990

0.4

0.5

3.9

4.0

6.6

6.7

-0.2

-0.8

1.7

1.2

1995

0.4

0.3

9.0

8.3

15.0

13.6

0.7

-0.8

5.2

3.3

With the MBE system, the EPDs for Simmentals and Simbrah are directly comparable. The genetic trends for purebred Simmental and purebred Simbrahs are shown for the five weight traits in table 2. Comparing the average EPDs of calves born in 1995, the differences in average transmitting ability between Simmental and Simbrah are -.7 for birth weight, +12.3 for weaning weight, +23.1 for yearling weight, +1.3 for maternal milk, and +7.4 for maternal weaning weight. The differences between Simmental and Simbrah come from the differences between Simmental and Brahman that are included in the evaluation. Regardless of the base, the differences between Simmental and Simbrah will remain the same for each trait. The genetic trends show the change in each breed from 1983 to 1995. Using weaning weight as an example, the change in average weaning weight EPD from 1983 to 1995 was +11.1 for Simmental and +10.4 for Simbrah. The genetic trends for Simbrah are roughly parallel to the Simmental trends except for birth weight where Simbrah has increased birth weight EPD about 1 lb. more compared to Simmental.

 

BWT

WWT

YWT

MMK

MWW

 

SM

SMBH

SM

SMBH

SM

SMBH

SM

SMBH

SM

SMBH

1983

-0.3

-0.6

-2.8

-14.4

-4.6

-26.2

0.3

-2.4

-1.1

-9.6

1985

-0.1

-0.2

-0.8

-12.3

-1.4

-22.1

0.1

-1.5

-0.3

-7.7

1987

0.1

0.1

0.8

-11.4

1.4

-20.9

-0.2

-1.8

0.2

-7.5

1989

0.3

0.5

2.9

-9.2

4.9

-17.4

-0.7

-1.9

0.8

-6.5

1991

0.5

0.8

5.4

-6.7

8.9

-13.9

-0.9

-2.1

1.8

-5.4

1993

0.5

1.0

6.8

-4.9

11.2

-11.0

-0.7

-2.5

2.7

-4.9

1995

0.3

1.0

8.3

-4.0

13.6

-9.5

-0.8

-2.1

3.3

-4.1

It would be difficulty to compute a genetic trend for breeds other than Simmental or Simbrah. The ASA data base does not have enough purebred animals from other breeds to compute meaningful trends for those breed groups. However, the ASA data contains many animals with some Angus genes, some Hereford genes, some Brahman genes etc. All animals with a fraction of genes from a breed group contribute to the gametic trend for that breed group. The gametic trend is the average merit of genes from a breed group represented in calves born in a particular year. The trend is expressed on an EPD scale. Every calf contributes to the gametic trend of a breed group if the calf possesses genes from that breed group. Gametic trends are computed for the breed groups included in the MBE analysis: Simmental, Angus, Hereford, Brahman, Charolais, Limousin, Gelbvieh, American, British, Continental, Dairy, and Mixed.

In tables 3 to 5, the average effect of Simmental, Angus, Hereford, and Brahman genes are shown for birth weight, yearling weight, and maternal milk. In addition to the four breeds, gametic trends were computed for the F1 Simmental-Angus cross and purebred Simbrah. Using the gametic trends of the twelve breed groups, trends can be computed for any possible combination of the twelve breed groups. For example, the gametic trend for Simmental-Angus was created by averaging the Simmental and Angus trends. The purebred Simbrah gametic trend was computed as a weighted average equal to 5/8ths of the Simmental trend plus 3/8ths of the Brahman trend.

Compared to the average Simmental genes expressed in calves born in 1995, the difference between Angus, Hereford, and Brahman genes and Simmental genes were 7.6 lb., 9.4 lb., and 0.1 lb. of birth weight, respectively. The average merit of F1 Simmental-Angus genes was intermediate to the Simmental and Angus gene values, -2.5 lb. From 1970 to 1995, the average Simmental genes for birth weight increased 0.5 lb. while the average Angus genes in the ASA data increased 3.5 lb. The average Brahman genes sampled to create Simbrah increased 2.4 lb. from 1970 to 1995.

 

SM

AN

HH

BR

SM-AN

SMBH

1970

0.8

-9.8

-6.4

-1.2

-4.5

0.0

1975

0.2

-9.4

-6.1

-1.1

-4.6

-0.3

1980

0.1

-8.5

-6.0

-1.2

-4.2

-0.4

1985

0.5

-7.5

-6.0

-0.7

-3.5

0.0

1990

1.0

-6.7

-7.2

0.3

-2.8

0.8

1995

1.3

-6.3

-8.1

1.2

-2.5

1.

 

Examining the yearling weight gametic trends, the selection for increased weight is evident regardless of the breed contributing genes. From 1970 to 1995, the increase was 33.3 lb. for Simmental, 23.7 lb. for Angus, 22.4 lb. for Hereford, and 11.5 lb. for Brahman. For F1 Simmental-Angus and Purebred Simbrah genes, the increase in yearling weight transmitting ability was 28.5 and 25.1 lb., respectively. On an EPD scale, the difference between Simmental genes and Angus genes for calves born in 1970 was 49.5 lb. The difference was 59.5 lb. in 1995 between Simmental and Angus.

 

SM

AN

HH

BR

SM-AN

SMBH

1970

-11.1

-60.6

-66.2

-65.3

-35.9

-31.4

1975

-5.8

-58.6

-64.9

-64.6

-32.2

-27.9

1980

-1.6

-54.2

-63.8

-64.8

-27.9

-25.3

1985

5.2

-50.4

-60.8

-62.8

-22.6

-20.3

1990

13.3

-44.4

-55.3

-58.2

-15.6

-13.5

1995

22.2

-36.9

-43.8

-53.8

-7.4

-6.3

For maternal milk, the average Simmental genes decreased 3.5 lb. from 1970 to 1995 while the average Angus genes in the ASA data decreased 1.1 lb. The gametic trends for Hereford and Brahman increased 9.4 lb. and 5.0 lb. from 1970 to 1995, respectively. For calves born in 1995, the average difference in the ASA data between Simmental and Angus genes was 12.6 lb. for maternal milk EPD. The average merit of F1 Simmental-Angus in 1995 was equal to the average Brahman genes in calves born the same year. The average merit of purebred Simbrah genes for maternal milk was 2.4 lb. less than Simmental and 3.9 lb. higher than F1 Simmental-Angus.

 

SM

AN

HH

BR

SM-AN

SMBH

1970

4.1

-10.6

-20.4

-10.4

-3.3

-1.4

1975

3.2

-10.3

-19.6

-9.3

-3.6

-1.5

1980

2.6

-10.5

-18.3

-8.1

-4

-1.4

1985

1.6

-9.8

-17.4

-6.5

-4.1

-1.4

1990

0.6

-11.3

-16.7

-5.2

-5.4

-1.6

1995

0.9

-11.7

-11

-5.4

-5.4

-1.5

Summary

With the MBE System, two types of trends can be produced, genetic and gametic. Genetic trends are produced for a defined group of animals such as purebred Simmentals or purebred Simbrahs. The trends represent the average EPD for calves born in each year. Gametic trends are the yearly average value of genes from a particular breed group in calves born each year. Every animal in the data contributes to the gametic trend depending upon the breeds represented in the animals pedigree. For example, a calf that is 25% Simmental, 50% Angus, and 25% Gelbvieh will contribute to the Simmental, Angus, and Gelbvieh gametic trends. The gametic trends can be used to produce trends for any particular cross of interest based on the information in the ASA data.

The genetic trends for purebred Simmental in the Fall 1996 evaluation and the MBE evaluation were very similar except for maternal milk in the 1970s and early 1980s. The difference between the trends was due to the differences in the records are handled by the two evaluation systems. The EPDs for Simmental and Simbrah animals are directly comparable using the MBE system.

The gametic trends describe breed differences based on all calves born each year. These gametic trends can be used to predict trends for crosses such as F1 Simmental-Angus or F1 Simmental-Brahman. The gametic trends can be used to set the base for any year and breed combination.

All EPDs are expressed relative to some zero point or base. For the purebred Simmental evaluation, the base is defined by making the average EPD of purebred Simmentals born in 1986 equal zero. The purebred Simbrah evaluation defines the base by making the average EPD of purebred Simbrahs born 1986 equal zero. The MBE will require some group to be set to zero. During a meeting at Cornell University, John Pollak said "The opportunity exists to set the base based on you want people to look at your EPDs and think about your cattle. We ask only that all traits be treated the same."

 

 



 

Multiple-Breed Genetic Evaluation Part 5

The Base is Set

Part 5 of a Series

The ASA Board of Trustees has made a decision regarding the base for the MBE Genetic Evaluation to implemented in June, 1997 for the Fall 1997 Sire Summary. They considered several different options for defining the base using the estimated gene effects from the MBE analysis: 1) Average Angus genes in 1991; 2) Average of Simmental, Angus, Hereford, and Brahman genes in 1991; 3) Average British genes in 1991; 4) 1986 Purebred Simmental; and 5) Average of twelve gene effects in 1991. The base chosen by the Board for the weight traits is the average Simmental, Angus, Hereford, and Brahman genes in 1991.

In table 1, the average EPDs for purebred Simbrah and Simmental calves born in 1996 are listed for the Spring '97 evaluation and the MBE Research Run using the current 1986 base and the base approved by the ASA Board. For Simmental breeders, the MBE EPDs will be higher for all traits compared to the PBE EPDs. Breeders can anticipate a 3 lb. increase in BWT EPD, 19 lb. increase in WWT EPD, 35 lb. increase in YWT EPD, 8 lb. increase in MMK EPD, and 21 lb. increase in MWW EPD due to setting the base using the average of Simmental, Angus, Hereford, and Brahman genes in 1991.

Simmental Spring '97 MB-NCE

 

BWT

WWT

YWT

MMK

MWW

SP'97, ASA

0.3

10.8

18.1

0.2

5.6

PB'86

0.2

9.4

15.9

-0.7

4.0

MBE'91

3.4

28.3

50.5

7.1

21.2

Simbrah Spring '97 MB-NCE

 

BWT

WWT

YWT

MMK

MWW

SP'97, ASA

0.6

4.2

6.4

2.5

4.6

PB'86

1.2

-1.8

-6.3

-2.7

-3.5

MBE'91

4.4

17.1

28.3

5.1

13.7

Regardless of the base chosen for the MBE system, the Simbrah EPDs are comparable to the Simmental EPDs. Compared to the Spring 1997 Simbrah evaluation, the Simbrah EPDs will be different since the MBE system uses the Simbrah animal's complete pedigree. The MBE system uses the difference between the average Simmental and Brahman genes in the ASA data to adjust the EPDs. Using the MBE system, the average purebred Simbrah calf born in 1996 is about 1 lb. heavier for BWT, 11 lb. lighter for WWT, 22 lb. lighter for YWT, 2 lb. lighter for MMK, and 8 lb. lighter for MWW. The differences between Simmental and Simbrah are the same regardless of the base.

Why the 1991 Four Breed Base?
  • The EPDs more accurately epresent the merit of Simmental cattle than the current 1986 base.
  • Many commercial cattle are British x Continental or British x Brahman and the EPDs produced will give a good approximation of the results to be expected by breeding to seedstock with the genetic make-ups.
  • The resulting milk EPDs will appropriately de-emphasize breeders and customers' concentration and consternation with our current distribution of maternal milk EPDs.
  • This base provides a blend of our strengths (growth and milk) coupled with adequate emphasis on traits creating challenges (birth weight).
  • The base is the average of the estimated gene effects for the four breeds having the greatest influence in the ASA data set.

During the last two months, the ASA and CSA Boards approved the combining of the U. S. and Canadian data files into a single North American evaluation. The final research run with the MBE system is being performed using the combined data from the American Simmental and the Canadian Simmental Association. Once this research run is completed, we will have the final look at the planned changes to the EPD system prior to the Fall '97 evaluation.

 

 

Michigan State University Extension
Joel Cowley, Extension Beef Specialist
Department of Animal Science
July 22, 1998

What are EPDs?


Expected Progeny Differences (EPDs) are the most current and accurate means to select cattle for the traits for which they are calculated. It has been suggested that selection based upon EPDs is five to nine times more accurate than selection based upon performance indexes and ratios.

EPDs are estimates of how a bull or cow’s future progeny will perform, on average, for a given trait. The words ‘on average’ are italicized, as this is a very important concept to keep in mind. A parent contributes only a sample half of its genes to each offspring. That sample, being random, might contain a large number of genes that have a positive effect on the trait in question (a good sample) or it could contain many genes that have a negative effect (a poor sample). This can be likened to a deck of cards in a poker game. Some hands are winners and some are losers, but they all come from the same deck. Therefore, EPDs do not predict the absolute performance of an animal’s offspring, but the average performance.

As an example, assume that Sire A has a Birth Weight EPD of +5lb. and the Birth Weight EPD of Sire B is —1 lb. We would expect the offspring of Sire A to average six pounds heavier at birth than the offspring of Sire B when the two sires were bred to a large number of comparable cows (i.e. 94 vs. 88 pounds). Not every calf sired by A will be heavier than every calf sired by B, but Sire A’s calves will be heavier on average.

 

How are EPDs calculated?


EPDs are usually calculated twice a year when a breed association gathers performance and pedigree information for their breed. The information is sent to an educational institution where a National Cattle Evaluation (NCE) is performed. Most NCEs currently utilize a multiple trait animal model to statistically analyze the data and generate EPDs. An animal model produces an EPD for every animal in the analysis, parent or non-parent, male or female. Animal models take into account all genetic relationships within a data set so that an animal’s own performance is combined and properly weighted with the performance of relatives (progeny, parents, grandparents, full and half-siblings, etc.) in order to generate an EPD. Multiple trait animal models take into account the genetic relationships that may exist between two or more traits and utilize these relationships as another source of information on a trait. As an example, weaning weight information can be used to help calculate Yearling Weight EPDs, as some of the same genes that affect weaning weight also have an influence on yearling weight. This can help to compensate for biases that might occur as a result of sequential culling (culling a sire’s offspring at weaning so that they have no yearling weight data) or selective reporting of yearling data.

The animal model approach also adjusts for the merit of mates. If a sire was mated to only the best cows, his EPD is adjusted to account for this so that he does not receive all of the credit for a superior set of calves.

The genetic change within a breed is also accounted for in an NCE. Therefore, comparisons may be made across generations of cattle. Based upon the available information, young bulls with no progeny can be directly compared with older bulls with a large number of progeny, meaning that more conservative estimates of an animal’s genetic worth are made when information is limited.

The animal model also separates out the maternal component of a trait. As an example, weaning weight is partitioned into the genetics for growth to weaning age (weaning weight direct) and the influence of mild (the maternal component of weaning weight).

It is important to remember that the EPDs generated by any NCE are only directly comparable with EPDs from the same evaluation (within the same breed).

For what traits are EPDs calculated?
EPDs are calculated for a number of, but not all, economically important traits. Most breeds report EPDs for Birth, Weaning and Yearling Weight as well as Milk. The following is a list of traits for which EPDs are calculated.

Birth Weight- Birth Weight EPDs are expressed in pounds and predict the average difference that can be expected in an animal’s offspring when compared with another animal in the same genetic evaluation. Birth weight EPDs are primarily used as an indicator of calving ease, with the age and size of the females to be bred usually dictating how much birth weight can be tolerated.

Weaning Weight- Weaning Weight EPDs are expressed in pounds and predict the average differences in weight that can be expected between the progeny of animals in the same genetic evaluation at 205 days of age. Weaning Weight EPDs do not account for differences in weaning weight that are due to milk.

Yearling Weight- Like Birth and Weaning Weight EPDs, Yearling Weight EPDs are expressed in pounds and predict the average differences that can be expected between the progeny of animals at one year of age.

Milk- Milk EPDs are expressed as pounds of calf weaned by a bull’s daughters. They reflect the average differences in weaning weight that can be expected in grandprogeny due to the milking ability of a bull’s daughters. Available feed resources will dictate the extent to which milking ability should be selected.

Total Maternal (Maternal Weaning Weight)- Like Milk EPD, Total Maternal EPDs are also measured in pounds of calf weaned by an animal’s daughters. They account for average differences that can be expected from both weaning weight direct as well as from milk, and measure a sire’s ability to transmit milk production and growth rate through his daughters. They are calculated by adding an animal’s Milk EPD to one-half of its Weaning Weight EPD.

Yearling Hip Height- Reported in inches. Predict the average difference in progeny hip height that can be expected at one year of age. (Angus).

Calving Ease Direct- Predict the average difference in ease with which a sire’s calves will be born when bred to first-calf heifers. Expressed as percentage of unassisted births with a higher value indicating greater calving ease (Gelbvieh, Simmental, Tarentaise).

Calving Ease Maternal- Predict the average ease with which a sire’s daughters will calve as first-calf heifers when compared to the daughters of another sire in the same evaluation. Expressed as percentage of unassisted births (Gelbvieh, Simmenal, Tarentaise).

Scrotal Circumference- Estimate the average differences that can be expected in scrotal circumference in male progeny. Expressed in centimeters. Of interest as larger scrotal circumference is favorably associated with fertility and age at puberty in a sire’s daughters (Limousin, Angus, Hereford).

Gestation Length- Predict average differences in gestation length. Expressed in days. Shorter gestation lengths are associated with less dystocia and longer post-partum intervals (Limousin and Gelbvieh).

Stayability- Expressed as the probability that an animal’s daughters will remain in production to at lease six years of age when compared to the daughters of another animal. A measure of sustained fertility that probably reflects traits such as fleshing ability and structural soundness. Expressed as deviations from a 50% probability, a higher value indicates increased stayability (Red Angus, Limousin).

Mature Daughter Height and Weight- Predict the average differences that can be expected in mature daughter size in inches and pounds, respectively. These EPDs can be used to match mature cow size to forage resources (Angus).

Carcass Weight- Estimate average differences in carcass weight. Expressed in pounds at a given age endpoint (Angus and Simmental).

Marbling- Predict the average difference in USDA Quality Grade in an animal’s progeny when compared to the progeny of another animal at a given age endpoint. Expressed in numerical marbling score where one point equals one USDA marbling score (Angus and Simmental).

Ribeye Area- Predict the average difference in ribeye area in an animal’s progeny when compared to the progeny of another animal at a given age endpoint. Expressed in square inches (Angus).

Fat Thickness- Estimate the average differences that are expected in fat thickness at the 12th and 13th rib between progeny of different animals. Expressed in inches at a given age endpoint (Angus).

Percent Retail Cuts- Predict the average differences in cutability that can be expected between the progeny of animals at a given age endpoint. Expressed as percent (Simmental).

Docility- Predict the percentage of an animal’s offspring that are expected to score favorably (1 or 2) on a five-point scoring system when compared to the offspring of another animal. Expressed as a percentage with higher values being favorable (Limousin).

How do I know if EPDs are high or low?
It is easy to determine which animal has the highest or lowest EPD, but what about the magnitude of the estimate relative to the breed? The genetic composition of the herd as well as the environmental conditions and marketing strategy, will determine the level to which traits should be selected. Breed averages can be used as a benchmark to determine where an animal ranks within the breed as well as whether or not an animal’s offspring will be suitable for a given set of environmental conditions. Average EPDs will vary between breeds due to differences in Reference Year (the year that all EPDs were arbitrarily set to zero) and Genetic Trend (what has happened in a trait since the Reference Year). Breed averages can be calculated for the entire breed or for a subset of animals. Table 1 lists breed average EPDs for animals born in 1997.   

Table 1. Average EPDs for Animals Born in 1997

Breed

BW

WW

YW

Milk

Angus

3.1

27.3

48.2

11.1

Charolais

1.7

14.6

21.1

2.0

Gelbvieh*

2.6

33.4

58.8

19.5

Hereford

4.1

31.0

53.0

8.0

Limousine

1.4

8.1

15.0

1.0

Maine Anjou

-.1

.8

1.5

.3

Red Angus

.8

24.8

41.6

9.7

Salers

.7

6.9

11.7

2.6

Shorthorn

2.3

15.5

24.8

3.6

Simmental

4.0

30.6

48.6

9.4

*Adjusted to reflect the Fall 1998 change in base 

 

Another method for comparing breeds based on genetic merit lies within the databases of several breed associations. The policy of many associations allows for the upgrading of percentage cattle to purebred status. As a result, these breed associations have performance in formation of several breeds within their database, information where animals of different breeds are competing within the same contemporary groups. The American Simmental Association implemented a Multiple-Breed Evaluation (MBE) system in their Fall 1997 genetic evaluation. All animals in their database were evaluated in the same statistical model. This allows the resulting EPDs to be directly compared regardless of breed. Such an evaluation would prove beneficial in defining genetic differences for commercial cattlemen. 

What does the Accuracy Value mean?


All EPDs are associated with an accuracy value that represents the reliability of the estimate. Accuracies are computed based upon the quantity and quality of information that went into the estimate and fall in a range between 0 and 1. An accuracy close to 1 indicates that an EPD merits a high level of confidence as it is the result of a great deal of information and is likely an accurate representation of the animal’s true, unknown average genetic value. Values close to 0 indicate a low level of reliability (or a high level of risk) associated with the estimate.

In addition to numeric accuracies, Interim (I) or Pedigree Estimate (P or PE) accuracies may be attached to an EPD. Interim EPDs are calculated when an animal’s own performance was not available or was edited from the most recent NCE. They are computed by averaging the parent’s EPDs and factoring in the animal’s own performance and contemporary group information. Pedigree Estimate EPDs are merely the average of the parental EPDs are do not include the animal’s own performance. Depending upon the trait, P(E) or I accuracies will generally correspond to numeric accuracies of from .10 to .30.

Higher accuracy values indicated that an EPD is less likely to change in subsequent evaluations. Sire summaries contain a table of Possible Change Values to allow you to determine the risk associated with different levels of accuracies for different traits.

A common misconception associated with accuracy is that a bull’s progeny will become more uniform as his accuracies increase. The bull is not changing as his accuracy values increase. He is still the same bull, throwing a random sample of the same genes and producing the same amount of variation in his offspring. The higher accuracy value simply indicates that we are more confident as to what those genes are and, therefore can more accurately predict what the average of his progeny will be when compared with the progeny of another sire.

Is there a way to compare EPDs across breeds?
Scientists at the U.S. Meat Animal Research Center (MARC) in Clay Center, NE have developed an adjustment procedure to convert EPDs from one breed(s) to a comparable scale for another breed. Actual performance differences between the breeds were determined through the comprehensive Germplasm Evaluation Project (GPE), initiated in 1969. Breeds in the GPE are evaluated by artificially inseminating Hereford and Angus cows to a sample of bulls from each breed. The resulting offspring are evaluated for several economically important traits.

By using the actual breed differences (in pounds) from the GPE and adjusting all data to a common base year, adjustment factors are developed to compare the EPDs of cattle of different breeds. Although Across-Breed EPDs appear to merit confidence for growth traits, Milk EPDs may be another matter due to the difficulty in measuring the trait. Other concerns with Across-Breed EPDs appear to merit confidence for growth traits, Milk EPDs may be another matter due to the difficulty in measuring the trait. Other concerns with Across-Breed EPDs are that they do not account for differences that may occur as a result of hybrid vigor and that it is unknown whether or not the same breed differences seen at MARC will hold true across other environments. The estimates listed in Table 2 are not EPDs. They are the most recent MARC adjustment factors that can be added to the EPDs of animals of different breeds in order to adjust them to an Angus equivalent (1996 base). They account for the breed differences observed at MARC as well as the differences in breed average EPDs. As an example, if we wanted to compare the average Angus, Charolais and Hereford animals (from Table 1) with regard to Birth Weight EPD, we could use the factors from Table 2 to adjust all three to an Angus equivalent. Birth Weight EPDs would be 3.1 (3.1 + 0.0), 12.9 (1.7 + 11.2) and 8.1 (4.1 + 4.0) pounds for the average Angus, Charolais and Hereford, respectively. Keep in mind that EPDs are not calculated for every economically important trait and there are reasons for choosing a breed other than just for birth weight, weaning weight, yearling weight, and milk.

 

Table 2. Across-Breed EPD adjustment factors to adjust breeds to a 1996 Angus Equivalent

Breed

BW

WW

YW

Milk

Angus

+0.0

+0.0

+0.0

+0.0

Charolais

+11.2

+2.0

+62.0

+1.7

Gelbvieh*

+7.8

+20.1

+3.3

+10.1

Hereford

+4.0

+3.0

+4.4

-9.6

Limousine

+8.1

+34.0

+29.2

-9.7

Maine Anjou

+12.3

+41.1

+53.9

+23.8

Salers

+6.5

+29.6

+34.9

+12.9

Shorthorn

+8.3

+29.4

+40.7

+10.7

Simmental

+7.3

+24.4

+42.2

+13.6

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