Genetics Analysis



----------------------------------------------------------------------------------------------------------------------------

Understanding Genetic Analysis

The use of genetic markers in describing cattle is still in its infancy.  Pfizer (formerly Bovigen) has
been a leader in the efforts to translate available DNA information to the Cattle buyer and producer.  
This has not been an easy job as the amount of information has been changing almost on a daily basis.

We started with Gene Star and Genetic Progeny Difference.  The GPD’s were based on four genetic
identifiers for feed efficiency, three for tenderness and four for quality grade or marbling.  The limited
number of markers were easily translated into stars to indicate to the casual observer the obvious
differences between animals.  The more stars you had the better the animals potential.  Cattlemen
could make a quick decision based on an obvious measure i.e. the number of stars.

But the analysis of the cattle genome was just beginning. More and more markers were being
identified and used to present a better and more correct picture of the animal’s makeup.  The Stars
system quickly became unwieldy as the markers increased.  Today our analysis is based on 56
markers to define three traits, Feed Efficiency, Tenderness and Quality.  The results are now
as Molecular Value Predictions.

The folks at Pfizer have come up with a scale for each of the traits, which can incorporate all the
inputs and present a picture of that trait in a range that is scientifically based.  Please review the
explanation put out by Pfizer.  They are a part of this web site and may be found by simply
clicking on “Pfizer, Understanding MVP results”.  This is a very thorough and complete
explanation of the DNA numbering evaluation that is presented for animals involved in our
embryo, semen or actual animal sales.
----------------------------------------------------------------------------------------------------------
EXPECTED BREEDING VALUES (EBV'S)
BACKGROUND
Breedplan was created over many years with funding of over $90 million by the Australian
government, the Australian beef industry and four research groups. Over 83 breed societies
worldwide utilize this evaluative system.

In 2009, the first GROUP BREEDPlAN analysis for the Wagyu breed in Australia was published.
The GROUP BREEDPLAN analysis included performance information from 27 different Wagyu
herds, with over 42,000 animals represented. Herds that participated in the GROUPBREEDPLAN
analysis have  been sent reports containing the GROUPEBVs for their animals  and comparing
them to all the other Wagyu in the study.

UNDERSTANDING EBV's
An animal's breeding value is its genetic merit, half of which will be passed on to its progeny.  
While the exact breeding value can not be known, for performance traits it is possible to
make good estimates.  These estimates are called
Estimated Breeding Values (EBVs).

EBVs report the breeding value of a variety of performance traits - from birth weight to mature cow
weight, eye muscle area to IMF%. The critical point here is that the value of any given performance
trait is determined by comparing it to those of other animals in the herd: particular animals are
valued as being either above or below the herd average (or 50%) - in the case of the GROUP
BREEDPLAN, the animals are valued as being either above or below the Wagyu Breed average.

EBV TRAITS AVAILABLE
The following EBVs  are shown in Breedplan graphs to the Wagyu herd:
• Birth Weight is based on the measured birth weight of progeny,  adjusted for dam age:
the lower the value, the lighter the calf at birth.
•200-day Growth is calculated from the weight of progeny taken between 80 and
300 days of age, adjusted to 200 days and for dam age.  
•400-day Growth is calculated from the weight of progeny taken between 301 and 500
days of age, adjusted to 400 days and for dam age.
·600-day Weight is calculated from the weight of progeny taken between 501 and 900
days of age, adjusted to 600 days and for dam age.
· Milk estimates milking ability: for sires, it indicates daughter's milking
ability as inherited from the sire.

• Rib Eye Area is calculated from live animal ultrasound scans at the 12th and 13th rib site,
adjusted to 500 days of age: the higher the value, the larger the eye muscle area, and
the better muscled and higher percentage yielding progeny will be produced .    
•Intramuscular Fat % estimates the genetic difference in percentage of scanned IMF
at the 12/13th rib site in a 500 day animal: the larger the percentage, the better.  

NOTE: The IMF%EBV should not be confused with Marbling - without actual carcass data this
EBV only serves to point in the direction of expected value. A direct correlation has not yet been proven.
--------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------
We at Down Under Genetics have analyzed the information presented and have put together a ranking
analysis that while not scientifically defensible will, we believe give the casual observer an idea of the relative
value of different animals.  This system merely takes the ranges of the measured traits and grades them from
bottom to top.  The bottom that is the least desirable side of the equation, whether a minus or a plus, is
expressed as a zero and the top as a hundred.  The resulting number is then multiplied by the % reliability for
that trait as supplied by Pfizer.  This is called the Trait Summary Number.  A TSN tells you the grading point
on a scale of one to 100 of the trait being evaluated multiplied by the reliability of the number.

For instance the Feed Efficiency Range is from –3.17 to 2.38, that’s a total of 5.55 lbs.  Changing that scale
from 5.55 to one hundred would mean that .18 would multiply each hundredth of a point.   The bottom number
(0) would translate to a positive 2.38 pounds and the top (100) would translate to a –3.17 pounds.  A bit more
math is involved but this is a fairly good summary of the resulting Trait Summary Number.

A reading of 0.0 would translate to 238 X .18= 43 X 30% = 13.

Looking at Marbling we have a range or 2.11.  Then each one hundreth of a point is worth .47 on a scale of
one to one hundred.  On this marker positive is better so the bottom number or zero here corresponds to
–1.00, and the top or 100 to 1.11.    Let’s take a score of 0.  That would translate to 47 on our one to one
hundred scale and then with the reliability of 26% we’d end up with a Trait Summary Number of 12

On Tenderness we have a range of 2.93 and on this is minus is positive.  A max force of 1.89 pounds would
translate to ) on our scale of zero to one hundred, and a top score of –1.04 would translate to one hundred.   
Each one hundredth would then have a value of .34 on the zero to one hundred scale.  Again let’s go with an
initial reading of zero this would translate to 189 X .34 =63 X our % reliability of 49% = 31

Taking the above animal it would have the following readings:
Feed efficiency 13
Marbling           12
Tenderness        31


All are of course relative to other numbers in their class and all have
been corrected for reliability.  We believe our Trait Summary Number is a real
working tool that can be easily applied and understood.   For a more complete
understanding and analysis refer to the Pfizer  Summary, but for a quick look
the Down Under Trait Summary is a useful tool.














Genetic Testing - DUG Sires Defect Free

Testing results for signs of genetic abnormalities in U.S. wagyu
are available along with information about the 5 defects tested for here:
American Wagyu Association

Australia has also conducted these genetic tests, and results show that
Down Under Genetics  two herd sires,  Maifuku and Marblemax, have
tested clean and free of any indicated markers or defects.  
The genetic testing results for our bulls can be found at
Australian Wagyu Tested Sires

For more information please read:
American Wagyu Associations' Genetic Disorder FAQ
and
Genetic Memo

Down Under Genetics LLC

For an explanation of the analysis that is involved in the
selection of
animals for breeding the reader should familiarize himself with
the different methods of selection employed by breeders and
then adapt the method with which he is most comfortable.