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Monthly Archives: July 2017

How do genomic proofs hold up?

We’re well into the genomic era. If you’re like most producers, you’re now comfortable incorporating genomic-proven bulls as part of your balanced breeding program.

Yet, you might still have questions about the difference you can expect between a bull’s first genomic proof and his daughter proof. To answer your questions, we’ve done an in-depth proof analysis of all industry bulls. Our goal was to find out how genomic proofs hold up. Do they become more or less accurate with time?

What did we learn?

Graph 1 shows the average change in TPI from initial genomic proofs to April 2017 daughter proofs. The TPI change from genomic to daughter proof is the amount of space that separates the blue and orange lines.

Graph1, which shows the change in TPI the average industry bulls see from their initial genomic release until their April 2017 daughter proof
Graph 1. Change in TPI from genomic release to April 2017 daughter proof

So, even though genomic numbers are still slightly inflated, the gap between genomic and daughter proofs changes less with each passing proof round.

Want more details?

Let’s look at the facts and figures in a different light. We’ll focus in on all 1,078 industry bulls released in 2013. We use this group because all bulls released in 2013 should now have a daughter proof for production, health and conformation traits.

The bell-shaped curve of Graph 3 shows the mean and standard deviation change in TPI on the 1,078 industry bulls released as genomic-proven sires in 2013.

Graph 3, which shows the bell-shaped curve distribution of TPI change from the initial genomic figures of bulls released in 2013 to their April 2017 daughter proof
Graph 3. Histogram of difference in TPI from genomic release in 2013 to April 2017 daughter proof

As you can see, on average, these bulls changed less than 100 points from their initial release in 2013 to their daughter proof in April 2017. One hundred of these bulls have a daughter-proven TPI within just twenty points of their original genomic TPI. Only about 40 bulls from the entire group of 1,078 lost more than 300 TPI points – that’s less than 4%.

We see the same trend for NM$. Graph 4 shows the average NM$ change and standard deviation of the same 1,078 industry bulls released in 2013. These sires changed about -103 NM$ from their initial genomic proof in 2013 to their daughter proof in April 2017.

Ninety-five bulls held steady within the small 20 point swing from genomic to daughter-proven NM$. Less than 20 bulls changed more than 300 NM$.

Graph 4, which shows the bell-shaped curve distribution of NM$ change from the initial genomic figures of bulls released in 2013 to their April 2017 daughter proof
Graph 4. Histogram of difference in NM$ from genomic release in 2013 to April 2017 daughter proof
Click the thumbnails below to find the average change in individual traits from a bull’s genomic release in 2013 to his daughter proof in 2017.
April 2017 Top Dtr-proven bullTPI
11HO11434 | AltaCR2531
11HO11379 | AltaRABO2476
11HO11348 | AltaBGOOD2474
11HO11143 | AltaEMBASSY2462
11HO11380 | AltaROBLE2461
11HO11283 | AltaMERCI2450
11HO11272 | AltaGILCREST2444
11HO11446 | AltaPITA2430
11HO11202 | AltaOAK2425
11HO11405 | AltaKADO2419
AVERAGE2457
April 2017 Top Genomic-proven bullsTPI
11HO11630 | AltaMORENO2742
11HO11778 | AltaROBSON2733
11HO11725 | AltaAMULET2712
11HO11724 | AltaSTEEL2684
11HO11826 | AltaLOBELLO2681
11HO11758 | AltaNIXER2676
11HO11672 | AltaKERMIT2667
11HO11736 | AltaRECOIL2656
11HO11734 | AltaPOLISH2651
11HO11720 | AltaFLYWHEEL2643
AVERAGE2685

Currently, our top daughter-proven sires average a solid 2457 TPI. Yet, the top, available genomic-proven group provides a 228 point TPI advantage!

Some bulls gain points and some bulls lose points. But your odds are nearly zero that every single bull atop the genomic-proven list would drop to rank lower than the current list of daughter-proven sires.

As you make your genetic selection decisions, keep in mind:

  1. Genomic proofs are slightly inflated. Yet, with each proof round, we see less change from genomic to daughter-proven TPI and NM$ because of model adjustments made along the way.
  2. The average TPI and NM$ change from genomic proof to daughter proof for bulls released in 2013 is about -100. Despite that change, you still make much faster genetic progress using a group of genomic-proven sires than a group of daughter-proven sires.
  3. Make sure the genetic progress you make is in the direction of your goals. Select a group of genomic-proven sires based on your customized genetic plan. Emphasize only on the production, health or conformation traits that matter most to you to boost your farm’s future profitability.

Proof analysis and graphs done by Ashley Mikshowsky, PEAK Geneticist

Click to download a printable PDF of this article.

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Proof terminology explained

The letters, numbers and acronyms on a proof sheet can be complicated. Here, we break down the meaning and explanation of the proof indexes, traits and terminology.
Selection indexes

Genetic selection indexes are set by national organizations or breed associations. Genetic indexes help dairy producers focus on a total approach to genetic improvement, rather than limiting progress by single trait selection.

However, each farm is unique, with different situations and future plans. With that in mind, it’s important to understand what traits are included in each industry standard index. When you know what’s included, you can more effectively evaluate if the index truly matches your farm’s goals.

TPI = Total Performance Index
TPI is calculated by the Holstein Association USA (HA-USA) and includes the following trait weightings.

Image to show the weights on production, health and type for the TPI Index

PRODUCTION TRAITS = 46%

21% Pounds of protein
17% Pounds of fat
8% Feed efficiency

HEALTH TRAITS = 28%

13% Fertility index
-5% Somatic cell score
4% Productive life
3% Cow livability
2% Daughter calving ease
1% Daughter stillbirth

TYPE TRAITS = 26%

11% Udder composite
8% PTA type
6% Foot & leg composite
-1% Dairy form

NM$ = Net Merit Dollars

NM$ is a genetic index value calculated by the Council on Dairy Cattle Breeding (CDCB). It describes the expected lifetime profit per cow as compared to the base of the population born in 2010. Trait weightings are generally updated approximately every five years and include emphasis on the following traits. The current trait breakdown is in place as of April 2017. Please note that trait weights are rounded to the nearest percentage.

Image to show trait weights for production, health and conformation within Net Merit $.

PRODUCTION TRAITS = 43%

24% Pounds of fat
18% Pounds of protein
-1% Pounds of milk

HEALTH TRAITS = 41%

13% Productive life
7% Cow livability
7% Daughter pregnancy rate
-6% Somatic cell score
5% Calving ability
2% Cow conception rate
1% Heifer conception rate

TYPE TRAITS = 16%

7% Udder composite
6% Body weight composite
3% Foot & leg composite

CM$ = Cheese Merit Dollars

CM$ is an index calculated to account for milk sold to be made into cheese or other dairy products. The current CM$ index was adjusted in April 2017 and the following trait weights are considered. Please take note that trait weights shown have been rounded to the nearest percentage.

Image showing the trait breakdowns for production, health and type within the Cheese Merit dollars formula

PRODUCTION = 50%

22% Pounds of protein
20% Pounds of fat
-8% Pounds of milk

HEALTH = 37%

12% Productive life
-7% Somatic cell score
6% Cow livability
6% Daughter pregnancy rate
4% Calving ability
1% Cow conception rate
1% Heifer conception rate

TYPE TRAITS = 13%

6% Udder
-5% Body weight composite
2% Foot & leg

GENERAL PROOF TERMS

CDCB: Council on Dairy Cattle Breeding
Calculates production and health trait information for all breeds

MACE: Multiple-trait across country evaluation
Denotes that a bull’s proof evaluation includes daughter information from multiple countries

PTA: Predicted transmitting ability
The estimate of genetic superiority or inferiority for a given trait that an animal is predicted to transmit to its offspring. This value is based on the animal’s own records and the records of known relatives.

EFI: Effective future inbreeding
An estimate, based on pedigree, of the level of inbreeding that the progeny of a given animal will contribute in the population if mated at random

GFI: Genomic future inbreeding
Similar to EFI, an animal’s GFI als predicts the level of inbreeding he/she will contribute in the population if mated at random. Yet, GFI provides a more accurate prediction. It takes into account genomic test results and the actual genes an animal has.

aAa: an independent method for making mating decisions

DMS: a separate, independent method for making mating decisions

 

PRODUCTION TRAITS

PTAM: Predicted transmitting ability for milk

PTAP: Predicted transmitting ability for protein

PTAF: Predicted transmitting ability for fat

PRel: the percent reliability of a sire’s production proof

 

HEALTH & FERTILITY TRAITS

PL: Productive Life
Measured as the total number of additional or fewer productive months that you can expect from a bull’s daughters over their lifetime. Cows receive credit for each month of lactation, with more credit given to the first months around peak production, and less credit given for months further out in lactation. More credit is also given for older cows than for younger animals.  

LIV: Cow livability
Measure of a cow’s ability to remain alive while in the milking herd.

SCS: Somatic cell score
The log score of somatic cells per milliliter.

DPR: Daughter pregnancy rate
Daughter Pregnancy Rate is defined as the percentage of non-pregnant cows that become pregnant during each 21-day period. A DPR of ‘1.0’ implies that daughters from this bull are 1% more likely to become pregnant during that estrus cycle than a bull with an evaluation of zero. Each increase of 1% in PTA DPR equals a decrease of 4 days in PTA days open.

HCR: Heifer conception rate
A virgin heifer’s ability to conceive – defined as the percentage of inseminated heifers that become pregnant at each service. An HCR of 1.0 implies that daughters of this bull are 1% more likely to become pregnant as a heifer than daughters of a bull with an evaluation of 0.0

CCR: Cow conception rate
A lactating cow’s ability to conceive – defined as the percentage of inseminated cows that become pregnant at each service. A bull’s CCR of 1.0 implies that daughters of this bull are 1% more likely to become pregnant during that lactation than daughters of a bull with an evaluation of 0.0.

MAST: expected resistance of an animal’s offspring to clinical mastitis
Daughters of a bull with a MAST value of +1.0 are expected to have 1% fewer cases of mastitis than the average herdmate.

METR: expected resistance of an animal’s offspring to metritis
Daughters of a bull with a METR value of +1.0 are expected to have 1% fewer recorded cases of metritis than the average herdmate.

KET: expected resistance of an animal’s offspring to ketosis
Daughters of a bull with a KET value of +1.0 are expected to have 1% fewer recorded cases of ketosis than the average herdmate.

DA: expected resistance of an animal’s offspring to displaced abomasum
Daughters of a bull with a DA value of +1.0 are expected to have 1% fewer recorded cases of displaced abomasum than the average herdmate.

MFEV: expected resistance of an animal’s offspring to milk fever (hypocalcemia)
Daughters of a bull with a MFEV value of +1.0 are expected to have 1% fewer recorded cases of milk fever than the average herdmate.

RP: expected resistance of an animal’s offspring to retained placenta
Daughters of a bull with a RP value of +1.0 are expected to have 1% fewer recorded cases of retained placenta than the average herdmate.

HRel: the reliability percentage for a sire’s health traits

 

CALVING TRAITS

SCE: Sire calving ease
The percentage of bull’s calves born that are considered difficult in first lactation animals. Difficult births include those coded as a score of 3, 4 or 5 on a scale of 1-5.

DCE: Daughter calving ease
The percentage of a bull’s daughters who have difficult births during their first calving. Difficult calvings are those coded as a 3, 4 or 5 on a scale of 1-5.

SSB: Sire stillbirth
The percentage of a bull’s offspring that are born dead to first lactation animals.

DSB: Daughter stillbirth
The percentage of a bull’s daughters who give birth to a dead calf in their first lactation.

 

TYPE / CONFORMATION TRAITS

PTAT, UDC and FLC are all calculated by the Holstein Association USA.

PTAT: Predicted transmitting for type – referring to the total conformation of an animal

UDC: Udder composite index; comprised of the following linear trait weights:
19% Rear udder height
17% Udder depth
-17% Stature
6% Rear udder width
13% Fore udder attachment
7% Udder Cleft
4% Rear teat optimum
4% Teat length optimum
3% Front teat placement

FLC: Foot and leg composite index; comprised of the following trait weights:
58% foot and leg classification score
18% rear legs rear view
-17% stature
8% foot angle

TRel = the percent reliability for a sire’s conformation/type proof

 

GENETIC CODES

POLLED
PO: observed polled
PC: genomic tested as heterozygous polled; means 50% of offspring are expected to be observed as polled
PP: genomic tested as homozygous polled; means that 100% of offspring are expected to be observed as polled

COAT COLOR
RC: carries the recessive gene for red coat color
DR: carries a dominant gene for red coat color

RECESSIVES & HAPLOTYPES

These codes, or symbols representing the code, will only show up on a proof sheet if an animal is a carrier or test positive for one of the following. The acronyms denoting that an animal is tested free of a recessive will only show up on its pedigree.

BY: Brachyspina
TY: Tested free of brachyspina

BL: BLADS, or Bovine leukocyte adhesion deficiency
TL: Tested free of BLADS

CV: CVM or Complex vertebral malformation
TV: Tested free of CVM

DP: DUMPS, or Deficiency of the uridine monophosphate synthase
TD: Tested free of DUMPS

MF: Mulefoot
TM: Tested free of mulefoot

HH1, HH2, HH3, HH4, HH5: Holstein haplotypes that negatively affect fertility
HCD: Holstein haplotype for cholesterol deficiency

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