A new era for the Montbeliarde genomic Proofs

A new way to calculate the genomic indexes

April 2015

A new way for the genomic indexation

All the information in this presentation comes from the data provided by the UMT 3G (Technical Department for Genetic and Genomic Studies).

April 2015

A new step forward for the genomic era The Montbeliard breeders were waiting for more reliability in the proofs. Since 10th April and the new proofs, this has been achieved.

By taking into account DNA tested females within the genomic calculation, the reference population has been multiplicated by 4. This population hadn’t been updated for 5 years prior to this achievment.

Moreover, for each trait, a new step forward is done: from 500 region with genetic information (QTL, Quantitative Trait Locus), we now take into account more than 3 000!

The genomc analysis is consequently far better. We definitely increase the reliability by 10 points in the Montbeliarde!

x4 x6

That’s the increase (in terms of size) of the Montbeliarde reference population

The number of regions on the genome where the information has been multiplicated by 6

RELIABILITY +10points

x4

Increase of the size of the Montbeliarde population

Until now, 1 500 DNA tested and proven sires were used as a reference population to calculate proofs of young bulls. This basis has been completed by 1 100 extra proven sires, coming from the last years.

Moreover, 20 000 DNA tested females with proofs (lactations and phenotypic evaluation) add more information to this population. That’s a huge asset because 5 DNA tested females with proofs bring as much information as 1 proven sire with daughters.

= 6300 1500 bulls

2010

+1 100 Proven bulls

+20 000 females

2015

equivalent bulls The reference population has increased from 1 500 (in 2010) to 6 300 bulls (in 2015)

x6

The number of QTL has been multiplicated by 6

Thanks to new statistic calculations and more powerful software, the reading of the genome is getting more and more reliable. In 2010, 500 QTL were used to assess one trait (like the milk). In 2015, for the same trait, 3 000 QTL are used! Moreover, we kept a small part of the polygenic information in the last indexes (coming from the parental indexes). This part has disappeared and the indexation is now 100% genomic.

Genomic indexation

Genomic indexation

2010

2015

Part

Source

% variability explained

Polygenic

pedigree

50%

Part

Source

% variability explained

10 000 SNP

25%

3 000 QTL

75%

Genomic Genomic

500 QTL

50%

A new step forward with the genomic selection

x4 Increase of the size of the Montbeliarde reference population x6 Increase of the number of QTL

RELIABILITY +10points Young bulls (<1 year) Milk production Type Fertility Lifespan

Reliability with Reliability with the old model the new model 58 68 54 67 51 60 47 56

Whatâ&#x20AC;&#x2122;s the reliability?

An index is not the true genetic value of the animal but an estimation of its breeding value.

The reliability gives us information about the precision of this breeding value.

The degree of confidence of the breeding value gets smaller when the reliability is close to 1.

113 kg

Rel= 50%

313 kg

Variations of a breeding value, depending on its reliability

1887 kg

Rel = 70%

439 kg

1687 kg

Rel = 80%

603 kg

1561 kg

Rel = 90% 710 kg

1397 kg Rel = 95%

1290 kg

INDEX = + 1000 kg milk

To what extent can breeding values vary?

Values of index have been calculated for different types of animals: • • • •

Females with lactations Young bulls, under 2 years old Young bulls already used Proven sires with daughters

The indexes from October 2014 (calculated with the old method) have been compared to the indexes from April 2015 (calculated with the new method).

To what extent can breeding values vary?

The graph below shows the distribution of the variations of young Montbeliard bulls.

A majority of animals are within a small variation area of +/- 6 pts ISU!

Candidates under 2 years old

Montbeliarde breed: young animals without any proof

Animals without proofs and females under 2 years old

To what extent can breeding values vary?

Young bulls <5 years old

Young bulls, used between 2 and 5 years old

Bulls from 6 to 10 years old

Montbeliarde breed Young bulls and proven sires

Sires with daughters in France and aged from 6 to 10 years old

Young bulls for whom the indexes have been published are impacted by this new method. The graph at the top shows the variations in this population. We can notice some important variations (increase and decrease), reaching 30 points.

However, most of the bulls remain in the area of +/- 12 points.

For the Proven sires, the situation is more stable. The new indexes are mainly explained by new daughters, coming into milk and/or phenotypying.

The change of the model does not impact the proven sires.

The new genomic indexes predict the coming proofs of the females much better .

The correlation between genomic indexes of DNA tested females and their proofs is clearly improving, as shown in the table below. This improvment is clear for all groups of traits; production, type and functional traits.

Montbeliarde breeders will make more precise decisions concerning their replacement heifers!

Montbeliarde breeders The new genomic indexes are fairly reliable predictors for the female side

Milk production Somatic cell Count Stature Udder development

Correlations between genomic indexes 2015 and proofs of DNA tested cows Lactation number

Last model

New model

L1 L2 L3 L1 L2 L3

0,27 0,40 0,41 0,27 0,33 0,38

0,50 0,63 0,70 0,43 0,52 0,60

-

0,46 0,39

0,80 0,65

The new genomic indexes of young bulls predict their next index, calculated with daughters, much better The correlation between the genomic indexes of DNA tested young bulls and their index, calculated with daughters, is clearly improving, as shown on the graph below.

This improvment is present for every group of traits; production, type and functional traits.

•In blue, it’s the correlation between the parental indexes and the indexes with daughters (0,35). We osberved that when testing bulls •In red, the genomic model 2010 allowed us to gain a correlation of 0,15.

•In green, the correlation which is calculated is now strong and reaches 0,55!

Validation works in the Montbeliarde breed

The new genomic index are fairly good predictors for the male side

Milk production

Type

Functional Traits

More information available for young bulls

With the increase of the reliability, more functional traits are published

To sum up, with the new method, we do more efficient mating plans, taking into account all traits.

For more information:

Presentation of daughters of proven sires during the COOPEXUMOTEST Show in 2015, held in Besançon-FRANCE.

Contact your partner

4, rue des Epicéas, 25640 Roulans-France export@coopex.com www.coopex.com