# Some opportunities and challenges regarding SNP international evaluations

Vincent Ducrocq

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## To cite this version:

Vincent Ducrocq. Some opportunities and challenges regarding SNP international evaluations. Interbull Technical Workshop, Feb 2017, Ljubljana, Slovenia. pp.22 slides, 2017. hal-01605561

HAL Id: hal-01605561

https://hal.science/hal-01605561

Submitted on 2 Jun 2020

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# Some opportunities and challenges regarding SNP international evaluations

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Vincent Ducrocq

GABI, INRA, Jouy-en-Josas, France

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# Genomic selection programmes in dairy cattle

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* Impose to obtain GEBV more frequently

* Easy if we assume estimates **of SNP effects** are stable between two official evaluations
# National genomic evaluations

* Two strategies :

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* At national level, the first strategy becomes complex ...
  because of too many animals...

(In France, in August 2016, > 300,000 Holstein genotyped animals
+ number of genotyped females increases by ~20 to 30% a year)

→ It does not make sense for **quick use** in genomic selection !
International genomic evaluations

→ More and more countries are moving towards SNP-BLUP

* **GMACE is not really used**, in particular in breeding programmes

* at international level, it is essentially viewed as a marketing tool...

* Heifers/cows **GEBV** do not benefit from GMACE

→ **SNP-MACE** is a big move towards:

> more reliable national GEBV

> easy to compute (quick)

> benefiting to all (including females)

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# Challenge 1 : redundant information = a big mess!

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* Interbull MACE results (= phenotypes of RP animals) are used in all countries (= « Mike's complications »)

* Consortia share their reference populations

* Quite a few « strategic » bulls are genotyped in more than one consortium

* e.g., two countries:

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* Easiest : use national data only ? → disconnect from MACE
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# Challenge 2 : How to include results from countries with genomic evaluations deviating from GBLUP? (+ SNP lists increasingly differ between countries)

e.g., France :

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An example : our genomic model

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## In practice...

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* Genomic relationships via EuroG10K chip:

System size= constant

* Easy and fast evaluation once a week

* Causal variants easy to include
By the way...

**Challenge 3 : How do we deal with the « residual polygenic » component in an International SNP model?**

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* Ignore? → suboptimal
decrease accuracy, increase inflation

* The French way?
Back to challenge 2: another way to see it...

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Expectations:

* More informative (haplotypes are more polymorphic)

* More stable over generations

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Validation results (27 to 41 traits / breed)

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Can we do better → haploblocks?

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(Jonas et al, 2017, in press)

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Validation results (Montbéliarde, 5 traits)

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Can we do better → haploblocks?

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→ **A reason to prefer Mike's « method 2b » ?**
= **international estimation of GEBV of *haploblock* regions ?**

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Set of
haplotypes

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## Challenge 4 : will it make Interbull work simpler ?

* No validation of genetic trend to worry about ??

* Validation?

* Need to find out when noise rather than new information is added to the system. How?

* Data management ?

* Fee system ?

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## Challenge 5 : will it be accepted?

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* So much effort to develop GMACE...

* Is SNP-MACE more politically acceptable than GMACE ?

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* Benefit to all: higher reliability of SNP effects higher reliability of GEBV for both sexes

* Open new horizons for understanding what we do (detection and use of causal variants, source of GxE, multibreed genomic evaluation,...)

Will it be enough ?

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# International genetic evaluations

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Country A
 export ing )

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Interbull
 MACE

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Country B
 (importing)

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Country C
 (importing)

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On scale of country A!

Country D
 (importing w/o genetic eval.)

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# International genomic evaluations

Initially Now ...

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Country A
 exportin g)

GEBV

pG<1

Interbull
GMACE

pG<1

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pG<1

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On scale of country A!

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Country B
(importing)

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Country C
(importing)

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Country D
(including w/o
**genomic** eval.)

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# International SNP evaluations

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Country A
 export (importing)

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$\rho G<1$

Interbull
SNP eval

$\rho G<1$

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$\rho G<1$

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Country B
(exporting)

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Country C
(Importing)

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Country D
(Importing w/o
**genomic** eval.)

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on a « close » scale
(ideally)

On scale of country A!
# Summary

* **Challenge 1**: redundant information

* **Challenge 2**: national genomic evaluations differing from GBLUP or with different sets of SNP

* **Challenge 3**: inclusion of a « residual polygenic » effect

* **Challenge 4**: Interbull chores and monitoring

* **Challenge 5**: acceptability ...
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# Summary

* **Opportunity 1:** added reliability for all (incl. females)

* **Opportunity 2:** end of the Interbull « white elephant » ?
  (« Rube Goldbert machine », « usine à gaz »)

* **Opportunity 3:** genomic selection in countries
  without national genomic evaluation yet

* **Opportunity 4:** easier multibreed evaluations?

* **Opportunity 5:** understand genetic
  background (causal variants, G x E, ...)

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Thank you!

THE FUTURE
IS EXCITING
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Some opportunities and
challenges regarding
SNP international
evaluations

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Vincent Ducrocq

GABI, INRA, Jouy-en-Josas, France

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