Genomic selection risks benefits alternatives Jack J. Windig - - PDF document

▶
genomic selection risks benefits alternatives
SMART_READER_LITE
LIVE PREVIEW

Genomic selection risks benefits alternatives Jack J. Windig - - PDF document

Jan 18, 2024 252 likes •360 views

Low Input Breeds ECO AB Symposium, 1516 24/03/2011 March, 2011 Genomic selection risks benefits alternatives Jack J. Windig Animal Breeding & Genomics Centre Animal Breeding & Genomics Centre Animal breeding Can be very

slide-1
SLIDE 1

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 1

Animal Breeding & Genomics Centre

Animal Breeding & Genomics Centre

Genomic selection risks benefits alternatives

Jack J. Windig

Animal Breeding & Genomics Centre

Animal breeding

Can be very effective

Scrapie incidence in the Netherlands

Even effective when heritability is low

Animal breeding works cumulative Effects are permanent

Right breeding goal is crucial

Too narrow breeding goal gives problems

  • Fertility problems and mastitis in Holstein
  • In general: production at the cost of welfare and health
slide-2
SLIDE 2

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 2

Animal Breeding & Genomics Centre

What is Genomic selection?

based on SNP data

3K -> 50K ->300K

Animal Breeding & Genomics Centre

Genomic selection

Breeding Value1205 = A1 + A2 + B1 + B1 + C1 + C2 + D2 + D2 + E1

slide-3
SLIDE 3

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 3

Animal Breeding & Genomics Centre

Genomic selection

Breeding value1205 = A1 + A2 + B1 + B1 + C1 + C2 + D2 + D2 + E…. Breeding value1211 = A1 + A1 + B1 + B2 + C1 + C2 + D1 + D2 + E….

Find animals with reliable beeding values

Based on performance (of relatives) and pedigree

Determine value of A1, A2, B1, B2 etc. Compute SNP-breeding value for animals without

performance data (of enough relatives)

Animal Breeding & Genomics Centre

Statistic model Reference Data base:

SNP1: T = +1 g milk A = -1 g milk SNP2: G = +2 g milk C = -2 g milk Etc, etc, etc, ………..

Measured performance SNPs Breeding value animals for genomic selection Reference population Young animals

slide-4
SLIDE 4

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 4

Animal Breeding & Genomics Centre

Generation interval in a typical dairy cattle program

  • ↓
  • ↓
  • !

↓

  • ↓

"#$ #%

  • ↓
  • Animal Breeding &

Genomics Centre

Accuracy in genomic selection

Size reference population

More is better Should capture the SNPs in the current population and their

combination with trait determining genes

Relationship with reference population

Linkage between SNPs and genes changes over time Additive (and non-additive) effects change with gene frequencies

Number of SNPs

More is better

slide-5
SLIDE 5

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 5

Animal Breeding & Genomics Centre

One step further

Velo- and Whizzo -genetics

Breeding in the lab

  • Cell cultures derived from oocytes
  • Select best cultures with genomic selection
  • Induce meiosis
  • Fertilization
  • Repeat X generations

10 (or more) generations squeezed into 1 Huge size of breeding program possible

Not yet feasible Ever feasible?

Acceptance by society is doubtful Doubtful if animal after x generations is as expected

  • Natural selection is turned off
  • Reference population in genomic selection functions for a limited time

Animal Breeding & Genomics Centre

Current situation

Large breeding companies are implementing

genomic selection, especially in dairy cattle

Global high input/high output breeds will increase

their genetic progress

slide-6
SLIDE 6

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 6

Animal Breeding & Genomics Centre

Low input breeds and Genomic Selection

Breeding value estimation for other than usual traits

Disease resistance Energy balance Methane emissions Performance on special diets Performance in special environments

Enables breeding value estimation in populations

without a reliable pedigree

Reliable reference population is crucial but can (will)

be problematic

Expertise and high investment needed

Animal Breeding & Genomics Centre

Breeding polled cattle as an alternative to dehorning?

Dehorned Polled

Dehorning is painful but necessary to prevent injuries later in life Breeding polled cattle is an alternative

Polledness based on a single gene but rare or absent in most breeds

slide-7
SLIDE 7

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 7

Animal Breeding & Genomics Centre

Situation 2009 in Holstein

Only 38 polled bulls (36 Pp and 2 PP) Farmers opinion

Will not use them

  • Too few to choose from
  • Too low production etc.
  • Dehorning is not a problem

If bulls with good breeding values available

  • Will certainly use them

Breeding program needed

Animal Breeding & Genomics Centre

Breeding program?

  • Was succesfull in Fleckvieh and Charolais
  • Now >90% of bulls in Fleckvieh for suckler cows are

polled

  • Classic introgression program
  • Takes > 20 years
  • Cannot close the gap completely
  • Genomic selection
  • Can produce bulls with high breeding values <10

years

slide-8
SLIDE 8

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 8

Animal Breeding & Genomics Centre

Social research under Dutch citizens

Livestock and breeding in general:

Citizens

  • Animal welfare is very important
  • The more natural the better
  • Strong negative opinion on genetic modification
  • No distinction between genetic modification and animal breeding

Farmers

  • Animal welfare is very important
  • Best farmer is a farmer that cares for its animals
  • Strong negative opinion on genetic modification
  • Distinction between genetic modification and animal breeding

Information changes the opinion of a part of the

citizens

Animal Breeding & Genomics Centre

Social research under Dutch citizens

Breeding polled cattle

Cows with horns are seen as more natural and better for animal

welfare than cows without horns

No distinction is being made between naturally polled cattle and

dehorned cattle

Opinions are not very strong

Breeding polled cattle only acceptable if

Distinction breeding - genetic modification is clear Polled cattle is seen as natural

slide-9
SLIDE 9

Low Input Breeds ECO AB Symposium, 1516 March, 2011 24/03/2011 9

Animal Breeding & Genomics Centre

Pros and cons

Polledness is a genetic defect Polledness is completely natural

Polledness occurs since prehistoric times

Horns are an integral part of the animal Animals function perfectly without horns

Compare with sheep

It is not ethical to adapt animals to the production

environment (should be the other way round)

Larger stables with space to avoid other cows also prevent injuries

It is not ethical to leave animals as they are when the

environment changes

In the past selection was against polled animals to adapt them to

tie stalls

Animal Breeding & Genomics Centre

Conclusions

Breeding goal comes first! Genomic selection

Accelerates animal breeding Can be beneficial for low input breeding Small population size is a handicap

General public

Distrusts genetics Whizzo-genetics will be totally unacceptable