Breeding Jersey cattle for Africa in the era of genomics

Prof Norman Maiwashe1,2 (PhD, Pri. Sci. Nat)

1ARC-Animal Production InstitutePrivate Bag X2

Irene 0062

2University of the Free StateP.O. Box 339

Bloemfontein 9300

20th International WJCB Conference , Western Cape, South Africa, 17 Sept 2014

Presentation Outline

• A breeder’s dilemma – Inbreeding versus Genetic progress

• How will genomics:– Complicate or Simplify breeding

• Summary

Genetic Improvement is a balancing act

Minimal Inbreeding

Rapid Genetic Progress

The curse is in the principle!– Superior animals (sires) are provided more breeding

opportunities

While:

– Inferior animals (sires) are denied breeding opportunities

Consequently:• Most of the progeny are from few outstanding sires and

are «likely to be outstanding themselves»

• When this progeny in turn become parents, they are more «likely to mate with their siblings»

Question 1:

Is the rate of inbreeding reaching critical levels in Jersey populations?

Inbreeding level in SA dairy cattle

Inbreeding level in SA Jersey 4.8%

Du Toit et al. (2012)

Inbreeding in Canadian Jerseys

Du Toit et al. (2012)

Inbreeding depression

• Inbreeding has a negative impact on longevity in SA Jersey cattle (Du Toit et al., 2012)

-0.14%

Mean longevity

-0.35%-0.22%

Lact. 1 Lact. 2 Lact. 3

A 1% increase in inbreeding is associated with ~0.5% reduction in longevity

Inbreeding in the genomic era• ΔF will increase due to shorter rapid generation interval

• Management of inbreeding will become more important

• Opportunity – Genomics may allow for new ways to control inbreeding

e.g. use of DNA to calculate genomic relatedness and inbreeding

Answers to Question 1:

• Inbreeding is real and should be managed– Use superior bulls that are less related to the population

• Genomics could lead to rapid inbreeding – but offer better tools for managing inbreeding (genomic mating

programs)

• Remember: Inbreeding is not bad per se – it is rapid inbreeding that is bad

• Mild inbreeding with intense selection is good

Question 2:

How was the Jersey breeder’s life before genomics?

Genetic trend for Calving Interval

Conformation and Udder TraitsFigure: Genetic trends for « conformation » and « udder » in SA Jersey

Theron et al. (2012)

Answers to Question 2

How was the Jersey breeder’s life before genomics?

Answer:• Good genetic progress made on measured traits (often

with high h2) albeit at a relatively slow pace

• Little progress on lowly heritable traits

• Progress was costly (time and money)

Question 3

How is the Jersey breeder’s life during genomics?

Genomic opportunities

1. Genomics for managing deleterious haplotype carriers (e.g JH1, JH2 and Fertility 1)

– Decreased reproductive efficiency (is accessible to the breeder)

2. Genomic selection (more about this later)– Selection of young animals with DNA test (with

reasonable reliability ~60%)

3. Parentage verification or discovery of missing ancestors (is accessible to the breeder)

Genomic selection• Requires a large number of animals with accurate proofs

e.g. >1000 animals

• Genotyping costs are still high – Use of cows in the reference population is a possibility– Genotyping a small group of animals with high density chips and

using imputation

• Important question: – Can I use genomic proofs from another country?

• Answer: – Advise: tread carefully– Genomic proofs are population-specific and their reliabilities may

erode in a different population• Using foreign scale could be hazardous for traits with low international

genetic correlations (Partry and Ducrocq, 2014)

Priorities during the Genomic Era

• Genomic exploitation strategy:– High value animals (influential)

• genotype with 50K or higher density SNP chip

– Low value animals • genotyped using low density chips for:

– Parentage verification – Genomic inbreeding – Deleterious haplotypes

The KEY to genomic selection

• Aggressive data collection (milk/performance recording)

• What kind of data?– Fertility– Adaptation to heat stress– Weights / growth– Feed efficiency – Methane production– Health

Answer to Question 3

How is the Jersey breeder’s life during genomics?

Answer?• Genomics for parentage verification and managing

deleterious haplotypes is a reality and beneficial

• Genomics proofs presented on foreign scale should be treated cautiously

Summary• Inbreeding is a threat to long-term genetic improvement

and should be managed

• Genomics presents an opportunity for fast-tracking genetic improvement

• More emphasis should be placed on:– collection of data on traits that are difficult to improve through

conventional selection

• Both public and private (industry) investment is key to exploitation of genomics selection

Thank You Dankie vir u andaag

Ndi a livhuwa