The feasibility of implementing SNP technology in the South African national dairy cattle genetic evaluation system

A Maiwashe (PhD, Pri Sci Nat)

ARC-Animal Production Institute Programme: Animal Breeding and Genetics Private Bag X2, Irene, 0062

Presentation Outline
Overview of the current SA national dairy cattle improvement programme and SNP technology Definition genomic selection The benefits of genomic selection The requirements for successful implementation of genomic selection in dairy cattle Challenges to implementation of SNP technology

Summary

The SA commercial dairy cattle producers needs The dairy cattle farmers are interested in improving profitability of their enterprise through use of breeding animals that carry superior genetics for traits of economic importance This need is addressed through a national dairy cattle improvement programme which looks:
Collecting of phenotypic data in traits of economic importance Providing information (breeding values) that allows farmers to identify superior breeding stock

SA national dairy cattle improvement programme (1) Three 4 dairy breeds currently participate in the programme:
Holstein, Jersey, Ayrshire and Guernsey

Traits of economic importance considered are:

Production (milk yield, protein and fat yield and their percentages) Udder health somatic cell count Fertility calving interval Type / conformation

These traits are only expressed in females and therefore selection of bulls is based daughter performance or so called progeny test results

SA national dairy cattle improvement programme (2)

Young bulls ( 10 months) are put through progeny test programme which is run by AI centers

Pre-selection of test bulls is based on pedigree and therefore only family selection is practiced
Bulls are considered ready for use in AI at the age of 6 years which is rather long time About 10 test bulls are required to identify 1 proven AI bull The progeny test cost in the order of R1.5 million for a cohort of 10 test bulls translating to about R150 000 per bull

Bottom line: progeny testing is expensive and takes a long time

SA national dairy cattle improvement programme (3)

The current dairy improvement programme presents opportunities that can be
Final bull selection can only be done at 6 years the generation interval is too long
Pre-selection of test bulls is only limited to family selection The reliability of pre-selection is too low reliability is in the order of 25-30% Progeny testing is expensive

There is therefore a need to look technologies that could be used to exploit the existing opportunities

SNP Technology
The sequencing of the bovine genome has led to the discovery of thousands of Single Nucleotide Polymorphism - SNPs Automated genotyping using dense marker panels led to the reduction genotyping cost 50 K Bovine SNP Chip This developments provided impetus for investigating the use of SNPs in both crop and livestock improvement - the so called genomic selection

What is genomic selection?

Genomic selection is a form of marker-assisted selection in which genetic markers covering the whole genome are used so that all quantitative trait loci are in linkage disequilibrium with at least one marker (Goddard and Hayes 2007). Genomic Breeding Values are calculated as the sum of the effects of genetic markers, or haplotypes of these markers, across the entire genome.

Genomic selection (1)

Meuwissen et al., (2001) demonstrated through simulation that high reliability of genetic values could be achieved using marker data alone genomic selection Schaeffer (2006) found that genomic selection was 3 to 4 times superior to traditional progeny testing in dairy cattle and saving in logistical costs of about 97%.

Genomic selection (2)

Development of software for genomic evaluation and the reduction in genotyping costs provided motivation for countries to implement genomic selection in dairy cattle national evaluation

Recently, a number of countries have implemented genomic selection in their national dairy cattle genetic evaluations
Australia, Canada, Ireland, France, Germany, New Zealand, Netherland, United States

Are genomic BV more reliable than traditional BV?

Trait

REL Parent Average (%) 25 29 -

REL Genomic Country BV (%) 49 41 48 United States Denmark Australia

Reference

All All Australian Selection Index All Milk yield

VanRaden et al (2009) Su et al (2010) Hayes et al (2009)

27 28

50 56

New Zealand Germany

Hayes et al (2009) Lui eta al (2011)

Earlier more accurate selection can be practiced with genomic BVs

100
GEBV
EBV

80
Reliability (%) 60
GEBV

40
20
GIGEBV EBV GIEBV

Age of bull (years)

Genomic selection Yes or No?

The benefits of genomic selection in dairy cattle is quite clear But a system should be put in place to facilitate smooth implementation of genomic selection

What is needed to implement genomic selection? (1)

1. A reference population for estimating and validation of SNP effects

- animals in the reference population should have phenotypes and DNA should be available for genotyping The number of animals in the reference population should be in the order of thousands to achieve reasonable reliability of genomic breeding values

The accuracy of GEBV and heritability determine the size of the reference population

Do we have sufficient progeny tested bulls in SA? (1)

About 10 bulls are enrolled in progeny testing in SA Holstein one of the two major dairy cattle breeds There is about 40 bulls with readily available semen from AI company An extensive effort should be placed into securing more semen from progeny tested bulls from farmers Thus, a reference population could not be established on local bulls alone

Do we have sufficient progeny tested bulls in SA? (2)

Semen on foreign bulls is also used extensively in SA These semen could be used to increase there reference population Most countries have signed agreements to share genotypes on foreign bulls to reduce genotyping costs The ARC is in the process of entering into such an agreement with Ireland It should therefore be feasible to increase the reference population in the short-term

What is needed to implement genomic selection? (2)

2. Access to genotyping facility
- The Biotechnology Platform of the ARC has recently purchased a high throughput genotyping equipment that uses the Illumina 50K Bovine BeadChip

3. The existence of a national genetic evaluation system

- Breeding values from a national evaluation center are required for estimating SNP effects - The ARC is currently responsible for conduct routine national genetic evaluation for SA dairy cattle breeds

A major challenge to application of SNP technology in dairy cattle genetic evaluation in SA

Availability of sufficient animals to create a reference population of that will lead to reasonable accurate genetic prediction The current cost of genotyping is quite high in the order of R2 million for a reference population of 1 000 animals a challenge? In comparison to progeny testing the cost of genotyping does not present a major challange

Summary (1)
The use of SNP technology in the form of genomic selection in dairy cattle has led to considerable increase in genetic response Implementation of genomic selection in SA dairy improvement program is feasible but the challenge of small reference population should receive immediate attention

The genotyping costs remains a major challenge for wide acceptance of this technology by farmers

Summary (2)
Implementation of DNA repository for dairy cattle should be considered for possible exploitation of future genetic marker technology Partnership should be established among research institutions, academia and industry to contribute to a DNA repository for dairy cattle. Strong liaison with AI companies and breed society is crucial for successful implementation of genomic selection Application of genomic technology should receive particular attention in training of animal breeding students