Session Outline

• Overview of the incorporation of genomics data into

Angus BREEDPLAN

• Discuss recent changes to the analytical software that

is used when incorporating genomics information into

Angus BREEDPLAN

• Differences between previous and new software

• Changes in EBVs

• Main feedback from members

Genomic Information in Angus BREEDPLAN

• 4 x genomic tests previously incorporated into Angus

BREEDPLAN genetic evaluation

Genomic

Product

Laboratory No. Traits No. Traits in Angus

BREEDPLAN

i50K Zoetis 22 14

HD50K Zoetis 22 14

GGP-LD GAA 20+ 11

GGP-HD GAA 20+ 11

• Also incorporated historic genomic information for Angus

animals tested in the Beef Co-operative Research Centre

• Genomic information has been included in Angus BREEDPLAN

since April 2011

• Includes genotypes from 17 different manifests (from 8K – 770K)

Incorporation of Genomic Information in the

Calculation of Estimated Breeding Values

• Results in more accurate selection decisions,

particularly:

• when an animal is young

• for difficult to measure traits

• for traits that can’t be measured prior to breeding age

• for traits with a low heritability

• in situations where collecting effective performance

information is problematic (small herds, animals removed

from contemporary group)

• Does not replace the need to collect pedigree and

performance information

Genomics is an evolving

science

Software for incorporating

genomic information into the

calculation of EBVs is also

evolving

Utilisation of Genomics in Angus

BREEDPLAN

Previous Procedure

• Involved a multi-step approach

Pedigree &

performance

data

Traditional

EBV

• Step 1 – Pedigree and performance data used to calculate a traditional

estimated breeding value

Genomic

Prediction

• Step 2 - Genomic data used to calculate a genomic prediction (e.g.

Zoetis MVPs)

“Genomically

Enhanced”

EBV

• Step 3 – Traditional EBV “blended” with genomic prediction to

generate genomically enhanced EBV

New Procedure

• Multi-step approach was most sophisticated approach at the time, but

a new “single step” approach has now been developed

Pedigree &

performance

data“Genomically

Enhanced”

EBV

• Traditional breeding value and genomic prediction no longer calculated

• New approach simultaneously utilises pedigree, performance and

genomic information at the one time to calculate an EBV

Benefits of Single Step Procedure

• Main benefit in determining how genetic relationships between animals

are determined

• Traditional pedigree approach assumes full siblings have 50% of genes in

common

• In reality, siblings may have 40 – 60% of genes in common

• New approach uses genomic information to determine exact genetic

relationship

• Also accommodates animals that may be unrelated by pedigree, but have

some genes in common

• Ensures appropriate emphasis given to pedigree, performance and

genomic information based on an animal’s relationship to reference

population

Benefits of Single Step Procedure

• Overcomes any pedigree errors (if animals have genomic information)

• Genomic information contributes to EBVs for relatives, not just

genotyped animals

• Genomic information contributes to all EBVs in the main multi-trait

analysis

• Removes the need to regularly recalibrate prediction equations used to

calculate genomic predictions

►CALCULATION OF IMPROVED EBVs

How Much Did EBVs Change?

• No change in average EBVs

• Change in EBV accuracies

• Considerable re-ranking for

animals with genomics

See Technical Bulletin

Value of Genomics

• No change in average EBVs

• Increase in spread of EBVs

(similar to inclusion of performance information)

Value of Genomics

• Most additional accuracy when initial EBV accuracy is low

• Additional accuracy now differs subject to animal’s

relationship to reference population

• Additional accuracy highest for hard to measure traits

What Does Additional Accuracy Mean?

* No animals = 9122

• More EBV spread as accuracy increases

• Re-ranking considerable enough to change selection

decisions

Take Home Messages

• “Single-Step” BREEDPLAN will make better use of

genomics data to produce more reliable EBVs for

animals.

• Some EBVs have changed with the implementation of

“Single-Step” BREEDPLAN (especially for genotyped

animals).

• Inclusion of genomics will result in:

• No change in average EBV

• Increased spread in EBVs

• Increased EBV accuracy (and re-ranking)