where next for terminal sire recording?
TRANSCRIPT
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Where next for
Terminal Sire Recording?
Samuel Boon, Signet Manager
and EBLEX Breeding Specialist
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Performance recording has
been a great success......
High rates of genetic gain
for growth and carcase traits
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Success
• Breeders are using EBVs to add value
to ram sales
• Increase in demand for recorded rams
• Commercial understanding is increasing
(but still a long way to go)
Number of flocks recording is limited
and hence industry impact could be
higher
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Challenges
Breeding Values are getting bigger......
Is it time to rebase?
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Challenges
Breeders are looking for more regular
BLUP information – 3 runs a year is
limiting
More crossbred animals and crossbred
flocks are looking for useful EBVs
Current BLUP solutions are limited
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Commercial demand.......
At every sheep meeting I have spoken at for 15+
years someone has said “can we compare breeds”
Would an indirect “comparison” – if promoted sensibly
- assist breeders (and breeds) of high genetic merit
sheep?
Should Signet be helping the industry to find the
sheep with the best genes – regardless of breed?.....
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We have been here before.....
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Current approach In
de
x /
EB
V
1990 2013
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Current approach In
de
x /
EB
V
1990 2013
Charollais
Suffolk
Texel
Meatlinc
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Across breed
approach In
de
x /
EB
V
1990 2013
Charollais
Suffolk
Texel
Meatlinc
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Combined breed evaluations
What are other people doing?
£ £
UK Dairy
Evaluations
“Everyone in one
pot”, but breeds
reported separately
Lambplan
Combined runs
for Merino + Rest
SIL
Central Progeny Test
ICBF
Beef in Ireland
Sheep Ireland
(future?)
Starting with a simple approach
– doesn’t preclude more advanced solutions in the future
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Where will we get crossbred
data?
• Existing members with crosses?
• New members with crosses?
• Other sources? Test flocks?
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Advantages
(potentially)
• More regular EBV updates
– More efficient use of money to produce
EBVs
• More accurate EBVs for crossbreds
– Greater accuracy values for all
• Clearer message for commercial
producers
• Even greater interest in top end
genetics
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Independence
• Within breed rankings remain
• EBVs across breeds
– but breed specific indexes are possible
• Breed specific genetic group solutions
• For those not interested in other
breeds
– not really an issue
– business as usual
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Crossbreds - are they
inevitable?
The introduction of Composites has not only
lifted sheep performance by their own merit,
it has also put a sharper focus on breeding
and performance of purebred sheep
Mark Young, Heartland Sheep October 2013
Threat? Opportunity?
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Summary
This is a major opportunity to improve
the way we identify and promote
terminal sires with superior genes
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Thank you
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Combined breed analysis ~ technical issues
Kirsty Moore
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Introduction
• Improved efficiency
– Increased number of evaluations
– Increased accuracies
• Ability to evaluate cross bred animals
• Commercial producer
• Be on par with international methods and systems
• No impact if not interested in benefits
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Issues along the way
• Heterosis
• Genetic parameters
• Breed effects
• Genetic groups
• Rebasing
• Different indices
• Running time
• Publishing results
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The road is partially paved ...
• Combined breed analysis is not a new concept
• UK dairy evaluations have been combined breed
since ~2010
• 2013 EasyRams SPARK award
• Have started a test terminal combined breeds
evaluation
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Some of the easier questions
• Heterosis
• Genetic parameters
• Breed effects
• Genetic groups
• Rebasing
• Different indices
• Running time
• Publishing results
Benchmark EBVs across runs over time. 1990 born animals have an average EBV of 0. Modernise the ‘base animals’
Yes breeds can have different indices depending on their different breeding goals
Yes it will take longer to run but we have the computing power and software to handle this. The dairy evaluation ~ 20 million milk records
The changes proposed concern the calculation of EBVS we can still publish onto BASCO, web search, extract specific groups etc
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Heterosis / Hybrid Vigour
• When cross bred progeny perform better than expected given the 2 parental breeds – Reproduction
– Survival
– fitness
• In this example we expected 55kg but observed 65kg. The extra 10kg is due to hybrid vigour
50kg 60kg 55kg
65kg
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Heterosis / Hybrid Vigour
• But heterosis is not genetic!
• If we ignore heterosis
– estimate that an animal (and its relatives) is better/worse genetically than it really is
• Relatively easy to account for
– Different crosses express different amounts of heterosis
– knowledge of the breed makeup
– Proportion of Each Breed (PEB)
• Based on information from BASCO/breed 16ths
• many breeds to be present
• records breed make up as a %
• Good agreement with existing breed 16ths
• Better able to record breed of complex breed crosses
– Breed or breed type?
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Genetic parameters
• Can only use 1 set
• Review of parameters
– show very similar heritabilities/correlations
– In some cases differences in variances
• Not sure if this a true reflection of the data today
– Need to extract some data and look at the phenotypic
variances to see if there are breed differences
• Not a problem if variances are different as we can model this
• Dairy pre scale data so variances are comparable
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Breed effects / genetic groups
• Genetic group definitions will need to revised to
include breed
– Provide the opportunity to improve the definitions
• We will need to account for breed effects
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EasyRams SPARK award
• Opportunity in a small dataset to start to work with
some of the issues
• Robyn Hulme
– Suffolk, Texel and SufTex
– NZ importations
• 2 parts to the SPARK
– Across country
– Combined breed
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The data
• Data from 2007-2012
– Robyn’s flocks or flocks with a number of progeny from a
All Black ram produced by Robyn
– ~4,500 with data
– ~18,000 5 generation pedigree
• PEB procedures / breed makeup
• Data extraction
– Some modifications required
• Dam breed
• Genetic groups
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The EBVS
• EBVs produced for All Black animals
– 8wk weight
– scan weight
– muscle depth
– fat depth
• Correlation between the combined breed EBV and within breed EBV
– 0.69 – 0.94
– Indicates that heterosis does change the ranking but not radically
– Some of the re-ranking is due to changes in models and data sets
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How did EBVs compare with phenotype
SWT MD FD
R(phen & within breed)
combined breed)
within breed)
combined breed)
within breed)
combined breed)
Suffolk 0.41 0.44 0.54 0.55 0.62 0.62
SufTex 0.48 0.63 0.60 0.63 0.51 0.59
Mostly Tex 0.22 0.39 0.81 0.76 0.63 0.70
n=~1300 animals
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EBVs for 17 sires
-2
0
2
4
6
8
10
12
14
-4 -2 0 2 4 6 8
Wit
hin
Bre
ed
EB
V
Combined Breed EBV
SWT
MD
FD
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Summary
• We have started an combined terminal breed
analysis test run
– Still working out which methods and approaches are
appropriate for our data
• A massive step forward for the UK sheep industry
– Vast improvements in efficiency
– Better service the users
– Improvement in EBVs and accuracy of the EBVs
– Utilising cross bred data
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Multi-Breed Genetic Evaluations
Lessons from UK Dairy evaluations
Marco Winters
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DairyCo Breeding+
• Responsible for Genetic Evaluation in UK
– Independent and Paid for by dairy farmers
• All breeds and crosses :
– Production traits
– SCC
– Lifespan
– Fertility Index
– Type (excl. B&W)
– Calving Ease
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Who do we work with? Breed Societies Milk Recording Service partner
Critical success factors;
• Recording (ICAR accredited)
• Collaboration – (inter)nationally
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The Breeders ‘toolbox’
• Dairy breeding has never been so easy !
– Many bulls on offer from many breeds
– Many genetic indexes available to use
• However, they only add value if they are used !
– Regardless of heritability
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Yield 1977 – 2006 (Year of Birth) (Milk Genetics vs. 1st Lact. yields)
3000
3500
4000
4500
5000
5500
6000
6500
7000
7500
8000
-3500 -3000 -2500 -2000 -1500 -1000 -500 0 500
HOL
SHO
AYR
JER
GUE
FRI
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Impact of Genetics – lower h2
0
50
100
150
200
250
300
-35 -25 -15 -5 5 15 25 35
Dtr
Lacta
tio
n A
vg
. S
CC
Sire PTA
Lact.1
Lact.2
Lact.3
Lact.4
• Daughter average – Lactation SCC
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Standardised Genetic Gains (based on insemination data)
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Future Challenges - Competitiveness
• What are the future genetic needs ?
– Consider future economic conditions
– Consider different ‘non-economic’ demands
• E.g. environment, welfare, consumer
– Consider ever-widening range of production systems
• What are implications for Genetic evaluations ?
– Are we making best use of available data?
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Genetic Evaluations
• Performance = Genetics + Environment
• Genetic evaluations based on:
– Pedigree information
– (Genomic information)
– Performance recording (e.g. Milk, SCC)
• Correcting for environmental effects
– Progeny performance • Proper adjustment for genetic merit of mate
• Genetic gain improves with higher accuracy
– (but there is a trade-off with Generation Interval)
Time & Accuracy
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UK situation – Pre 2010 • Aim: How can we maximise the accuracy of evaluations?
– Using all existing data
– Without bias to existing evaluations
• Not all recorded data was being used – Some breeds excluded altogether
– Crossbreds largely excluded
– Not all breeds had full set of traits evaluated
• Not all data was being used optimally – Split proofs for the same bulls across breeds
– Suboptimal use of pedigree contributions
– Herdmate contemporaries not always included
• Growing interest in crossbreeding
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Breed proportion - Changes
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Breed proportions 2013 – Live cows
• 20% of cows not pure (>87.5% purity)
– Most are result of breed replacement
– 89% are >75% ‘pure’
• 5.3% are 1st generation crosses – Up 1.5% during last five years
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Dealing with mixed breed data
• Correction for difference in variance
• Fitting full pedigree – Separate groups for unknown parents by breed
– Widespread use of AI has established many links
• Correction for Heterosis / Recombination – Crosses between four main breed groups considered
• Holstein
• British Friesian
• Reds (Ayrshire, Shorthorn, Brown Swiss, Montbeliarde)
• Other (Jersey, Guernsey, rest)
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Example animal - 11779014
• Animal Breed Code %Breed Origin
• 11779014 68 50.00 NZ Jersey
• 11779014 76 12.50 N. American Jersey
• 11779014 04 6.25 UK Jersey
• 11779014 66 6.25 Danish Jersey
• 11779014 78 25.00 NZ Ayrshire
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Heterosis of 5% • Offspring better than average of its parents
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
Breed 1 Offspring Breed 2
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Useful Heterosis • Offspring are better than either of their parents
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
Breed 1 Offspring Breed 2
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All breed evaluations- background
• Already routinely used in other countries: – E.g. Ireland, The Netherlands, New Zealand, and USA
• DairyCo commissioned feasibility study (‘07/08)
• Results of feasibility were promising – EGENES undertook further development work (08/09)
– International validation run in August 2009 (interbull)
– Implementation in January 2010
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Impact
Largest changes for:
– Bulls used heavily in crossbreeding
– Bulls with limited information • Few daughters
• Few herds
• Therefore;
– Smaller breed populations relatively more change
• But also have largest gains in reliability
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All-breed evaluations • Best use of all data; Two examples
• Morwick Sand Ranger (Red Holstein)
– Pure-bred analysis;
• 399 daughters in Holstein proof
• 392 daughters in Ayrshire proof
• 12 daughters in Shorthorn proof
– All-breed 837 dtrs in combined proof
• B Jurist (Swedish Red)
– Pure-bred analysis; • 0 dtrs in Holstein proof (not allowed)
• 127 dtrs in Ayrshire proof
• 21 dtrs in Shorthorn proof
– All-breed 766 dtrs in combined proof
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Presentation of proofs
• Each animal receives only one proof • Post evaluation
– Animals get assigned to breed groups
– Each breed group has own genetic base • Reset in January 2010 to average of cows born in 2005
• Example:
• £PLI index applied to all breeds (Guernsey has own Merit Index)
Bull name Original PTA Re-based PTA
Milk SCC Base Milk SCC
Rosedale Advantage-Red -269 11 HOL -269 11
T-Bruno -279 -6 AYR 414 -4
Lakemead Rancher -275 7 FRI 406 13
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On-going requirements
• Accurate data needed (lots of it !)
– Currently >100M records used
• Accurate animal identification
• Harmonised trait definitions (ICAR)
• Sharing (pooling) of Data
– Internationally
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Conclusion and Future
• All-breed evaluations implemented in 2010 • Improved Accuracy of evaluations – within and across breeds
• New breed and trait evaluations added
• Industry response has been positive – Separate breed lists helped this situation
– However, one single list would help those x-breeding
• Future possibly All-breed genomic evaluations – Within breed genomics for Holstein - 2012
– More R&D needed to ‘translate’ DNA info to other breeds