Animal Phenomics | Aaron Ingham
Animal Phenomics
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Animal Phenomics | Aaron Ingham2 |
What is phenomics?
• A partner term for genomics• The process of measuring many or ‘deep’ phenotypes/traits
– Traits span
group animal molecular
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– Transcript– Protein– Metabolite
– Weight– Morphology – Behaviour
– Mother/offspring– Social hierarchy
Animal Phenomics | Aaron Ingham3 |
Measurable Responses
Social disruptionClimatic extremesPathogensPredators
Physiology Immune Behaviour
Stimuli
Responses
HungerHusbandry practices
Stress
Morphology Productivity
Animal Phenomics | Aaron Ingham
Why Phenomics?
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A natural distribution of performance exists for many phenotypes but can only be utilised for selective breeding when animals are easily identified / ranked
BUT many important phenotypes are not measured or difficult to measure
Disease resistant?
Animal Phenomics | Aaron Ingham5 |
A short history of phenotyping
Domestication began in the Near East some 8,000 to 10,000 years ago.
People have been working with, and measuring things on, animals for a long time.
Animal Phenomics | Aaron Ingham
For much of this time Phenotypic Selection drove Breeding Decisions
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Aurochs
Artistic interpretation
Dairy
Beef
10,000 years
Animal Phenomics | Aaron Ingham
So in the age of the $1000 genome what do we measure on animals?
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Surely this has progressed beyond what an animal looks like…
Animal Phenomics | Aaron Ingham
Contemporary Australian Breeding Programs
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Trait Likely Response Contribution to economic gain
(%)
Fleece Weight +2.8% 11%
Fibre diameter -1.3μm 47%
Body Weight +1.1kg 1%
CV of FD -0.9% 3%
Staple Strength +4.6 N.ktex 29%
Worm Egg Count
-12% 2%
Curvature +1.8 deg/mm 1%
Number of Lambs Weaned
+3% 6%
MerinoSelect – Wool SheepBREEDPLAN – Beef Cattle
Animal Phenomics | Aaron Ingham
And we must know everything about genes…
• ~ 40% of the human protein coding genes have no defined function
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In mice, there are many genes that you knock out and you don’t see a phenotype, and one concludes that they are redundant.
I say, have you taken your mice to the opera?
Can they still tell Wagner from Mozart? Wolpert et al 1998 (Int J Dev Biol 42)
Animal Phenomics | Aaron Ingham
• Disease resistance
• Feed intake – growth efficiency
• Preferred behaviours – stress tolerance
• Reproductive performance
What different things might you measure?
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…and how might you measure them??
Animal Phenomics | Aaron Ingham
• We can’t reliably measure individual intake of pasture on any scale– This precludes direct estimates of efficiency
• Current feed conversion values determined only on growing animals and
using intensive feeding approaches
BUT• Over 60% of economic costs of meat production are associated with the
breeding herd/flock, more if replacements are costed
• The national breeding herds/flocks, and most other classes of stock, are pasture-fed
Pasture intake – efficiency
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Animal Phenomics | Aaron Ingham
Is feed conversion efficiency really a big ticket item?
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Selective breeding for feed conversion efficiency in chickens over 30 years has reduced the amount of feed each bird requires to hit target weight in a set time period. Image courtesy Rachel Hawken, Cobb-Vantress.
Animal Phenomics | Aaron Ingham
• Typically for a steer of ~ 450 kg fed a concentrate based diet• 1928 - 12 to 13 kg of feed consumed per kg of liveweight gain.
– Ref: Henry WA and Morrison FB (1928) Feeds and feeding. 19th Ed. The Henry-Morrison Company, Ithaca NY.
• 2015 - 9 kg of feed consumed per kg of liveweight gain is possible – Beef CRC.
• Retail yield being 36% of liveweight
Feed conversion in cattle
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30kg feed
0.8 kg steak
1.2 kg steak
1928
2015
0.0045% compound annual increase over 90 years
Animal Phenomics | Aaron Ingham
Pasture intake – efficiency
• What is required to calculate feed conversion efficiency?
INTAKE• Animal behaviour can be measured • Pasture disappearance can be measured• Behaviour can be correlated with D pasture = IntakeLIVEWEIGHT CHANGE• Walkover weighing (WOW) enables regular measures
• Growers…Intake / weight gain = Measure of efficiency• Breeders…Intake / calves weaned
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Animal Phenomics | Aaron Ingham
Pasture intake - Behaviours
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On animal sensors Data analysed for features Behaviour classification and annotation
Animal Phenomics | Aaron Ingham
Pasture intake – Weight change / Body condition
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Walk Over Weighing
LIDAR
Weight
Time
Animal Phenomics | Aaron Ingham
Pasture intake – Pasture depletion
•Biomass disappearance- Quadrats (calibration)- Capacitance probes- Electronic plate meters- C-DAX pasture meter- Crop circle NDVI- Exclusion cages (regrowth)- UAVs, LIDAR- Satellite
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Animal Phenomics | Aaron Ingham18 |
Closing thoughts 1
• A natural distribution of performance exists for many phenotypes but can only be utilised when easily identified
• Many important traits are hard to measure
• The accuracy of genomic prediction is highest for traits that have the most records
• For traits that are measured categorical phenotypes limit understanding as most processes are multivariate and continuous
• Phenotypes are necessary for defining magnitude of G x E
• Functional annotation of the genome remains essential
Animal Phenomics | Aaron Ingham
Closing thoughts 2
• Deconstructing complex phenotypes• Do the component traits of complex traits have improved
heritability values?• Is this the key question?
• For example…Feed intake• Grazing duration• Appetite (endocrine levels)• Energy partitioning• Daily activity score• Muscle mitochondrial content (maintenance costs)
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Animal Phenomics | Aaron Ingham
Closing thoughts 3
• Sensor attachment to animals• Automated pattern recognition (annotation) in data• Big data (audio ~ 6,000 data points / second)• Identifying critical times for trait measurement• Standardised approaches for measurement required
• Linkage to industry breed improvement programs is vital• Trait relationships / selection indexes• Measurement in natural environment• Molecular models (tissues, genes, proteins, metabolites)
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Peter HuntDavid PaullSabine SchmoelzlGregory Bishop-HurleyBryce LittleHeather BrewerDominic NiemeyerGrant UphillMoira MenziesBradley Hine
Jody McNallyJessica McLeodKeith EllisIan PurvisSinead CorvanLauren WilliamsPaul GreenwoodIan ColditzSonja DominikPhil Valencia
LIVESTOCK PHENOMICS / AGRICULTURE FLAGSHIP
Thank you
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