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