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©2019 Alltech, Inc. All rights reserved. How precision dairy will influence animal breeding Jeffrey Bewley, PhD, PAS Alltech Dairy Housing and Analytics Specialist
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How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

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Page 1: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

©2019 Alltech, Inc. All rights reserved.

How precision dairy will influence animal

breedingJeffrey Bewley, PhD, PAS

Alltech Dairy Housing and Analytics Specialist

Page 2: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Genetic Interest• The first sire book that I studied

cover to cover was as an 8-year-old

• Internship with AI company (NOBA) during college

• Mentors told me I’d never find a job in genetics

• Involved in breeding with partners in Kentucky

Page 3: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Genetics Environment Phenotype+ =

Page 4: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

The Opportunity

• Considerable opportunities for measuring novel phenotypes

• Previously unavailable, consistent, objective measures for traits that have been difficult to measure in the past

• Traits may be incorporated into robustness assessments focused on measuring animal health, reproduction, behavior, and longevity (Hocquette et al., 2012)

Page 5: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 6: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Analytics is The Next Scientific Breakthrough

Page 7: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 8: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

What Can We Learn From Basketball?

Page 9: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

From Basketball to Cows

Page 10: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Efficient Players

• Nothing flashy

• No one knows her name

• High production

• Feed efficient

• Doesn’t get sick

• Breeds back quickly

• Nothing flashy

• No one knows his name

• Moderate points

• Scores when needed

• Top notch defense

• Wins games

Page 11: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Basketball Analytics

• Effective field goal percentage: takes into account that 3 pointers are worth more than 2 pointers

• Value added: what a player adds to a team above what a replacement player would

• Player efficiency rating: Overall rating of a player’s per minute statistical production

Page 12: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Dairy Cow Analytics

• Money corrected milk: revenue-based metric, considers value of components

• Longevity corrected milk: adjust milk yield to herd distribution of 30% 1st lactation, 20% 2nd lactation, 50% 3rd + lactation

• Retention pay-off: the value of a cow’s future net revenues compared to her replacement

• Summer:winter ratios: compare milk, SCC, conception, etc. by season to monitor heat stress management

Page 13: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Dynamic Comparison

Conception

Likelihood

Lameness

Risk

Mastitis Risk

Mastitis

Recovery

Survival

Likelihood

Basketball dynamically calculates shot

percentages

Dairy can do the same within a lactation

Page 14: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Precision Dairy Monitoring

Milk Behavior

Physiology Conformation

Page 15: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Precision Dairy Monitoring Applications

• Estrus Detection

• Mastitis Detection

• Fresh Cow Disease Detection

• Lameness Detection

• Calving Detection

• Management Monitoring

Page 16: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Wearables, Images, and Milk Analyses

Page 17: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 18: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Wearable Technologies

Page 19: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 20: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 21: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 22: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Real Time Location Systems

Page 23: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Future is Image and Milk Analysis

Page 24: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 25: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Body Condition Scoring

Page 26: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Calculated Angles

1 & 15 Hook Anterior Angles 5 & 11 Hook Posterior Angles

2 & 14 Hook Anterior Curvatures 6 & 10 Thurl to Pin Angles

3 & 13 Hook Angles 7 & 9 Tailhead Depressions

4 & 12 Hook Posterior Curvatures 8 Tailhead Angle

Page 27: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Example

USBCS 2.50

Predicted BCS 2.63

Posterior Hook Angle 150.0°

Hook Angle 116.6°

USBCS 3.50

Predicted BCS 3.32

Posterior Hook Angle 172.1°

Hook Angle 153.5°

Page 28: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Lau,

Zhao,

Shelley,

and

Bewley,

2019

Page 29: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Feed Intake: 3D Imaging (99% R2)

Page 30: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Video Behavior

Page 31: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Zhao et al., 2018

Page 32: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

New Phenotypes

Mastitis

MIR-fatty acids

Milk properties

Body condition scoring

3D cow

Estrus intensity

Fresh cow diseases

Heat stress

Robotic milking selection

Calf data

Page 33: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

0 0.1 0.2 0.3 0.4 0.5

Udder health

SCC

Elecrical conductivityFertility diseases

Ovarian IssuesLuteal activity startMetabolic diseases

Lameness

TemperamentAMS flow rateAMS behavior

ActivityFatty acids

Residual feed intakeMethane emissions

HERITABILITY

TRA

IT

Page 34: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Linear Evaluation for Genetic Evaluations

Page 35: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Body condition score for the top (× and *) and bottom (+ and ●) two sires ranked on profit index (PIN)

BCS

Heritability ~

0.20

Page 36: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Heat Stress Genetics

Page 37: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Rectal temperatures from Florida

study (Dikmen and Hanse,

2009)

Page 38: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 39: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

• SNPs identified• Rectal

temperature

• Respiration rate

• Sweating rate

Page 40: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Methane Emissions

Page 41: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Estrus and Fertility

Page 42: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

0.16

0.18

0.20

Tim

e to

fir

st e

pis

od

e

Du

rati

on

Stre

ngt

h

Tim

e to

fir

st e

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od

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Du

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on

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on

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Her

itab

ility

First episode,

first parityFirst episode,

all parities

All episodes,

all paritiesHigh

activity

for

cows

and

heifers

Page 43: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Robotic Milking

Page 44: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

These traits especially include Rear Teat Placement (RTP), Teat Length (TL), Udder Depth (UD), Rear Leg Rear View (RLRV) and Milking Speed (MSP)

Page 45: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Based on data from six million robot milkings a week for 500,000 cows on over 4000 dairy farms

H2 = 0.12 H2 = 0.07 H2 = 0.27

Page 46: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Automated calf feeders

• Daily intake

• Drinking speed

• Average daily gain

• Meal size

• Disease

Page 47: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Genetic Evaluations

• May provide information previously unavailable for genetic evaluations

• New or improved traits (i.e. feed intake, lameness, BCS, heat tolerance, fertility)

• Improved data accuracy (i.e. yield, fat, protein, SCC, health traits)

• More data, fewer erroneous measurements

Page 48: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Branded Genetics

• Could bull studs supplement technology costs in large progeny test herds in exchange for data?

• Reduction in data collection costs

• May be a new form of product differentiation

Page 49: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Genomics

Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits

But, need enough high-quality phenotypic data to calculate the SNP effects

More data needed for lowly heritable traits

Page 50: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Challenges and Limitations

Brand differences in measures

Technology failures

Standardization

Calibration Data ownershipWho pays for what?

Page 51: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Are we measuring the targets we intend to?

Can’t

forget the

need for

third party

validations

Page 52: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

X ≠ X and Y ≠ Y

Tsai et al., 2019

Means for 135

cows

DIM 1-21

Page 53: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Disappearing Data

847 cow days (29%) out of possible 2898

Tech 3

Tech 2

Tech 1

• 138 cows

• DIM 1 to 21

• 2898 cow days

• 7 technologies

Tsai et al., 2019

Page 54: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

Data Silos

DHIA Sensors GeneticsMilk

BuyerNutrition Financial

Page 55: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough
Page 56: How precision dairy will influence animal breeding · 2019. 7. 10. · Precision Dairy Farming/genomic selection synergies may lead to improvement in health traits But, need enough

©2019 Alltech, Inc. All rights reserved.

Jeffrey Bewley, PhD, [email protected]

@bewleydairy

www.linkedin.com/in/jeffreybewley