Angus Genetic Evaluation Update

Dan Moser, AGI President and AAA Director of Performance Programs

Stephen Miller, AGI Genetic Research Director

Kelli Retallick, AGI Genetic Services Director

North Carolina Angus Field Day

Key Topics

I. Genetic Evaluation update

A. Enhancements

B. Validation

C. Changes

II. $Values, Economic Assumptions

III. Questions & Discussion

Angus Genetics Inc.

• Wholly-owned subsidiary of the American Angus Association

– Four geneticists

– Seven customer service representatives

– Receive significant support from AAA Information Systems, Angus Media

– Strategic partnerships

Genetic Evaluation Services

• AGI is the world’s leading provider of beef genetic information

• Deliver genetic evaluation services to the American Angus Association, and five other breed organizations

Dan Moser, Ph.DAGI President

Stephen Miller, Ph.DAGI Genetic Research

Director

Kelli Retallick, M.S.AGI Genetic Service

Director

Lizhen Wang, Ph.DAGI Research

Geneticist

Lou Ann AdamsDirector of

Information Systems

Janice BlairProgrammer

Gayle BillupsProgrammer

Marg DressmanSoftware Engineer

Jason KenyonAssistant Director of Information Systems

Ignacy Misztal, Ph.D Daniela Lourenco, Ph.D

Yutaka Masuda, Ph.D Shogo Tsruuta, Ph.D

Romdhane Rekaya, Ph. D

J. Keith Bertrand, Ph.D

New and Improved Angus Genetic

Evaluation Released 7/7/17

JULY 2017"Different isn’t always better, but better is always different." - Author Unknown

The Evolution of Livestock Measurement

WEANING AND YEARLING WEIGHTS

WITHIN HERD RATIOS

EXPECTED PROGENY DIFFERENCES

$ VALUES: BIO-ECONOMIC INDEXES

GENOMICALLY ENHANCED EPDs

and INDEXES and INDEXES

Enhancements to Angus

Evaluation on 7/7/17• Single Step Genomics• Improved models for carcass

traits• Additional genotypes and

data• Updated heritability and

genetic correlation estimates• Annual update of economic

assumptions for $Values

Multistep vs. Single Step

GE-EPDs Combine Multiple

Sources of Information

GE-EPD

Pedigree

PerformanceGenomic Testing

Progeny Data

Implementing the Kachman

correlated trait model

0.38 0.7

0.99

CWT

CWT_50K

Fit genomic prediction as a correlated trait

Relationship b/w MBV and CWT

h2+rg RIB CWT LWT URIB_B URIB_C URIB_S CWT_M1 RIB_M1 CWT_M2 RIB_M2 CWT_50K RIB_50K

RIB X X X X X X X X X X X X

CWT X X X X X X X X X X X

LWT X X X X X X X X X X

URIB_B X X X X X X X X X

URIB_C X X X X X X X X

URIB_SX

X X X X X X

CWT_M1 X X X X X X

RIB_M! X X X X X

CWT_M2 X X X X

RIB_M2 X X X

CWT_50K X X

RIB_50K

X

Single-Step Approach

• Redefines pedigree relationships among animals based on genetic markers

PGS

S

PGD

X

MGS

D

MGDAguilar et al, 2010

Single-Step Approach

• Redefines pedigree relationships among animals based on genetic markers

PGS

S

50% PGD

X

MGS

25% D

MGDAguilar et al, 2010

Genomics captures more

variation in relationships

6 - Full Sibs

• Pedigree – 0.59

• Genomics 0.49 – 0.65

232 – ½ sibs

• Pedigree min = 0.29

• Genomic min = 0.19

Dr. Daniela Laurenco, UGA

h2+rg RIB CWT LWT URIB_B URIB_C URIB_S

RIB X X X X X X

CWT X X X X X

LWT X X X X

URIB_B X X X

URIB_C X X

URIB_SX

Single Step allows a more

DIRECT model

h2+rg RIB CWT LWT URIB_B URIB_C WWT UFAT_B UFAT_C FAT

RIB X X X X X X X X X

CWT X X X X X X X X

LWT X X X X X X X

URIB_B X X X X X X

URIB_C X X X X X

WWTX

X X X

UFAT_B X X X

UFAT_C! X X

FAT X

Single Step allows a more COMPLETE model

Adding weaning weight reduces

selection biasA selected group is

chosen to be scanned:

Above average for

growth a weaning time

Half are below average

for ultrasound scan

weight – even though

all were pre-selected high performers

Penalized unfairly for

carcass weight

Single Step

proves

superior in

USMARC

validation

Correlations with MARC

EPDs

Trait MS SS

Birth 0.59 0.60

CWT 0.32 0.35

FAT 0.24 0.42

MILK 0.40 0.40

MARB 0.44 0.51

REA 0.24 0.27

Weaning 0.43 0.43

YWT 0.51 0.52

196 Sires

R-Square – SS predicts AAA

performance better

0 0.02 0.04 0.06 0.08 0.1 0.12 0.14 0.16 0.18 0.2

Birth EX SS

Birth EX MS

Weaning EX SS

Weaning EX MS

Yearling Gain EX SS

Yearling Gain EX MS

Single Step Weights Genomics

Variably Across the Population

• Multi-step = “One size fits all”

• Single Step• Weights genomics more for animals genetically

“closer” to the data

• Like having an accuracy value for the genomic component of the EPD

• Animals distant from data will change less from DNA testing, and have lower EPD accuracy

h2 SS Prog Equiv

Ave. SS. Acc

CED 0.19 28 0.36BW 0.46 21 0.48WW 0.28 26 0.42YW 0.27 21 0.38Milk 0.12 33 0.30DMI 0.34 8 0.24HP 0.15 14 0.20SC 0.48 13 0.40YHT 0.51 11 0.39Doc 0.44 10 0.34MW 0.37 11 0.31MH 0.62 8 0.36CWT 0.44 9 0.32MARB 0.48 9 0.34REA 0.32 12 0.30Fat 0.33 10 0.29

Angus Progeny Equivalents with SS EPD

Genotyped non-parent animals (2014-2016 born). Average accuracy and number of progeny required to reach that accuracy.

Genotypes in Angus Genetic

EvaluationDate Genotypes

Oct. 2012 11,000

Oct. 2013 42,000

Oct. 2014 89,000

Oct. 2015 159,000

Oct. 2016 262,000

Current 355,000

Data + DNA = Selection Tools that Work

• 7.8M birth weights• 8.6M weaning weights• 4.2M post-weaning gain records• 1.5M heifer calving ease scores• 115K carcass records• 1.9M ultrasound records• 20K individual intake records• 256K docility scores• 60K heifer pregnancy observations• 203K mature cow weights• 355K Genotypes

SS Genetic Trends more stable

• Inflating trends with MS

• SS and Classic trends very similar

-0.3

-0.1

0.1

0.3

0.5

0.7

1972

1977

1982

1987

1992

1997

2002

2007

2012

Marb

SS Full Classic Adjust

-4

-3

-2

-1

0

1

2

319

72

1974

1976

1978

1980

1982

1984

1986

1988

1990

1992

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

MS SSNewBase

Birth EPD Trend is Flatter

Yearling EPD Trend is Steeper

-60

-40

-20

0

20

40

60

80

10019

72

1974

1976

1978

1980

1982

1984

1986

1988

1990

1992

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

MS SSNewBase

Milk EPD Trend is Flatter

-5

0

5

10

15

20

25

3019

72

1974

1976

1978

1980

1982

1984

1986

1988

1990

1992

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

MS SSNewBase

h2+rg RIB CWT LWT URIB_B URIB_C WWT UFAT_B UFAT_C FAT

RIB X X X X X X X X X

CWT X X X X X X X X

LWT X X X X X X X

URIB_B X X X X X X

URIB_C X X X X X

WWTX

X X X

UFAT_B X X X

UFAT_C! X X

FAT X

Single Step allows a more COMPLETE model

Carcass Weight EPD

-20

-10

0

10

20

30

40

5019

72

1974

1976

1978

1980

1982

1984

1986

1988

1990

1992

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

MS SSNewBase

Recent $B Trend very similar

-40

-20

0

20

40

60

80

100

120

140

1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016

SS $B MS $B

Recent $W Trend very similar

-60

-40

-20

0

20

40

60

1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016

$W SS $W MS

DMI EPD

-0.8

-0.6

-0.4

-0.2

0

0.2

0.419

72

1974

1976

1978

1980

1982

1984

1986

1988

1990

1992

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

MS SSNewBase

Summary of Changes

• More variation in DMI EPD• Narrower ranges for some traits, greater ranges

for others• More variation among half- and full-sibs• More current, real-time use of genomic

information• More accurate prediction of progeny performance• Friday data cut-off for weekly evaluation

A New Angus-CattleFax

Partnership

• Lance Zimmerman and Mike Murphy of CattleFax provided data and insight for this year’s economic updates

• Long-term partner, for consistency going forward

Economic assumptions for $Weaned

Dec-13 Dec-14 Jul-15 Jul-16 Jul-17

Ranch Assumptions:Base Calf Price 145 180 205 185 185Cow/Heifer Mix 80%/20% 80%/20% 80%/20% 80%/20% 80%/20%Cow Weight 1300 lb 1300 lb 1300 lb 1300 lb 1300 lbFeed energy cost 0.090 0.115 0.115 0.095 0.090

Economic assumptions for $BeefDec-13 Dec-14 Jul-15 Jul-16 Jul-17

Feedlot assumptions:Time on feed (days) 160 160 165 170 170Ration cost (per dry ton) 305 305 305 275 250Fed market (per cwt. Live) 115 130 140 135 130

Grid assumptions:Quality components:

Prime premium (above Choice) $14.00 $14.00 $14.00 $14.00 $14.00 CAB premium (above Choice) $4.00 $4.00 $4.00 $4.00 $4.00 Choice-Select spread $10.00 $10.00 $10.00 $10.00 $10.00 Standard discount ($22.00) ($22.00) ($22.00) ($22.00) ($25.00)

Yield components:YG 1 premium $4.50 $4.50 $4.50 $4.50 $4.50 YG 2 premium $2.25 $2.25 $2.25 $2.25 $2.25 YG 3 base $0.00 $0.00 $0.00 $0.00 $0.00 YG 4 & 5 discount ($18.00) ($18.00) ($18.00) ($18.00) ($18.00)Avg. carcass wt., lb. 816 816 816 836 861Heavyweight discount ($20.00) ($20.00) ($20.00) ($20.00) ($23.00)Discount weight 950 950 1,000 1,000 1,050

More Spread in $B, $WSlight increase in average values

Old $W New $W Old $B New $B

Max 102 102 198 215

25% 56 56 127 130

50% 46 46 107 108

75% 36 36 85 84

Min -55 -55 -105 -80

Rebuilding Angus $Values

• Propose a frame-off restoration

• Complete Model Rebuild for all $Values

• $W

– CEM

– HP

– DMI

• $Total Profit – from Long-Range Strategic Plan

Changes Coming in 2018

• Economic updates implemented in June, instead of first of July

• Comprehensive review and updating of $Value definitions, traits included, additional $Values

Birth without weaning

implemented on August 8th

• Birth weights submitted before this date will be processed as normal

• Basic principles still apply: – Set of 2 or more animals; best to work towards a

CG of at least 10

– CG of 1, not useful for NCE

– Registered vs. commercial recipient dams

• Birth growth-correlations now in NCE

• Separate sex at birth contemporary grouping.

• Weights, ultrasound scans, calving ease scores, scrotal measurements, etc. are more important than ever.

Genomic technologies are only as strong as our database. It is important to feed this database in order to continue critiquing and improving these technologies.

In the era of genomics,

PHENOTYPE is king.

Questions?Dan W. Moser, Ph.D. AGI Presidentdmoser@angus.org 816-383-5196

Kelli Retallick, M.S. Genetic Service Directorkretallick@angus.org 816-383-5190

Stephen Miller, Ph.D. Genetic Research Directorsmiller@angus.org 816-383-5157