Extending genomic evaluations to direct health traits in Jerseys - - PowerPoint PPT Presentation

Extending genomic evaluations to direct health traits in Jerseys

Laura Jensen, Kristen Parker Gaddis, Duane Norman Council on Dairy Cattle Breeding, Bowie, MD

Introduction

• Disease resistance through genetic selection is another tool to

reduce on farm expenses

• CDCB currently has health evaluations for Holsteins (April 2018)
• Jerseys are the second most prevalent breed in the U.S.
• Traits (measured as disease resistance): Milk Fever, Displaced

Abomasum, Ketosis, Mastitis, Metritis, Retained Placenta

ADSA 2019 Annual Meeting, 25 June 2019 – 2

PHENOTYPIC SUMMARY

ADSA 2019 Annual Meeting, 25 June 2019 – 3

Phenotypic Data

Re sistanc e T

• Animals

Obse r vations

Milk F e ve r 42,842 65,502 Displa c e d Ab o ma sum 40,707 59,874 K e to sis 23,783 39,716 Ma stitis 60,980 97,507 Me tritis 46,811 70,214 Re ta ine d Pla c e nta 38,834 59,808 T

• ta l

79,334 134,403

ADSA 2019 Annual Meeting, 25 June 2019 – 4

All Parities Incidence Rates

Milk Fever = 1.1% Displaced Abomasum = 0.7% Ketosis = 2.6% Mastitis = 11.7% Metritis = 5.3% Retained Placenta = 2.1%

ADSA 2019 Annual Meeting, 25 June 2019 – 5

0% 2% 4% 6% 8% 10% 12% 14% 16% 18% 1 2 3 4 5 Dise ase Oc c ur r e nc e L ac tation MF E V DA KE T O MAST ME T R RE T P

GENETIC EVALUATIONS

ADSA 2019 Annual Meeting, 25 June 2019 – 6

Methodology

• Univariate linear animal repeatability model
• Same model used for Holstein health

evaluations

• Fixed effects: year-season, age at calving by

parity, and regression on inbreeding

• Random effects: herd-year, additive genetic,

permanent environment, and residual

ADSA 2019 Annual Meeting, 25 June 2019 – 7

Overview

• 79k markers (those used in CDCB

routine genomic evaluations)

• SNP effects estimated using a

model similar to BayesA

• 310,232 Jerseys genotyped
• RELs ~15 points lower than

Holsteins

ADSA 2019 Annual Meeting, 25 June 2019 – 8

Re sistanc e T

• Ave r

age RE L

Milk F e ve r 29% Displa c e d Ab o ma sum 30% K e to sis 30% Ma stitis 35% Me tritis 31% Re ta ine d Pla c e nta 30%

Genomic Reliabilities of Old and Young Jerseys (n=310,232)

ADSA 2019 Annual Meeting, 25 June 2019 – 9

Re sista nc e T

• Old/ yng

MAX g e nRE L ME AN g e nRE L SD g e nRE L

Milk F e ve r Old 85% 32% 5% Milk F e ve r Yng 46% 29% 4% Displa c e d Ab o ma sum Old 90% 34% 5% Displa c e d Ab o ma sum Yng 52% 30% 4% K e to sis Old 87% 32% 5% K e to sis Yng 47% 29% 4% Ma stitis Old 97% 42% 7% Ma stitis Yng 69% 34% 5% Me tritis Old 92% 35% 6% Me tritis Yng 55% 31% 4% Re ta ine d Pla c e nta Old 90% 33% 5% Re ta ine d Pla c e nta Yng 50% 30% 4%

Genomic EBVs of Jerseys (n=310,232)

ADSA 2019 Annual Meeting, 25 June 2019 – 10

Re sistanc e T

• Min gE

BV Max gE BV Me an gE BV SD gE BV

Milk F e ve r

• 1.42

0.84

• 0.12

0.14 Displa c e d Ab o ma sum

• 2.55

1.11 0.08 0.23 K e to sis

• 3.22

2.14

• 0.03

0.48 Ma stitis

• 10.57

8.74 0.24 1.59 Me tritis

• 5.20

3.27 0.20 0.81 Re ta ine d Pla c e nta

• 3.52

1.16 0.02 0.30

PTA CORRELATIONS

ADSA 2019 Annual Meeting, 25 June 2019 – 11

Overview

• Instead of doing bivariate or multivariate

models we used PTA correlations to predict the genomic correlations

• Health traits measure disease resistance
• Bulls with NM$ >99 REL, born before 1990
• n = 137 bulls

ADSA 2019 Annual Meeting, 25 June 2019 – 12

PTA Correlations for Health and Yield Traits (n=137)

ADSA 2019 Annual Meeting, 25 June 2019 – 13

Re sista nc e T

• Bre e d

Milk F a t Prote in SCS

Milk F e ve r Je rse y

• 0.34*
• 0.28*
• 0.29*

0.12 Milk F e ve r Ho lste in

• 0.07
• 0.01
• 0.09
• 0.02

Displa c e d Ab o ma sum Je rse y 0.09

• 0.07

0.09 0.07 Displa c e d Ab o ma sum Ho lste in 0.09 0.12* 0.22*

• 0.18*

K e to sis Je rse y 0.20* 0.39* 0.35*

• 0.07

K e to sis Ho lste in 0.08 0.24* 0.28* 0.47* Ma stitis Je rse y

• 0.34*
• 0.18*
• 0.31*
• 0.41*

Ma stitis Ho lste in 0.01 0.12* 0.06

• 0.70*

Me tritis Je rse y 0.18* 0.18* 0.30*

• 0.02

Me tritis Ho lste in 0.25* 0.28* 0.32*

• 0.14*

Re ta ine d Pla c e nta Je rse y 0.03 0.28* 0.20*

• 0.16

Re ta ine d Pla c e nta Ho lste in 0.03 0.05

• 0.06
• 0.02

*sig nific a ntly diffe re nt fro m 0 a t p<0.05

PTA Correlations for Health and Functional Traits (n=137)

ADSA 2019 Annual Meeting, 25 June 2019 – 14

Re sista nc e T

• Bre e d

PL L IV DPR HCR CCR

Milk F e ve r Je rse y

• 0.06

0.36* 0.05 0.08 0.16 Milk F e ve r Ho lste in

• 0.04

0.11*

• 0.03
• 0.03
• 0.07

Displa c e d Ab o ma sum Je rse y 0.13 0.29* 0.08 0.13

• 0.02

Displa c e d Ab o ma sum Ho lste in 0.43* 0.44* 0.29* 0.20* 0.23* K e to sis Je rse y 0.18* 0.12 0.06 0.05 0.06 K e to sis Ho lste in 0.47* 0.40* 0.37* 0.21* 0.28* Ma stitis Je rse y 0.27* 0.18* 0.19* 0.01 0.18* Ma stitis Ho lste in 0.51* 0.37* 0.31 0.15* 0.30* Me tritis Je rse y 0.26* 0.30* 0.21 0.23* 0.25* Me tritis Ho lste in 0.44* 0.34* 0.37* 0.19* 0.37* Re ta ine d Pla c e nta Je rse y 0.16 0.13 0.09 0.15 0.23* Re ta ine d Pla c e nta Ho lste in 0.12* 0.10 0.09 0.09 0.09

*sig nific a ntly diffe re nt fro m 0 a t p<0.05

PTA Correlations between Health Traits (n=137)

ADSA 2019 Annual Meeting, 25 June 2019 – 15

Re sista nc e T

• Bre e d

Avg RE L MF E V DA KE T O MAST ME T R RE T P

Milk F e ve r JE 51% 1 Milk F e ve r HO 76% 1 Displa c e d Ab o ma sum JE 57% 0.22* 1 Displa c e d Ab o ma sum HO 87% 0.16* 1 K e to sis JE 53% 0.05 0.24* 1 K e to sis HO 85% 0.13* 0.66* 1 Ma stitis JE 77% 0.04

• 0.14
• 0.22*

1 Ma stitis HO 95% 0.08 0.15* 0.20* 1 Me tritis JE 61% 0.07 0.25* 0.33*

• 0.08

1 Me tritis HO 89%

• 0.05

0.30* 0.35* 0.20* 1 Re ta ine d Pla c e nta JE 56% 0.14

• 0.09

0.40*

• 0.02

0.46* 1 Re ta ine d Pla c e nta HO 88% 0.09 0.03 0.08 0.16* 0.48* 1

*sig nific a ntly diffe re nt fro m 0 a t p<0.05

GENOMIC AND PHENOTYPIC TRENDS

ADSA 2019 Annual Meeting, 25 June 2019 – 16

Milk Fever Resistance

ADSA 2019 Annual Meeting, 25 June 2019 – 17

• 1
• 0.5

0.5 1 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 wE BV Birth Ye a r

Ge ne tic T re nds

Holste in Je rse y 70 75 80 85 90 95 100 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Re sista nc e Ra te Birth Ye a r

F irst L a c ta tion Phe notypic T re nds

Holste in Je rse y

Displaced Abomasum Resistance

ADSA 2019 Annual Meeting, 25 June 2019 – 18

• 1
• 0.8
• 0.6
• 0.4
• 0.2

0.2 0.4 0.6 0.8 1 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 wE BV Birth Ye a r

Ge ne tic T re nds

Holste in Je rse y 70 75 80 85 90 95 100 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Re sista nc e Ra te Birth Ye a r

F irst L a c ta tion Phe notypic T re nds

Holste in Je rse y

Ketosis Resistance

ADSA 2019 Annual Meeting, 25 June 2019 – 19

• 1
• 0.8
• 0.6
• 0.4
• 0.2

0.2 0.4 0.6 0.8 1 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 wE BV Birth Ye a r

Ge ne tic T re nds

Holste in Je rse y 70 75 80 85 90 95 100 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Re sista nc e Ra te Birth Ye a r

F irst L a c ta tion Phe notypic T re nds

Holste in Je rse y

Mastitis Resistance

ADSA 2019 Annual Meeting, 25 June 2019 – 20

• 2
• 1.5
• 1
• 0.5

0.5 1 1.5 2 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 wE BV Birth Ye a r

Ge ne tic T re nds

Holste in Je rse y 70 75 80 85 90 95 100 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Re sista nc e Ra te Birth Ye a r

F irst L a c ta tion Phe notypic T re nds

Holste in Je rse y

Metritis Resistance

ADSA 2019 Annual Meeting, 25 June 2019 – 21

• 1
• 0.5

0.5 1 1.5 2 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 wE BV Birth Ye a r

Ge ne tic T re nds

Holste in Je rse y 70 75 80 85 90 95 100 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Re sista nc e Ra te Birth Ye a r

F irst L a c ta tion Phe notypic T re nds

Holste in Je rse y

Retained Placenta Resistance

ADSA 2019 Annual Meeting, 25 June 2019 – 22

• 1
• 0.8
• 0.6
• 0.4
• 0.2

0.2 0.4 0.6 0.8 1 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 wE BV Birth Ye a r

Ge ne tic T re nds

Holste in Je rse y 70 75 80 85 90 95 100 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Re sista nc e Ra te Birth Ye a r

F irst L a c ta tion Phe notypic T re nds

Holste in Je rse y

SUMMARY

ADSA 2019 Annual Meeting, 25 June 2019 – 23

Increasing health records

• Current Jersey health records submitted (May

2019)

• Milk fever = 102,509  57% increase
• Displaced Abomasum = 80,746  35% increase
• Ketosis = 59,252  49% increase
• Mastitis = 213,271  119% increase
• Metritis = 105,994  51% increase
• Retained Placenta = 101,830  70% increase

ADSA 2019 Annual Meeting, 25 June 2019 – 24

What’s next?

• Internal test run using Aug. 2019 data
• Release preliminary results to appropriate

collaborators

• Implement Jersey health evaluations
• Include in Interbull test run for mastitis

ADSA 2019 Annual Meeting, 25 June 2019 – 25

Special thanks to:

• DRPCs
• American Jersey Association and Cari Wolfe
• Dairy Producers
• Thais Cassel for the beautiful paintings

throughout the presentation

26

ADSA 2019 Annual Meeting, 25 June 2019 – 27

Thank you!