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 o 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 o ta l 79,334 134,403 ADSA 2019 Annual Meeting, 25 June 2019 – 4

18% All Parities 16% Incidence Rates 14% 12% Milk Fever = 1.1% e nc e r Dise ase Oc c ur Displaced Abomasum = 0.7% 10% Ketosis = 2.6% 8% Mastitis = 11.7% 6% Metritis = 5.3% 4% Retained Placenta = 2.1% 2% 0% 1 2 3 4 5 L ac tation MF E V DA KE T O MAST ME T R RE T P ADSA 2019 Annual Meeting, 25 June 2019 – 5

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 • Re sistanc e T o Ave r age RE L routine genomic evaluations) Milk F e ve r 29% SNP effects estimated using a • Displa c e d 30% Ab o ma sum model similar to BayesA K e to sis 30% 310,232 Jerseys genotyped Ma stitis 35% • Me tritis 31% RELs ~15 points lower than • Re ta ine d Pla c e nta 30% Holsteins ADSA 2019 Annual Meeting, 25 June 2019 – 8

Genomic Reliabilities of Old and Young Jerseys (n=310,232) Re sista nc e T o Old/ yng MAX ME AN SD g e nRE L g e nRE L 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% ADSA 2019 Annual Meeting, 25 June 2019 – 9

Genomic EBVs of Jerseys (n=310,232) Re sistanc e T o 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 ADSA 2019 Annual Meeting, 25 June 2019 – 10

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) Re sista nc e T o 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 ADSA 2019 Annual Meeting, 25 June 2019 – 13

PTA Correlations for Health and Functional Traits (n=137) Re sista nc e T o 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 ADSA 2019 Annual Meeting, 25 June 2019 – 14

PTA Correlations between Health Traits (n=137) Re sista nc e T o 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 ADSA 2019 Annual Meeting, 25 June 2019 – 15

GENOMIC AND PHENOTYPIC TRENDS ADSA 2019 Annual Meeting, 25 June 2019 – 16

Milk Fever Resistance Ge ne tic T re nds F irst L a c ta tion Phe notypic T re nds 1 100 95 Re sista nc e Ra te 0.5 90 BV 0 85 wE 80 - 0.5 75 - 1 70 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Birth Ye a r Birth Ye a r Holste in Je rse y Holste in Je rse y ADSA 2019 Annual Meeting, 25 June 2019 – 17

Displaced Abomasum Resistance Ge ne tic T re nds F irst L a c ta tion Phe notypic T re nds 1 100 0.8 95 0.6 Re sista nc e Ra te 0.4 90 0.2 BV 0 85 wE - 0.2 80 - 0.4 - 0.6 75 - 0.8 - 1 70 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Birth Ye a r Birth Ye a r Holste in Je rse y Holste in Je rse y ADSA 2019 Annual Meeting, 25 June 2019 – 18

Ketosis Resistance Ge ne tic T re nds F irst L a c ta tion Phe notypic T re nds 1 100 0.8 95 0.6 Re sista nc e Ra te 0.4 90 0.2 BV 0 wE 85 - 0.2 - 0.4 80 - 0.6 75 - 0.8 - 1 70 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Birth Ye a r Birth Ye a r Holste in Je rse y Holste in Je rse y ADSA 2019 Annual Meeting, 25 June 2019 – 19

Mastitis Resistance Ge ne tic T re nds F irst L a c ta tion Phe notypic T re nds 2 100 1.5 95 1 Re sista nc e Ra te 90 0.5 BV 0 85 wE - 0.5 80 - 1 75 - 1.5 - 2 70 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Birth Ye a r Birth Ye a r Holste in Je rse y Holste in Je rse y ADSA 2019 Annual Meeting, 25 June 2019 – 20

Metritis Resistance Ge ne tic T re nds F irst L a c ta tion Phe notypic T re nds 2 100 1.5 95 Re sista nc e Ra te 1 90 BV 0.5 85 wE 0 80 - 0.5 75 - 1 70 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Birth Ye a r Birth Ye a r Holste in Je rse y Holste in Je rse y ADSA 2019 Annual Meeting, 25 June 2019 – 21

Retained Placenta Resistance Ge ne tic T re nds F irst L a c ta tion Phe notypic T re nds 1 100 0.8 95 0.6 Re sista nc e Ra te 0.4 90 0.2 BV 0 85 wE - 0.2 80 - 0.4 - 0.6 75 - 0.8 - 1 70 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Birth Ye a r Birth Ye a r Holste in Je rse y Holste in Je rse y ADSA 2019 Annual Meeting, 25 June 2019 – 22

SUMMARY ADSA 2019 Annual Meeting, 25 June 2019 – 23