genetic selection for milk quality where are...

GENETIC SELECTION FOR MILK QUALITY – WHEREARE WE?

David Erf

Dairy Technical Services Geneticist

Zoetis

OVERVIEW

» The history of genetic evaluations

» The importance of direct selection for a trait

» Selection for improving mastitis today

» How the information is working in the field

HEADLINES: Holstein is ‘invisible cow': Trouble-free

animal nears lifetime milk record in just 10 lactations

Betzoldvale Scott Mar.

• 11-year-old Holstein has

produced 348,450

pounds of milk in her

lifetime (as of May 2011)

• Became pregnant on her

first service insemination

every year

www.thecountrytoday.com/front_page/article_ec780704-86d1-11e0-8571-

001cc4c002e0.html Accessed January 2, 2016

http://www.thecountrytoday.com/front_page/article_ec780704-86d1-11e0-8571-001cc4c002e0.html

RECOVERING HEIFER RAISING COSTS TAKES TIME

Adapted from Ferguson and Galligan, WCDS, 1995.

LONGEVITY-DRIVEN PROFIT

0%

5%

10%

15%

20%

25%

30%

35%

40%

45%

70

75

80

85

90

95

100

105

110

115

1 2 3 4 5 6 7 8

% o

f To

tal

Milk

/Co

w/D

ay u

sin

g 3

05

M

Parity Group

Performance and Percent of Herd by ParityCows >100DIM

Milk/Day

% of Herd

Data on file, Dec. 2015 Herd example, Zoetis, Inc.

IMPACT OF MORBIDITY IS SIGNIFICANT IN DAIRY COWS

Incidence per

Lactation Range

Cost ($) per

Case

Culling

Risk1 (%)

Displaced Abomasum 3-5% 1,2,3,4,13 $494 4 26.9

Ketosis 5-14% 1,3,4,13 $117-289 4,5 32.5

Lameness 10-48% 2,4,6,13 $177-469 4,7 16 2

Mastitis 12-40% 1,2,3,4,8,13 $155-224 4,8,9 32.7

Metritis 2-37% 1,3,10,11,13 $300-358 10,11 17.1

Retained Placenta 5-15% 1,2,3,4,11,12 $206-315 4,12 31.71 Grohn, Y. et al. 1998. Effect of Diseases on the Culling of Holstein Dairy Cows in New York State. J. of Dairy Sci, 81(4):966-978.2 USDA. 2008. Dairy 2007, Part II: Changes in the U.S. Dairy Cattle Industry, 1991–2007 USDA-APHIS-VS, CEAH. Fort Collins, CO #N481.0311.3 Bar, D., et al. 2007. Effect of repeated episodes of generic clinical mastitis on milk yield in dairy cows. Journal of dairy science 90(10):4643-4653.4 Guard, C. 2009. The costs of common diseases of dairy cattle. Central Veterinary Conference Proceedings. Kansas City, MO..5 McArt, J.A. et al, 2015. Hyperketonemia in early lactation dairy cattle: a deterministic estimate of component and total cost per case. J. of Dairy Sci. 98(3):2043-2054.e Bicalho, R.C. Lameness in Dairy Cattle: A debilitating disease or a Disease of Debilitated Cattle? Western Dairy Management Conference, 2011. Pg 73-83.7 Cha, E. et al. 2010. The cost of different types of lameness in dairy cows calculated by dynamic programming. Preventive veterinary medicine 97(1):1-8.8 Cha, E, et al. 2014. Optimal insemination and replacement decisions to minimize the cost of pathogen-specific clinical mastitis in dairy cows. Journal of dairy science 97(4):2101-2117.9 Cha, E, et al. 2011. The cost and management of different types of clinical mastitis in dairy cows estimated by dynamic programming. Journal of dairy science 94(9):4476-4487.10 Overton, M. and J. Fetrow. 2008. Economics of postpartum uterine health. Proc Dairy Cattle Reproduction Council:39-44.11 "The Value of Uterine Health: the diseases, the causes, and the financial implications." Dairy Cattle Reproduction Council article.12 Guard, C., 1999. Retained Placenta: Causes and Treatments. Advances in Dairy Technology (1999) Vol. 11, page 81.13 Zwald, N.R., K.A. Weigel, Y.M. Chang, R.D. Welper and J.S. Clay. 2004. Genetic selection of Health Traits using Producer-Recorded Data. I. Incidence Rates, Heritability Estimates and Sire

Breeding Values. J. of Dairy Sci., 87:4287-4294.

THE HISTORY OF NEW TRAITS IN GENETIC EVALUATIONS

» Prior to 1994 – Milk, Fat, Protein and Type

» 1994 – Net Merit (NM$), SCS, Productive Life (PL)

» 2003 – Daughter Pregnancy Rate (DPR)

» 2008 – Stillbirth – Daughter and Sire

» 2011 – Heifer Conception Rate (HCR), Cow Conception Rate

(CCR)

» 2016 - Livability

WELLNESS IS NOW A

PROFITABLE CHOICE

CLARIFIDE® PLUS FOR HOLSTEINS

CDCB Official Evaluation

• Parentage

• Production

• Reproduction

• Health

• Type

Wellness Traits

• Mastitis

• Lameness

• Metritis

• Retained Placenta

• Displaced Abomasum

• Ketosis

Genetic Conditions

• Polled (no fee)

• Milk Components

• Infertility Haplotypes

• Other genetic conditions*

* CVM, Brachyspina and Beta Casein

A2 available with add-on fee.

DWP$TM

Animal Ranking

CREATING WELLNESS TRAIT GENOMIC PREDICTIONS

PHENOTYPIC MEANS, STANDARD DEVIATIONS, AND HERITABILITIES USED IN THE ANALYSES

Trait Unit Mean SD h2

MastitisCase per

animal/lactation0.23 0.42 0.069

LamenessCase per


MetritisCase per


Retained placenta

Case per animal/lactation

0.05 0.22 0.073

Displaced abomasum

Case per animal/lactation

0.02 0.15 0.081

KetosisCase per


• Each trait was defined as a Holstein female recorded with the presence or absence of a disease/disorder in a

given lactation

• Every cow was assigned with 0 (no incidence) or 1 (recorded one or more incidences) per lactation

Source: Data on file, Zoetis internal data, August 2015, Zoetis Inc.

MILLIONS OF RECORDS CONTRIBUTE TO AVERAGE RELIABILITIES OF 49 OR HIGHER

Trait

Reliabilities (%) of young genotyped and

pedigreed females

GPTA ReliabilityTraditional Parent

Average Reliability

MAST 51 19

LAME 50 18

METR 49 17

RETP 50 17

DA 49 16

KET 50 16

29,901 heifer observations (<2 years old)


Reliabilities are similar or better than Reliability of some core CDCB traits (i.e. HCR & DSB)

CLARIFIDE® PLUS GENOMIC PREDICTIONS

» Wellness traits are expressed as a standardized transmitting

ability (STA)

– Centered at 100 with a standard deviation of 5

– Higher numbers represent animals with lower expected risk of disease

relative to herdmates with lower STA values

– Generally range from 75 to 120 for all traits

+/- 2 SD

SOMATIC CELL SCORE FOR HOLSTEIN’S HAS BEEN IMPROVING OVER TIME

Data on file, Enlight herd data, Accessed Dec 2015, Zoetis Inc.

Genetic Progress for SCS (heritability = 0.12)

0

10

20

30

40

50

60

70

1996 2001 2007

Disease Trends

Displaced Abomasum

Other Reproductive Problems(e.g. dystocia, metritis)

Infertility Problems (not pregnant150 days after calving)

Retained Placenta

Lameness

Clinical Mastitis

YET DAIRY COW MORBIDITY HAS NOT BEEN IMPROVING FOR MASTITIS OR OTHER TRAITS

USDA. 2008. Dairy 2007, Part II: Changes in the U.S. Dairy Cattle Industry, 1991–2007 USDA-APHIS-VS, CEAH. Fort Collins, CO #N481.0311.

SOME TRAITS HAVE HIGH CORRELATION BETWEEN

EACH OTHER, LIKE MILK AND PROTEIN

0

10

20

30

40

50

60

70

-500 0 500 1000 1500 2000

GP

TA

Pro

tein

[lb

s]

GPTA Milk [lbs]

Correlation in Breed = 0.83a

Observed Correlation=0.81

a http://aipl.arsusda.gov/reference/nmcalc-2014.htm, Accessed Dec. 15, 2015

Data on file, Dec. 2014 Data package n = 30, Zoetis Inc.

Yet selecting for Protein, to get more protein, is best

http://aipl.arsusda.gov/reference/nmcalc-2014.htm

SOME TRAITS HAVE MEDIUM OR LOW CORRELATION, LIKE MILK AND FAT

0

10

20

30

40

50

60

70

80

90

100

-500 0 500 1000 1500 2000

GP

TA

Fat

[lb

s]

GPTA Milk [lbs]

Correlation in Breed = 0.43a

Observed Correlation=0.20

a http://aipl.arsusda.gov/reference/nmcalc-2014.htm, Accessed Dec. 15, 2015

Data on file, Dec. 2014 Data package n = 30, Zoetis Inc.

Here direct selection for Fat is highly necessary if you want to improve fat

http://aipl.arsusda.gov/reference/nmcalc-2014.htm

BOTTOM LINE, DIRECT SELECTION IS BEST!

» To make the most genetic and phenotypic progress in a trait,

use direct selection, not indirect

» Examples:

Goal Indirect

trait

Direct trait Estimated

correlation

Improve

reproductionPL

Daughter Pregnancy Rate

(DPR)0.64

Reduce mastitis

casesSCS New genomic Mastitis trait -0.45

Reduce

lameness

PL New genomic Lameness trait 0.28

FLC New genomic Lameness trait 0.00

Reduce metritis PL New genomic Metritis trait 0.32


DIRECT SELECTION IS BEST!

Genomic Prediction – Quintiles

Ave

rag

e D

ise

as

e In

cid

en

ce

• Data includes Ref.

Pop. n= 76K

• Not useful for

validation purposes

since phenotypic

records are

contributing to the

Mastitis Prediction

• Good example we

can expect from

the validation data

of how direct

selection is best

Genomic Mastitis vs GPTA for SCS


STUDY TIMELINE

Health Records collection

Year 1 Year 2 Year 3

September 2015Enrollment & DNA Sample collection prior to calving

Oct 2016 Oct 2017 Oct 2018

August 2016

DISTRIBUTION OF ENROLLED HERDS

LOCATION AND SAMPLING OF ANIMALS

Herd State Number of Sampled Animals

1 MI 3182 MN 3083 ID 3444 CA 3505 CA 3506 WI 2927 NY 2538 GA 3059 CA 334

10 WI 36311 ID 350

Animals Sampled 3567

Animals eliminated* -692

Animals included in the study 2875(66% Nulliparous, 33% Primiparous)

Source: Data on file, Zoetis internal data, October 2016, Zoetis Inc.

* Animals eliminated due to calving date outside desired window, breed conflict, sample failures

DEFINING AFFECTED AND HEALTHY RECORDS

First and second lactation records were assigned to one of three possible phenotypes by trait:

1. “Healthy” (0): no documented incidence of the health event before 306 DIM

2. “Diseased” (1): a documented incidence of the health event before 306 DIM

3. “Excluded” (.): missing lactation record and/or animals that were healthy and sold/died before the 90th percentile DIM by trait

Calving

DIM 0305 Day Lactation

RP

4 DIM

METR

DIM 9

MAST

DIM 250

KET

DIM 16

LAME

DIM 265DA

DIM 66

ASSOCIATION BETWEEN MAST STA GROUPS AND MASTITIS EVENTS

15.9%A

11.2%B11.1%B

8.5%C

92.3W

97.7X

101.1Y

105.2Z

85

90

95

100

105

110

0.0%

5.0%

10.0%

15.0%

20.0%

Worst 25% 26-50% 51-76% Best 25%

LS-M

eas

STA

Mar

gin

al M

ean

s

Genetic Groups


Prevalence: P<0.0001; STA: P<0.0001

15.9%A

11.2%B11.1%B

8.5%C

92.3W

97.7X

101.1Y

105.2Z

85

90

95

100

105

110

0.0%

5.0%

10.0%

15.0%

20.0%

Worst 25% 26-50% 51-76% Best 25%

LS-M

eas

STA

Mar

gin

al M

ean

s

Genetic Groups

ASSOCIATION BETWEEN MAST STA GROUPS AND MASTITIS EVENTS

Genetic Group Est. Cost per Cow5

Bottom 25% $35.7426-50% $25.0751-75% $24.71Top 25% $18.81

5 Cha et al ., 2011. Journal of Dairy Science 94(9):4476-4487.


Prevalence: P<0.0001; STA: P<0.0001

EXPECTED PHENOTYPIC PREVALENCE IN FIRST LACTATION


0%

5%

10%

15%

20%

25%

30%

35%

40%

90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110

MetritisMastitisLameness

SUMMARY AND CONCLUSIONS

» We have made great progress genetically on Somatic Cell Score –

It has been and continues to be a good tool.

» But, we have a new tool for genetic selection for lower incidences

of mastitis and it is working out in the field.

» To make the most progress in reducing mastitis – it will take a

combination of the best management practices along with a focus

on the genetic side to give the best results.

genetic selection for milk quality where are...

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