Effects of -Calpain DNA Tests on Tenderness

R. Mark Thallman

U.S. Meat Animal Research CenterClay Center, NE

-Calpain

• Quantitative Trait Locus (QTL) for WB Shear Force on Bovine Chromosome 29

-calpain gene located in the region of the QTL-calpain is a proteolytic enzyme that plays a key

role in postmortem tenderization of meat

MARC -Calpain Team

• Tim Smith• Eduardo Casas• Roger Stone• Brent Page• Stephen White• Mohammad Koohmaraie• Tommy Wheeler• Steven Shackelford

• Renee Godtel• Kevin Tennill• Steve Simcox• Linda Flathman

Tests for -Calpain are Marketed By:

• Frontier Beef Systems - TenderGENE

• Genetic Solutions – GeneStar Tenderness II

• MMI Genomics – plan to market with their parentage products

QTL on Bovine Chromosome 29

L×JP×A

BTA29 BTA29

Tough Tender Tough Tender

What is an SNP?(Single Nucleotide Polymorphism)

FunctionalGenotype

TestResult

+/-

FunctionalMutation

+/-

TestLocation

AGAATTTGAATTGTGATGAACACTCCACAGAATATGAATTGTGATGAACAGTCCAC

+/++/+ AGAATTTGAATTGTGATGAACACTCCACAGAATTTGAATTGTGATGAACACTCCAC

Association between test result and functional mutation

Or, the test polymorphism may actually be the functional polymorphism, but that is difficult to prove and not really necessary.

SNP Association

L×JP×A

G|

A

Tough Tender Tough Tender

C|

G

316

530

G|

A

C|

G

316

530

Possible Test Results Can be Viewed from Two Perspectives

GG AG AA

CC CCGG

CCAG

CCAA

CG CGGG

CG AG

CG AA

GG GG GG

GG AG

GGAA

SNP316

SNP 530 C G

G G

G A

C A

C G

CCGG

CGGG

CG GA

CC GA

G G

GCGG

GG GG

GG GA

GC GA

G A

GC AG

GG AG

GG AA

GC AA

C A

CC AG

CG AG

CG AA

CC AA

Haplotype

Haplo

type

Reporting Results with Multiple SNP

GG AG AA

CC +/+4.0

+/?0.4

?/?0.0

CG +/?22.3

+/-8.8

-/?0.8

GG ?/?27.0

-/?28.4

-/-8.2

SNP316

SNP 530 C G

G G

G A

C A

C G

+/+4.0

+/?11.2

+/-4.0

+/?0.2

G G

+/?11.2

?/?27.0

-/?14.2

?/?0.4

G A

+/-4.0

-/?14.2

-/-8.2

-/?0.4

C A

+/?0.2

?/?0.4

-/?0.4

?/?0.0

Haplotype

Haplo

type

Genotype frequencies

Genotypic Effects on WB Shear Force (lb)(higher is tougher)

GG AG AA

CC -1.35 ± 0.792%

-0.58 ± 1.091%

N/A0%

CG -0.36 ± 0.3512%

-0.29 ± 0.3316%

-0.99 ± 0.931%

GG 024%

0.0 ± 0.2733%

0.82 ± 0.3710%

SNP316

SNP 530

ASA 362 hd

Two Possible Models for Observed Intermediate Haplotype Effect

Avg. Effect ofHaplotype

Tender

Intermediate

Tough

Too Rare to Estimate Well

CG

316

530

GA

316

530

GG

316

530

CA

316

530

CG

316

530

GA

316

530

GG

316

530

CA

316

530

GG

Three FunctionalAlleles

Mixture of TwoFunctional Alleles

Effect

-.22 .07

0

.09 .06

-.10 .34

Freq.

.193

.527

.268

.011

GPE Cycle VII-2 557 hd

A Challenge and …

B×H

Tough Tender

G|

G

G|

G

316

530

• Heterozygous for QTL, but homozygous at test loci.

• Red vs blue alleles in progeny are determined by flanking microsatellites

… an Opportunity

B×H

Tough Tender

G|

G|T

G|

G|

C

316

530

• This situation suggests rather strongly that the G-G haplotype is actually associated with a mixture of functional alleles.

• Provides opportunity to make the test more powerful by adding SNP

SNP X?

Why Did We Discover this Opportunity to Improve the Test?

• Because we looked

• Because we had an appropriate population in which to find it

We Are Learning a Great Deal From the -Calpain DNA Test

• Multiple SNP present some challenges.

• The test works very well as it is.

• I am confident that it will work even better when we add a few more SNP to it.

Conclusions• DNA testing is not as simple as it first

appears.• DNA tests should be viewed as very fluid

systems.• The potential benefits are enormous.• It will eventually become widespread in

cattle breeding.

• It is important that producers have realistic expectations