Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC...

20 April 2006Choctaw, MS

Beef Improvement Federation(NBCEC Validation Update)

Quaas, Thallman & Van Eenennaam

Commercial DNA Tests

NBCEC Validations

Dick Quaas, Cornell UniversityMark Thallman, USMARC

Alison Van Eenennaam, UC-Davis




Home

Background

Sample Populations

Marker Assisted

Selection

Ancillary Results

Glossary

The purpose of the NBCEC commercial DNA test validation is to independently verify associations between genetic tests and traits as claimed by the commercial genotyping company using phenotypes and DNA from reference cattle populations. The validation process is a partnership of the owners of DNA and phenotypes (e.g., breed associations) and genomics companies, facilitated by the NBCEC

Commercial genetic test validations

IGENITY TenderGeneTM

GeneSTAR® Quality Grade

GeneSTAR® Tenderness

www.nbcec.orgvalidation




Marker Assisted ???

Marker Assisted Selection (MAS)Select Breeding StockNBCEC validation is for MAS

Marker Assisted Management (MAM)Sort cattle for management purposes, e.g.,

Feedlot cattle optimal endpointFeedlot cattle implant regime

NBCEC does not validate MAM tools




Bovigen Marker Validation: Done

GeneSTAR Quality Grade (reported @ ‘05 BIF)TG5 (original GeneSTAR Marbling) + M2CMP Charolais only(CMP Herefords 99:1 M2 allele freq.)

GeneSTAR Tenderness (reported @ ‘05 BIF)T1 = CAST & T2 = CAPN1 316CMP Charolais & Herefords




Merial Marker Validation: Done

Igenity TenderGENE

UoG-Cast1 + CAPN1 316 + CAPN1 4751

CMP Charolais, Red Angus, Brangus & Brahmans




Bovigen Marker Validation: Near Done

GeneSTAR TendernessT1 = CAST & T2 = CAPN1 316T3 = CAPN1 4751 & “Tx”CMP Charolais & Herefords + LSU

BrahmansCMP Brahmans

Tx is almost fixed in (European) TaurusNo association in Brahmans; Bovigen will

not include in GeneSTAR Tenderness

New




Quality/Fatness Marker Summary

Bovigen: GeneSTAR Quality GradeResults

Small, nonsignificant effect on marbling

Significant effect on % Choice or betterSimilar findings w/ TG5 in Simm-Angus

ConclusionModestly effective, primarily due to

TG5, Stars aren’t equal; TG5 >>>M2




Quality/Fatness Marker Summary

Merial submitted 4 leptin SNP + GHRUASM1, UASM2, exon2fb, A252T

Traits analyzed: Carcass wt, REA, Fat thick., YG, Marbling score

Results:Leptin SNP not associated with

traits; (A252T not polymorphic)GHR associated with REA & YG

but favorable allele rare




Quality/Leanness Marker Summary

Merial (leptin SNP)Not for seedstock selection for carcass

traitsPossibly for “marker assisted management”

Results to be included under Ancillary Analyses on website

Future leptin studies of other traits, e.g. female fertility




Tenderness Marker Summary

Bovigen & Merial each market 3 tenderness SNP2 identical calpain SNP: CAPN1 316 & 4751

from MARC1 calpastatin SNP

Bovigen: CAST-T1 (Genetic Solutions)

Merial: UoG-CAST1 (U. of Guelph)Current NBCEC Consensus

3-SNP Tenderness Panels are effective & equally so





Calpastatin SNP (UoG-CAST1 or T1) Taurus: 60-90% favorable allelesBrahmans: ~40-60% favorable

Calpain 316 (T2)Taurus: ~20 % favorableBrahmans: ~2% favorable

Calpain 4751 (T3)Taurus: ~50 % favorableBrahmans: ~5-10% favorable





Current NBCEC Consensus

3-SNP Tenderness Panels are effective & equally so

About 2.25 lbs difference between “best” & ”worst” genotypes

Should expect .75-1.5 lb. by making herd homozygous depending on breed




Current Test Conundrum

Tenderness:Phenotypes not available for EPDsTests are effectiveWhat’s the economic return?

Quality/Yield Grade:Huge economic returnTests are ‘modestly’ effectiveUltrasound EPDs available and very

effective




www.nbcec.org

(validation tab)

Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC...

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