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Commercial DNA Tests NBCEC Validations. Dick Quaas, Cornell University Mark Thallman, USMARC Alison Van Eenennaam, UC-Davis. Commercial genetic test validations. GeneSTAR ® Tenderness. GeneSTAR ® Quality Grade. IGENITY Tender Gene TM.

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commercial dna tests nbcec validations

Commercial DNA TestsNBCEC Validations

Dick Quaas, Cornell University

Mark Thallman, USMARC

Alison Van Eenennaam, UC-Davis

Beef Improvement Federation(NBCEC Validation Update)

www nbcec org

Commercial genetic test validations

GeneSTAR® Tenderness

GeneSTAR® Quality Grade

IGENITY TenderGeneTM

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

Home

Background

Sample Populations

Marker Assisted Selection

Ancillary Results

Glossary

www.nbcec.org

validation

Beef Improvement Federation(NBCEC Validation Update)

marker assisted
Marker Assisted ???
  • Marker Assisted Selection (MAS)
    • Select Breeding Stock
    • NBCEC validation is for MAS
  • Marker Assisted Management (MAM)
    • Sort cattle for management purposes, e.g.,
      • Feedlot cattle  optimal endpoint
      • Feedlot cattle  implant regime
    • NBCEC does not validate MAM tools

Beef Improvement Federation(NBCEC Validation Update)

bovigen marker validation done
Bovigen Marker Validation: Done
  • GeneSTAR Quality Grade (reported @ ‘05 BIF)
    • TG5 (original GeneSTAR Marbling) + M2
    • CMP Charolais only
    • (CMP Herefords 99:1 M2 allele freq.)
  • GeneSTAR Tenderness (reported @ ‘05 BIF)
    • T1 = CAST & T2 = CAPN1 316
    • CMP Charolais & Herefords

Beef Improvement Federation(NBCEC Validation Update)

merial marker validation done
Merial Marker Validation: Done
  • Igenity TenderGENE
    • UoG-Cast1 + CAPN1 316 + CAPN1 4751
    • CMP Charolais, Red Angus, Brangus & Brahmans

Beef Improvement Federation(NBCEC Validation Update)

bovigen marker validation near done
Bovigen Marker Validation: Near Done
  • GeneSTAR Tenderness
    • T1 = CAST & T2 = CAPN1 316
    • T3 = CAPN1 4751 & “Tx”
    • CMP Charolais & Herefords + LSU Brahmans
    • CMP Brahmans
    • Tx is almost fixed in (European) Taurus
    • No association in Brahmans; Bovigen will not include in GeneSTAR Tenderness

New

Beef Improvement Federation(NBCEC Validation Update)

quality fatness marker summary
Quality/Fatness Marker Summary
  • Bovigen: GeneSTAR Quality Grade
    • Results
      • Small, nonsignificant effect on marbling
      • Significant effect on % Choice or better
      • Similar findings w/ TG5 in Simm-Angus
    • Conclusion
      • Modestly effective, primarily due to TG5, Stars aren’t equal; TG5 >>>M2

Beef Improvement Federation(NBCEC Validation Update)

quality fatness marker summary8
Quality/Fatness Marker Summary
  • Merial submitted 4 leptin SNP + GHR
      • UASM1, 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

Beef Improvement Federation(NBCEC Validation Update)

quality leanness marker summary
Quality/Leanness Marker Summary
  • Merial (leptin SNP)
    • Not for seedstock selection for carcass traits
    • Possibly for “marker assisted management”
    • Results to be included under Ancillary Analyses on website
    • Future leptin studies of other traits, e.g. female fertility

Beef Improvement Federation(NBCEC Validation Update)

tenderness marker summary
Tenderness Marker Summary
  • Bovigen & Merial each market 3 tenderness SNP
    • 2 identical calpain SNP: CAPN1 316 & 4751 from MARC
    • 1 calpastatin SNP
      • Bovigen: CAST-T1 (Genetic Solutions)
      • Merial: UoG-CAST1 (U. of Guelph)
  • Current NBCEC Consensus
    • 3-SNP Tenderness Panels are effective & equally so

Beef Improvement Federation(NBCEC Validation Update)

tenderness marker summary11
Tenderness Marker Summary
  • Calpastatin SNP (UoG-CAST1 or T1)
      • Taurus: 60-90% favorable alleles
      • Brahmans: ~40-60% favorable
  • Calpain 316 (T2)
      • Taurus: ~20 % favorable
      • Brahmans: ~2% favorable
  • Calpain 4751 (T3)
      • Taurus: ~50 % favorable
      • Brahmans: ~5-10% favorable

Beef Improvement Federation(NBCEC Validation Update)

tenderness marker summary12
Tenderness Marker Summary
  • 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

Beef Improvement Federation(NBCEC Validation Update)

current test conundrum
Current Test Conundrum
  • Tenderness:
    • Phenotypes not available for EPDs
    • Tests are effective
    • What’s the economic return?
  • Quality/Yield Grade:
    • Huge economic return
    • Tests are ‘modestly’ effective
    • Ultrasound EPDs available and very effective

Beef Improvement Federation(NBCEC Validation Update)

www nbcec org validation tab

www.nbcec.org(validation tab)

Beef Improvement Federation(NBCEC Validation Update)