IGENITY Tenderness:
Igenity profile Tenderness is a DNA genetic marker panel test comprised of three markers (UoGCAST1, Calpain 4751 and Calpain 316). An increase in “tenderness” is associated with substituting a “C” allele at calpastatin (UoGCAST1) and a “C” allele at both μ-calpain loci (Calpain 4751 and Calpain 316). The following table shows the decrease in “toughness” (Warner-Bratzler Shear Force, lb) for each of the possible genotypes contrasted to the least tender genotype (i.e. UoG-Cast1 “GG”, Capn4751 “TT”, Capn316 “GG”) calculated from a combined analysis of 1209 cattle from four sample populations (Brangus, Charolais x Angus cross, Red Angus and Brahman) used in the validation study.
| Genotype | Estimate (lbs.) |
Standard Error | Number Obs. | % | ||
|---|---|---|---|---|---|---|
| UoG-Cast1 | Calpain 316 | Calpain 4751 | ||||
| CC | CC | CC | -2.3 | 0.4 | 18 | 1.5 |
| CT | -1.1 | 0.6 | 8 | 0.7 | ||
| TT | 0.1 | 1.0 | 0 | 0.0 | ||
| CG | CC | -1.9 | 0.3 | 60 | 5.0 | |
| CT | -1.5 | 0.3 | 123 | 10.2 | ||
| TT | -0.4 | 0.5 | 9 | 0.7 | ||
| GG | CC | -1.6 | 0.3 | 60 | 2.7 | |
| CT | -1.2 | 0.3 | 181 | 15.0 | ||
| TT | -0.8 | 0.2 | 212 | 17.5 | ||
| CG | CC | CC | -1.9 | 0.3 | 9 | 0.7 |
| CT | -0.7 | 0.5 | 1 | 0.1 | ||
| TT | 0.5 | 1.0 | 0 | 0.0 | ||
| CG | CC | -1.5 | 0.2 | 42 | 3.5 | |
| CT | -1.1 | 0.2 | 74 | 6.1 | ||
| TT | 0.1 | 0.5 | 4 | 0.3 | ||
| GG | CC | -1.2 | 0.3 | 23 | 1.9 | |
| CT | -0.8 | 0.2 | 91 | 7.5 | ||
| TT | -0.4 | 0.1 | 204 | 16.9 | ||
| GG | CC | CC | -1.4 | 0.3 | 2 | 0.2 |
| CT | -0.2 | 0.5 | 1 | 0.1 | ||
| TT | 1.0 | 1.0 | 0 | 0.0 | ||
| CG | CC | -1.1 | 0.2 | 7 | 0.6 | |
| CT | -0.7 | 0.1 | 9 | 0.7 | ||
| TT | 0.5 | 0.5 | 0 | 0.0 | ||
| GG | CC | -0.8 | 0.3 | 5 | 0.4 | |
| CT | -0.4 | 0.1 | 30 | 2.5 | ||
| TT | 0 | 63 | 5.2 | |||
The yellow shaded genotypes involve the rare "T-C" haplotype. The low number of animals with this genotype in the data set made it difficult to accurately estimate the size of its effect.
The Calpastatin marker (UogCAST1) and the Calpain haplotypes based on CAPN4751 and CAPN316) were each highly significant. The combination of all three even more so. Each calpastatin “C” was associated with a decrease of 0.4 lb of Warner-Bratzler Shear Force, and substituting the Calpain 4751 “C” - 316 “C” haplotype for the Calpain 4751 “T” - 316 “G” was associated with a decrease of 0.7 lb of Warner-Bratzler Shear Force. Among genotypes with sufficient information there was a 2.3 lb. difference in WBSF between the best (homozygous C at all three markers) and the worst GG-TT-GG (UoGCAST1-CAPN4751-CAPN316). Breeders should not expect gains this large because no herd will consist 100% of the ‘least tender’ genotype.
Igenity profile Tenderness is a DNA genetic marker panel test offered by Igenity. Increase in “tenderness” is associated with favorable alleles of a marker panel that includes Calpain 4751 (i.e. a “C” allele at the 4751 SNP of calpain ), Calpain 316 (i.e. a “C” allele at the 316 SNP of calpain ), and UofG-CAST1 (i.e. a “C” allele at the UofGCAST1).
Polymorphisms analyzed
- CAPN1 316 = SNP “316” in μ -calpain (micromolar calcium activated neutral protease 1).
- CAPN1 4751 = SNP “4751” in μ -calpain (micromolar calcium activated neutral protease 1).
- UofG-CAST1 = SNP in calpastatin (calpain inhibitor). Note this is a different SNP from CAST-T1 (GeneSTAR® Tenderness).
Cattle Used for Validation
- Brahman Sired ARS, Brooksville cattle (344 animals)
* Brahman sires, Brahman dams - Brangus Sired CMP* cattle (219 animals)
* Brangus sires, primarily Brangus and some Brangus cross dams - Charolais Sired CMP* cattle (435 animals)
* Charolais sires, Black Angus dams - Red Angus Sired CMP* cattle (307 animals)
* Red Angus sires, mostly Red Angus dams, some crossbred - Black Angus cattle (394 animals)
* Angus sires, Black Angus dams
* CMP = carcass merit project; influential sires in their breed in the 1990s were utilized ("legacy bulls")
| Reference Population | CALPAIN 4751 | CALPAIN 316 | UoG-CAST1 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| CC | CT | TT | CC | GC | GG | GG | GC | CC | ||
| Combined | Genotype No. | 426 | 724 | 556 | 113 | 561 | 1042 | 175 | 604 | 896 |
| Genotype % | 25 | 42 | 33 | 7 | 33 | 61 | 14 | 48 | 71 | |
| Allele % | 46% | 54% | 23% | 77% | 28% | 9448% | ||||
| Total No. | 1706 | 1716 | 1268 | |||||||
| Brangus | Genotype No. | 64 | 111 | 44 | 5 | 67 | 145 | 10 | 65 | 128 |
| Genotype % | 29 | 51 | 20 | 2 | 31 | 67 | 5 | 32 | 63 | |
| Allele % | 55% | 45% | 18% | 82% | 21% | 79% | ||||
| Total No. | 219 | 217 | 203 | |||||||
| Charolais x Angus | Genotype No. | 82 | 234 | 119 | 19 | 163 | 253 | 20 | 137 | 255 |
| Genotype % | 19 | 54 | 27 | 4 | 37 | 58 | 5 | 33 | 62 | |
| Allele % | 46% | 54% | 23% | 77% | 26% | 74% | ||||
| Total No. | 307 | 307 | 305 | |||||||
| Red Angus | Genotype No. | 63 | 165 | 79 | 15 | 110 | 182 | 23 | 111 | 171 |
| Genotype % | 21 | 54 | 26 | 5 | 36 | 59 | 8 | 36 | 56 | |
| Allele % | 47% | 53% | 23% | 77% | 26% | 74% | ||||
| Total No. | 307 | 307 | ||||||||
| Brahman | Genotype No. | 5 | 45 | 280 | 10 | 333 | 113 | 163 | 68 | |
| Genotype % | 2 | 14 | 85 | 3 | 97 | 33 | 47 | 20 | ||
| Allele % | 8% | 92% | 1% | 99% | 57% | 43% | ||||
| Total No. | 330 | 343 | 344 | |||||||
| Black Angus | Genotype No. | 212 | 169 | 34 | 74 | 211 | 129 | 9 | 128 | 274 |
| Genotype % | 51 | 41 | 8 | 18 | 51 | 31 | 2 | 31 | 67 | |
| Allele % | 71% | 29% | 43% | 57% | 18% | 82% | ||||
| Total No. | 415 | 414 | 411 | |||||||
* These are the frequencies in the data analyzed and are not necessarily reflective of any purebred population.
IGENITY profile Tenderness Results :
A.
*** The Angus CMP population was analyzed at a later date than the other sample populations and so this data is not included in the combined analysis.
** ITG = Igenity profile Tenderness combined marker panel = total number of favorable UofG-Cast1 alleles & CAPN1 haplotypes.
*effect of UofG-Cast1 and CAPN1 haplotype estimated separately; CAPN1 haplotype has a larger effect than UofG-Cast1.
* Genotype effects constructed from effects estimated in the haplotype analysis (Table B)
B. Combined Three-marker Genotype Effects (contrasted to UoG-Cast1 “GG”, Capn316 “GG”, Capn4751 “TT”), Standard Errors and Frequencies* in Reference Samples
| Genotype | Estimate (lbs.) |
Standard Error | Number Obs. | % | ||
|---|---|---|---|---|---|---|
| UoG-Cast1 | Calpain 316 | Calpain 4751 | ||||
| CC | CC | CC | -2.3 | 0.4 | 18 | 1.5 |
| CT | -1.1 | 0.6 | 8 | 0.7 | ||
| TT | 0.1 | 1.0 | 0 | 0.0 | ||
| CG | CC | -1.9 | 0.3 | 60 | 5.0 | |
| CT | -1.5 | 0.3 | 123 | 10.2 | ||
| TT | -0.4 | 0.5 | 9 | 0.7 | ||
| GG | CC | -1.6 | 0.3 | 60 | 2.7 | |
| CT | -1.2 | 0.3 | 181 | 15.0 | ||
| TT | -0.8 | 0.2 | 212 | 17.5 | ||
| CG | CC | CC | -1.9 | 0.3 | 9 | 0.7 |
| CT | -0.7 | 0.5 | 1 | 0.1 | ||
| TT | 0.5 | 1.0 | 0 | 0.0 | ||
| CG | CC | -1.5 | 0.2 | 42 | 3.5 | |
| CT | -1.1 | 0.2 | 74 | 6.1 | ||
| TT | 0.1 | 0.5 | 4 | 0.3 | ||
| GG | CC | -1.2 | 0.3 | 23 | 1.9 | |
| CT | -0.8 | 0.2 | 91 | 7.5 | ||
| TT | -0.4 | 0.1 | 204 | 16.9 | ||
| GG | CC | CC | -1.4 | 0.3 | 2 | 0.2 |
| CT | -0.2 | 0.5 | 1 | 0.1 | ||
| TT | 1.0 | 1.0 | 0 | 0.0 | ||
| CG | CC | -1.1 | 0.2 | 7 | 0.6 | |
| CT | -0.7 | 0.1 | 9 | 0.7 | ||
| TT | 0.5 | 0.5 | 0 | 0.0 | ||
| GG | CC | -0.8 | 0.3 | 5 | 0.4 | |
| CT | -0.4 | 0.1 | 30 | 2.5 | ||
| TT | 0 | 63 | 5.2 | |||
The yellow shaded genotypes involve the rare "T-C" haplotype. The low number of animals with this genotype in the data set made it difficult to accurately estimate the size of its effect.
C. Effect of One Copy of a UoGCAST1 Allele or CAPN1 Haplotype on the Target Trait
The yellow shaded genotypes involve the rare "T-C" haplotype. The low number of animals with this genotype in the data set made it difficult to accurately estimate the size of its effect.
*** The Angus CMP population was analyzed at a later date than the other sample populations and so this data is not included in the combined analysis.