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Commercial Genetic Test Validation

Ancillary Results

Leptin

  1. Test Details
  2. Sample Populations
  3. Allele Frequencies
  4. Results
  5. Igenity website

GHR

  1. Test Details
  2. Sample Populations
  3. Allele Frequencies
  4. Results
  5. Igenity website

Leptin:

Test Details

Polymorphisms analyzed

  • UASMS2 = a C/T SNP at position 528 of 5’ untranslated promoter region of the bovine leptin gene (GenBank Accession No. AB070368)
  • EXON2-FB = a C/T SNP that results in an amino acid change from Arginine to Cysteine in exon 2 of the bovine leptin gene at (position 121 of GenBank Accession No. AB070369)

Sample Populations

Cattle Used for Validation

  1. Brahman Sired ARS, Brooksville cattle (344 animals)
    * Brahman sires, Brahman dams
  2. Brangus Sired CMP* cattle (219 animals)
    * Brangus sires, primarily Brangus and some Brangus cross dams
  3. Charolais Sired CMP* cattle (435 animals)
    * Charolais sires, Black Angus dams
  4. Red Angus Sired CMP* cattle (307 animals)
    * Red Angus sires, mostly Red Angus dams, some crossbred

* CMP = carcass merit project; influential sires in their breed in the 1990s were utilized ("legacy bulls")

Reference Population Allele Frequencies

Reference Population   UASM S2 EXON2-FB
CC CT TT CC CT TT
Combined (1+2+3+4) Genotype No.
Genotype %
Allele %
Total No.		 998
77
87%
 		 267
21

1299 		 34
3
13%
 		 439
33
55%
 		 569
43

1311 		 303
23
45%
 
Brangus (1) Genotype No.
Genotype %
Allele %
Total No.		 119
56
73%
 		 72
34

213 		 22
10
27%
 		 45
21
43%
 		 96
44

218 		 77
35
57%
 
Charolais x Angus (2) Genotype No.
Genotype %
Allele %
Total No.		 342
78
89%
 		 96
22

438 		 0
0
11%
 		 133
30
55%
 		 216
49

438 		 89
20
45%
 
Red Angus (3) Genotype No.
Genotype %
Allele %
Total No.		 212
69
83%
 		 85
28

307 		 10
3
17%
 		 20
7
34%
 		 168
55

307 		 119
39
66%
 
Brahman (4) Genotype No.
Genotype %
Allele %
Total No.		 329
98
99%
 		 7
2

336 		 0
0
1%
 		 241
70
82%
 		 82
24

343 		 20
6
18%
 

* These are the frequencies in the data analyzed and are not necessarily reflective of any purebred population.

Results

A. Significance of gene effects under an additive model (regression on number of alleles).

Population TRAIT Number Head Marker b SE F P
Combined (1+2+3+4) Marbling 1281
1293		 UASMS2
EXON-2FB		 0.01
-0.03		 4.63
3.34		 0.00
0.00		 1.00
0.99
Yield Grade 1281
1293		 UASMS2
EXON-2FB		 0.01
-0.02		 0.04
0.03		 0.05
0.48		 0.82
0.49
Carcass Weight 1283
1295		 UASMS2
EXON-2FB		 -1.19
-0.59		 4.24
3.07		 0.08
0.04		 0.78
0.85
Rib Eye Area 1282
1294		 UASMS2
EXON-2FB		 -0.08
0.03		 0.07
0.05		 1.28
0.38		 0.26
0.54
Fat thickness 1249
1261		 UASMS2
EXON-2FB		 -0.01
0.00		 0.01
0.01		 1.78
0.01		 0.18
0.93

 

Growth Hormone Receptor:

Test Details

Polymorphisms analyzed

  • GHR = a T/A substitution that results in an amino acid change from Asparagine to Threonine in exon 8 of the bovine growth hormone receptor gene (position 279 of GenBank Accession No. CAA49635)

Sample Populations

Cattle Used for Validation

  1. Brahman Sired ARS, Brooksville cattle (344 animals)
    * Brahman sires, Brahman dams
  2. Brangus Sired CMP* cattle (219 animals)
    * Brangus sires, primarily Brangus and some Brangus cross dams
  3. Charolais Sired CMP* cattle (435 animals)
    * Charolais sires, Black Angus dams
  4. Red Angus Sired CMP* cattle (307 animals)
    * Red Angus sires, mostly Red Angus dams, some crossbred

* CMP = carcass merit project; influential sires in their breed in the 1990s were utilized ("legacy bulls")

Reference Population Allele Frequencies

Reference Population   GHR
AA AT TT
Combined (1+2+3+4) Genotype No.
Genotype %
Allele %
Total No.		 8
1%
28%
 		 146
11%

1310 		 1156
88%
94%
 
Brangus (1) Genotype No.
Genotype %
Allele %
Total No.		 0
0
7%
 		 31
14

216 		 185
86
93%
 
Charolais x Angus (2) Genotype No.
Genotype %
Allele %
Total No.		 5
1
9%
 		 68
15

439 		 366
83
91%
 
Red Angus (3) Genotype No.
Genotype %
Allele %
Total No.		 4
1
9%
 		 45
15

307 		 258
84
91%
 
Brahman (4) Genotype No.
Genotype %
Allele %
Total No.		 0
0
0.4%
 		 3
1

344 		 341
99
99.6%
 

* These are the frequencies in the data analyzed and are not necessarily reflective of any purebred population.

Results

A. Significance of gene effects under an additive model (regression on number of alleles).

Population TRAIT Number Head Marker b SE F P
Combined (1+2+3+4) Marbling 1292 GHR 2.57 6.44 0.16 0.69
Yield Grade 1292 GHR 0.13 0.05 5.88 0.02
Carcass Weight 1294 GHR -2.44 5.86 0.17 0.68
Rib Eye Area 1293 GHR -0.31 0.10 9.24 0.002
Fat thickness 1260 GHR 0.02 0.01 1.61 0.20