Table 4.
AR and Tex11 SNP association analysis in the tropical composite population
| Trait | SNP | P | Allele | Effect | SE | %Va |
|---|---|---|---|---|---|---|
| PNS18 |
AR1_In4 |
0.0127 |
T |
−6.384 |
2.551 |
5.646 |
| PNS18 |
Tex11_r38k |
0.0072 |
G |
−6.181 |
2.29 |
6.911 |
| PNS18 |
Tex11_g297d |
0.5780 |
A |
−1.655 |
2.992 |
0.299 |
| PNS18 |
Tex11_r696h |
0.0063 |
G |
−6.266 |
2.282 |
7.169 |
| PNS24 |
AR1_In4 |
0.0784 |
T |
−4.137 |
2.347 |
2.368 |
| PNS24 |
Tex11_r38k |
0.0002 |
G |
−7.838 |
2.101 |
11.102 |
| PNS24 |
Tex11_g297d |
0.0594 |
A |
−5.127 |
2.715 |
2.863 |
| PNS24 |
Tex11_r696h |
0.0006 |
G |
−7.31 |
2.121 |
9.746 |
| SC12 |
AR1_In4 |
5.02 x 10-6 |
T |
−1.427 |
0.3097 |
7.976 |
| SC12 |
Tex11_r38k |
4.00 x 10-15 |
G |
−2.155 |
0.2669 |
23.754 |
| SC12 |
Tex11_g297d |
3.35 x 10-5 |
A |
−1.517 |
0.3628 |
7.096 |
| SC12 |
Tex11_r696h |
2.22 x 10-16 |
G |
−2.28 |
0.2691 |
26.837 |
| SC18 |
AR1_In4 |
4.98 x 10-7 |
T |
−1.565 |
0.3077 |
10.584 |
| SC18 |
Tex11_r38k |
4.88 x 10-14 |
G |
−2.066 |
0.2674 |
24.086 |
| SC18 |
Tex11_g297d |
7.45 x 10-4 |
A |
−1.222 |
0.3604 |
5.079 |
| SC18 |
Tex11_r696h |
1.44 x 10-14 |
G |
−2.137 |
0.2705 |
26.009 |
| SC24 |
AR1_In4 |
1.66 x 10-7 |
T |
−1.548 |
0.2922 |
10.772 |
| SC24 |
Tex11_r38k |
3.03 x 10-12 |
G |
−1.839 |
0.2579 |
19.853 |
| SC24 |
Tex11_g297d |
0.0066 |
A |
−0.9469 |
0.3471 |
3.173 |
| SC24 | Tex11_r696h | 2.18 x10-12 | G | −1.865 | 0.2597 | 20.607 |
Significance (P), allele substitution effect (Effect) for the named allele of each SNP, its standard error (SE) and percentage of additive variance (%Va) explained by 3 SNP genotypes in Tex11 and 1 SNP in AR on Scrotal Circumference (SC) at 12, 18 and 24 months of age and on the percentage of normal sperm (PNS) at 18 and 24 months of age.