Table 7.
The most significant (P < 5 × 10-8) SNPs from the best variable GWAS (SNP, w/i B. taurus ( Bt ), and w/i B indicus ( Bi )) across traits and the frequency of the B allele across and within subspecies origins
| Trait | Most significant variable 1 | CHR | Position | Effect | SE | P value |
Frequency of B allele |
||
|---|---|---|---|---|---|---|---|---|---|
| Across | B. taurus | B. indicus | |||||||
| LLPF |
B w/i Bi |
1 |
7901376 |
0.01 |
0.00 |
2.39E-08 |
0.252 |
0.388 |
0.117 |
| X_lwt |
SNP |
3 |
80105316 |
-7.43 |
1.22 |
1.12E-09 |
0.552 |
0.269 |
0.852 |
| RFI |
A w/i Bi |
3 |
88904960 |
0.15 |
0.03 |
3.44E-08 |
0.816 |
0.925 |
0.712 |
| PW_lwt |
B w/i Bi |
4 |
7139260 |
-2.62 |
0.44 |
3.64E-09 |
0.171 |
0.316 |
0.050 |
| CP8 |
A w/i Bi |
4 |
75484332 |
0.80 |
0.13 |
1.11E-09 |
0.333 |
0.458 |
0.195 |
| X_lwt |
A w/i Bt |
5 |
47594268 |
-8.87 |
1.35 |
5.17E-11 |
0.739 |
0.997 |
0.523 |
| PW_hip |
B w/i Bi |
5 |
47866991 |
1.36 |
0.14 |
1.11E-16 |
0.515 |
0.979 |
0.135 |
| HUMP |
SNP |
5 |
48623407 |
7.42 |
1.17 |
2.78E-10 |
0.368 |
0.038 |
0.592 |
| CIMF |
SNP |
5 |
48876680 |
0.25 |
0.04 |
1.22E-08 |
0.447 |
0.957 |
0.125 |
| CRIB |
A w/i Bi |
5 |
49341986 |
-0.51 |
0.09 |
1.24E-08 |
0.510 |
0.089 |
0.841 |
| PW_lwt |
B w/i Bi |
5 |
50511526 |
3.99 |
0.48 |
2.22E-16 |
0.032 |
0.030 |
0.034 |
| PW_hip |
SNP |
6 |
40093712 |
-1.59 |
0.17 |
1.11E-16 |
0.948 |
1.000 |
0.905 |
| PW_lwt |
B w/i Bi |
6 |
40093712 |
7.20 |
0.89 |
6.66E-16 |
0.948 |
1.000 |
0.905 |
| X_hip |
B w/i Bi |
6 |
40093712 |
2.16 |
0.39 |
3.53E-08 |
0.948 |
1.000 |
0.905 |
| LLPF |
SNP |
6 |
68101121 |
-0.02 |
0.00 |
6.20E-11 |
0.620 |
0.986 |
0.352 |
| CIMF |
A w/i Bt |
6 |
103056415 |
0.71 |
0.12 |
1.15E-08 |
0.114 |
0.018 |
0.206 |
| CRBY |
SNP |
7 |
93287387 |
-0.55 |
0.08 |
2.45E-11 |
0.767 |
0.575 |
0.951 |
| LLPF |
SNP |
7 |
98540675 |
-0.02 |
0.00 |
1.11E-16 |
0.833 |
0.901 |
0.763 |
| RFI |
SNP |
8 |
88601164 |
-0.15 |
0.03 |
3.68E-08 |
0.483 |
0.792 |
0.213 |
| CIMF |
SNP |
9 |
81368713 |
0.21 |
0.03 |
6.75E-10 |
0.481 |
0.821 |
0.196 |
| CRBY |
SNP |
9 |
99124601 |
-0.62 |
0.11 |
3.37E-08 |
0.318 |
0.004 |
0.642 |
| LLPF |
SNP |
10 |
94456158 |
0.01 |
0.00 |
2.29E-10 |
0.260 |
0.009 |
0.526 |
| CIMF |
SNP |
10 |
96286865 |
-0.19 |
0.03 |
1.84E-09 |
0.497 |
0.175 |
0.798 |
| PW_hip |
A w/i Bi |
11 |
103650142 |
0.64 |
0.10 |
2.58E-10 |
0.882 |
0.813 |
0.935 |
| PW_lwt |
A w/i Bt |
11 |
104721167 |
-2.74 |
0.45 |
1.33E-09 |
0.910 |
0.941 |
0.883 |
| HUMP |
SNP |
12 |
28414761 |
6.82 |
1.21 |
2.09E-08 |
0.400 |
0.004 |
0.697 |
| LLPF |
A w/i Bi |
12 |
35342256 |
0.01 |
0.00 |
4.52E-09 |
0.792 |
0.649 |
0.929 |
| CP9 |
SNP |
14 |
24573257 |
-0.68 |
0.10 |
1.41E-12 |
0.699 |
0.909 |
0.366 |
| RFI |
SNP |
14 |
24621142 |
0.18 |
0.03 |
3.52E-09 |
0.300 |
0.085 |
0.643 |
| X_hip |
SNP |
14 |
24973324 |
1.19 |
0.19 |
2.89E-10 |
0.731 |
0.972 |
0.361 |
| PW_hip |
SNP |
14 |
25015640 |
0.96 |
0.09 |
1.11E-16 |
0.707 |
0.949 |
0.356 |
| PW_lwt |
SNP |
14 |
25015640 |
4.38 |
0.45 |
1.11E-16 |
0.707 |
0.949 |
0.356 |
| X_lwt |
SNP |
14 |
25015640 |
12.70 |
1.24 |
1.11E-16 |
0.707 |
0.949 |
0.356 |
| PWIGF |
A w/i Bi |
14 |
25284162 |
40.70 |
5.26 |
2.56E-14 |
0.263 |
0.022 |
0.621 |
| CRIB |
SNP |
14 |
26244461 |
0.38 |
0.07 |
1.03E-08 |
0.489 |
0.391 |
0.594 |
| CIMF |
B w/i Bt |
14 |
49295027 |
0.31 |
0.05 |
4.00E-12 |
0.714 |
0.814 |
0.626 |
| LLPF |
B w/i Bi |
14 |
57668819 |
0.01 |
0.00 |
1.38E-08 |
0.183 |
0.042 |
0.318 |
| X_hip |
B w/i Bi |
16 |
11142022 |
-11.30 |
1.72 |
5.78E-11 |
0.979 |
0.966 |
0.993 |
| LLPF |
A w/i Bt |
16 |
73527778 |
-0.01 |
0.00 |
3.08E-09 |
0.856 |
0.947 |
0.776 |
| CRIB |
B w/i Bt |
17 |
25138316 |
0.41 |
0.07 |
4.49E-08 |
0.522 |
0.358 |
0.692 |
| LLPF |
SNP |
17 |
49580330 |
0.01 |
0.00 |
2.56E-08 |
0.870 |
0.767 |
0.965 |
| X_lwt |
B w/i Bt |
20 |
4873556 |
11.38 |
1.75 |
7.42E-11 |
0.900 |
0.807 |
0.983 |
| PW_hip |
SNP |
20 |
16773483 |
-0.57 |
0.10 |
4.95E-08 |
0.559 |
0.942 |
0.232 |
| CIMF |
A w/i Bt |
20 |
28193857 |
-0.20 |
0.04 |
3.14E-08 |
0.348 |
0.277 |
0.411 |
| PW_lwt |
A w/i Bt |
21 |
21396681 |
-3.04 |
0.55 |
3.91E-08 |
0.241 |
0.308 |
0.183 |
| PW_hip |
A w/i Bt |
21 |
21751432 |
-0.86 |
0.15 |
4.69E-09 |
0.531 |
0.198 |
0.823 |
| CRBY |
A w/i Bt |
21 |
27166480 |
0.47 |
0.08 |
1.86E-08 |
0.761 |
0.773 |
0.751 |
| X_lwt |
SNP |
21 |
32790802 |
-6.49 |
1.11 |
4.65E-09 |
0.599 |
0.366 |
0.837 |
| CRIB |
A w/i Bt |
25 |
10486776 |
0.45 |
0.08 |
8.00E-09 |
0.576 |
0.549 |
0.601 |
| LLPF |
A w/i Bi |
25 |
25631487 |
0.01 |
0.00 |
6.17E-09 |
0.334 |
0.285 |
0.383 |
| CIMF |
A w/i Bt |
29 |
36095196 |
1.40 |
0.23 |
1.21E-09 |
0.089 |
0.009 |
0.162 |
| LLPF | A w/i Bi | 29 | 45556241 | 0.02 | 0.00 | 1.11E-16 | 0.456 | 0.105 | 0.806 |
1B w/i Bi = B allele within Bos indicus; A w/i Bi = A allele within Bos indicus; A w/i Bt = A allele within Bos taurus; B w/i Bt = B allele within Bos taurus.