Table 5.
Interaction GWAS: number of the SNPs significant (P < 10-4) for one or more of the three contrasts: origin of sub-species (O), allele within B. taurus (T), and allele within B. indicus (I) for each trait
| Trait | OTI Nb | OT- Nb | O-I Nb | O-- Nb | -TI Nb | -T- Nb | --I Nb |
|---|---|---|---|---|---|---|---|
| RFI |
0 (0) |
12 (0) |
31 (2) |
435 (0) |
0 |
328 (97) |
274 (55) |
| LLPF |
2 (2) |
25 (5) |
77 (48) |
3675 (142) |
19 (19) |
182 (59) |
529 (303) |
| CRBY |
0 |
11 (1) |
13 (0) |
552 (0) |
0 |
294 (104) |
113 (10) |
| CIMF |
0 |
39 (1) |
3 (1) |
1154 (0) |
0 |
671 (186) |
37 (25) |
| CP8 |
0 |
12 (0) |
41 (0) |
490 (15) |
0 |
117 (12) |
430 (161) |
| CRIB |
0 |
33 (2) |
5 (0) |
651 (0) |
0 |
444 (117) |
150 (76) |
| PW_lwt |
0 |
19 (2) |
45 (15) |
2656 (66) |
36 (36) |
406 (146) |
670 (411) |
| X_lwt |
0 |
17 (0) |
125 (38) |
1719 (17) |
24 (24) |
295 (141) |
1335 (716) |
| PWIGF |
0 |
138 (0) |
60 (29) |
170 (28) |
0 |
143 (3) |
608 (368) |
| PW_hip |
0 |
35 (2) |
93 (46) |
5121 (215) |
21 (21) |
193 (46) |
1537 (1041) |
| X_hip |
0 |
79 (0) |
24 (1) |
243 (13) |
0 |
184 (14) |
310 (86) |
| HUMP | 0 | 0 | 10 (0) | 10 (0) | 0 | 6 (0) | 444 (227) |
Column headed OTI Nb = number of SNPs that have significant effects for subspecies origin (O), allele within B. taurus (T) and allele within B. indicus (I); OT- Nb = number of SNPs that have significant effects due to sub-species of origin and alleles within B. taurus but not for alleles within B. indicus; Numbers in brackets = number of SNPs that are significant for all three contrasts and that are also significant in the conventional GWAS for one or more of the 3 one-degree-of-freedom contrasts (see Table 3).