Table 7.
Genome-wide significant SNPs for mammary system traits
| Trait | SNP name | Chr. | Position (bp) | Nearest gene | Distance (bp) | Heritability/-log 10 ( P ) b | Threshold |
|---|---|---|---|---|---|---|---|
| Rear udder |
ARS-BFGL-NGS-111920 |
14 |
44029634 |
LOC100337279 |
within |
0.01330 |
0.00891 |
| Hapmap50827-BTA-94026 |
24 |
2166631 |
LOC100336384 |
39,890 |
0.01130 |
0.00891 |
|
| Udder texture |
ARS-BFGL-NGS-104839 |
3 |
88712390 |
LOC100295233 |
within |
0.00873 |
0.00872 |
| BTA-41935-no-rs |
17 |
72284836 |
DRG1 |
within |
0.01670 |
0.00872 |
|
| BTB-01236227 |
20 |
15824409 |
HTR1A |
264,560 |
0.00941 |
0.00872 |
|
| Median suspensory |
BTB-00089278 |
2 |
26942975 |
LRP2 |
within |
0.01080 |
0.00874 |
| BTB-01007411 |
4 |
37145925 |
SEMA3E |
960 |
0.00995 |
0.00874 |
|
| ARS-BFGL-NGS-35982 |
5 |
5693439 |
NAP1L1 |
81,318 |
0.00941 |
0.00874 |
|
| ARS-BFGL-NGS-29118 |
13 |
8497369 |
MACROD2 |
within |
0.01490 |
0.00874 |
|
| ARS-BFGL-NGS-52278a |
12 |
89182471 |
RAB20 |
within |
7.85b |
6.02c |
|
| Fore attachment |
ARS-BFGL-NGS-114960 |
29 |
36024434 |
NTM |
448,744 |
0.01050 |
0.00965 |
| Fore teat Placement |
ARS-BFGL-NGS-113245 |
19 |
59068269 |
SLC39A11 |
within |
0.01290 |
0.00892 |
| Teat length |
BTB-01255458 |
10 |
99270875 |
PDIA6 |
80,295 |
0.01030 |
0.00911 |
| Rear attach height |
ARS-BFGL-NGS-20052 |
2 |
107616903 |
CDK5R2 |
3,609 |
0.00988 |
0.00904 |
| Hapmap43038-BTA-76203 |
6 |
50316616 |
LOC100298058 |
12,846 |
0.00997 |
0.00904 |
|
| Rear attach Width |
BTB-01478363 |
20 |
17370437 |
BAG1 |
210,690 |
0.00938 |
0.00924 |
| Rear teat Placement |
ARS-BFGL-NGS-31730 |
11 |
44265651 |
SH3RF3 |
within |
0.00927 |
0.00864 |
| BTB-01230622 | 15 | 62600934 | DCDC5 | 61,622 | 0.01200 | 0.00864 |
Note: Heritability and threshold were obtained using the LASSO method; -log10(P) was calculated using SMMA. aSNP detected by SMMA only; b-log10(P) obtained from SMMA; cthreshold of SMMA. Nearest gene are symbols of gene full name in the NCBI database (http://www.ncbi.nlm.nih.gov/).