Table 2.
Genomic regions under selection in cattle and sheep identified using composite selection signals (CSS)
| Regiona | Chr | Positionb (Mb) |
Number of significant SNPs |
Total genesc | Known genesd | Gene function | |||
|---|---|---|---|---|---|---|---|---|---|
| CSS | XPEHH | FST | ΔDAF | ||||||
|
A1 |
1 |
1.01-2.63 |
10* |
9 |
1 |
- |
15 |
POLL locus
|
Polledness |
| A5 |
13 |
63.90-65.97 |
18 |
23* |
1 |
5 |
26 |
UQCC, GDF5 |
Stature |
| A7 |
14 |
23.78-25.61 |
11 |
7 |
5* |
10* |
12 |
PLAG1, CHCHD7 |
Stature |
|
B1 |
2 |
6.15-7.82 |
10* |
11* |
3 |
- |
9 |
MSTN
|
Double muscle |
| B2 |
6 |
66.55-68.11 |
11 |
8 |
- |
- |
6 |
COX7B2, FRYL |
Reproduction |
| B6 |
16 |
44.49-46.05 |
11 |
11 |
1 |
- |
12 |
NMNAT1, PIK3CD, SPSB1, SLC |
Embryonic growth, immunity |
| B8 |
18 |
13.34-15.03 |
5 |
3 |
1 |
- |
33 |
MC1R |
Coat colour |
|
C5 |
10 |
28.54-30.05 |
26* |
17* |
34* |
5* |
9 |
RXFP2
|
Polledness |
| C8 |
13 |
66.97-68.50 |
7 |
- |
7 |
3 |
17 |
ASIP |
Coat colour |
| C10 |
25 |
6.67-8.29 |
14 |
10 |
- |
2 |
16 |
LRP4 |
Bone growth |
| D2 |
2 |
119.62-122.30 |
20 |
11* |
10 |
16 |
26 |
- |
- |
| D4 | 2 | 124.25-128.05 | 28* | 22 | 27 | 27 | 47 | MSTN | Double muscle |
Cluster of a minimum of three significant SNPs within a window spanning 1 Mb genomic locations centred on a core SNP above the threshold (top 0.1%) in CSS (smoothed statistics) are reported and are compared with the constituent tests.
aPrefix (A, B, C and D) with each region number represents the dataset as defined in Table 1 and rows in bold indicate the genomic regions containing candidate genes. A complete list of 36 genomic regions, their positions, range of all significant clusters (for each test) and genes under clusters of significant SNPs is shown in [Additional file 10: Table S4].
bPosition of genomic regions includes a 0.5 Mb extension on both sides of boundaries of the main cluster identified by CSS to compare constituent tests and count of genes (see Methods). Large sized (> 1 Mb) regions are formed by joining successive (<1 Mb apart) clusters.
cGenes mapped on bovine (UMD3.1) and ovine (OARv1.0) assemblies within the boundaries of genomic regions.
dCandidate genes with known functional/structural effects for a particular trait present in the contrasting panels of multiple breeds.
*Indicates the cluster of highest ranked SNPs (raw scores) for a particular selection test.