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Table 2 Genomic regions under selection in cattle and sheep identified using composite selection signals (CSS)

From: Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

Regiona

Chr

Positionb(Mb)

Number of significant SNPs

Total genesc

Known genesd

Gene function

CSS

XPEHH

F ST

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

  1. 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.
  2. 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].
  3. 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.
  4. cGenes mapped on bovine (UMD3.1) and ovine (OARv1.0) assemblies within the boundaries of genomic regions.
  5. dCandidate genes with known functional/structural effects for a particular trait present in the contrasting panels of multiple breeds.
  6. *Indicates the cluster of highest ranked SNPs (raw scores) for a particular selection test.