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Table 1 Genomic regions under recent selection in French Large White pigs

From: Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

ID

Chr

Start (Mb)

End (Mb)

L (kb)

WG tests

Category

Genes

SSC1:16

1

16.33

16.36

34

hapFLK

div

KATNA1 GINM1

SSC1:95

1

95.44

95.63

186

LWS

conv

3

SSC1:110

1

110.37

111.69

1328

hapFLK

div

6

SSC1:230

1

230.43

230.44

6

LWD

LWD

GNA14

SSC1:238

1

238.38

239.9

1518

LWD

conv(LWD)

20

SSC1:253

1

253.31

253.45

134

LWD

LWD

3

SSC2:1

2

1.22

1.53

305

LWD,LWS

conv

12

SSC2:45

2

45.74

45.76

20

LWS

conv(LWS)

PTH (+1)

SSC2:145

2

145.18

145.18

0

LWD

conv(LWD)

0

SSC2:151

2

151.01

151.38

371

hapFLK

div

10

SSC3:3

3

3.85

3.86

6

LWD

conv(LWD)

SLC29A4

SSC3:124

3

124.83

124.84

1

LWS

LWS

0

SSC4:18

4

18.01

18.03

17

hapFLK

div

0

SSC4:54

4

54.79

54.8

5

LWS

conv(LWS)

SNX16

SSC5:94

5

94.16

94.17

18

hapFLK

div

0

SSC6:13

6

13.87

13.87

1

LWS

LWS

(+1)

SSC6:72

6

72.3

72.31

15

LWS

conv(LWS)

VPS13D RF00156

SSC7:18

7

18.6

18.62

11

hapFLK

div

0

SSC7:85

7

85.68

85.69

1

LWS

LWS

(+1)

SSC8:80

8

80.67

80.75

72

hapFLK

div

ARHGAP10

SSC8:124

8

124.62

124.62

0

hapFLK

LWS

BMPR1B

SSC9:19

9

19.37

19.9

538

LWS

conv(LWS)

13

SSC9:96

9

96.7

98.42

1721

LWD

conv(LWD)

5

SSC9:101

9

101.3

104.51

3206

LWD

conv

26

SSC9:107

9

107.83

108.62

784

LWS

conv(LWS)

8

SSC10:23

10

23.7

23.7

2

LWS

conv(LWS)

PKP1

SSC10:62

10

62.92

62.93

12

LWS

conv(LWS)

0

SSC11:7

11

7.66

7.79

130

LWD,hapFLK

LWD

HSPH1 B3GLCT (+1)

SSC11:51

11

51.15

51.16

5

LWD

LWD

0

SSC13:99

13

99.09

99.09

3

LWS

conv

0

SSC13:109

13

109.1

110.15

1046

LWS

conv

9

SSC13:113

13

113.97

114.2

233

LWS

conv(LWS)

NAALADL2

SSC13:191

13

191.52

191.54

14

hapFLK

div

0

SSC16:69

16

69.96

70.9

941

LWD

LWD

6

SSC17:1

17

1.86

4.02

2153

LWD

LWD

8

SSC17:43

17

43.48

43.91

434

LWS

conv(LWS)

3

SSC17:60

17

60.33

60.79

466

hapFLK

div

0

SSC18:10

18

10.54

10.56

20

hapFLK

div

ZC3HAV1

  1. Columns ‘ID’, ’Chr’, ’Start (Mb)’ and ’End (Mb)’ indicate the name and the genomic position of each region and column ‘L (kb)’ gives its length in kb. The ’WG tests’ column provides the whole genome test(s) that detected this region as significant; LWD (resp. LWS) stands for time-LWD+LS (resp. time-LWS-LS) to simplify the notations. The ’Type’ column indicates the selection scenario proposed for this region (as described in “Methods” section). The ’Genes’ column reports the number of genes found in the region. Gene names are reported for regions when there is a maximum of two genes with gene names, in this case the number of genes without gene name (only an Ensembl ID) is given in parenthesis. The full list of genes for all regions is provided in Additional file 3
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Genetics Selection Evolution

ISSN: 1297-9686