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Table 3 Focus on a few biological functions under selection in LW

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

Biological term

Database

Region category

Nb. genes

Nb. regions

Candidate genes

Body weight

MGI

Dam

8

6

LPIN1, CAMK2A, KITLG, NR3C1

Body weight

MGI

Both.Sire

16

8

RELN, EPG5, GATA3, NRCAM, IGF2, TNIK, PNPLA8, PLCG1

Body size

MGI

Dam

9

7

B3GLCT, PDGFRB, LPIN1, KITLG, NR3C1

Body size

MGI

Both.Sire

11

6

RELN, IGF2, SFRP4, PLCG1

PI3K signaling ptw.

KEGG

Dam

3

2

PDGFRB, KITLG

PI3K signaling ptw.

KEGG

Both.Sire

5

3

MAGI2, RELN, IGF2

Preweaning lethality

MGI

Dam

9

8

KATNA1, ARHGAP10, TMTC3, RBM26, SLC6A7

Perinatal lethality

MGI

Dam

4

4

KITLG, NR3C1, PDGFRB

Calcium signaling ptw.

KEGG

Dam

3

2

PDGFRB, CAMK2A, GNA14

Osteoporosis

MGI

Dam

4

3

NR3C1

Lipid metabolic process

GOBP

Both.Sire

5

5

LPIN1, PNPLA8, PLCG1

Fatty acid metabolic process

GOBP

Both.Sire

3

3

LPIN1, PNPLA8

Insulin secretion

KEGG

Both.Sire

3

3

LPIN1

Glycogen biosynthetic process

GOBP

Both.Sire

3

2

IGF2, PTH

  1. Biological functions listed in this table are highlighted because they are among the most significantly enriched in signatures of selection (body weight, body size and PI3K signaling pathway) or because they are specifically associated with one category of signatures of selection (other terms). The ‘Nb. genes’ column gives the number of genes associated with a given biological function and located within (or flanking) a region from a specific region category. The ‘Nb. regions’ column gives the number of distinct regions where these genes are located. The ‘Candidate genes’ column reports the genes that can be considered among the best candidate genes within their candidate region (among those counted in the ‘Nb. genes’ column). The determination of candidate genes within a candidate region is based on the local values of the statistics used to detect selection in this region, and on expression data when available. It does not account for functional information concerning the genes. Details regarding this determination procedure can be found in (see Additional file 2: Table S1). The full list of biological functions showing significant enrichment in signatures of selection is in Additional file 6