Genome-wide selection signature analysis identified new candidate genes for the teat number in three distinct strains of Large White pigs

Figures (6) Tables (2)

Figure 1.
Analysis of the population structure in four Large White pigs. (a) Principal component analysis. (b) Neighbor-joining tree.
Figure 2.
Manhattan plots for selective sweep analyses of CG strain with the (a) CLR, (b) iHS, (c) nSL, and (d) XP-EHH analyses.
Figure 3.
Manhattan plots for selective sweep analyses of Cooperl strain with the (a) CLR, (b) iHS, (c) nSL, and (d) XP-EHH analyses.
Figure 4.
Manhattan plots for selective sweep analyses of Topigs strain with the (a) CLR, (b) iHS, (c) nSL, and (d) XP-EHH analyses.
Figure 5.
The Venn diagram illustrates the overlap of genes between four different approaches. (a) CG, (b) Cooperl, (c) Topigs.
Figure 6.
Results of the PheWAS analysis based on the identified candidate genes.

Groups	N¹	Min²	Max³	Mean⁴ ± SE⁵
French CG Large White pigs	50	16	20	18.27 ± 0.10
French Cooperl Large White pigs	50	18	20	18.32 ± 0.07
Dutch Topigs Large White pigs	50	18	19	18.26 ± 0.06
Danish Large White pig	50	10	13	12.40 ± 0.09
¹ Number of individuals with phenotypic records. ² Minimum of phenotype. ³ Maximum of phenotype. ⁴ Mean of phenotype. ⁵ Standard error.

Table 1.

Descriptive statistics of the number of teats in 50 Large White pigs of each strain.

Group	Methods	Genes	Trait
CG	nSL	PAFAH1B1	Teat number
		UBE2G1	Teat number
		DNAH12	Teat number
		PCM1	Teat number
		PACC1	Teat number
	iHS	CDH13	Teat number
	CLR	JAZF1	Teat number
Cooperl	CLR	ARL4C	Teat number
Cooperl	CLR	RAPGEF2	Teat number
Topig	nSL	DOCK1	Teat number
	nSL	PCM1	Teat number
	CLR	DNAH12	Teat number
		DOCK1	Teat number
		PCM1	Teat number
* This table is based on the information retrieved in the pig QTLdb database (accessed on 2 April 2024).

Table 2.

Potential candidate genes detected using all methods*.