Table 5.

Most significant (in italics) and suggestive SNPs in identified vQTL for litter size variability^a

SSC	Name	Position (Mb)	MAF	SNP effect (with SE)	Genetic. variance explained	Phenotypic variance explained	− log(p-value)	SNP location	Candidate genes	Previously detected QTL
1	AX-116127462	129.07	0.01	− 0.083 (0.020)	0.013	0.002	4.57	Intron	GANC	None
	AX-116127463	129.08	0.01	− 0.100 (0.021)	0.017	0.003	5.53	Intron	GANC
	AX-116127466	129.09	0.01	− 0.097 (0.020)	0.018	0.003	6.02	Intron	GANC
	AX-116702728	129.17	0.01	− 0.083 (0.018)	0.015	0.003	5.30	Intron	VPS39
	AX-116127269	127.69	0.03	− 0.047 (0.012)	0.012	0.002	4.23	Non-coding	Nonea
7	AX-116317099	36.59	0.47	0.020 (0.005)	0.016	0.003	4.35	Non-coding	NCR2	Birthweight variability [66]; number mummified piglets [67]; age at puberty [68]
	AX-116317159	36.80	0.49	0.019 (0.004)	0.015	0.003	4.78	Non-coding	NRN1
	AX-116317552	38.26	0.36	0.018 (0.005)	0.013	0.002	4.03	Intron	CUL9
	AX-116317553	38.26	0.36	0.018 (0.005)	0.013	0.002	4.07	Intron	CUL9
	AX-116317740	38.97	0.36	− 0.019 (0.005)	0.015	0.003	4.43	Non-coding	Nonea
	AX-116689108	41.80	0.01	0.106 (0.018)	0.020	0.003	8.50	Non-coding	ADGRF1; ADGRF5
18	AX-116596013	18.07	0.05	− 0.039 (0.009)	0.012	0.002	4.60	Intron	LMBR1	Litter weight [69]; litter size [69]; litter weight of piglets born alive [69]; birthweight [70]
	AX-116596024	18.19	0.09	− 0.030 (0.007)	0.013	0.002	4.83	Non-coding	KLF14; TSGA13; COPG2
	AX-116596140	18.88	0.04	0.045 (0.011)	0.01	0.002	4.08	Intron	UBE2H
	AX-116596204	19.30	0.07	− 0.034 (0.008)	0.012	0.002	4.53	Intron	AHCYL2
	AX-116596216	19.37	0.09	− 0.029 (0.007)	0.011	0.002	5.01	Intron	AHCYL2
	AX-116596225	19.40	0.06	− 0.041 (0.009)	0.015	0.003	5.56	Intron	AHCYL2
	AX-116596239	19.45	0.05	− 0.039 (0.009)	0.013	0.002	4.82	Intron	SMO

SSC Sus scrofa chromosomes; SNPs on each SSC present confirmed candidate QTL region

MAF minor allele frequency

^aObtained with a log-transformed variance of residuals

^bWithin ± 50 kb