Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs

Sell-Kubiak, Ewa; Knol, Egbert F.; Lopes, Marcos

doi:10.1186/s12711-021-00692-5

Genetics Selection Evolution

Table 6 Most significant (in italics) and suggestive SNPs in identified vQTL for litter size variability^a

From: Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs

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
7	AX-116317026	36.25	0.016	0.055 (0.013)	0.007	0.002	4.59	Non-coding	None^a	Birthweight variability [66]; number mummified piglets [67]; age at puberty [68]
	AX-116317099	36.59	0.470	0.022 (0.004)	0.016	0.004	5.93	Non-coding	NCR2
	AX-116317136	36.72	0.480	− 0.020 (0.004)	0.014	0.004	5.36	Non-coding	FOXP4
	AX-116317145	36.74	0.310	− 0.025 (0.005)	0.019	0.005	5.60	Non-coding	FOXP4
	AX-116317156	36.79	0.310	− 0.026 (0.005)	0.019	0.005	5.76	Exon	FOXP4
	AX-116317159	36.80	0.490	0.017 (0.004)	0.011	0.003	4.88	Non-coding	MDFI; FOXP4
	AX-116317341	37.52	0.332	0.017 (0.004)	0.008	0.002	4.06	Intron	TRERF1
	AX-116317343	37.53	0.332	0.017 (0.004)	0.008	0.002	4.06	Intron	TRERF1
	AX-116317552	38.26	0.361	0.017 (0.004)	0.009	0.002	4.04	Intron	CUL9
	AX-116317553	38.26	0.361	0.017 (0.004)	0.009	0.002	4.05	Intron	CUL9
	AX-116689108	41.80	0.010	0.110 (0.016)	0.018	0.005	11.57	Non-coding	ADGRF1; ADGRF5
7	AX-116320104	50.68	0.312	0.020 (0.004)	0.012	0.003	5.15	Non-coding	None^a	Teat number [71]; number mummified piglets [67]
	AX-116320268	51.43	0.248	0.019 (0.005)	0.009	0.002	4.41	Intron	SH3GL3
	AX-116320489	52.20	0.345	0.017 (0.004)	0.009	0.002	4.25	Non-coding	FSD2; AP3B2
	AX-116320491	52.20	0.332	0.02 (0.004)	0.012	0.003	5.10	Non-coding	FSD2; AP3B2
	AX-116320493	52.21	0.330	0.021 (0.004)	0.013	0.003	5.43	Intron	AP3B2
	AX-116689308	52.22	0.332	0.019 (0.004)	0.011	0.003	4.71	Intron	AP3B2
	AX-116320498	52.22	0.332	0.019 (0.004)	0.011	0.003	4.53	Intron	AP3B2
	AX-116320499	52.23	0.339	0.020 (0.004)	0.012	0.003	5.30	Intron	AP3B2
	AX-116320501	52.23	0.331	0.019 (0.004)	0.011	0.003	4.53	Intron	AP3B2
	AX-116320502	52.23	0.242	0.019 (0.005)	0.009	0.002	4.52	Intron	AP3B2
	AX-116321160	57.08	0.069	− 0.028 (0.007)	0.007	0.002	4.00	Non-coding	PSTPIP1; RCN2
	AX-116321525	58.97	0.057	− 0.035 (0.008)	0.009	0.002	4.35	Intron	ARID3B
11	AX-116416565	5.71	0.018	− 0.048 (0.012)	0.006	0.002	4.30	Intron	FLT1	Teat number [72]; number mummified piglets [67]; uterine horn length [73]
	AX-116416787	6.87	0.036	0.041 (0.010)	0.008	0.002	4.43	Non-coding	None⁴
	AX-116416839	7.04	0.05	0.038 (0.008)	0.009	0.002	5.50	Intron	KATNAL1
	AX-116416845	7.08	0.036	0.041 (0.010)	0.008	0.002	4.49	Intron	KATNAL1
	AX-116779844	7.30	0.036	0.041 (0.010)	0.008	0.002	4.53	Non-coding	USPL1
	AX-116416878	7.32	0.038	0.038 (0.010)	0.007	0.002	4.14	Non-coding	USPL1
	AX-116779846	7.37	0.039	0.037 (0.009)	0.007	0.002	4.28	Non-coding	USPL1; ALOX5AP
	AX-116851433	7.39	0.039	0.037 (0.009)	0.007	0.002	4.28	Non-coding	USPL1; ALOX5AP
	AX-116650934	8.77	0.231	0.020 (0.005)	0.01	0.003	4.16	Non-coding	FRY; ZAR1L

SSC Sus Scrofa chromosomes; two clusters of SNPs on SSC7 and one on SSC11 present confirmed candidate QTL regions
MAF minor allele frequency
^aObtained with Double Hierarchical GLM
^bWithin ± 50 kb

Back to article page

ISSN: 1297-9686

Contact us

Submission enquiries: helene.hayes@inrae.fr
General enquiries: info@biomedcentral.com