Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations

Zhang, Wanchang; Zhang, Junjie; Cui, Leilei; Ma, Junwu; Chen, Congying; Ai, Huashui; Xie, Xianhua; Li, Lin; Xiao, Shijun; Huang, Lusheng; Ren, Jun; Yang, Bin

doi:10.1186/s12711-016-0184-2

Genetics Selection Evolution

Table 2 Genome-wide significant QTL for fatty acid composition in Erhualian, Laiwu and DLY pig populations

From: Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations

Chr	Trait	Pop	Nsnp	Range of Nsnp (Mb)	Top SNP	Position (bp)	P-value	Var (%)	Candidates
6	C16:1	Laiwu	1	71.01	ASGA0106005	71011913	1.97E−07	4.95
7	C20:1	Laiwu	18	27.35–31.80	H3GA0020505	29416373	2.25E−08	7.91
7	C14:0	Laiwu	15	29.54–33.59	ALGA0039950	31500144	2.60E−08	17.78
7	C16:1	Laiwu	21	29.42–34.06	DRGA0007448	31628039	1.27E−08	8.03
7	C20:2n6	Laiwu	6	29.42–34.06	DRGA0007448	31628039	5.61E−07	6.55
7	C20:1	Laiwu	9	133.96–134.54	ASGA0037322	133962789	3.54E−17	35.18	ELOVL5
7	C20:1	Erhualian	6	134.15–134.54	ALGA0114746	134540651	1.51E−17	26.43
8	C16:1	DLY	7	119.73–121.47	H3GA0025321	119887525	1.54E−13	8.31	ELOVL6
8	C16:0	Laiwu	20	118.82–123.41	ALGA0049254	120996107	2.66E−07	8.89
8	C16:1	Erhualian	11	125.08–129.51	ALGA0049349	127072110	6.18E−09	9.77
9	C20:1	DLY	4	6.29–7.58	ALGA0105252	6304559	4.27E−07	3.99
9	C14:0	DLY	4	13.26–14.31	ALGA0107040	13826057	2.15E−08	3.33	THRSP
9	C14:0	DLY	4	13.26–14.31	MARC0100725	14217867	3.23E−07	4.00
12	C14:0	Laiwu	6	0.25–2.52	ASGA0099260	248014	4.06E−10	9.01
12	C14:0	Erhualian	2	0.46–4.12	MARC0063090	1779278	6.05E−12	26.81	FASN
12	C16:0	Erhualian	3	0.46–4.12	MARC0063090	1779278	9.24E−09	19.56
12	C16:1	Erhualian	4	0.46–4.12	MARC0063090	1779278	2.01E −10	13.07
12	C18:1n9c	Erhualian	4	0.46–4.12	MARC0063090	1779278	1.14E−06	17.44
12	C20:1	Erhualian	5	0.46–4.12	MARC0063090	1779278	1.03E−07	10.97
14	C16:0	DLY	11	120.39–121.95	ALGA0081087	120972588	4.00E−08	6.25	SCD
14	C20:0	DLY	4	120.97–121.50	CASI0010164	121305916	1.04E−07	3.51
14	C18:0	DLY	45	119.03–123.48	MARC0063250	121500518	2.82E−25	26.35
14	C16:1	DLY	35	120.51–123.29	ASGA0066120	121515129	1.47E−13	11.13
16	C20:0	Erhualian	20	32.43–36.85	ASGA0072949	34715842	6.97E−13	12.07
16	C20:0	DLY	37	41.14–45.83	DRGA0016155	43534471	4.32E−31	31.79	ELOVL7
16	C20:0	Laiwu	4	43.53–45.31	DRGA0016169	45313348	7.41E−14	25.50

P-values were calculated using the GenABEL package in R
Phenotypic variation explained by the top SNPs was estimated by (V_reduce−V_full)/V_resuce, where V_reduce and V_full are the residual variances of models with and without including SNP genotypes as predictor variables, respectively
Chr chromosome, Pop population, N _snp number of significant SNPs, Position genomic position on the Sscrofa 10.2 pig genome assembly, Var (%) percentage of phenotypic variance explained by each locus

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ISSN: 1297-9686

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