Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)

Dvergedal, Hanne; Harvey, Thomas Nelson; Jin, Yang; Ødegård, Jørgen; Grønvold, Lars; Sandve, Simen Rød; Våge, Dag Inge; Moen, Thomas; Klemetsdal, Gunnar

doi:10.1186/s12711-020-00587-x

Genetics Selection Evolution

Table 1 Single-nucleotide polymorphisms (SNP) with genome-wide significant (p < 10^–7) associations with weight gain (WG), relative weight gain (RG), atom % ¹³C muscle (AMC), atom % ¹⁵N muscle (AMN), atom % ¹³C liver (ALC), and atom % ¹⁵N liver (ALN)

From: Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)

Trait	Chr	SNP	Base pair	A1	A2	Freq	b	se	p
WG	5	ctg7180001180119_4244_SCT	33597277	C	T	0.141	1.063	0.190	2.28E−08
	5	ctg7180001923117_1435_SAG	31819838	A	G	0.097	1.153	0.215	7.63E−08
	9	ctg7180001197157_4756_SAG	89517134	G	A	0.356	− 1.016	0.166	9.54E−10
	9	ctg7180001818540_14626_SGT	96172057	G	T	0.233	0.991	0.163	1.23E−09
	9	ctg7180001818540_11784_SCT	96174899	C	T	0.234	0.976	0.163	1.98E−09
	9	ctg7180001664612_2468_SCT	91842480	C	T	0.234	0.967	0.163	3.00E−09
	9	ctg7180001664612_1619_SAG	91841631	G	A	0.234	0.958	0.163	4.19E−09
	9	ctg7180001545661_2981_SGT	16416138	G	T	0.402	0.819	0.140	4.53E−09
	9	ctg7180001832507_11515_SCG	75470675	G	C	0.448	− 0.847	0.145	5.35E−09
	9	ctg7180001868348_9058_SAG	15945100	G	A	0.492	− 0.781	0.137	1.18E−08
	9	ctg7180001628780_1051_SAG	17214390	G	A	0.414	− 0.871	0.153	1.20E−08
	9	ctg7180001197157_4700_SAC	89517078	A	C	0.311	0.859	0.151	1.40E−08
	9	ctg7180001894494_11001_SAG	89556217	G	A	0.310	0.851	0.152	2.08E−08
	9	ctg7180001911598_32299_SCT	17106888	C	T	0.436	− 0.808	0.146	2.88E−08
	9	ctg7180001802227_6890_SAC	78211162	A	C	0.216	0.972	0.176	3.34E−08
	9	ctg7180001806806_477_SAC	78242149	A	C	0.216	0.969	0.176	3.67E−08
	9	ctg7180001588841_1060_SGT	86047894	G	T	0.234	0.855	0.155	3.77E−08
	9	ctg7180001926947_6570_SGT	81306559	T	G	0.247	0.885	0.161	3.86E−08
	9	ctg7180001380355_4100_SGT	96979010	G	T	0.422	0.721	0.133	5.50E−08
	9	ctg7180001921692_473_SGT	95413530	G	T	0.212	0.946	0.175	6.46E−08
	9	ctg7180001898405_11116	82286805	A	C	0.312	0.818	0.152	7.65E−08
	9	ctg7180001678561_512_SGT	90982168	T	G	0.335	0.769	0.143	7.99E−08
	9	GCR_cBin45958_Ctg1_101	19444985	G	A	0.386	0.825	0.154	8.16E−08
	9	ctg7180001859612_1950_SCT	106163425	T	C	0.426	0.837	0.157	9.45E−08
	20	ctg7180001900661_2996_SAG	29391087	A	G	0.472	0.651	0.116	1.97E−08
	20	ctg7180001900661_8312_SAC	29385772	A	C	0.472	0.632	0.116	4.75E−08
	20	ctg7180001403181_749_SGT	32398670	T	G	0.413	0.701	0.131	7.97E−08
RG	9	ctg7180001820745_5080_SAG	23240272	G	A	0.202	2.191	0.337	7.98E−11
	9	ctg7180001604256_10823_SAG	23113694	G	A	0.156	2.406	0.380	2.39E−10
	9	GCR_cBin45958_Ctg1_101	19444985	G	A	0.386	2.035	0.339	1.99E−09
	9	ctg7180001789610_1630_SCT	25039628	C	T	0.349	− 1.669	0.288	7.03E−09
	9	ctg7180001841302_7054_SGT	21739717	G	T	0.184	2.112	0.367	8.33E−09
	9	ctg7180001841302_7076_SGT	21739695	T	G	0.191	2.046	0.365	2.02E−08
	9	ctg7180001809374_3372_SCT	19466507	C	T	0.373	1.900	0.343	3.03E−08
	9	ctg7180001847789_6042_SAG	16428841	A	G	0.263	2.034	0.367	3.07E−08
	9	ctg7180001857693_2711_SAG	85086045	G	A	0.278	1.814	0.329	3.60E−08
	9	ctg7180001545661_2981_SGT	16416138	G	T	0.402	1.704	0.310	3.68E−08
	9	ctg7180001468960_5703_SCT	14756989	C	T	0.226	2.035	0.370	3.83E−08
	9	ctg7180001931759_8478_SAG	16329499	G	A	0.217	2.046	0.376	5.14E−08
	9	ctg7180001898949_10269_SAG	22638682	A	G	0.482	− 1.584	0.292	5.86E−08
AMC	9	ctg7180001628780_1051_SAG	17214390	G	A	0.415	− 0.013	0.002	1.04E−09
	9	ctg7180001820745_5080_SAG	23240272	G	A	0.202	0.013	0.002	2.45E−09
	9	ctg7180001789610_1630_SCT	25039628	C	T	0.349	− 0.011	0.002	5.22E−09
	9	ctg7180001763729_3905_SAG	15474718	A	G	0.283	0.013	0.002	8.27E−09
	9	ctg7180001763729_4055_SGT	15474568	T	G	0.283	0.013	0.002	1.14E−08
	9	ctg7180001872184_4046_SAC	59521565	A	C	0.267	− 0.012	0.002	1.69E−08
	9	ctg7180001847789_6042_SAG	16428841	A	G	0.261	0.013	0.002	1.91E−08
	9	ctg7180001903467_551_SGT	30327474	T	G	0.175	− 0.013	0.002	2.06E−08
	9	ctg7180001700380_482_SGT	15707203	G	T	0.282	0.013	0.002	2.08E−08
	9	GCR_cBin45958_Ctg1_101	19444985	G	A	0.385	0.012	0.002	3.47E−08
	9	ctg7180001911598_32299_SCT	17106888	C	T	0.436	− 0.011	0.002	3.78E−08
	9	ctg7180001903534_19011_SGT	13431163	T	G	0.283	− 0.013	0.002	3.98E−08
	9	ctg7180001872184_453_SCT	59517972	T	C	0.265	− 0.012	0.002	4.40E−08
	9	ctg7180001604256_10823_SAG	23113694	G	A	0.157	0.013	0.002	4.58E−08
	9	ctg7180001343223_1775_SCT	67759885	T	C	0.411	0.011	0.002	5.85E−08
	9	ctg7180001545661_2981_SGT	16416138	G	T	0.401	0.011	0.002	6.44E−08
	9	ctg7180001833924_2266_SCT	24557694	T	C	0.429	0.011	0.002	6.65E−08
	9	ctg7180001794986_4059_SAC	20044519	C	A	0.262	− 0.012	0.002	6.93E−08
	9	ctg7180001898949_10269_SAG	22638682	A	G	0.481	− 0.010	0.002	7.33E−08
AMN	9	ctg7180001820745_5080_SAG	23240272	G	A	0.202	0.034	0.005	3.24E−11
	9	ctg7180001841302_7054_SGT	21739717	G	T	0.184	0.036	0.006	1.47E−10
	9	ctg7180001604256_10823_SAG	23113694	G	A	0.157	0.037	0.006	1.87E−10
	9	ctg7180001841302_7076_SGT	21739695	T	G	0.192	0.033	0.006	1.33E−09
	9	ctg7180001898949_10269_SAG	22638682	A	G	0.481	− 0.027	0.004	1.51E−09
	9	ctg7180001909530_3368_SAC	30671958	A	C	0.289	0.032	0.006	1.69E−08
	9	ctg7180001857693_2711_SAG	85086045	G	A	0.278	0.028	0.005	2.38E−08
	9	ctg7180001628780_1051_SAG	17214390	G	A	0.415	− 0.028	0.005	2.78E−08
	9	ctg7180001912930_10973_SAC	59822403	C	A	0.446	− 0.026	0.005	4.30E−08
	9	ctg7180001343223_1775_SCT	67759885	T	C	0.411	0.026	0.005	4.62E−08
	9	ctg7180001911598_32299_SCT	17106888	C	T	0.436	− 0.026	0.005	8.19E−08
	9	ctg7180001254975_135_SCT	30005989	T	C	0.328	0.017	0.003	9.72E−08
ALC	12	ctg7180001233434_1518_SCT	45935004	C	T	0.418	− 0.009	0.001	1.79E−10
	12	ctg7180001878331_16006_SAG	67415693	A	G	0.411	− 0.008	0.001	3.95E−10
	12	ctg7180001589944_2780_SAC	67420787	C	A	0.410	− 0.008	0.001	5.82E−10
	12	ctg7180001917752_6118_SAG	68229784	A	G	0.342	− 0.008	0.001	6.01E−09
	12	ctg7180001926810_6994_SGT	59975663	T	G	0.445	− 0.008	0.001	8.58E−09
	12	ctg7180001924417_6623_SAC	66355729	A	C	0.178	− 0.010	0.002	1.38E−08
	12	ctg7180001863800_134_SAC	54013376	C	A	0.495	− 0.008	0.001	1.71E−08
	12	ctg7180001930970_12364_SCT	34715679	C	T	0.460	0.007	0.001	1.86E−08
	12	ctg7180001787629_3714_SGT	63703424	G	T	0.441	− 0.008	0.001	1.92E−08
	12	ctg7180001926810_5584_SCT	59974253	C	T	0.435	− 0.008	0.001	2.17E−08
	12	ctg7180001759831_1827_SCT	45916216	C	T	0.364	− 0.007	0.001	2.33E−08
	12	ctg7180001481690_187_SAG	73548289	G	A	0.438	− 0.008	0.001	3.22E−08
	12	ctg7180001912956_2486_SGT	36748230	T	G	0.416	− 0.007	0.001	3.25E−08
	12	ctg7180001926810_6801_SAG	59975470	A	G	0.444	− 0.007	0.001	3.28E−08
	12	ctg7180001899463_4736_SCT	45925520	C	T	0.365	− 0.007	0.001	3.78E−08
	12	ctg7180001874153_6984_SAC	59968424	C	A	0.444	− 0.007	0.001	3.82E−08
	12	ctg7180001903261_15275_SCT	36741726	T	C	0.419	− 0.007	0.001	4.80E−08
	12	ctg7180001802518_8127_SAG	38630722	G	A	0.264	− 0.008	0.002	5.60E−08
	12	ctg7180001895532_9980_SAC	52536172	C	A	0.150	− 0.010	0.002	8.47E−08
ALN	9	ctg7180001820745_5080_SAG	23240272	G	A	0.202	0.034	0.005	1.71E−10
	9	ctg7180001604256_10823_SAG	23113694	G	A	0.157	0.037	0.006	3.95E−10
	9	ctg7180001902776_3165	44544043	A	G	0.030	− 0.082	0.013	1.00E−09
	9	ctg7180001297112_1053_SAC	44743511	C	A	0.029	− 0.079	0.013	3.51E−09
	9	ctg7180001846444_1581_SAG	27624708	G	A	0.050	− 0.060	0.010	3.64E−09
	9	ctg7180001898949_10269_SAG	22638682	A	G	0.481	− 0.027	0.005	6.84E−09
	9	ctg7180001841823_6182_SGT	27830435	G	T	0.050	− 0.059	0.010	8.19E−09
	9	ctg7180001841823_8622_SAG	27832875	A	G	0.051	− 0.058	0.010	9.34E−09
	9	ctg7180001897675_6237_SCG	26358698	C	G	0.050	− 0.058	0.010	1.04E−08
	9	ctg7180001841302_7076_SGT	21739695	T	G	0.192	0.033	0.006	1.28E−08
	9	ctg7180001841302_7054_SGT	21739717	G	T	0.184	0.033	0.006	1.39E−08
	9	ctg7180001516979_6848_SCT	26634813	T	C	0.050	− 0.058	0.010	1.54E−08
	9	ctg7180001905112_13597_SAC	25462494	C	A	0.061	− 0.052	0.009	1.57E−08
	9	ctg7180001516979_7200_SCT	26635165	C	T	0.050	− 0.057	0.010	2.04E−08
	9	GCR_cBin3500_Ctg1_117	27426856	C	G	0.081	− 0.044	0.008	3.60E−08
	9	ctg7180001927229_6536	84462126	A	G	0.448	0.027	0.005	4.58E−08
	9	ctg7180001905111_1804_SAC	25477875	C	A	0.062	− 0.050	0.009	4.77E−08
	9	ctg7180001322796_3617_SGT	50798901	G	T	0.113	− 0.037	0.007	6.77E−08
	9	ctg7180001796082_675_SAC	19872408	C	A	0.148	− 0.035	0.006	7.31E−08

SNPs are ranked within trait and chromosome. Significant associations that are common between traits are indicated in italic characters
A1: reference allele; A2: alternative allele; Freq: frequency of A1; b: SNP effect (the effect of increasing the genotype with one extra reference allele) with associated standard error (se) and p-value (p)

Back to article page

ISSN: 1297-9686

Contact us

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