Table 1.

Statistics of non-imprinted QTL

			Peak	Flanking markers c				Estimate d
Chr	Trait a	Groups	(cM) b	Left	Right	F-value	LOD	a	s.e a	d	s.e d	% var e
1	Gastro**	pQTL	23	rs3696088	rs13472794	35.40	14.84	-0.0417	0.0054	-0.0239	0.0073	6.73
1	Pec**	pQTL	23	rs3696088	rs13472794	53.84	22.19	-0.0084	0.0089	-0.0503	0.0120	9.88
1	Tnni1	eQTL	23	rs3696088	rs13472794	8.73	3.75	-0.3433	0.0965	-0.2555	0.1282	2.23
1	AI**	pQTL	24	rs3696088	rs13472794	13.00	5.57	0.0813	0.0165	0.0332	0.0219	2.64
1	Fat**	pQTL	24	rs3696088	rs13472794	13.54	5.80	0.0817	0.0167	0.0367	0.0222	2.68
1	Edl**	pQTL	25	rs3696088	rs13472794	7.19	3.10	-0.0327	0.0086	0.0010	0.0112	1.44
2	Edl	pQTL	78	rs3144393	rs13476878	6.79	2.93	-0.0179	0.0052	0.0107	0.0082	1.36
2	Gastro**	pQTL	80	rs3144393	rs13476878	9.40	4.04	-0.0117	0.0033	0.0124	0.0053	1.88
2	AI**	pQTL	88	rs3144393	rs13476878	18.65	7.95	0.0519	0.0091	-0.0263	0.0138	3.65
2	Fat**	pQTL	88	rs3144393	rs13476878	19.62	8.35	0.0535	0.0092	-0.0279	0.0140	3.84
3	Pec	pQTL	44	rs13477174	rs3670634	9.84	4.23	0.0143	0.0049	0.0243	0.0069	1.96
3	Gastro	pQTL	56	rs3663873	rs13477430	6.51	2.81	0.0084	0.0032	0.0134	0.0050	1.31
3	Edl	pQTL	64	rs3663873	rs13477430	5.45	2.35	0.0179	0.0058	0.0145	0.0103	1.10
4	IGF1	eQTL	68	rs6324470	rs3659226	8.46	3.63	0.0985	0.0312	-0.1273	0.0516	2.17
5	Gastro	pQTL	49	rs6256504	CEL-5_52953963	4.51	1.95	-0.0050	0.0030	0.0113	0.0048	0.91
6	Gastro	pQTL	0	-	rs13478602	6.64	2.86	-0.0058	0.0028	0.0125	0.0041	1.33
6	AI**	pQTL	27	rs13478727	rs13478839	10.27	4.41	0.0393	0.0090	-0.0121	0.0136	1.99
6	Fat**	pQTL	28	rs13478727	rs13478839	9.97	4.29	0.0394	0.0091	-0.0122	0.0137	1.98
6	lengthNT**	pQTL	45	rs3676254	rs3656205	13.45	5.76	0.2921	0.0578	0.1200	0.0975	2.58
7	Gastro	pQTL	47	rs3676254	rs3656205	5.65	2.44	0.0227	0.0068	-0.017	0.0073	1.14
7	Pec**	pQTL	47	rs3676254	rs3656205	10.54	4.53	0.0445	0.0113	-0.0169	0.0122	2.10
8	Gastro	pQTL	37	rs13479657	rs13479757	7.22	3.11	0.0134	0.0036	-0.0032	0.0060	1.45
8	Fat**	pQTL	68	rs3678433	rs6182338	15.00	6.42	0.0556	0.0102	0.0022	0.0163	2.96
8	AI**	pQTL	69	rs3678433	rs6182338	15.38	6.58	0.0546	0.0100	0.0032	0.016	2.95
9	Gastro	pQTL	0	-	rs13480071	4.28	1.85	-0.0039	0.0029	-0.0100	0.0039	0.86
9	AI	pQTL	23	rs8259427	rs6213724	8.94	3.85	0.0311	0.0091	0.0334	0.0139	1.79
9	Fat	pQTL	23	rs8259427	rs6213724	9.18	3.95	0.0320	0.0091	0.0336	0.0140	1.83
10	lengthNT	pQTL	26	rs13480578	CEL-10_58149652	7.96	3.43	0.1970	0.0519	-0.0946	0.0792	1.58
10	Gastro	pQTL	30	rs13480579	CEL-10_58149653	4.50	1.94	-0.0082	0.0028	-0.0033	0.0041	0.91
11	Tail**	pQTL	25	rs6276300	rs6199956	16.87	7.21	0.2461	0.0425	0.024	0.0682	3.29
11	lengthNT**	pQTL	26	rs6276300	rs6199956	21.55	9.16	0.3596	0.0556	0.0833	0.0892	4.15
11	BMI	pQTL	49	rs13481054	rs3701609	8.23	3.55	0.5312	0.1385	0.2684	0.1978	1.64
11	Gastro	pQTL	68	rs3653651	rs13481216	4.86	2.10	0.0086	0.0028	0.0026	0.0040	0.98
14	Gastro	pQTL	34	rs8251329	rs3712401	7.77	3.35	0.0118	0.0030	0.0030	0.0042	1.56
17	AI**	pQTL	17	rs13482893	rs3719497	11.2	4.81	0.0418	0.0091	-0.0079	0.0145	2.14
17	Fat**	pQTL	17	rs13482893	rs3719497	10.94	4.70	0.0415	0.0091	-0.0097	0.0144	2.14
17	Edl**	pQTL	33	rs3023442	rs6395919	7.74	3.34	-0.0187	0.0049	0.0072	0.0079	1.55
17	Gastro**	pQTL	68	rs6257479	rs3663966	9.62	4.14	-0.0128	0.0029	0.0024	0.0042	1.92
18	lengthNT	pQTL	34	rs3670254	rs3718618	8.39	3.62	0.2128	0.0522	0.0373	0.078	1.67
18	lengthNA	pQTL	35	rs3670254	rs3718618	8.62	3.72	0.1345	0.0325	0.0149	0.0486	1.71

^aTrait abbreviations: lengthNA nasal to anal length (cm), lengthNT nasal to tail length (cm), AI adiposity index, BMI body mass index, Tail tail length (cm), Soleus soleus muscle weight percentage, Gastro gastrocnemius muscle weight percentage, Edl EDL muscle weight percentage, Pec pectoralis muscle weight percentage, Fat average gonadal fat pad weight percentage (epididymal for males and perimetrial for females). Tnni1 troponin I type 1 expression, IGF1 insulin-like growth factor 1 expression. QTL with an F-value that exceeded 1% genome-wide permutation threshold are denoted by **; QTL without ** exceeded 5% genome-wide permutation threshold.

^bPeak position of QTL detected in Kosambicentimorgans.

^cFlanking markers (left and right) of the QTL peak. A“-“ notation denotes the end of the chromosome. See Additional file 1: Table S6 for marker information.

^da: additive effect; s.e_a: standard error of additive effect; d: dominance effect; s.e_d: standard error of dominance effect.

^e% var: percentage of phenotypic variance that a given QTL position could account for.