Table 2.

Location of the most significant QTL, limited to the top 5 per breed which were associated with development of loin, and the genes located within these QTL within each breed

Breed	Chr	Start	End	Number of suggestive and significant SNPs	Most significant SNP	P-value	Allele frequency of + allele					Candidate genes within this QTL
							AA	CH	HE	LM	SI
AA	1	39155170	40155196	3	39655188a	1.06 × 10−6	0.003	0.015	0.000	0.967	0.976
	10	5741208	6752759	54	6241208a	3.45 × 10−6	0.181	0.105	0.090	0.773	0.872	GCNT4, HMGCR
	11	21539414	22560915	4	22049725c	6.26 × 10−6	0.032	0.928	0.904	0.000	0.068	CDKL8, MAP4K3
	15	53716499	55635294	27	55096343a	1.43 × 10−6	0.993	0.000	0.000	0.000	0.996	RAB6A, MRPL48, UCP2, UCP3d, PPME1, NEU3
	19	12894306	13934964	9	13430257a	2.23 × 10−6	0.045	0.088	0.969	0.102	0.044	USP32, MYO19, ACACA
CH	1	142705947	143712126	78	143205947c	3.50 × 10−6	0.000	0.010	0.005	0.972	0.993	BACE2, RIPK4, PRDM15, C2CD2
	2	37387	8714844	1728	6808074a	1.19 × 10−26	0.000	0.079	0.000	0.028	0.004	WDR75e, ASNSD1e, MFSD6e, MSTNe, PMS1e, ORMDL1, COL3A1e, COL5A2e, ANKARe, SLC40A1e
	10	84923776	85960329	2	85423776a	4.45 × 10−7	0.000	0.007	0.000	0.000	0.024	PSEN1, ACOT2, ACOT4, DNAL1, ZNF410, FAM161B, COQ6
	16	32025893	33120555	127	32558878a	4.12 × 10−7	0.975	0.884	0.135	0.898	0.093	SMYD3, KIF26B, EFCAB2
	24	45933369	46937392	5	46437392b	1.20 × 10−6	0.000	0.006	0.012	0.000	0.019	PSTPIP2, ST8SIA5
HE	2	79648265	81037622	15	80168803b	1.42 × 10−6	0.000	0.994	0.996	0.987	0.997	STAT1, MYO1Bd, NABP1
	4	3339555	4351559	4	3851559a	1.16 × 10−7	0.014	0.034	0.025	0.884	0.952	ENSBTAG00000044810
	11	17934758	18942324	3	18442324a	1.11 × 10−6	0.876	0.011	0.011	0.964	0.988	CRIM1
	16	75812761	76823259	3	76312761a	1.94 × 10−6	0.911	0.000	0.030	0.000	0.937	ENSBTAG00000044497
	29	9233633	10275049	26	9733633a	1.80 × 10−6	0.650	0.417	0.304	0.378	0.801	EED, SYTL2, CREBZF, TMEM126A, TMEM126B
LM	2	5545383	8287013	748	6747317a	6.69 × 10−10	0.198	0.409	0.617	0.073	0.511	WDR75d, ASNSD1d, MFSD6, MSTNd, PMS1d, ORMDL1, COL3A1, COL5A2d, ANKARe, SLC40A1d
	3	99009887	100073842	5	99509887b	5.78 × 10−7	0.041	0.000	0.047	0.934	0.883	CYP4X1, CYP4A22
	5	71738658	72751064	6	72238658b	2.70 × 10−6	0.000	0.819	0.163	0.251	0.830	SYN3, TIMP3, MGC137211, MGC137014, LARGE1d
	6	110629080	112106706	11	111176155a	3.30 × 10−7	0.126	0.868	0.898	0.830	0.211	HS3ST1
	12	32803688	33961156	7	33461156b	5.12 × 10−7	0.000	0.000	0.000	0.997	0.975	USP12, SHISA2
SI	7	58665425	60243933	10	59590500a	3.37 × 10−7	0.002	0.016	0.046	0.000	0.990	SH3RF2d
	8	90813081	91857894	14	91313081a	5.24 × 10−7	0.957	0.627	0.064	0.346	0.291	SPIN1, FBXW12
	14	79527472	81070931	18	80091780b	3.45 × 10−7	0.908	0.052	0.981	0.114	0.070	E2F5
	17	69082585	70268366	4	69646862b	1.04 × 10−7	0.975	0.010	0.987	0.992	0.003	PITPNBd
	22	33231032	34644069	14	34044822b	9.77 × 10−9	0.000	0.960	0.946	0.000	0.004	FAM19A1, SUCLG2e, KBTBD8

SNP classification: ^aintergenic, ^bintron, ^cdownstream gene variant

Significance of SNPs within genes: ^dgene contains at least one suggestive SNP, ^egene contains at least one significant SNP