Table 3.

Location of the most significant QTL, limited to the top 5 per breed, which were associated with development of inner thigh, 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	146687440	147685998	7	147187440b	9.55 × 10−7	0.988	0.712	0.073	0.179	0.631	TRAPPC10, COL18A1, SLC19A1, PCBP3e, COL6A1, COL6A2
	4	69229353	70999401	38	70373241a	4.19 × 10−7	0.991	0.015	0.990	0.014	0.900	HOXA1, HOXA2, HOXA3, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, HOXA10, HOXA11, HOXA13
	24	36998437	38030390	4	37530390bd	2.24 × 10−7	0.977	0.000	0.014	0.036	0.983	NDC80, EMILIN2e, MYOM1, MYL12A, MYL12B
	25	35042698	36122096	6	35542698a	3.50 × 10−7	0.998	0.000	0.000	0.000	0.002	POLR2J, MYL10, ALKBH4, COL26A1
	29	23787949	24826548	7	24290699a	1.82 × 10−7	0.048	0.043	0.937	0.939	0.919	SLC6A5, PRMT3
CH	2	7850	10711228	5075	6808074a	9.07 × 10−49	0.000	0.079	0.000	0.028	0.005	WDR75f, ASNSD1f, NAB1f, MFSD6f, MSTNf, PMS1f, ORMDLe COL3A1, COL5A2f, ANKARf, SLC40A1f
	14	33353270	34360874	4	33855595a	2.20 × 10−7	0.013	0.026	0.054	0.054	0.018	ARFGEF1, CPA6, PREX2
	14	67849241	68850085	4	6834924a	2.69 × 10−6	0.000	0.062	0.000	0.000	0.000	STK3, KCNS2, POP1, RPL30, MATN2
	16	60443313	62320499	4	60943313a	6.72 × 10−6	0.904	0.230	0.063	0.853	0.821	RASAL2, ANGPTL1, TOR3A, ABL2, SOAT1
	29	21313583	22460213	38	21917306a	3.58 × 10−6	0.000	0.989	0.000	0.978	0.000	GAS2, FANCF
HE	4	3924012	5000928	3	4424012a	4.05 × 10−7	0.755	0.032	0.082	0.000	0.939	ENSBTAG00000023806
	7	72100887	73679002	67	72608186b	9.09 × 10−7	0.000	0.998	0.046	0.000	0.995	EBF1e, ADRA1B
	13	6038290	8341939	9	7003978a	1.84 × 10−7	0.000	0.000	0.002	0.004	0.000	ESF1, NDUFAF5, FLRT3
	14	57257740	58269158	3	57757740a	7.98 × 10−7	0.262	0.122	0.758	0.104	0.000	TRHR
	25	37995664	39005834	3	38505834c	2.68 × 10−7	0.160	0.928	0.097	0.056	0.071	LMTK2, PMS2, EIF2AK1, USP42
LM	2	313343	3758925	102	3226165a	5.94 × 10−10	0.907	0.032	0.997	0.066	0.057	NIPA1, NIPA2e, ARHGEF4
	2	4973733	11101064	2441	6747317a	2.20 × 10−28	0.802	0.409	0.617	0.074	0.490	WDR75, ASNSD1f, NAB1f, MFSD6e, MSTNf, PMS1f, ORMDL1e, COL3A1e, COL5A2f, ANKARf, SLC40A1f
	2	11556240	12618550	36	12116324a	1.36 × 10−8	0.308	0.402	0.231	0.195	0.556	ZNF804A
	2	13935604	14957932	55	14447892bc	1.67 × 10−6	0.433	0.562	0.374	0.394	0.524	PDE1Ae, PPP1R1C, NEUROD1
	4	23124509	24137261	59	23630609b	2.52 × 10−7	0.096	0.027	0.996	0.994	0.010	AGMOe, MEOX2
SI	1	22558133	23622641	49	23117106a	5.21 × 10−6	0.949	0.043	0.866	0.060	0.870	ENSBTAG00000046369
	14	79492849	80610485	17	80090294b	2.33 × 10−7	0.104	0.052	0.980	0.886	0.072	E2F5
	17	21615210	22651417	8	22115210a	1.47 × 10−6	0.474	0.619	0.639	0.359	0.297	ENSBTAG00000044703
	21	17057917	18336523	18	17836523a	5.30 × 10−8	0.003	0.010	0.000	0.000	0.997	ENSBTAG00000045960
	22	33706576	34737653	10	34236342b	2.08 × 10−6	0.000	0.995	0.000	0.987	0.002	SUCLG2e, KBTBD8

SNP classification: ^aintergenic, ^bintron, ^cupstream gene variant, ^ddownstream gene variant

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