Table 4.

Location of the most significant QTL, limited to the top 5 per breed, which were associated with thigh width, 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	11	53741952	54849531	2	54349531a	2.65 × 10−6	0.017	0.047	0.000	0.997	0.994	CTNNA2
	13	78082912	79223584	10	78722523b	2.99 × 10−7	0.191	0.232	0.866	0.157	0.108	ZNFX1, B4GALT5, SLC9A8f, UBE2V1
	14	22612620	23619374	3	23116129a	1.99 × 10−6	0.026	0.994	0.074	0.962	0.971	OPRK1, ATP6V1H, RGS20
	16	1654734	2669694	4	2169248a	5.14 × 10−6	0.986	0.980	0.985	0.056	0.979	ETNK2, GOLT1A, PPP1RI5B, PIK3C2B, NFASC
	16	63066185	64073838	2	63066185d	4.07 × 10−6	0.027	0.948	0.991	0.072	0.000	ACBD6, STX6, MR1
CH	2	7850	10186234	1860	6808074a	4.09 × 10−25	0.000	0.079	0.000	0.028	0.004	WDR75g, ASNSD1g, NAB1g, MFSD6g, MSTNg, PMS1g, ORMDL1, COL3A1g, COL5A2g, ANKARg, SLC40A1g
	9	12470065	13731582	11	12970065e	8.65 × 10−9	0.000	0.013	0.000	0.003	0.000	KHDC3Lg, EEF1A1
	20	61727533	63246384	5	62296495b	7.78 × 10−9	0.997	0.010	0.000	0.000	0.000	CTNND2f, DAP, FAM173B
	28	9234253	24087892	1025	16275379a	4.17 × 10−9	0.581	0.829	0.476	0.430	0.523	ANK3f, CDK1, RHOBTB1, EGR2
	28	24331178	40249741	1322	26134688a	3.87 × 10−9	0.388	0.810	0.424	0.591	0.486	SIRT1, MYPNf, DNA2f, SLC25A16, SRGNf, COL13A1f, AIFM2, ADAMTS14f, SGLP1, PCBD1, SPOCK2f, ANAPC16f, DDIT4, MYOZ1
HE	5	17326996	18595093	3	18095093a	1.75 × 10−6	0.000	0.996	0.003	0.985	0.000	C5H12orf50, C5H12orf29, CEP290
	7	75039465	75039465	2	75539465d	4.24 × 10−6	0.990	0.000	0.997	0.000	0.000	GABRA6f
	10	87480123	88487031	3	87980123b	1.72 × 10−6	0.959	0.034	0.020	0.981	0.033	TTLL5f, TGFB3
	20	35840468	37412173	5	36340468a	1.30 × 10−6	0.342	0.589	0.421	0.230	0.328	LIFR, EGFLAM, GDNF
	20	39512041	41162914	10	40272197b	1.01 × 10−6	0.015	0.985	0.985	0.994	0.003	C1QTNF3, ADAMTS12f
LM	2	4973607	10670961	1526	7772897a	2.88 × 10−15	0.617	0.571	0.000	0.116	0.642	WDR75f, ASNSD1g, NAB1f, MFSD6f, MSTNf, PMS1f, ORMDL1, COL3A1, COL5A2, ANKARg, SLC40A1g
	2	11570479	12640428	43	12083258a	1.01 × 10−7	0.561	0.205	0.057	0.097	0.809	ZNF804A
	2	13916060	14952210	55	14450953b	1.92 × 10−6	0.434	0.565	0.374	0.394	0.477	PDE1Af, PPP1R1C
	9	36716988	37719425	4	37216988a	6.31 × 10−7	0.245	0.649	0.547	0.247	0.286	HS3ST5
	27	35767035	36785436	7	36267035c	8.03 × 10−6	0.057	0.000	0.998	0.997	0.000	SFRP1, GOLGA7, GPAT4, ANK1
SI	9	32996000	34105290	5	33604527b	4.82 × 10−7	0.969	0.980	0.981	0.985	0.019	NEPN, GOPC
	14	76746937	78193017	13	77271966a	1.65 × 10−7	0.712	0.107	0.052	0.916	0.085	MMP16f, SLC2A5
	24	17511696	18515510	3	18015356a	8.99 × 10−7	0.461	0.449	0.299	0.506	0.378	ENSBTAG00000045320, ENSBTAG00000011094
	26	35041033	36071133	3	35541033a	1.97 × 10−6	0.000	0.006	0.004	0.994	0.995	AFAP1L2, ABLIM1, ATRNL1
	29	47398869	48688066	30	47898869a	5.42 × 10−7	0.790	0.197	0.886	0.850	0.108	CCND1, FGF19, FGF4

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

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