Table 1.

Location of the most significant QTL, limited to the top five per breed, which were associated with development of hind quarter 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	72069526	130071811	8	120584401a	3.69 × 10−6	0.940	0.940	0.061	0.949	0.951	DLG1, FAM43A, APOD, OPA1, OSTN, GHSR
	8	72017409	73103211	16	72569526b	3.25 × 10−6	0.276	0.565	0.264	0.332	0.687	ADAM28
	10	5155837	6179062	11	5655837d	7.60 × 10−6	0.032	0.133	0.000	0.073	0.036	SFXN1, DRD1e
	23	20541063	21541072	2	21041063b	3.34 × 10−7	0.995	0.977	0.000	0.000	0.005	PTCHD4e
	24	35913368	37107434	16	36567715a	8.07 × 10−7	0.918	0.050	0.958	0.941	0.903	ENOSF1, ADCYAP1
CH	2	35194	10711228	5128	6808074a	9.07 × 10−49	0.000	0.079	0.000	0.028	0.004	WDR75f, ASNSD1f, ARHGEF4f, MYO7Bf, IWS1e, NAB1f, MFSD6f, MSTNf, PMS1f, ORMDL1e, COL3A1f, COL5A2f, ANKARf, SLC40A1f
	4	89299122	90487119	12	89799122a	4.67 × 10−6	0.000	0.007	0.002	0.000	0.992	GPR37e, POT1
	14	33353270	34360874	4	33855595a	2.20 × 10−7	0.013	0.026	0.054	0.054	0.982	PREX2
	21	34538609	35572213	47	35062974b	9.70 × 10−7	0.617	0.521	0.594	0.000	0.451	UBL7, SEMA7A, PML
	28	15669176	18516719	77	16273851a	2.95 × 10−8	0.574	0.827	0.580	0.416	0.520	ANK3, CDK1, RHOBTB1
HE	1	68813144	73614763	228	69348458b	5.23 × 10−7	0.764	0.531	0.237	0.317	0.480	KALRNe, ITGB5e
	7	83591608	84673367	26	84122153a	3.16 × 10−7	0.177	0.851	0.913	0.000	0.910	ACOT12, ATG10
	12	48965278	50129513	4	49465278a	1.84 × 10−6	0.020	0.995	0.996	0.983	0.000	KLF12
	13	2761800	3761897	2	3261897a	7.44 × 10−7	0.681	0.761	0.795	0.269	0.695	MRPL33
	23	12056019	13111217	5	12571991b	1.09 × 10−6	0.220	0.000	0.094	0.885	0.100	GLO1, GLP1R
LM	2	4293223	12640428	2610	6622189a	3.22 × 10−30	0.491	0.447	0.250	0.043	0.799	WDR75, ASNSD1f, MYO7B, IWS1, NAB1f, MFSD6e, MSTNf, PMS1f, ORMDL1e, COL3A1f, COL5A2f, ANKARf, SLC40A1f, ZNF804A
	2	13916060	14987913	113	14446207bc	4.83 × 10−8	0.567	0.562	0.374	0.394	0.523	PDE1Ae, PPP1R1C
	5	59612855	60696179	7	60112855a	1.58 × 10−7	0.000	0.000	0.000	0.997	0.996	AMDHD1
	11	12163298	13181229	7	12676690a	1.56 × 10−6	0.486	0.283	0.000	0.231	0.163	CYP26B1, DYSF, ZNF638
SI	6	76112104	77238886	16	76612104a	1.28 × 10−6	0.997	0.993	0.000	0.000	0.993	ENSBTAG00000043492
	7	103195804	104247192	3	103695804b	1.78 × 10−6	0.000	0.000	0.000	0.005	0.005	SLCO4C1e, SLC06A1
	9	65068999	66303927	4	65712927a	4.56 × 10−7	0.000	0.000	0.000	0.003	0.996	TBX18e, MRAP2
	23	41204249	42287354	9	41747427a	1.48 × 10−7	0.009	0.008	0.994	0.962	0.990	JARID2
	25	22649471	23937019	6	23400365a	1.00 × 10−7	0.985	0.993	0.000	0.993	0.998	AQP8, ZKSCAN2

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

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