Table 5.

Location of the most significant QTL, limited to the top 5 per breed, which were associated with width of withers, 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	40642399	41670931	3	41142399b	2.49 × 10−6	0.997	0.998	0.009	0.991	0.000	EPHA6d
	6	90992982	92064889	10	91513217a	2.34 × 10−9	0.008	0.019	0.009	0.995	0.005	EREG, AREG, RCHY1
	14	9414135	10414890	9	9914135b	3.85 × 10−6	0.016	0.936	0.144	0.969	0.951	TG, KCNQ3d
	14	17744843	18889304	16	18244843b	1.59 × 10−6	0.957	0.007	0.977	0.000	0.977	ANXA13, KLHL38, FBXO32
	15	66035436	67113172	4	66535436b	3.42 × 10−7	0.004	0.996	0.930	0.003	0.992	APIP, PDHX
CH	2	218127	8714844	1227	6808074a	2.02 × 10−21	0.000	0.079	0.000	0.028	0.004	WDR75e, ASNSD1d, NAB1e, MFSD6e, MSTNe, PMS1e, ORMDL1, COL3A1e, COL5A2e, ANKARe, SLC40A1e
	4	63740415	65180447	6	64680447a	3.32 × 10−7	0.000	0.003	0.000	0.000	0.991	NT5C3A, KBTBD2
	14	67870173	68870239	7	68370173a	2.98 × 10−7	0.028	0.060	0.965	0.053	0.024	STK3, KCNS2, POP1, RPL30, MATN2
	28	15669176	17454059	6	16943776a	1.52 × 10−8	0.640	0.868	0.525	0.690	0.729	ANK3, CDK1, RHOBTB1
	28	31765108	33148059	7	32634467a	1.61 × 10−7	0.367	0.889	0.664	0.511	0.468	KCNMA1
HE	7	63750754	64814905	15	64309256b	1.46 × 10−7	0.022	0.949	0.008	0.011	0.009	RPS14, MYOZ3, ZNF300, GPX3d, ANXA6
	11	89579990	90599173	5	90079990a	5.13 × 10−6	0.664	0.280	0.163	0.800	0.217	RNF144A, RSAD2
	18	11547513	12549350	5	12047513a	4.85 × 10−6	0.479	0.565	0.507	0.532	0.446	GSE1, IRF8, FOXC2
	20	25429449	27124758	9	25929649a	3.38 × 10−6	0.532	0.000	0.559	0.000	0.480	FST
	26	32810942	33810987	3	33310942b	2.78 × 10−6	0.000	0.000	0.998	0.000	0.000	GPAM, ACSL5
LM	2	5547713	8495179	725	6622189a	8.77 × 10−12	0.490	0.447	0.250	0.043	0.800	WDR75, ASNSD1d, NAB1, MFSD6, MSTN, PMS1d, ORMDL1, COL3A1, COL5A2e, ANKARd, SLC40A1e
	2	9053737	10527711	26	9559686a	1.53 × 10−6	0.464	0.504	0.213	0.127	0.456	ITGAV, ZC3H15
	2	13916060	14957655	68	14450953b	6.10 × 10−8	0.433	0.564	0.626	0.394	0.479	PDE1Ad, PPP1R1C, NEUROD1
	2	20539841	21539862	3	21039862a	6.85 × 10−10	0.000	0.000	0.000	0.998	0.000	HOXD1, HOXD3, HOXD4, HOXD9, HOXD10, HOXD11, HOXD12, HOXD13
	6	19014612	21121181	13	19817910a	8.15 × 10−9	0.000	0.000	0.008	0.995	0.000	NPNT, GSTCDd
SI	1	79028842	80104503	3	79604503b	3.81 × 10−7	0.022	0.040	0.000	0.964	0.004	LPPd
	4	57566849	58584434	5	58084434d	6.35 × 10−8	0.902	0.261	0.457	0.248	0.229	IMMP2Ld, LRRN3
	9	32996000	34471196	16	33604527b	5.67 × 10−8	0.969	0.979	0.019	0.985	0.019	NEPN, GOPCd
	12	28061051	29073791	3	28561051d	7.49 × 10−7	0.008	0.020	0.084	0.016	0.998	PDS5B
	20	65137216	66168943	4	65668943a	1.76 × 10−7	0.000	0.009	0.000	0.977	0.007	FASTKD3, ADCY2d

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