TABLE 5.

The location of the most significant QTLs, limited to the top 5, which were associated with chest depth, and the genes located within these QTLs within each breed.

				No of suggestive and significant SNPs	Most significant SNP		Allele frequency of positive allele
Breed	Chr	Start	End			P-Value	AA	CH	HE	LM	SI	Candidate genes within this QTL
Angus	4	109535218	110566320	118	110035226a	2.08 × 10–7	0.003	0.000	0.000	0.000	0.998	CNOT4*
	8	51491571	52874502	6	52374502b	1.55 × 10–7	0.004	0.011	0.998	0.990	0.000	OSTF1, PCSK5*
	18	42431986	42811277	6	41931986a	8.41 × 10–8	0.004	0.003	0.000	0.014	0.996
	19	25487490	26528596	129	25988404b	2.68 × 10–7	0.003	0.953	0.003	0.977	0.076	PITPNM3*, UBE2G1, MYBBP1A, GGT6, PIMREG
	23	27713725	28798254	34	28273994c	6.31 × 10–7	0.043	0.104	0.023	0.023	0.904	MIC1, TCF19, CCHCR1, VARS2, PPP1R18, TRIM26, TRIM15, TRIM10, TRIM40, TRIM31, TRIM39*, PPP1R11
Charolais	4	103847357	105940963	3	104347357b	2.48 × 10–6	0.000	0.006	0.000	0.993	0.005	HIPK, SLC37A3, WEE2, SSBP1, PARP12*
	10	29295461	30295461	12	29796031b	4.91 × 10–6	0.808	0.756	0.252	0.672	0.000	TMCO5B, SCG5
	10	75515119	76535772	7	76015119b	1.17 × 10–6	0.006	0.995	0.995	0.980	0.987	KCNH5, PPP2R5E*, SYNE2
	12	81616525	82648669	15	82139001a	4.14 × 10–6	0.053	0.100	0.000	0.027	0.921	NALCN, ITGB1
	14	49295193	50325837	6	49825837b	1.24 × 10–6	0.916	0.795	0.285	0.185	0.860	UTP23, EIF3H*
Hereford	3	63308338	64320629	4	63808996a	1.19 × 10–6	0.990	0.000	0.038	0.063	0.919
	5	99016506	100071368	31	99516506a	6.26 × 10–7	0.100	0.056	0.070	0.966	0.046
	17	61625220	62663494	3	62157617a	1.37 × 10–6	0.000	0.003	0.969	0.000	0.000	TBX3, TBX5
	18	41115715	42140232	4	41635699a	3.00 × 10–6	0.997	0.014	0.002	0.997	0.000	ZNF536, TSHZ3
	20	9677922	10679487	5	10177922b	2.93 × 10–6	0.863	0.257	0.741	0.666	0.219	MCCC2, BDP1, SERF1A, SMN2, SLC30A5
Limousin	5	26076148	27084460	3	26576148c	8.02 × 10–7	0.000	0.004	0.007	0.009	0.000	HOXC4, HOXC5, HOXC6, HOXC8, HOXC8, HOXC9, HOXC10, HOXC11, HOXC12, HOXC13
	6	32350666	34308736	456	33560360a	2.14 × 10–7	0.060	0.049	0.053	0.097	0.968
	6	37037069	40568831	211	38075438b	2.92 × 10–9	0.087	0.000	0.000	0.131	0.368	PPM1K, ABCG2∧, PKD2∧, SPP1, MEPE, LAP3, NCAPG*, LCORL*
	7	16966648	17927749	15	17466648a	5.13 × 10–7	0.991	0.956	0.978	0.052	0.941	EBF1*
	11	77828096	78855720	3	78355720a	5.74 × 10–7	0.000	0.000	0.000	0.003	0.000	GDF7, RHOB, SDC1
Simmental	2	97634951	98536954	3	98035848b	2.77 × 10–7	0.000	0.002	0.000	0.000	0.004	KANSL1L, ACADL, MYL1
	11	42337336	43357452	3	42837336a	4.45 × 10–7	0.865	0.815	0.000	0.975	0.991	BCL11A, GTF2A1L*
	21	50755259	51864196	11	51364196a	4.44 × 10–8	0.000	0.002	0.000	0.002	0.998	LRFN5
	24	49238747	50334349	12	49739134d	4.03 × 10–7	0.997	0.002	0.005	0.005	0.995	CDH2*, DYM, ACAA2, MYO5B
	27	9276392	10276408	3	9776396a	3.29 × 10–7	0.000	0.007	0.000	0.975	0.998

AA, Angus; CH, Charolais; HE, Hereford; LM, Limousin; SE, Simmental; HF, Holstein-Friesian. Superscript denotes SNP classification:^aintergenic, ^bintron, ^cupstream gene variant, ^ddownstream gene variant. Symbols denote the significance of SNPs within genes: * gene contained at least one suggestive (p ≤ 1 × 10^–5) SNP ^∧ gene contained at least one significant (p ≤ 1 × 10^–8) SNP.