Table 5.

Summary of the windows within the three chromosomes and three genomic regions that explained the higher genomic variance for carcass quality traits in crossbred pigs with a list of annotated genes in the proximity of each window¹

Trait	Windows	Chr	σ 2, %	Start, Mb	Stop, Mb	Genes	SNP	σ 2 CB, %	σ 2 PB, %	P-value
Back fat	5	7	1.88	1.07	1.64	GMDS, MYLK4	rs320534160	0.035	0.00088	1.45 × 10–4
	6	18	1.85	10.6	11.4	KIAA1549, ATP6V0A4, ENSSSCG00000035963, ENSSSCG00000018723, SVOPL, RIM24, TRIM24, ZC3HAV1L	rs346337753	0.012	0.0021	2.94 × 10–4
	4	5	1.37	71.9	72.5	ENSSSCG00000000784, ENSSSCG00000027998, CNTN1, ENSSSCG00000039178	rs81385196	0.022	0.000065	1.23 × 10–4
Loin depth	4	18	1.29	25.3	26.1	FAM3C, WNT16, CPED1, TSPAN12, ING3	rs81467885	0.024	0.0021	1.79 × 10–4
	5	3	1.28	111.1	111.8	RBKS, ENSSSCG00000034129, ENSSSCG00000033248, SLC4A1AP, SUPT7L, GPN1, ENSSSCG00000039695, ZNF512, C2orf16, GCKR, FNDC4, IFT172, KRTCAP3, NRBP1, PPM1G, ZNF513, SNX17, EIF2B4, GTF3C2	rs81374918	0.024	0.0026	1.33 × 10–4
	2	6	1.23	133.5	133.8	TOX3, ENSSSCG00000027421	rs318606636	0.036	0.011	1.52 × 10–4
ADG	4	4	1.54	140.2	140.6		rs80915915	0.0074	0.0032	1.20 × 10–6
	6	1	1.40	191.9	193.8	AGBL1, ENSSSCG00000034903, ESR2	rs81349654	0.0011	0.00074	1.04 × 10–6
	9	7	1.32	139.8	140.7	TMEM266, ETFA, ISL2, SCAPER, ENSSSCG00000039452, ENSSSCG00000032875, NRG4	rs80885610	0.0078	0.00007	7.22 × 10–7

¹SNP = marker with largest variance within windows.

²Genetic variance of the marker with largest impact within window for crossbred (σ²_CB) and purebred (σ²_PB) expressed as percentage of total genetic variance, respectively.