Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms

Table 3 Relevant genomic windows with the explained genetic variances and associated candidate genes

Trait	Genomic window^a		Variance (%)^b		Candidate genes
Trait	Chr	Positions (bp)	Int	Slo	Candidate genes
TNB	SSC3	5,934,183–5,978,000	0.61	0.00	TRRAP
	SSC12	37,811,479–37,872,427	0.27	0.60	ENSSSCG00000039473
	SSC14	134,570,084–134,625,180	0.06	0.59	None
	SSCX	7,243,129–7,307,313	0.52	0.16	MID1
		19,844,004–19,985,584	0.11	0.89	ACOT9, SAT1, APOO, CXorf58
		19,885,476–20,012,307	0.15	1.09
		19,911,826–20,026,618	0.10	0.74
		91,905,396–92,010,688	0.37	0.77	TRPC5
NBA	SSC5	69,872,903–70,055,268	0.54	0.00	ENSSSCG00000000769, MICAL3
	SSC12	37,811,479–37,872,427	0.20	0.56	ENSSSCG00000039473
	SSCX	7,198,352–7,278,758	0.53	0.20	MID1
		7,213,512–7,293,780	0.60	0.15
		7,243,129–7,307,313	0.61	0.07
		19,844,004–19,985,584	0.01	0.60	ACOT9, SAT1, APOO
		19,885,476–20,012,307	0.02	0.74	ACOT9, SAT1, APOO
		91,889,310–91,994,567	0.14	0.57	TRPC5
		91,905,396–92,010,688	0.23	0.98
		91,966,658–92,025,442	0.13	0.55
		91,979,985–92,034,525	0.10	0.58
		122,118,491–122,263,709	0.40	0.52	MAMLD1, MTM1
		122,149,267–122,298,170	0.41	0.52
		122,194,006–122,365,194	0.49	0.62
WW	SSC1	141,889,209–142,070,404	0.52	0.47	UBE3A, ENSSSCG00000050514*
	SSC5	41,461,124–41,616,882	0.64	0.46	PKP2, YARS2, ENSSSCG00000000530
		69,770,951–70,055,268	0.51	0.37	ATP6V1E1, BCL2L13, ENSSSCG00000000769, MICAL3
		69,872,903–70,106,805	0.56	0.39	ATP6V1E1, BCL2L13, ENSSSCG00000000769, MICAL3
	SSCX	91,438,755–91,518,334	0.18	0.54	DCX

TNB, total number of piglets born; NBA, number of piglets born alive; WW, weaning weight (kg)
^aGenomic windows are defined by the five adjacent SNPs that explained 0.5% or more of the total additive genetic variance; Chr, chromosome; positions refer to Sscrofa11.1
^bExplained genetic variances in percent for intercept (Int) and slope (Slo) by five adjacent SNPs; explained variances with ≥ 0.5% are denoted in italics.
Candidate genes are represented by the gene symbol when available, otherwise by the Ensembl gene ID. The long noncoding RNA genes are marked by marked by an asterisk (^*)

ISSN: 1297-9686