Recombination rates in pigs differ between breeds, sexes and individuals, and are associated with the RNF212, SYCP2, PRDM7, MEI1 and MSH4 loci

Table 5 Top SNPs identified in genome-wide association analyses of ACC for each breed and both sexes

Chr	Breed	Sex	SNP position	Frequency of allele 1	Effect of allele 1	SE	P-value	% V_p	Candidate gene
4	LR	F	124741468	0.20	0.41	0.07	2.70E−09	0.73
5	LR	F	6863929	0.45	0.32	0.06	1.54E−08	0.66	MEI1
6	LR	F	61205	0.18	0.55	0.07	1.36E−14	1.22	PRDM7
	LW	F	28051609	0.20	0.48	0.08	7.14E−09	0.71
	LR	F	137566317	0.18	0.86	0.07	3.02E−33	2.91	MSH4
	SY	F	137825063	0.48	0.42	0.08	8.51E−08	1.08	MSH4
7	LW	F	78531203	0.39	0.43	0.07	6.83E−10	0.80	RNF212B/REC8*
	LR	F	113235081	0.41	0.56	0.06	9.39E−24	2.06
	DU	F	23426839	0.34	− 0.72	0.12	3.19E−10	2.29
8	LR	F	562791	0.06	1.47	0.12	8.51E−35	3.06	RNF212
	LW	F	164462	0.29	− 1.37	0.07	7.35E−79	7.00
	LW	M	1197996	0.36	− 0.72	0.12	4.76E−09	12.28
	SY	F	164462	0.63	1.16	0.08	7.16E−50	7.73
	SY	M	144871	0.65	0.60	0.11	2.89E−08	12.79
	DU	F	178951	0.18	− 1.41	0.14	2.87E−23	5.53
	DU	M	794886	0.20	− 1.03	0.17	5.94E−10	16.87
	PI	F	1543451	0.18	1.34	0.13	9.50E−24	6.95
	PI	M	1324636	0.24	0.87	0.15	3.11E−09	15.39
9	LR	F	123194749	0.43	0.30	0.06	6.95E−08	0.60	–
12	LR	F	43697634	0.39	0.32	0.06	2.35E−08	0.65	–
15	LR	F	115153652	0.20	− 0.55	0.07	2.03E−15	1.30	–
15	LR	F	35743431	0.35	− 0.37	0.06	1.02E−10	0.86	–
17	LR	F	59924616	0.27	− 0.67	0.06	6.05E−27	2.35	SYCP2
	LW	F	59845939	0.50	− 0.55	0.07	2.58E−16	1.41
	SY	F	59911489	0.36	− 0.53	0.08	2.32E−11	1.67

SNP positions are in base pairs, SE standard error of the effect, P P value, %V_p is the proportion of phenotypic variance explained by the SNP, LR Landrace, DU Duroc, LW Large White, PI Pietrain, SY Synthetic
^*Relatively distant from the peaks; REC8 position: 75118744–75139630 and RNF212B position: 75796882–75829620

ISSN: 1297-9686