Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

Table 3 Candidate genes located in genomic regions with a high frequency of ROH associated with pig economic traits

Breed	CHR	Start (Mb)	End (Mb)	No SNPs	No genes	Candidate genes	Gene function	Traits related to QTL
BER	6	5.52	6.51	52	5	CDH13	Meat	Lean meat percentage (7632)
	9	129.04	130.63	81	9	PROX1	Meat	Carcass weight (12,786)
	9	129.04	130.63	81	9	FLVCR1	Meat/ Production	Average daily gain (2896)
	14	65.87	68.09	48	7	EGR2	Meat	NA
	15	15.76	17.03	40	11	CCNT2	Meat	Meat colour score (3009)
	17	4.39	5.63	54	10	FGF20	Meat/Production	Average daily gain (28,911)
PIE	13	29.59	29.89	10	9	MYL3	Meat	Loin muscle area (5499)
	13	29.59	29.89	10	9	SETD2	Production	Body weight (21,843)
	16	49.85	52.75	60	17	FGF18	Production	Average daily gain (28,900)
WNHUAZ	1	111.18	117.45	86	6	LIPC	Fatness	Palmitoleic acid content (168,357)
	1	142.77	145.30	41	14	MCEE	Fatness	Intramuscular fat content (17,747)
	1	142.77	145.30	41	14	TJP1	Reproduction	Gestation length (10,617)
	8	64.83	68.48	52	6	STAP1	Health	Palmitoleic acid content (168,374)
	16	48.62	51.50	47	15	ZNF366	Reproduction	Teat number (8812)
	16	48.62	51.50	47	15	DUSP1	Health	NA
HZ	8	66.23	67.50	25	16	SULT1E1	Reproduction/ Fatness	Teat number (124,206)
HZ	8	66.23	67.50	25	16	CSN1S1	Reproduction	Corpus luteum number (492)

The distance between genes and ROH regions was calculated as follows: The starting coordinate of the gene minus the starting coordinate of the ROH region; all candidate genes are located in the ROH region; the number within brackets in the last column represents the QTL-ID

ISSN: 1471-2164