Genome-wide association and identification of candidate genes for age at puberty in swine

Nonneman, Dan J.; Schneider, James F.; Lents, Clay A.; Wiedmann, Ralph T.; Vallet, Jeffrey L.; Rohrer, Gary A.

doi:10.1186/s12863-016-0352-y

BMC Genomic Data

Table 2 Most significant QTL for age at puberty in pigs

From: Genome-wide association and identification of candidate genes for age at puberty in swine

SSC	Start¹	End¹	Marker 1	Marker 5	GenVar (%)	Rank²	p-value	-log(p)	Gene	Human trait or function
12	14,910,939	15,006,310	M1GA0016274	ASGA0053410	9.7332	1	0.0001	4.000	GH1	growth/height
6	68,823,187	68,890,361	ASGA0091283	ALGA0035583	0.3064	35	0.001	3.000	TMEM51
1	291,202,322	291,277,150	ALGA0009830	M1GA0001507	0.6121	10	0.003	2.523	BRINP1
3	26,517,667	26,631,496	MARC0007734	ALGA0018104	0.5091	15	0.003	2.523	GPR139
7	43,190,587	43,400,560	ALGA0040857	ASGA0033098	0.1673	75	0.003	2.523	UBR2	obesity
7	75,121,635	75,460,294	INRA0026429	H3GA0022045	7.1362	2	0.003	2.523	C14orf23, PRKD1	BMI/obesity
15	42,527,231	43,052,985	H3GA0044224	ALGA0114567	1.7467	3	0.003	2.523	ANGPT2	ovulation
3	11,143,547	11,286,978	H3GA0008684	ASGA0013430	0.5400	13	0.004	2.398	GTF2IRD1
9	142,232,369	142,338,853	ASGA0044888	ASGA0044901	1.4283	4	0.004	2.398	SMYD2
10	18,347,386	18,665,600	ASGA0046792	DRGA0010326	0.3992	24	0.004	2.398	SDCCAG8	obesity
3	11,960,567	12,093,180	ALGA0017578	ALGA0017611	1.0870	6	0.005	2.301	GATSL2
14	138,428,984	138,850,067	DRGA0014684	ALGA0082115	0.4572	19	0.005	2.301	SLC18A2	dopamine transport
1	121,626,075	121,978,687	M1GA0001099	ASGA0004239	0.4196	21	0.006	2.222	RORA	menarche
3	21,596,232	22,794,763	ASGA0013855	ASGA0094123	0.1765	70	0.006	2.222	AQP8	menarche
3	27,054,931	27,208,960	MARC0085816	ALGA0124353	1.1368	5	0.006	2.222	GPRC5B	BMI/obesity
6	127,194,648	127,655,907	MARC0001714	ASGA0029572	0.3900	25	0.006	2.222	ACADM	metabolite levels
15	148,542,045	148,722,557	ASGA0071543	ASGA0071569	0.1564	83	0.007	2.155	HJURP
8	15,600,021	15,671,195	DRGA0008334	ASGA0037920	0.2543	41	0.008	2.097	SLIT2
8	109,067,052	109,213,652	H3GA0025237	MARC0017963	0.2658	39	0.008	2.097	TRPC3
11	55,668,610	55,844,999	ALGA0062350	ALGA0062355	0.3136	34	0.008	2.097	RNF219
16	44,362,264	44,481,215	ALGA0090494	MARC0073104	0.2123	50	0.008	2.097	IPO11
18	50,837,228	51,030,054	DRGA0017050	ASGA0105879	0.5142	14	0.008	2.097	SNX10	visceral adipose tissue
2	133,313,068	133,376,955	INRA0009763	MARC0038747	0.2935	36	0.009	2.046	ZNF608	BMI/obesity
10	40,710,979	40,868,229	MARC0038064	ALGA0058443	0.0985	149	0.009	2.046	LINGO2	BMI/obesity
15	142,893,866	142,992,475	MARC0112236	ALGA0087841	0.3401	29	0.009	2.046	KPNA4
2	157,110,989	157,223,320	MARC0039166	M1GA0003373	0.2571	40	0.01	2.000	ABLIM3
2	157,270,386	157,362,402	H3GA0008275	ALGA0017005	0.4738	17	0.01	2.000	AFAP1L1	obesity

¹Start and End refer to SNP position in Sus scrofa Build 10.2
²Windows are ranked is by % genetic variance

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ISSN: 2730-6844

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