Population structure and genomic inbreeding in nine Swiss dairy cattle populations

Signer-Hasler, Heidi; Burren, Alexander; Neuditschko, Markus; Frischknecht, Mirjam; Garrick, Dorian; Stricker, Christian; Gredler, Birgit; Bapst, Beat; Flury, Christine

doi:10.1186/s12711-017-0358-6

Genetics Selection Evolution

Table 4 Genomic coordinates (chromosome and start- and stop-position) of the 32 windows with d _i higher than 10, the corresponding population (in brackets, other populations for which the window was significant) and their candidate genes

From: Population structure and genomic inbreeding in nine Swiss dairy cattle populations

BTA	Start position	End position	d _i	Population (other populations)	Candidate genes	Associated trait	References
4	53,358,285	55,358,285	13.424	ER/EV
4	78,602,192	80,602,192	10.036	ER/EV	INHBA	Feed intake	[71]
5	16,275,624	18,275,624	10.760	SF (BV, OB, ER/EV)	KITLG		[80]
5	46,225,174	48,225,174	11.852	RH (HO, SF, ER/EV)
5	46,225,174	48,225,174	11.511	HO (RH, SF, ER/EV)
5	55,558,224	57,558,224	13.108	SI (RH, SF)	STAT6	Growth efficiency, carcass traits	[81]
5	60,520,962	62,520,962	12.197	SI
5	75,148,807	77,148,807	10.435	SI (BV, BS)	SYT10	Longevity	[82]
5	76,432,958	78,432,958	10.735	BS (BV, OB)	SYT10	Longevity	[82]
6	32,407,621	34,407,621	11.691	BV (BS)
6	69,255,003	71,255,003	13.069	SI (BV, BS, HO, SF)	KIT	White spotting	[80]
6	77,416,656	79,416,656	12.928	HO (BS, BV, RH, SF, BS, BV)
6	77,416,656	79,416,656	11.932	RH (BS, BV, HO, SF,)
11	65,512,895	67,512,895	12.856	OB	PROKR1	Fertility	[48]
11	67,608,705	69,608,705	17.985	OB (BV, SF, SI, ER/EV)	CAPN14, CAPN13, LBH, LCLAT1, GFPT1, EHD3, GMCL1, PCBP1	Fertility, meat quality	[48, 75, 76]
11	67,608,705	69,608,705	11.660	SI (BV, OB, SF, ER/EV)		Fertility, meat quality	[48, 75, 76]
14	23,392,111	25,392,111	18.647	RH (BS, BV, OB, HO, SF, SI, ER/EV)	PLAG1, CHCHD7, LYN, TGS1	Stature, fertility	[69, 70]
14	23,392,111	25,392,111	15.509	SF (BS, BV, OB, HO, RH, SI, ER/EV)
14	23,392,111	25,392,111	15.050	HO (BS, BV, OB, RH, SF, SI, ER/EV)
14	23,392,111	25,392,111	10.466	OB (BS, BV, HO, RH, SF, SI, ER/EV)
16	24,736,714	26,736,714	15.161	BV (BS, OB, RH, SF, SI)	HLX	Feed efficiency	[83]
16	24,736,714	26,736,714	14.335	BS (BV, OB, RH, SF, SI)	HLX	Feed efficiency	[83]
16	26,450,435	28,450,435	10.846	BS (BV, OB)	TLR5, CAPN8, CAPN2	Disease resistance, meat quality	[75, 84,85,86]
18	13,233,845	15,233,845	25.720	HO (OB, RH, SF, SI)	MC1R, SLC7A5, CDH15, GALNS, FANCA	Coat color	[31,32,33, 87]
18	13,233,845	15,233,845	24.272	RH (OB, HO, SF, SI)
18	13,233,845	15,233,845	10.451	SF (OB, HO, RH, SI)
18	14,373,569	16,373,569	13.715	RH (HO, SF)	FANCA		[87]
20	29,194,786	31,194,786	14.835	HO (RH)	MRPS30, FGF10	Milk yield. Protein percentage	[88, 89]
20	43,561,002	45,561,002	10.593	HO (RH)
20	46,566,649	48,566,649	12.743	HO (RH, SF, SI)	CDH9	Clinical mastitis	[90]
20	46,566,649	48,566,649	10.759	RH (HO, SF, SI)	CDH9	Clinical mastitis	[90]
26	21,528,510	23,528,510	13.360	ER/EV (OB)	FGF8, SCD	Carcass quality, fertility, fatty acid composition	[72,73,74]

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ISSN: 1297-9686

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