Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Porto-Neto, Laercio R; Sonstegard, Tad S; Liu, George E; Bickhart, Derek M; Da Silva, Marcos VB; Machado, Marco A; Utsunomiya, Yuri T; Garcia, Jose F; Gondro, Cedric; Van Tassell, Curtis P

doi:10.1186/1471-2164-14-876

BMC Genomics

Table 1 Positive selection: regions in the top 1% smoothed F_STvalues

From: Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Region	BTA	SNP start pos	SNP end pos	Highest sFST	CNV [21]	Within cattle type**	Candidate genes	Cross reference
P1	2	47,857,335	48,065,161	0.387	1
P2*	2	71,565,086	72,885,823	0.498	1	Hol		[24]
P3	3	19,689,648	20,166,059	0.399	0	Hol, Nor, Bro	CDC42SE1
P4	3	94,742,479	95,401,345	0.396	0
P5	4	12,106,878	12,361,811	0.384	0
P6	4	46,670,940	46,814,875	0.380	0			[25]
P7	5	48,229,556	48,336,996	0.381	0			[9, 12, 24]
P8	5	55,881,766	56,801,729	0.424	1	Hol	STAT6, GLI1	[24, 25]
P9	7	21,008,805	21,606,667	0.391	0	Gue	ITGB1BP3	[24, 25]
P10	7	47,299,497	47,859,329	0.433	3	Lim	SPOCK, PPP2CA	[12]
P11*	7	50,951,861	53,757,384	0.826	5	Ang, Cha, Gue, Nor, Gir	CD14, CDC23, EGR1, MYOT, TMEM173	[24]
P12	8	39,288,115	39,800,492	0.393	0		CD274	[24]
P13	8	53,490,845	54,592,381	0.440	1	Nor		[26]
P14	8	58,649,674	58,727,004	0.380	0
P15	8	61,543,379	62,874,750	0.464	1
P16	8	69,691,214	70,488,061	0.493	0	Ang	POLR3D, PPP3CC
P17	8	73,617,355	73,704,634	0.382	0
P18	10	36,488,829	37,051,537	0.416	0	Her	CHP	[25]
P19	12	27,935,604	29,508,940	0.439	1	Hol		[24, 25]
P20	13	34,119,211	35,054,048	0.402	0		ZEB1
P21	13	48,893,096	49,816,619	0.408	0	Guz		[9]
P22	14	24,603,090	25,298,972	0.395	0	Nor	PLAG1, XKR4, MOS	[10]
P23	14	36,715,710	37,511,658	0.444	0	Gue		[24]
P24	14	38,919,669	39,027,008	0.383	0	Gue
P25	14	42,121,450	42,376,970	0.389	0
P26	14	45,478,315	46,437,276	0.430	0			[24]
P27	16	40,318,965	40,656,961	0.390	0
P28	16	40,886,797	41,149,860	0.383	0
P29	16	41,564,542	42,407,997	0.440	0	Jer
P30	16	43,250,880	43,501,100	0.390	0			[27]
P31*	16	44,277,286	45,534,177	0.510	2		PIK3CD
P32	18	11,298,096	11,959,392	0.409	0	Bro	IRF8	[24]
P33	18	14,171,624	14,702,657	0.423	0		ACSF3, SPATA2L	[10]
P34	20	13,714,109	15,135,107	0.429	0			[24]
P35*	20	71,629,018	71,967,622	0.508	0
P36*	21	83,766	2,416,432	0.564	0	Gue
P37*	21	31,681,776	33,273,658	0.530	1	Her
P38	21	45,793,883	45,979,589	0.391	0
P39	21	68,349,152	68,943,249	0.448	0	Ang	HSP90AA1, PPP2R5C
P40	24	24,114,816	24,452,344	0.383	1	Nor
P41	29	51,452,986	52,452,986	0.382	1
P42	30	33,064,381	50,329,406	0.810	0		IRAK1, BCAP31, CETN2, GAB3, IKBKG, KIR3DL2, MTM1, SRPK3
P43	30	53,439,167	57,258,157	0.711	0		BTK
P44	30	68,834,838	71,300,049	0.861	0		CYLC1	[12]
P45	30	72,360,206	79,580,964	0.844	0			[12]
P46	30	84,352,052	85,706,219	0.764	0		IL2RG	[12]
P47	30	96,229,383	100,603,158	0.699	0		ALAS2, SMC1A, LOC524601, SPIN2, VSIG4
P48	30	130,500,087	132,116,040	0.670	0		RS1

^*Regions containing smoothed FST (sFST) in the top 0.1%.
^**Regions at sFST top 1% of within taurine and within zebu breeds. Full table of within cattle type results for candidate regions under positive selection is on Additional file 6: Table S3. Ang – Angus; Bro – Brown Swiss, Cha – Charolais, Gue – Guernsey, Jer – Jersey, Her – Hereford, Hol – Holstein, Lim – Limousin, Nor – Norwegian Red, Guz – Guzera, Nel – Nelore.

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ISSN: 1471-2164

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