Genome changes due to artificial selection in U.S. Holstein cattle

BMC Genomics

Table 1 Allele frequency changes since 1964 in selected genes. (‘Allele 1’ is the lower-ranked letter of any pair of A, C, G, T)

SNP^a			frequency of ‘allele 1’ in population
chr	position (bp)	gene	I ^b	II ^b	III ^b	Current ^c	AFD ^d
X	114,995,979	ADGRG2 ^e	0.99	0.62	0.45	0.39	0.60
10	28,703,125	AVEN ^e	0.02	0.30	0.51	0.59	0.56
X	116,153,810	DMD ^f	0.05	0.46	0.53	0.58	0.53
3	98,450,919	SPATA6 ^e	0.08	0.53	0.57	0.59	0.51
2	100,376,419	ERBB4 ^e	0.08	0.29	0.47	0.56	0.48
23	27,215,001	SKIV2L ^e	0.37	0.58	0.78	0.84	0.47
1	88,050,696	USP13 ^g	0.22	0.57	0.63	0.64	0.42
11	6,724,678	IL1R2 ^g	0.68	0.33	0.29	0.26	0.42
13	76,932,968	SULF2 ^e	0.19	0.38	0.51	0.61	0.41
26	17,465,791	BLNK ^g	0.41	0.74	0.79	0.83	0.41
19	24,812,617	SPATA22 ^e	0.80	0.49	0.42	0.39	0.40
23	25,552,635	BOLA-DRB2 ^g	0.22	0.49	0.60	0.62	0.40
1	65,433,706	GSK3B ^g	0.54	0.21	0.17	0.16	0.38
12	35,934,370	LATS2 ^{e, g}	0.42	0.23	0.14	0.08	0.34
9	90,155,533	ESR1 ^e	0.45	0.24	0.16	0.13	0.32
20	32,030,332	GHR ^e	0.42	0.61	0.70	0.73	0.31
11	28,602,889	EPAS1 ^{e, g}	0.41	0.60	0.64	0.71	0.30
1	95,258,770	SPATA16 ^e	0.92	0.65	0.69	0.62	0.30
11	31,296,603	FSHR ^e	0.03	0.23	0.25	0.26	0.23
20	39,017,985	PRLR ^e	0.70	0.61	0.50	0.49	0.21
14	1,801,116	DGAT1 ^h	0.93	0.71	0.82	0.77	0.16

^a These SNPs were selected based on three criteria: AFD is large among all SNPs, the SNP is in a gene with known fertility or immunity function, or other well established functions (DGAT1 and DMD)
^b I, II, III represent Groups I, II and III respectively, where Group I was unselected, Group II was subjected to 20 years of selection, and Group III was subjected to 40 years of selection since 1964
^c The current population had 294,079 cows with 98% of the cows born in 2006–2015
^d This is the absolute allele frequency difference between Group I and the current population approximately due to 50 years of selection
^e Associated with fertility
^f Associated with muscle diseases
^g Associated with immunity
^h Widely confirmed to have the most significant effects on milk production traits in dairy cattle

ISSN: 1471-2164