A post-GWAS confirming effects of PRKG1 gene on milk fatty acids in a Chinese Holstein dairy population

Shi, Lijun; Lv, Xiaoqing; Liu, Lin; Yang, Yuze; Ma, Zhu; Han, Bo; Sun, Dongxiao

doi:10.1186/s12863-019-0755-7

BMC Genomic Data

Table 2 Associations of six SNPs in PRKG1 gene with milk fatty acid traits (LSM ± SE)

From: A post-GWAS confirming effects of PRKG1 gene on milk fatty acids in a Chinese Holstein dairy population

SNP	Genotype (No.)	C6:0 (%)	C8:0 (%)	C10:0 (%)	C11:0 (%)	C12:0 (%)	C13:0 (%)	C14:0 (%)	C14:1 (%)	C15:0 (%)	C16:0 (%)	C16:1 (%)	C17:0 (%)
g.8344262A > T	AA(424–459)	0.4901 ± 0.0122	0.9658 ± 0.0107	2.8472 ± 0.0321^Aa	0.0577 ± 0.0023	2.9861 ± 0.0418	0.0988 ± 0.0028	10.2891 ± 0.0702	0.6447 ± 0.0180	0.9972 ± 0.0122	34.7950 ± 0.1771	1.3324 ± 0.0248^ab	0.5664 ± 0.0031
	AT(259–393)	0.4735 ± 0.0125	0.9467 ± 0.0109	2.7685 ± 0.0332^Bb	0.0581 ± 0.0025	2.9584 ± 0.0423	0.0991 ± 0.0030	10.1625 ± 0.0716	0.6598 ± 0.0187	0.9947 ± 0.0127	34.7954 ± 0.1822	1.3529 ± 0.0257^a	0.5714 ± 0.0032
	TT(96–104)	0.4769 ± 0.0174	0.9366 ± 0.0150	2.8580 ± 0.0438^ABa	0.0559 ± 0.0035	2.9889 ± 0.0572	0.0965 ± 0.0047	10.3280 ± 0.0951	0.6555 ± 0.0271	0.9880 ± 0.0188	34.9466 ± 0.2566	1.2643 ± 0.0356^b	0.5709 ± 0.0047
	P	0.2405	0.0177	0.0012^**	0.8124	0.6385	0.8615	0.0297	0.6391	0.8733	0.7983	0.0295	0.1829
g.6904047G > T	GG(420–458)	0.4580 ± 0.0133	0.9292 ± 0.0119	2.8354 ± 0.0350	0.0580 ± 0.0026	3.0006 ± 0.0449	0.0988 ± 0.0032	10.2605 ± 0.0777^a	0.6579 ± 0.0199	0.9950 ± 0.0133	34.8344 ± 0.1923	1.2995 ± 0.0272^a	0.5621 ± 0.0034
	GT(179–196)	0.4682 ± 0.0155	0.9361 ± 0.0131	2.8250 ± 0.0394	0.0584 ± 0.0030	2.9910 ± 0.0502	0.0987 ± 0.0039	10.0941 ± 0.0865^b	0.6642 ± 0.0229	1.0011 ± 0.0159	34.9128 ± 0.2225	1.3677 ± 0.0312^b	0.5678 ± 0.0040
	TT(21–24)	0.5161 ± 0.0316	0.8947 ± 0.0258	2.8551 ± 0.0727	0.0538 ± 0.0064	3.0339 ± 0.0974	0.0947 ± 0.0085	10.1180 ± 0.1720^ab	0.6469 ± 0.0489	0.9967 ± 0.0346	34.7830 ± 0.4581	1.3050 ± 0.0656^ab	0.5592 ± 0.0085
	P	0.1453	0.2466	0.8812	0.7751	0.8935	0.8846	0.0377	0.9145	0.9096	0.9003	0.0304	0.2151
g.6903810G > A	AA(17–21)	0.5425 ± 0.0347	1.0524 ± 0.0269^A	2.7307 ± 0.0780	0.0547 ± 0.0070	2.8806 ± 0.1040	0.0922 ± 0.0096	10.3798 ± 0.1808	0.6550 ± 0.0523	0.9345 ± 0.0366	34.3377 ± 0.4963	1.2467 ± 0.0677	0.5534 ± 0.0091
	AG(179–191)	0.4720 ± 0.0146	0.9352 ± 0.0127^B	2.7669 ± 0.0373	0.0580 ± 0.0029	2.9549 ± 0.0484	0.0977 ± 0.0037	10.2389 ± 0.0820	0.6663 ± 0.0225	1.0024 ± 0.0153	34.8727 ± 0.2159	1.3247 ± 0.0301	0.5686 ± 0.0039
	GG(681–741)	0.4849 ± 0.0114	0.9418 ± 0.0102^B	2.8293 ± 0.0309	0.0592 ± 0.0022	3.0072 ± 0.0393	0.1001 ± 0.0026	10.2294 ± 0.0664	0.6561 ± 0.0169	0.9969 ± 0.0114	34.7215 ± 0.1659	1.3250 ± 0.0233	0.5674 ± 0.0029
	P	0.1040	<.0001^**	0.0464	0.7411	0.1944	0.6019	0.6868	0.8697	0.1831	0.4741	0.4903	0.2478
g.6903365C > A	AA(93–107)	0.4439 ± 0.0206^Aa	0.9343 ± 0.0169^A	2.8432 ± 0.0489	0.0586 ± 0.0041	3.0238 ± 0.0635	0.1018 ± 0.0053	10.4947 ± 0.1101	0.6549 ± 0.0305	1.0037 ± 0.0211	34.7232 ± 0.2894	1.2476 ± 0.0410	0.5653 ± 0.0053
	CC(361–381)	0.5229 ± 0.0138^Bb	0.9924 ± 0.0122^B	2.8967 ± 0.0367	0.0592 ± 0.0027	3.0341 ± 0.0471	0.0997 ± 0.0033	10.3851 ± 0.0799	0.6661 ± 0.0206	0.9927 ± 0.0140	34.9631 ± 0.2004	1.3330 ± 0.0283	0.5662 ± 0.0035
	CA(49–55)	0.4626 ± 0.0240^ABa	0.9379 ± 0.0196^A	2.8406 ± 0.0566	0.0576 ± 0.0048	2.9559 ± 0.0745	0.1039 ± 0.0063	10.1970 ± 0.1278	0.6478 ± 0.0365	0.9746 ± 0.0254	34.2494 ± 0.3514	1.2822 ± 0.0488	0.5598 ± 0.0063
	P	<.0001^**	<.0001^**	0.2980	0.9415	0.5068	0.7647	0.0958	0.8336	0.6052	0.0875	0.0569	0.5867
g.6902878 T > G	GG(189–202)	0.4323 ± 0.0169^A	0.9624 ± 0.0144^Aa	2.8052 ± 0.0423	0.0559 ± 0.0033	2.9744 ± 0.0550	0.0973 ± 0.0042	10.1691 ± 0.0957^a	0.6547 ± 0.0252	0.9966 ± 0.0172	34.7964 ± 0.2433	1.3831 ± 0.0341	0.5667 ± 0.0044
	GT(2)	0.7892 ± 0.0983^B	1.3588 ± 0.0820^B	3.1626 ± 0.2348	0.0560 ± 0.0212	3.0685 ± 0.3132	0.0971 ± 0.0288	11.5294 ± 0.5289^b	0.5671 ± 0.1627	0.9937 ± 0.1135	34.7693 ± 1.5091	1.1787 ± 0.2088	0.5358 ± 0.0283
	TT(306–334)	0.4942 ± 0.0161^C	0.9916 ± 0.0137^Ab	2.8670 ± 0.0409	0.0595 ± 0.0032	3.0380 ± 0.0527	0.1015 ± 0.0040	10.2332 ± 0.0918^a	0.6368 ± 0.0243	1.0049 ± 0.0166	34.8385 ± 0.2325	1.3627 ± 0.0326	0.5671 ± 0.0042
	P	<.0001^**	<.0001^**	0.0426	0.4274	0.2875	0.5502	0.0249	0.6194	0.8525	0.9768	0.4788	0.5390
g.6901713 T > G	GG(21–27)	0.5161 ± 0.0328^AB	1.0577 ± 0.0246^A	2.8817 ± 0.0710^AB	0.0539 ± 0.0064	2.8762 ± 0.0928	0.1008 ± 0.0083	10.0821 ± 0.1607^ab	0.5555 ± 0.0474	0.9906 ± 0.0333	34.1191 ± 0.4451	1.3422 ± 0.0617	0.5699 ± 0.0083
	GT(266–289)	0.4958 ± 0.0132^A	0.9797 ± 0.0116^B	2.9305 ± 0.0345^A	0.0579 ± 0.0026	3.0584 ± 0.0448	0.1000 ± 0.0033	10.3430 ± 0.0756^a	0.6518 ± 0.0201	0.9971 ± 0.0137	34.8534 ± 0.1956	1.3099 ± 0.0273	0.5649 ± 0.0035
	TT(591–637)	0.4628 ± 0.0116^B	0.9230 ± 0.0103^C	2.8342 ± 0.0310^B	0.0579 ± 0.0023	3.0024 ± 0.0397	0.0982 ± 0.0027	10.1984 ± 0.0673^b	0.6604 ± 0.0171	0.9930 ± 0.0115	34.9830 ± 0.1682	1.3285 ± 0.0237	0.5711 ± 0.0030
	P	0.0029^*	<.0001^**	0.0004^**	0.8083	0.0545	0.8097	0.0181	0.0734	0.9357	0.1082	0.6493	0.1080
SNP	Genotype (No.)	C17:1 (%)	C18:0 (%)	C18:1cis-9 (%)	C18index (%)	C20:0 (%)	C14index (%)	C16index (%)	C17index (%)	SFA (%)	UFA (%)	SFA/UFA (%)	Total index (%)
g.8344262A > T	AA(374–460)	0.1906 ± 0.0025^a	14.0884 ± 0.0864	18.9343 ± 0.1167^a	56.9012 ± 0.2735^ab	0.1685 ± 0.0017	6.0733 ± 0.1384	3.6217 ± 0.0636^AB	24.8838 ± 0.2156^a	68.1683 ± 0.1617	30.2498 ± 0.1462	2.2891 ± 0.0212	27.5332 ± 0.1278^A
	AT(331–393)	0.1957 ± 0.0026^b	14.0342 ± 0.0907	19.2495 ± 0.1212^b	57.3243 ± 0.2805^a	0.1706 ± 0.0017	6.2370 ± 0.1435	3.6885 ± 0.0659^A	24.9935 ± 0.2245^a	67.9305 ± 0.1671	30.4415 ± 0.1520	2.2709 ± 0.0221	27.9090 ± 0.1313^B
	TT(82–104)	0.1889 ± 0.0036^ab	14.2026 ± 0.1381	18.7636 ± 0.1828^a	56.3603 ± 0.4109^b	0.1699 ± 0.0027	6.1182 ± 0.2045	3.4344 ± 0.0913^B	24.1599 ± 0.3177^b	68.4212 ± 0.2469	29.9512 ± 0.2243	2.3224 ± 0.0329	27.1715 ± 0.1948^A
	P	0.0218	0.4469	0.0031^*	0.0323	0.3960	0.3704	0.0101	0.0154	0.0770	0.0628	0.2492	<.0001^**
g.6904047G > T	GG(382–459)	0.1909 ± 0.0027^Aa	14.0083 ± 0.0952	19.0595 ± 0.1295	57.3442 ± 0.2994	0.1668 ± 0.0020^a	6.2722 ± 0.1517	3.6249 ± 0.0698	24.9868 ± 0.2379^A	68.0210 ± 0.1771	30.3843 ± 0.1611	2.2734 ± 0.0232	27.7337 ± 0.1392
	GT(173–196)	0.1951 ± 0.0031^ABa	14.0877 ± 0.1147	19.0396 ± 0.1519	56.9780 ± 0.3490	0.1718 ± 0.0023^b	6.3520 ± 0.1778	3.7536 ± 0.0798	25.1566 ± 0.2723^A	68.1127 ± 0.2102	30.3983 ± 0.1887	2.2768 ± 0.0275	27.7040 ± 0.1642
	TT(22–24)	0.2129 ± 0.0064^Bb	14.2950 ± 0.2501	18.9209 ± 0.3330	56.8847 ± 0.7389	0.1642 ± 0.0045^ab	6.0245 ± 0.3750	3.5526 ± 0.1650	26.8471 ± 0.5501^B	67.8471 ± 0.4476	30.4643 ± 0.4116	2.2507 ± 0.0598	27.7666 ± 0.3516
	P	0.0010^**	0.4300	0.9118	0.4383	0.0190	0.6321	0.1072	0.0021^*	0.7890	0.9791	0.9099	0.9710
g.6903810G > A	AA(16–21)	0.1852 ± 0.0068	14.2381 ± 0.2711	19.4313 ± 0.3637	57.8248 ± 0.8116	0.1630 ± 0.0053^AB	5.8672 ± 0.3861	3.5731 ± 0.1706	25.0782 ± 0.5779	67.6381 ± 0.4921	30.6643 ± 0.4476	2.1938 ± 0.0634	28.8024 ± 0.3790^Aa
	AG(154–191)	0.1907 ± 0.0030	14.2502 ± 0.1111	18.9316 ± 0.1477	56.9864 ± 0.3386	0.1751 ± 0.0021^A	6.1871 ± 0.1691	3.6361 ± 0.0768	24.9321 ± 0.2611	68.1679 ± 0.2033	30.2696 ± 0.1845	2.3059 ± 0.0266	27.4558 ± 0.1589^Bb
	GG(622–743)	0.1907 ± 0.0023	14.0972 ± 0.0800	19.1316 ± 0.1076	57.5775 ± 0.2508	0.1692 ± 0.0016^B	6.1143 ± 0.1313	3.6545 ± 0.0602	24.8228 ± 0.2058	67.8738 ± 0.1482	30.4623 ± 0.1352	2.2670 ± 0.0196	27.8031 ± 0.1169^ABc
	P	0.6965	0.3037	0.1962	0.1177	0.0027^*	0.6719	0.8620	0.8107	0.2087	0.4195	0.1027	0.0006^**
g.6903365C > A	AA(86–107)	0.1840 ± 0.0041	13.8722 ± 0.1550	19.4709 ± 0.2047^a	57.9027 ± 0.4677	0.1597 ± 0.0031^A	6.0759 ± 0.2298	3.4734 ± 0.1041	24.7990 ± 0.3588	67.7737 ± 0.2806	30.7073 ± 0.2542^a	2.2474 ± 0.0368	28.0306 ± 0.2207^a
	CC(322–383)	0.1898 ± 0.0028	14.0896 ± 0.1003	18.8996 ± 0.1348^b	57.0679 ± 0.3097	0.1652 ± 0.0020^AB	6.2036 ± 0.1599	3.6362 ± 0.0727	25.0637 ± 0.2475	68.2830 ± 0.1841	30.0458 ± 0.1674^b	2.3118 ± 0.0244	27.4913 ± 0.1448^b
	CA(44–55)	0.1908 ± 0.0049	14.0436 ± 0.1845	19.2701 ± 0.2468^ab	57.5534 ± 0.5502	0.1736 ± 0.0037^B	6.2137 ± 0.2664	3.5773 ± 0.1236	25.4468 ± 0.4221	67.8333 ± 0.3333	30.3655 ± 0.3056^ab	2.2236 ± 0.0451	28.0080 ± 0.2610^ab
	P	0.2709	0.3586	0.0103	0.1432	0.0032^*	0.8193	0.2198	0.3687	0.0975	0.0221	0.0476	0.0114
g.6902878 T > G	GG(162–202)	0.1990 ± 0.0034^a	14.1712 ± 0.1255	19.2493 ± 0.1668	57.8214 ± 0.3823	0.1723 ± 0.0025	6.2335 ± 0.1958	3.7811 ± 0.0867	25.7488 ± 0.2926	67.8664 ± 0.2288	30.4505 ± 0.2085	2.2678 ± 0.0303	27.9791 ± 0.1799
	GT(1–2)	0.1396 ± 0.0210^b	15.1152 ± 0.8492	17.5963 ± 1.1241	55.1627 ± 2.4664	0.2174 ± 0.0205	4.6700 ± 1.1690	3.2808 ± 0.5268	22.3692 ± 1.7890	70.2243 ± 1.4970	27.7265 ± 1.3769	2.6772 ± 0.1992	25.8210 ± 1.1776
	TT(298–334)	0.1937 ± 0.0033^a	13.9941 ± 0.1205	19.0195 ± 0.1603	57.8556 ± 0.3675	0.1697 ± 0.0024	6.0736 ± 0.1867	3.6985 ± 0.0842	25.3001 ± 0.2887	68.1192 ± 0.2203	30.2583 ± 0.1994	2.2932 ± 0.0291	27.8464 ± 0.1728
	P	0.0035^*	0.1368	0.1045	0.5484	0.0342	0.2492	0.3232	0.0318	0.1353	0.0844	0.0802	0.1353
g.6901713 T > G	GG(23–27)	0.1820 ± 0.0064^AB	14.2657 ± 0.2465	19.3224 ± 0.3331	57.4973 ± 0.7218	0.1618 ± 0.0046	5.3282 ± 0.3472^a	3.6417 ± 0.1598	24.7738 ± 0.5396^AB	67.7758 ± 0.4361	30.6385 ± 0.4050	2.2379 ± 0.0579	28.0440 ± 0.3424
	GT(241–289)	0.1866 ± 0.0027^A	14.0054 ± 0.0977	18.9266 ± 0.1306	57.1601 ± 0.3031	0.1707 ± 0.0019	6.0394 ± 0.1533^ab	3.6135 ± 0.0702	24.4844 ± 0.2400^A	68.2066 ± 0.1805	30.1259 ± 0.1638	2.2896 ± 0.0240	27.4588 ± 0.1422
	TT(524–639)	0.1960 ± 0.0024^B	14.1040 ± 0.0818	19.1405 ± 0.1105	57.1691 ± 0.2570	0.1715 ± 0.0016	6.2935 ± 0.1335^b	3.6568 ± 0.0609	25.1479 ± 0.2074^B	68.0575 ± 0.1524	30.3322 ± 0.1387	2.2695 ± 0.0201	27.7208 ± 0.1193
	P	<.0001^**	0.3793	0.1310	0.8921	0.0925	0.0034^*	0.7300	0.0019^*	0.4593	0.2162	0.4936	0.0446

Note: LSM least square mean, SE standard error. P indicates the significances of the association analysis between each SNP and milk fatty acid traits. P is the raw value. *: P < 0.0083 (the significant association analysis after multiple testing, 0.05/N). ^**: P < 0.0017 (the significant association analysis after multiple testing, 0.01/N). N is the number of SNPs. Different letter (small letters: P < 0.05; capital letters: P < 0.01) superscripts indicate significant differences among the genotypes. The number in the brackets represents the number of cows for the corresponding genotype

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