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. 2021 Mar 8;12:640039. doi: 10.3389/fgene.2021.640039

TABLE 1.

GWAS for milk production traits in DSN.

Chr Position (bp) SNP-ID Ref Alt MA MAF Trait N β SE(β) PBF
1 77,049,090 rs110516247 A C C 0.11 Milk kg (LA3) 846 −515 100 0.00679
Protein kg (LA3) 844 −16.3 3.3 0.02351
79,757,250 rs43246393 C T T 0.34 Milk kg (LA3) 856 −390 76 0.00020
Protein kg (LA3) 854 −13.2 2.5 0.00007
Protein kg (LAm) 679 −10.3 2.2 0.02641
Fat kg (LA3) 857 −13.4 3.1 0.01868
115,539,332 rs42347234 C T T 0.11 Milk kg (LA1) 1355 336 70 0.03846
Protein kg (LA1) 1357 11.9 2.4 0.01140
128,503,005 rs109686415 C T C 0.49 Fat % (LA2) 1115 −0.082 0.016 0.00357
Fat % (LAm) 660 −0.082 0.016 0.01599
143,812,919 rs41255272 A G A 0.50 Milk kg (LA1) 1367 204 41 0.01478
Protein kg (LA1) 1369 6.6 1.4 0.04613
2 123,100,345 rs110278850 A C C 0.45 Protein kg (200 days) 1436 3.5 0.8 0.04941
3 15,947,663 rs110565504 T C T 0.24 Fat % (200 days) 1458 0.056 0.019 0.03398
4 47,674,986 rs110143001 G A G 0.42 Fat % (LA3) 844 0.086 0.019 0.04275
91,071,208 rs42753220 C T C 0.40 Milk kg (LA1) 1370 213 44 0.01390
5 62,094,191 rs29009717 A G A 0.18 Fat % (LA3) 853 −0.125 0.032 0.09655
83,959,138 rs41660560 G T G 0.35 Protein kg (LA2) 1160 9.4 2.1 0.01767
93,953,629 rs109945272 T C T 0.24 Fat % (LA2) 1136 −0.077 0.024 0.08780
114,935,739 rs41652414 C T T 0.19 Milk kg (LA1) 1357 220 71 0.02814
Milk kg (100 days) 1457 64 24 0.08596
Milk kg (200 days) 1452 141 46 0.00923
Protein kg (LA1) 1359 7.2 2.4 0.04450
Protein kg (100 days) 1459 2 0.7 0.08697
Protein kg (200 days) 1457 4.1 1.4 0.02288
Fat kg (200 days) 1447 5.1 1.7 0.07535
6 60,162,206 rs41605188 G A A 0.34 Milk kg (200 days) 1469 119 29 0.09377
61,733,082 rs135571989 C A A 0.21 Milk kg (LA1) 1320 −195 71 0.07717
Milk kg (200 days) 1416 −110 45 0.08954
62,988,117 rs42436495 T G G 0.30 Milk kg (LA1) 1370 225 49 0.01789
Milk kg (200 days) 1469 136 32 0.03921
63,010,380 rs42436482 A G G 0.29 Milk kg (LA1) 1368 220 52 0.04884
Milk kg (200 days) 1467 132 34 0.09298
64,928,624 rs42482917 T C C 0.32 Milk kg (200 days) 1463 111 30 0.09593
77,688,509 rs41652041 A G G 0.35 Milk kg (LA1) 1372 −212 49 0.06866
Milk kg (200 days) 1470 −138 31 0.03904
80,530,130 rs110291935 T C T 0.41 Milk kg (LA1) 1370 −209 42 0.01362
Milk kg (100 days) 1474 −71 14 0.00519
Milk kg (200 days) 1469 −132 27 0.00655
80,626,467 rs109872424 T C T 0.33 Milk kg (100 days) 1473 −64 16 0.06727
Milk kg (200 days) 1468 −124 30 0.02416
86,112,142 rs109592101 A G A 0.42 Milk kg (LA1) 1372 −193 41 0.01990
Milk kg (100 days) 1476 −78 14 0.00009
Milk kg (200 days) 1471 −119 26 0.04162
Protein kg (100 days) 1478 −1.8 0.4 0.08431
87,266,808 rs41591365 C T C 0.46 Protein kg (100 days) 1473 2.1 0.4 0.03608
88,164,411 rs41622837 A G A 0.14 Protein kg (200 days) 1444 −6 1.3 0.07033
8 53,663,120 rs41793393 C T T 0.19 Milk kg (LA3) 847 −356 115 0.00508
Milk kg (LAm) 673 −316 97 0.03554
53,867,972 rs109542652 G A A 0.14 Milk kg (LA3) 846 −489 101 0.02538
59,101,606 rs43550935 A G G 0.19 Milk kg (LAm) 685 −271 95 0.07475
Protein kg (LAm) 685 −9.1 3.2 0.02661
100,876,785 rs108983661 G A A 0.25 Fat kg (LAm) 683 12.5 3 0.05697
9 10,638,013 rs133869947 A C A 0.38 Milk kg (LA3) 818 −297 70 0.06280
Milk kg (LAm) 645 −270 60 0.04397
26,353,699 rs110314239 G T T 0.48 Fat kg (LA1) 1366 −6.8 1.5 0.05814
10 3,611,602 rs42697353 T C C 0.49 Fat % (200 days) 1449 −0.061 0.013 0.03506
11 69,443,503 rs110564084 T C T 0.30 Protein kg (LA2) 1157 11.9 2.5 0.05681
92,712,210 rs110540697 T C C 0.41 Fat % (200 days) 1454 0.057 0.013 0.09715
12 66,340,756 rs41629344 T G G 0.39 Fat % (200 days) 1452 0.06 0.013 0.00380
14 26,340,400 rs41727315 G A A 0.06 Protein kg (100 days) 1470 4 0.9 0.06447
16 11,516,923 rs41623175 A G A 0.21 Fat % (200 days) 1459 −0.082 0.02 0.05676
30,668,830 rs43041491 G T G 0.11 Fat % (LA3) 835 0.153 0.031 0.02338
32,105,683 rs798259422 A G G 0.29 Fat % (200 days) 1458 −0.055 0.015 0.05996
33,789,714 rs41796289 C T C 0.39 Fat % (LA2) 1134 −0.061 0.015 0.02776
Fat % (200 days) 1450 −0.049 0.013 0.09433
40,391,486 rs41804404 A G G 0.46 Fat % (200 days) 1446 0.058 0.012 0.04642
46,683,276 rs110777881 A G G 0.36 Protein kg (100 days) 1444 −1.8 0.5 0.05105
46,773,225 rs43719805 T C C 0.47 Protein kg (100 days) 1472 1.9 0.4 0.04084
18 53,596,284 rs109907036 C T T 0.37 Fat % (LA2) 1136 0.086 0.017 0.00477
20 50,879,180 rs41948928 T C T 0.10 Fat % (200 days) 1445 −0.118 0.023 0.00777
71,448,297 rs110353352 C T C 0.13 Milk kg (LA2) 1137 484 86 0.00040
Protein kg (LA2) 1143 15 2.9 0.00503
Fat kg (LA2) 1137 17.3 3.5 0.01434
21 42,828,439 rs41978846 T G T 0.33 Protein kg (200 days) 1450 −4.2 0.9 0.09136
24 16,789,760 rs110860585 C T T 0.41 Milk kg (LA3) 862 −348 72 0.01192
30,250,034 rs110476141 G A G 0.36 Protein kg (LA1) 1355 −7 1.5 0.01207
Protein kg (200 days) 1453 −4.1 0.9 0.03475
Fat kg (LA1) 1348 −8.5 1.7 0.02349
25 7,944,597 rs109583598 T C C 0.29 Fat % (200 days) 1456 0.065 0.016 0.01082
9,711,895 rs110469759 A G A 0.17 Fat kg (LA1) 1368 10.8 3.5 0.00392
Fat kg (200 days) 1467 5.7 2 0.02959
1,1019,450 rs109027867 G T G 0.48 Milk kg (200 days) 1445 −128 26 0.03396
27 13,864,569 rs110009442 C G C 0.32 Fat % (LA2) 1125 0.061 0.018 0.08067
Fat % (200 days) 1442 0.06 0.015 0.09215
18,527,112 rs42957103 G A A 0.41 Fat kg (LA1) 1367 7.5 1.7 0.09536
28 25,196,334 rs41587054 A G G 0.10 Protein kg (100 days) 1419 3.8 0.8 0.06929
29 50,217,955 rs109241029 G A A 0.44 Fat % (LA2) 1137 0.076 0.016 0.04229
50,260,533 rs109840529 A G G 0.42 Fat % (LA2) 1118 −0.082 0.016 0.00338
50,326,170 rs110740589 A G A 0.41 Fat % (LA2) 1113 −0.09 0.016 0.00022
X 12,896,716 rs109188619 T A T 0.18 Milk kg (LA3) 860 546 122 0.02488
116,886,837 rs41626783 T C C 0.38 Protein kg (200 days) 1476 −4.6 1.1 0.08409
117,691,901 rs110011913 A T T 0.31 Protein kg (LA3) 851 −13.5 2.7 0.01321
Protein kg (LAm) 676 −10.8 2.4 0.07065
133,244,405 rs29018822 G T T 0.35 Fat kg (200 days) 1409 −6.8 1.4 0.07242

For each trait, significantly associated SNPs are listed with chromosome number (Chr), chromosomal position in base pairs (bp), the SNP reference ID (SNP-ID), the given allele on the forward strand in the reference genome ARS-UCD1.2 (Ref), the alternative allele (Alt), the minor allele in the examined DSN population (MA), and the minor allele frequency (MAF). Furthermore, the associated trait, the number of cows in the specific analysis of this trait (n), the allele substitution effect of the minor allele (β), the standard error [SE(β)], and the p-value after Bonferroni-correction (PBF) are given. P-values of PBF < 0.1, PBF < 0.05, and PBF < 0.01 were considered as suggestive (highlighted in gray), significant, or highly significant (highlighted in bold), respectively.