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Table 2 Top SNP groups explaining most total additive genetic variation for wavenumbers, which interact with different chemical bonds

From: Genome-wide association study on Fourier transform infrared milk spectra for two Danish dairy cattle breeds

Danish Holstein
Chemical bond Peak region All associated wvn pVarA
Peak CHR LL UL Candidate genes
 Alkanes 6_b 6 80394422 88006286 CSN-cluster 1449 0.54
11_a 11 69240871 75495975   1449 0.4
13_a 13 53205470 58871642   1449 0.37
14 14 1463676 5428037 DGAT1 1449 2.04
19_a 19 32148966 37552530 SREBF1 1449 0.39
29_a 29 6893054 12147907   1449 0.48
 C=O 5_b 5 91118692 98515360 MGST1 1735, 1696 0.43
14 14 1463676 5428037 DGAT1 1735, 1696 9.76
17_a 17 12545331 18398611   1735 0.39
 C-H 5_b 5 91118692 98515360 MGST1 2988, 2872 0.39
14 14 1463676 5428037 DGAT1 2988, 2872 7.88
17_a 17 12545331 18398611   2988 0.36
20_b 20 56721394 61566803 ANKH 2988 0.36
21_a 21 6241052 11219294 IGF1R 2988 0.36
 C-O 3_c 3 49704834 58434544   1226, 1114, 1060 0.42
5_b 5 91118692 98515360 MGST1 1226, 1180, 975 0.47
11_a 11 69240871 75495975   1226, 1114 0.43
14 14 1463676 5428037 DGAT1 1226, 1180, 1114, 1060, 975 8.55
17_a 17 12545331 18398611   1180 0.37
19_c 19 57592897 62235799   1226, 1114, 1060 0.52
21_a 21 6241052 11219294 IGF1R 1226, 1114, 1060 0.35
21_c 21 62530384 67845758   975 0.35
25 25 47181 4689960   1226, 1180, 1114, 1060, 975 0.37
28_a 28 2313753 7557315   1226, 1180, 1114, 1060, 975 0.39
29_a 29 6893054 12147907   1226, 1114, 1060 0.54
 CO-N 5_b 5 94381154 101721892 MGST1 1500 0.36
6_b 6 86819633 92465869 CSN-cluster 1500 0.35
14 14 1463676 5428037 DGAT1 1500 5.19
 N-H 5_b 5 91118692 98515360 MGST1 1604 0.5
6_b 6 80394422 88006286 CSN-cluster 1557 0.55
14 14 1463676 5428037 DGAT1 1604, 1557 9.73
17_a 17 12545331 18398611   1604 0.37
20_b 20 54443531 59156949 ANKH 1604, 1557 0.53
 -OH 14 14 1463676 5428037 DGAT1 1295 1.12
19_c 19 58318121 63354178   1295 0.38
20_b 20 56721394 61566803 ANKH 1295 0.4
21_a 21 6241052 11219294 IGF1R 1295 0.36
29_a 29 6893054 12147907   1295 0.45
Danish Jersey
Chemical bond Peak All associated wvn pVarA
Peak CHR LL UL Candidate gene(s)
 Alkanes 3_a 3 10619258 19193451 GBA 1449 0.57
5_a 5 69483211 76659850   1449 0.6
6_b 6 81119938 88592295 CSN-cluster 1449 2.25
11_b 11 101802657 106804258 PAEP 1449 0.48
12_b 12 67073994 78212571   1449 0.47
14 14 1463676 5601692 DGAT1 1449 2.1
16_a 16 37904090 46625869   1449 0.54
18_b 18 29414941 37188964   1449 0.41
19_a 19 31087581 36437188 SREBF1 1449 0.55
20_a 20 28803514 35940949 GHR, MRPS30 1449 0.67
21_b 21 53369113 61180711 PI 1449 0.4
25 25 1127441 5948405   1449 0.35
 C=O 3_b 3 31035370 37101347   1735, 1696 0.35
5_a 5 72082602 79640097   1735, 1696 0.42
6_a 6 41496235 46788536 PPARGC1A 1696 0.4
9_a 9 123525 5981648   1735, 1696 0.39
11_b 11 100858404 105845271 PAEP 1735, 1696 0.44
12_b 12 67073994 78212571   1735, 1696 0.54
14 14 1463676 5601692 DGAT1 1735, 1696 5.11
16_a 16 40846801 48806575   1696 0.36
19_a 19 32148966 37582865 SREBF1 1735, 1696 0.54
20_a 20 28803514 35940949 GHR, MRPS30 1735, 1696 0.6
21_b 21 52091583 59665710 PI 1696 0.39
22_a 22 162018 5884558   1735, 1696 0.37
 C-H 1_b 1 143831554 148893434 SLC37A1, AGPAT3 2988, 2872 0.62
5_a 5 70897603 77988054   2988, 2872 0.46
6_a 6 41496235 46788536 PPARGC1A 2988, 2872 0.47
8_a 8 50575791 55477297   2988, 2872 0.35
9_a 9 123525 5981648   2988, 2872 0.39
11_b 11 100858404 105845271 PAEP 2988, 2872 0.44
12_b 12 67073994 78212571   2988, 2872 0.63
14 14 1463676 5601692 DGAT1 2988, 2872 5.38
16_a 16 44176019 51011081   2988, 2872 0.37
17_c 17 66304866 71192864   2872 0.36
18_a 18 162653 6934625   2988, 2872 0.4
19_a 19 32148966 37582865 SREBF1 2988, 2872 0.62
20_a 20 28803514 35940949 GHR, MRPS30 2988, 2872 0.64
21_b 21 53369113 61180711 PI 2988, 2872 0.46
23 23 33645739 40993370 PRL 2988, 2872 0.37
24 24 31982958 37002274   2988, 2872 0.35
25 25 1127441 5948405   2988, 2872 0.38
27_b 27 32800374 38436906 AGPAT6 2988, 2872 0.37
29_b 29 40344120 45817015 FADS1 2988, 2872 0.35
 C-O 1_b 1 141807977 146940031 SLC37A1, AGPAT3 1226, 1183 0.71
2_a 2 1826336 8188132   1226, 1183, 1114, 1056, 979 0.41
3_a 3 15658202 24149985 GBA 1226, 1114, 979 0.38
4 4 116209319 120641946   1114 0.43
5_a 5 70897603 77988054   1226, 1183, 1114, 1056, 979 0.51
6_b 6 81119938 88592295 CSN-cluster 1226, 1183, 1114 0.88
7_a 7 244816 5027447   1226, 1183, 1114, 1056, 979 0.41
8_b 8 102776706 108556349   1226, 1183, 979 0.38
9_a 9 123525 5981648   1226, 1183, 1114, 1056, 979 0.37
9_b 9 23322608 29910981   1226, 1183, 1114, 979 0.37
10_a 10 26527257 32295516   1226, 1183, 1114, 979 0.37
11_b 11 100858404 105845271 PAEP 1226, 1183, 979 0.51
12_b 12 67073994 78212571   1226, 1183, 1114, 1056, 979 0.67
14 14 1463676 5601692 DGAT1 1226, 1183, 1114, 1056, 979 5.27
16_b 16 66365432 71735866   1226, 1183, 1114, 1056, 979 0.43
17_c 17 67193210 72005076   1226, 1183, 1114, 1056, 979 0.38
17_c 17 66304866 71192864   1226, 1183, 1114, 1056, 979 0.38
18_a 18 162653 6934625   1226, 1183, 1114, 1056, 979 0.41
18_b 18 32335701 38197798   1226, 1183, 1114, 979 0.41
19_a 19 31087581 36437188 SREBF1 1226, 1183, 1114, 979 0.68
19_b 19 48007453 53568928 GH, FASN, CCDC57 1056, 979 0.66
20_a 20 28803514 35940949 GHR, MRPS30 1226, 1183, 1114, 979 0.63
21_b 21 53369113 61180711 PI 1226, 1183, 1114, 1056, 979 0.46
22_b 22 47619247 54132903 LTF 1226, 1183, 1114, 1056, 979 0.43
25 25 47181 4952802   1226, 1183, 1114, 1056, 979 0.39
25 25 1127441 5948405   1226, 1183, 1114, 1056, 979 0.39
28_b 28 17171751 23666465   1226, 1114, 979 0.47
 CO-N 6_b 6 81119938 88592295 CSN-cluster 1500 1.04
10_b 10 49435552 54012929   1500 0.37
11_b 11 101802657 106804258 PAEP 1500 0.41
12_a 12 15817583 23340411   1500 0.39
14 14 1463676 5601692 DGAT1 1500 1.9
16_a 16 40846801 48806575   1500 0.44
17_a 17 42892776 47808938   1500 0.42
20_a 20 27422842 34474873 GHR, MRPS30 1500 0.36
21_a 21 38947 8955497 IGF1R 1500 0.35
23 23 28021047 35406968 PRL 1500 0.43
24 24 33000605 37958693   1500 0.35
29_b 29 40344120 45817015 FADS1 1500 0.49
 N-H 1_a 1 68997018 76331663   1604, 1557 0.4
2 2 108823285 114517270   1557 0.36
2 2 27374270 31731639   1604, 1557 0.36
3 3 10619258 19193451 GBA 1604, 1557 0.73
5_a 5 69483211 76659850   1604, 1557 0.65
6_b 6 81119938 88592295 CSN-cluster 1604, 1557 2.32
7_a 7 5955666 16564424   1604, 1557 0.36
7_b 7 73511189 78936990   1604, 1557 0.36
8_a 8 50575791 55477297   1604 0.35
9_a 9 123525 5981648   1604 0.38
10_b 10 48475000 52884624   1604 0.36
11_b 11 101802657 106804258 PAEP 1604, 1557 0.45
12_a 12 15817583 23340411   1604, 1557 0.44
13_b 13 74795835 79730805   1604, 1557 0.35
14 14 1463676 5601692 DGAT1 1604 4.89
16_a 16 37003329 44151335   1604, 1557 0.49
18_a 18 8061697 14038121   1604, 1557 0.49
19_a 19 31087581 36437188 SREBF1 1604, 1557 0.38
20_a 20 27422842 34474873 GHR, MRPS30 1604, 1557 0.52
20_b 20 55992767 60817895 ANKH 1604 0.49
22_a 22 162018 5884558   1604 0.36
23 23 28021047 35406968 PRL 1604, 1557 0.4
24 24 29942533 34992601   1604, 1557 0.36
29_b 29 40344120 45817015 FADS1 1604, 1557 0.41
 -OH 1_b 1 142832701 147841620 SLC37A1, AGPAT3 1299 0.39
5_b 5 87904220 94858411 MGST1 1299 0.38
6_b 6 81119938 88592295 CSN-cluster 1299 1.09
14 14 1463676 5601692 DGAT1 1299 0.52
16_a 16 40846801 48806575   1299 0.46
18_b 18 27578257 35583594   1299 0.36
19_b 19 49037959 54488129 FASN, CCDC57 1299 0.42
23 23 38521106 44428685   1299 0.36
27_a 27 20369666 25633356   1299 0.35
28_b 28 17171751 23666465   1299 0.39
  1. The table shows wavenumbers for which the peak SNP-group explained > 0.35% of total additive genetic variation, the upper-, and lower limit of the peak SNP-group, and candidate genes which have been previously associated to milk composition traits. Wavenumbers in boldface are those with the highest percentage total additive genetic variation explained by the peak SNP-group