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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 bondPeak regionAll associated wvnpVarA
PeakCHRLLULCandidate genes
 Alkanes6_b68039442288006286CSN-cluster14490.54
11_a116924087175495975 14490.4
13_a135320547058871642 14490.37
141414636765428037DGAT114492.04
19_a193214896637552530SREBF114490.39
29_a29689305412147907 14490.48
 C=O5_b59111869298515360MGST11735, 16960.43
141414636765428037DGAT11735, 16969.76
17_a171254533118398611 17350.39
 C-H5_b59111869298515360MGST12988, 28720.39
141414636765428037DGAT12988, 28727.88
17_a171254533118398611 29880.36
20_b205672139461566803ANKH29880.36
21_a21624105211219294IGF1R29880.36
 C-O3_c34970483458434544 1226, 1114, 10600.42
5_b59111869298515360MGST11226, 1180, 9750.47
11_a116924087175495975 1226, 11140.43
141414636765428037DGAT11226, 1180, 1114, 1060, 9758.55
17_a171254533118398611 11800.37
19_c195759289762235799 1226, 1114, 10600.52
21_a21624105211219294IGF1R1226, 1114, 10600.35
21_c216253038467845758 9750.35
2525471814689960 1226, 1180, 1114, 1060, 9750.37
28_a2823137537557315 1226, 1180, 1114, 1060, 9750.39
29_a29689305412147907 1226, 1114, 10600.54
 CO-N5_b594381154101721892MGST115000.36
6_b68681963392465869CSN-cluster15000.35
141414636765428037DGAT115005.19
 N-H5_b59111869298515360MGST116040.5
6_b68039442288006286CSN-cluster15570.55
141414636765428037DGAT11604, 15579.73
17_a171254533118398611 16040.37
20_b205444353159156949ANKH1604, 15570.53
 -OH141414636765428037DGAT112951.12
19_c195831812163354178 12950.38
20_b205672139461566803ANKH12950.4
21_a21624105211219294IGF1R12950.36
29_a29689305412147907 12950.45
Danish Jersey
Chemical bondPeakAll associated wvnpVarA
PeakCHRLLULCandidate gene(s)
 Alkanes3_a31061925819193451GBA14490.57
5_a56948321176659850 14490.6
6_b68111993888592295CSN-cluster14492.25
11_b11101802657106804258PAEP14490.48
12_b126707399478212571 14490.47
141414636765601692DGAT114492.1
16_a163790409046625869 14490.54
18_b182941494137188964 14490.41
19_a193108758136437188SREBF114490.55
20_a202880351435940949GHR, MRPS3014490.67
21_b215336911361180711PI14490.4
252511274415948405 14490.35
 C=O3_b33103537037101347 1735, 16960.35
5_a57208260279640097 1735, 16960.42
6_a64149623546788536PPARGC1A16960.4
9_a91235255981648 1735, 16960.39
11_b11100858404105845271PAEP1735, 16960.44
12_b126707399478212571 1735, 16960.54
141414636765601692DGAT11735, 16965.11
16_a164084680148806575 16960.36
19_a193214896637582865SREBF11735, 16960.54
20_a202880351435940949GHR, MRPS301735, 16960.6
21_b215209158359665710PI16960.39
22_a221620185884558 1735, 16960.37
 C-H1_b1143831554148893434SLC37A1, AGPAT32988, 28720.62
5_a57089760377988054 2988, 28720.46
6_a64149623546788536PPARGC1A2988, 28720.47
8_a85057579155477297 2988, 28720.35
9_a91235255981648 2988, 28720.39
11_b11100858404105845271PAEP2988, 28720.44
12_b126707399478212571 2988, 28720.63
141414636765601692DGAT12988, 28725.38
16_a164417601951011081 2988, 28720.37
17_c176630486671192864 28720.36
18_a181626536934625 2988, 28720.4
19_a193214896637582865SREBF12988, 28720.62
20_a202880351435940949GHR, MRPS302988, 28720.64
21_b215336911361180711PI2988, 28720.46
23233364573940993370PRL2988, 28720.37
24243198295837002274 2988, 28720.35
252511274415948405 2988, 28720.38
27_b273280037438436906AGPAT62988, 28720.37
29_b294034412045817015FADS12988, 28720.35
 C-O1_b1141807977146940031SLC37A1, AGPAT31226, 11830.71
2_a218263368188132 1226, 1183, 1114, 1056, 9790.41
3_a31565820224149985GBA1226, 1114, 9790.38
44116209319120641946 11140.43
5_a57089760377988054 1226, 1183, 1114, 1056, 9790.51
6_b68111993888592295CSN-cluster1226, 1183, 11140.88
7_a72448165027447 1226, 1183, 1114, 1056, 9790.41
8_b8102776706108556349 1226, 1183, 9790.38
9_a91235255981648 1226, 1183, 1114, 1056, 9790.37
9_b92332260829910981 1226, 1183, 1114, 9790.37
10_a102652725732295516 1226, 1183, 1114, 9790.37
11_b11100858404105845271PAEP1226, 1183, 9790.51
12_b126707399478212571 1226, 1183, 1114, 1056, 9790.67
141414636765601692DGAT11226, 1183, 1114, 1056, 9795.27
16_b166636543271735866 1226, 1183, 1114, 1056, 9790.43
17_c176719321072005076 1226, 1183, 1114, 1056, 9790.38
17_c176630486671192864 1226, 1183, 1114, 1056, 9790.38
18_a181626536934625 1226, 1183, 1114, 1056, 9790.41
18_b183233570138197798 1226, 1183, 1114, 9790.41
19_a193108758136437188SREBF11226, 1183, 1114, 9790.68
19_b194800745353568928GH, FASN, CCDC571056, 9790.66
20_a202880351435940949GHR, MRPS301226, 1183, 1114, 9790.63
21_b215336911361180711PI1226, 1183, 1114, 1056, 9790.46
22_b224761924754132903LTF1226, 1183, 1114, 1056, 9790.43
2525471814952802 1226, 1183, 1114, 1056, 9790.39
252511274415948405 1226, 1183, 1114, 1056, 9790.39
28_b281717175123666465 1226, 1114, 9790.47
 CO-N6_b68111993888592295CSN-cluster15001.04
10_b104943555254012929 15000.37
11_b11101802657106804258PAEP15000.41
12_a121581758323340411 15000.39
141414636765601692DGAT115001.9
16_a164084680148806575 15000.44
17_a174289277647808938 15000.42
20_a202742284234474873GHR, MRPS3015000.36
21_a21389478955497IGF1R15000.35
23232802104735406968PRL15000.43
24243300060537958693 15000.35
29_b294034412045817015FADS115000.49
 N-H1_a16899701876331663 1604, 15570.4
22108823285114517270 15570.36
222737427031731639 1604, 15570.36
331061925819193451GBA1604, 15570.73
5_a56948321176659850 1604, 15570.65
6_b68111993888592295CSN-cluster1604, 15572.32
7_a7595566616564424 1604, 15570.36
7_b77351118978936990 1604, 15570.36
8_a85057579155477297 16040.35
9_a91235255981648 16040.38
10_b104847500052884624 16040.36
11_b11101802657106804258PAEP1604, 15570.45
12_a121581758323340411 1604, 15570.44
13_b137479583579730805 1604, 15570.35
141414636765601692DGAT116044.89
16_a163700332944151335 1604, 15570.49
18_a18806169714038121 1604, 15570.49
19_a193108758136437188SREBF11604, 15570.38
20_a202742284234474873GHR, MRPS301604, 15570.52
20_b205599276760817895ANKH16040.49
22_a221620185884558 16040.36
23232802104735406968PRL1604, 15570.4
24242994253334992601 1604, 15570.36
29_b294034412045817015FADS11604, 15570.41
 -OH1_b1142832701147841620SLC37A1, AGPAT312990.39
5_b58790422094858411MGST112990.38
6_b68111993888592295CSN-cluster12991.09
141414636765601692DGAT112990.52
16_a164084680148806575 12990.46
18_b182757825735583594 12990.36
19_b194903795954488129FASN, CCDC5712990.42
23233852110644428685 12990.36
27_a272036966625633356 12990.35
28_b281717175123666465 12990.39
  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