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

Zaalberg, R. M.; Janss, L.; Buitenhuis, A. J.

doi:10.1186/s12863-020-0810-4

BMC Genomic Data

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
Chemical bond	Peak	CHR	LL	UL	Candidate genes	All associated wvn	pVarA
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
Chemical bond	Peak	CHR	LL	UL	Candidate gene(s)	All associated wvn	pVarA
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

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

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