Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Tiplady, Kathryn M.; Lopdell, Thomas J.; Reynolds, Edwardo; Sherlock, Richard G.; Keehan, Michael; Johnson, Thomas JJ.; Pryce, Jennie E.; Davis, Stephen R.; Spelman, Richard J.; Harris, Bevin L.; Garrick, Dorian J.; Littlejohn, Mathew D.

doi:10.1186/s12711-021-00648-9

Genetics Selection Evolution

Table 3 Peak variants for FT-MIR wavenumbers with co-localized eQTL

From: Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Chr	Position	Tag variant ID	Iter	Top wvn (cm⁻¹)	N of hits	P-value	Gene	Top eQTL variant ID	Top eQTL variant p-value	LD	Pearson	Pearson window (Mb)
1	5120248	rs42317521	2	2794	55	4.0e−18	CLDN8	rs42317521	4.3e−17	1	0.764	0.5
1	144377960	rs208161466	0	2592	22	2.3e−85	SLC37A1	rs208161466	4.1e−15	1	0.710	1.0
1	146481250	rs383691757	1	1071	1	4.7e−15	CSTB	rs210595016	1.4e−52	0.992	0.938	0.5
1	154125158	rs207836083	0	1130	142	3.6e−68	SH3BP5	rs207836083	2.6e−32	1	0.816	0.5
3	15411459	rs134900385	1	1022	6	4.3e−19	KRTCAP2	rs133285846	9.7e−09	0.996	0.938	1.0
3	15550598	rs380597285	0	1462	325	1.3e−54	SLC50A1	rs380597285	8.7e−16	1	0.854	0.5
3	34387618	rs109030498	1	1466	157	3.5e−25	ELAPOR1	rs109030498	3.2e−30	1	0.817	0.5
3	53755929	rs209271975	1	1089	15	8.6e−22	LRRC8C	rs466686834	3.5e−39	0.99	0.927	0.5
5	75729880	rs384734208	1	1466	44	5.0e−47	CSF2RB	rs210641868	9.2e−27	0.926	0.752	1.0
5	75732526	rs210305241	1	1458	5	4.4e−42	NCF4	rs209273109	9.3e−16	0.91	0.813	1.0
5	93945738	rs211210569	0	1171	544	1.8e−131	MGST1	rs209372883	3.2e−43	0.919	0.925	1.0
6	46568418	rs210515595	3	1772	5	7.7e−22	SLC34A2	rs110805476	2.5e−07	0.979	0.805	0.5
6	87388064	rs379473589	1	1436	17	1.1e−97	CSN3	rs208009847	9.9e−33	0.963	0.878	0.5
9	21637056	rs209222932	0	1003	33	9.4e−20	YRMY5A	rs209222932	2.8e−36	1	0.634	0.5
9	26534109	rs208123385	0	1462	36	1.9e−24	RNF217	rs208173647	1.3e−16	0.986	0.856	0.5
9	87585031	rs110986237	1	1470	6	7.4e−15	TAB2	rs110986237	9.5e−12	1	0.851	0.5
9	102874726	rs137238900	0	1768	1	1.0e−14	MPC1	rs134094426	6.9e−15	0.969	0.849	0.5
10	46581015	rs109326466	0	1246	15	2.0e−46	USP3	rs109326466	2.0e−31	1	0.961	0.5
11	14180010	rs110527112	1	2760	23	3.6e−29	XDH	rs207554031	8.8e−26	0.978	0.709	0.5
11	78868975		1	1112	10	1.2e−19	LAPTM4A	rs110552157	1.3e−40	0.998	0.920	0.5
11	103292402	rs383398415	0	2548	1	3.5e−56	PAEP	rs109333988	1.2e−29	0.933	0.956	0.5
11	104229609	rs110534892	0	3648	10	1.2e−21	ABO	rs109750996	3.9e−28	0.944	0.803	0.5
14	1754287	rs135443540	0	1085	3	1.6e−39	DGAT1	rs137202508	8.9e−42	0.905	0.944	0.5
15	57266467	rs136337092	0	3935	1	2.7e−13	CAPN5	rs136208815	9.3e−46	0.997	0.940	0.5
16	66314547	rs42579412	2	1425	1	1.0e−15	RGL1	rs42579412	6.3e−14	1	0.727	0.5
16	67730371	rs380453838	1	1757	125	3.8e−21	IVNS1ABP	rs380453838	4.5e−27	1	0.876	0.5
18	2203322	rs132899112	1	1466	7	1.4e−15	FA2H	rs137235970	1.9e−27	0.998	0.875	0.5
19	33517487	rs434248431	0	1100	23	2.9e−46	PMP22	rs434248431	8.6e−38	1	0.832	0.5
19	43036265	rs210324533	1	1029	11	5.3e−43	GHDC	rs381442991	1.8e−22	0.945	0.975	0.5
19	57079881	rs381175117	2	1220	9	2.0e−23	HID1	rs109407913	1.2e−32	0.936	0.803	0.5
19	61134515	rs41923843	0	1130	45	3.2e−46	KCNJ2	rs41923843	1.7e−26	1	0.882	0.5
20	58454531	rs135636613	0	1391	23	4.3e−441	ANKH	rs135636613	2.4e−16	1	0.860	0.5
22	53519865	rs109233889	0	1235	7	5.3e−15	LTF	rs109233889	1.3e−32	1	0.813	0.5
24	58817202	rs208779762	0	1220	23	6.8e−34	LMAN1	rs207893260	1.3e−27	0.958	0.713	1.0
27	36211708	rs209855549	0	1731	157	6.2e−188	GPAT4	rs209855549	3.7e−21	1	0.848	0.5
27	41267242	rs109068627	1	2977	23	3.5e−26	THRB	rs109068627	1.7e−22	1	0.704	0.5
29	9546217	rs380868305	0	1130	8	4.6e−186	PICALM	rs380868305	2.4e−54	1	0.831	0.5
29	44579245	rs439384463	2	1548	3	4.3e−16	MUS81		3.0e−21	0.924	0.913	0.5

Peak variants for FT-MIR wavenumbers with a co-localized eQTL. Co-localized eQTL are defined such that: the Pearson correlation between the –log₁₀(p-values) of the trait QTL and the –log₁₀(p-values) of the eQTL is higher than 0.7; and the LD between the tag variant for the trait QTL and the top eQTL variant is higher than 0.9. The Pearson correlation shown is the highest from two different size windows (0.5 Mbp and 1 Mbp), centred on the top tag variant. Iterations are defined relative to the base GWAS, with the base GWAS represented as iteration 0. N of hits: number of wavenumbers for which the variant was selected as the representative (most significant) tag variant for a peak

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ISSN: 1297-9686

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