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 4 Peak variants for composite milk production traits with co-localized eQTL

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

Trait	Chr	Position	Tag variant ID	Iteration	P-value	Gene	Top eQTL variant ID	Top eQTL variant p-value	LD	Pearson	Pearson window (Mbp)
FP	3	34387618	rs109030498	2	6.0e−13	ELAPOR1	rs109030498	3.2e−30	1	0.832	0.5
FP	5	75698283	rs385866519	1	4.0e−19	CSF2RB	rs210641868	9.2e−27	0.910	0.701	1
FP	5	93945738	rs211210569	0	6.7e−106	MGST1	rs209372883	3.2e−43	0.919	0.928	1
FP	10	46483019	rs133089336	0	4.5e−13	USP3	rs208181306	2.0e−31	0.909	0.905	0.5
FP	11	104229609	rs110534892	1	2.6e−14	ABO	rs109750996	3.9e−28	0.944	0.727	1
FP	16	67730371	rs380453838	1	2.6e−19	IVNS1ABP	rs380453838	4.5e−27	1	0.886	0.5
FP	27	36211708	rs209855549	0	9.7e−132	GPAT4	rs209855549	3.7e−21	1	0.819	0.5
LP	1	154122887	rs42167460	0	1.2e−50	SH3BP5	rs380642859	2.6e−32	0.999	0.859	0.5
LP	3	15433518	rs109749506	1	1.3e−20	KRTCAP2	rs133285846	9.7e−09	0.995	0.940	1
LP	3	15545091	rs379353107	0	2.2e−42	SLC50A1	rs379353107	8.7e−16	1	0.806	0.5
LP	3	53994057	rs211488591	2	6.7e−18	LRRC8C	rs466686834	3.5e−39	0.986	0.753	1
LP	19	43036265	rs210324533	3	9.4e−40	GHDC	rs381442991	1.8e−22	0.945	0.963	0.5
LP	19	61134515	rs41923843	1	1.1e−46	KCNJ2	rs41923843	1.7e−26	1	0.857	0.5
LP	20	58448763	rs134813825	0	3.2e−18	ANKH	rs134813825	2.4e−16	1	0.809	0.5
LP	27	36204066	rs208306200	0	1.9e−21	GPAT4	rs208306200	3.7e−21	1	0.767	0.5
LP	29	9577372	rs380473328	0	2.1e−140	PICALM	rs384691767	2.4e−54	0.996	0.845	0.5
PP	3	15520971	rs109098377	2	7.5e−16	KRTCAP2	rs133285846	9.7e−09	0.989	0.928	0.5
PP	3	15550598	rs380597285	0	1.7e−37	SLC50A1	rs380597285	8.7e−16	1	0.832	0.5
PP	5	75680825	rs208925020	4	8.5e−23	CSF2RB	rs210641868	9.2e−27	0.947	0.871	1
PP	5	93945738	rs211210569	1	3.7e−42	MGST1	rs209372883	3.2e−43	0.919	0.817	0.5
PP	6	87387870	rs382652853	2	2.9e−45	CSN3	rs208009847	9.9e−33	0.963	0.891	0.5
PP	10	46581015	rs109326466	0	4.0e−38	USP3	rs109326466	2.0e−31	1	0.961	0.5
PP	18	2203,325	rs135350753	0	2.1e−13	FA2H	rs137235970	1.9e−27	0.997	0.831	0.5
PP	19	43035006	rs209494359	0	1.6e−40	GHDC	rs381442991	1.8e−22	0.945	0.976	0.5
PP	24	58817202	rs208779762	0	5.7e−26	LMAN1	rs207893260	1.3e−27	0.958	0.737	0.5

Peak variants for composite milk production traits 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. FP Fat %, LP Lactose %, PP Protein %

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ISSN: 1297-9686

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