Host genetic control on rumen microbiota and its impact on dairy traits in sheep

Martinez Boggio, Guillermo; Meynadier, Annabelle; Buitenhuis, Albert Johannes; Marie-Etancelin, Christel

doi:10.1186/s12711-022-00769-9

Genetics Selection Evolution

Table 5 Significant SNPs from the genome-wide association studies of the rumen bacteria on chromosomes that colocalized with dairy traits

From: Host genetic control on rumen microbiota and its impact on dairy traits in sheep

Genus	OTU name	SNP name	OAR	Position (bp)	Var (%)	− log₁₀ (P value)	Gene name
Lachnospiraceae_NK4A136_group	OTU2186	rs422351583	3	5,668,047	0.13	6.09
[Eubacterium]_coprostanoligenes_group /uG	OTU2438	rs420593841	3	8,693,890	0.05	5.37	GARNL3
[Eubacterium]_ventriosum_group	OTU355	rs415665472	3	27,430,018	0.14	5.95
Prevotella	OTU196	rs399829503	3	38,048,434	0.09	5.09	TIA1
Clostridia UCG-014/uF/uG	OTU2515	rs417512713	3	82,810,037	0.14	5.79
Prevotella	OTU196	rs407226710	3	87,932,154	0.37	5.07
Prevotellaceae_UCG-001	OTU906	rs419358934^a	3	89,802,120	0.33	6.24
Prevotella	OTU196	rs419358934^a	3	89,802,120	0.18	5.32
Prevotella	OTU196	rs430243701	3	89,808,523	0.14	6.78
Prevotellaceae_UCG-001	OTU906	rs424849255	3	99,246,368	0.09	5.25	IL18R1
Prevotellaceae_UCG-001	OTU906	rs404566475	3	112,090,102	0.23	5.92
Syntrophococcus	OTU509	rs409660427	3	138,657,389	0.14	5.27	ENDOU
Prevotella	OTU427	rs402872469	3	221,603,160	0.16	5.40
Possible_genus_Sk018	OTU1631	rs402307868^a	5	31,467,389	0.03	5.76
Prevotella	OTU1843	rs402307868^a	5	31,467,389	0.11	5.11
Prevotella	OTU1843	rs413547561	5	31,477,570	0.10	5.99
Fibrobacter	OTU1335	rs405557393	5	59,933,921	0.06	6.10	ANXA6
Rikenellaceae_RC9_gut_group	OTU546	rs410315179	5	72,275,014	0.38	6.75
Rikenellaceae_RC9_gut_group	OTU546	rs429334236	5	72,324,510	0.24	5.81
Fibrobacter	OTU1335	rs398177414	5	79,732,944	0.18	6.56
Ruminococcus	OTU1191	rs411645323	5	83,683,348	0.20	5.30
Ruminococcus	OTU1191	rs418870684	5	83,724,689	0.12	5.29	ENSOARG00000025325
Lachnospiraceae_UCG-008	OTU655	rs403619685	6	28,689,782	0.08	5.92
Lachnospiraceae_XPB1014_group	OTU947	rs400970883	6	36,655,091	0.05	6.20	SPP1
Prevotella	OTU1843	rs416815759	6	45,906,622	1.43	5.59	TBC1D19
Prevotella	OTU440	rs406261149	6	50,058,344	0.20	5.30
Acetitomaculum	OTU612	rs430647780	6	75,425,021	0.20	5.58
Acetitomaculum	OTU612	rs415319007	6	85,637,777	0.29	5.51
Prevotella	OTU399	rs428296445	10	16,139,981	0.33	5.57	W5PCY9_SHEEP
Clostridia UCG-014/uF/uG	OTU1386	rs423990418	10	16,216,118	0.21	6.28	W5PCZ6_SHEEP
Clostridia UCG-014/uF/uG	OTU1386	rs404163943	10	16,222,665	0.10	6.28	W5PCZ6_SHEEP
Prevotella	OTU13	rs408448649	10	46,573,078	0.25	5.58	DACH1
Muribaculaceae/uG	OTU803	rs403822645	10	80,687,261	0.08	4.87	ENSOARG00000026327
Ruminococcaceae/uG	OTU155	rs408532009	10	84,678,999	0.35	6.41	ANKRD10
Ruminococcaceae/uG	OTU501	rs422890024	11	7,826,874	0.04	5.40	MSI2
Christensenellaceae_R-7_group	OTU596	rs414408260	11	58,151,039	0.14	5.63
CAG-352	OTU304	rs421085019	11	61,946,606	0.23	5.48
CAG-352	OTU304	rs429659626	11	62,034,261	0.04	5.48	HELZ
Prevotella	OTU943	rs412819070	15	5,606,060	0.13	5.71	MMP20
Prevotella	OTU423	rs409362751^a	15	37,553,506	0.18	6.97	PDE3B
Prevotella	OTU80	rs409362751^a	15	37,553,506	0.16	5.84	PDE3B
Prevotella	OTU399	rs409362751^a	15	37,553,506	0.19	5.52	PDE3B
Prevotella	OTU399	rs426932216	15	44,445,054	0.14	5.13	LOC101105776
Blautia	OTU1025	rs425070593	15	80,043,367	0.20	5.34	TCN1
F082/uG	OTU167	rs412496804^a	26	28,316,180	0.31	6.06
Prevotella	OTU1336	rs412496804^a	26	28,316,180	0.20	5.98
Prevotellaceae_UCG-001	OTU906	rs412496804^a	26	28,316,180	0.20	5.20

SNPs that are in a quantitative trait locus region are in bold characters
OAR Ovis aries chromosome, Var (%) phenotypic variance explained for a window of 20 adjacent SNPs, uF unknown family, uG unknown genus
^aSNP shared between different OTU

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ISSN: 1297-9686

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