Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

Ghoreishifar, Seyed Mohammad; Eriksson, Susanne; Johansson, Anna M.; Khansefid, Majid; Moghaddaszadeh-Ahrabi, Sima; Parna, Nahid; Davoudi, Pourya; Javanmard, Arash

doi:10.1186/s12711-020-00571-5

Genetics Selection Evolution

Table 3 Genomic autosomal regions detected (through the DCMS analyses) as being under putative selection in Swedish native and commercial cattle breeds

From: Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

Region (Mb)	Q-value	Breed	Candidate gene (rank)	Trait	Citation
1: 1.58-2.39	0.00274	FNC	EVA1C (1), C1H21orf59 (2), SYNJ1 (3), PAXBP1 (4), C1H21orf62 (5), OLIG1 (6), LOC526226 (7), IFNAR2 (8)	Polled phenotype	[105]
1: 2.25-2.52	4.9E − 08	SMC	URB1 (1), EVA1C (2), MRAP (3), MIS18A (4)	Polled phenotype	[105]
1: 1.14-1.33	0.00289	SRP	CRYZL1 (5), DONSON (4), SON (3), GART (2), DNAJC28 (10)	Polled phenotype	[105]
1: 1.52-2.51	1.2E − 05	SRP	IL10RB (12), IFNAR2 (11), LOC526226 (10), OLIG1 (9), C1H21orf62 (8), PAXBP1 (7), SYNJ1 (6), C1H21orf59 (5), EVA1C (2), URB1 (1), NSBTAG00000023718 (3), MIS18A (4)	Polled phenotype	[105]
2: 71.46-71.66	0.00633	SRP	TMEM37 (1)	Disease resistance	[94]
3: 32.06-32.34	0.00325	SRC	CHIA (2), CHI3L2 (4)	Bacterial infection	[96, 97]
3: 9.23-9.72	0.00933	SRC	DCAF8 (1)	Altitude adaptation	[88]
3: 9.57-9.58	0.00933	SRC	PEA15 (2)	RFI	[77]
3: 54.20-54.22	6.8E − 05	SHF	GBP6 (4)	Bacterial infection	[103]
3: 54.34-54.36	6.87E − 05	SHF	GBP2 (3)	RFI	[77]
3: 54.64-54.68	6.8E − 05	SHF	GBP4 (11)	Stature	[106]
3: 54.25-54.26	6.8E − 05	SHF	GBP5 (2)	RFI	[77]
4: 77.43-77.70	0.00202	SHF	NPC1L1 (5), NUDCD3 (6)	Milk yield	[107]
5: 105.75-106.52	2.60e-13	FNC	KCNA6 (13), NDUFA9 (11), AKAP3 (10), C5H12orf4 (7), RAD51AP1 (6), FGF6 (2), TIGAR (3), CCND2 (4)	Body weight	[76, 77]
5: 105.75-106.52	2.60e-13	FNC	CCND2 (4)	Stature	[78]
5: 82.49-82.73	2.37e-09	FNC	PPFIBP1 (2), REP15 (3)	Bacterial infection	[99, 108]
5: 106.15-106.32	2.4E − 05	SHF	FGF6 (2), TIGAR (3), CCND2 (4)	Body weight	[76]
5: 106.15-106.32	2.4E − 05	SHF	CCND2 (4)	Stature	[78]
5: 9.30-9.56	0.00039	SMC	PPP1R12A (1)	Reproduction	[109]
5: 9.30-9.56	0.00039	SMC	PPP1R12A (1)	Altitude adaptation	[85, 86]
5: 24.92-25.02	8.17E − 05	SRC	FGD6 (3)	RFI	[77]
6: 37.06-37.27	5.7E − 06	SHF	TIGD2 (2)	Bacterial infection	[110]
6: 37.64-37.72	0.01986	SHF	PYURF (1)	Bacterial infection	[110]
7: 8.40-8.48	0.00159	SMC	CYP4F2 (1)	Disease resistance	[93, 94]
8: 76.23-76.78	0.00022	SMC	AQP3 (5), AQP7 (5)	Acclimation	[89]
11: 25.57-25.83	0.00433	SHF	ZFP36L2 (1)	Reproduction	[111]
12: 83.19-83.37	0.00082	SMC	SLC10A2 (1)	Bacterial infection	[95]
13: 40.38-42.28	0.00985	SRC	FOXA2 (6)	Growth traits	[63]
13: 43.40-43.42	0.00474	SRC	ASB13 (9)	RFI	[77]
13: 42.73-44.04	0.00474	SRC	ACSS1 (7)	Milk content	[112, 113]
14: 53.71-54.81	0.00068	FNC	CSMD3 (1)	Body length	[80]
14: 24.42-25.11	2.2E − 10	SHF	TMEM68 (2), TGS1 (1), LYN (3)	Growth traits	[114]
14: 24.42-25.11	2.2E − 10	SHF	TGS1 (1), LYN (3), RPS20 (4), MOS (5), PLAG1 (6), CHCHD7 (7)	Pleiotropic	[44, 48, 50, 56, 114]
14: 25.35-25.73	2.2E − 10	SHF	IMPAD1 (1)	Pleiotropic	[51, 64, 66]
14: 26.01-26.24	0.00031	SHF	FAM110B (1)	Pleiotropic	[64]
14: 24.00-24.89	2.8E − 06	SRC	XKR4 (1), TMEM68 (2)	Growth, feed intake	[114]
14: 25.50-25.58	0.00624	SRC	IMPAD1 (1)	Pleiotropic	[64, 115]
14: 33.02-33.41	0.00513	SRC	CSPP1 (1)	Reproduction	[116]
14: 33.02-33.41	0.00513	SRC	COPS5 (2)	Feed intake	[117]
14: 32.10-32.63	0.00137	SRC	CRH (1)	Growth	[60]
15: 53.10-54.25	5.6E − 05	FNC	FCHSD2 (1)	Milk fat content	[70]
15: 53.10-54.25	5.6E − 05	FNC	FCHSD2 (1), ARHGEF17 (5), RELT (6)	Bacterial infection	[92]
			UCP2 (13)	Hypoxia	[118]
			UCP2 (13), UCP3 (14)	Milk fat content, carcass quality	[71,72,73, 119]
15: 53.13-53.80	0.00073	SMC	FCHSD2 (1)	Milk fat content	[70]
15: 53.13-53.80	0.00073	SMC	FCHSD2 (1), ARHGEF17 (4), RELT (5)	Bacterial infection	[92]
15: 53.52-53.67	0.00178	SRC	ARHGEF17 (1), RELT (2)	Bacterial infection	[92]
15: 78.33-78.51	0.02265	SRP	SLC39A13 (1)	Stature	[120, 121]
16: 55.09-55.15	0.00963	SRC	PRDM2 (1)	Bacterial infection	[77, 99]
			PRDM2 (1), KDM5B (2)	Bacterial infection	[98, 99]
			PRDM2 (1)	RFI	[77]
16: 44.96-45.25	0.00299	SRP	SPSB1 (1)	Immune regulation	[100, 101]
17: 57.91-58.43	0.00011	SRC	HSPB8 (1)	Heat and cold stress	[122, 123]
19: 51.21-51.30	0.01373	SMC	SLC16A3 (1)	Altitude adaptation	[88]
19: 35.10-35.14	0.00442	SHF	GID4 (1), ATPAF2 (2)	Milk protein	[124]
20: 71.49-71.80	0.00272	SHF	CEP72 (3), SLC9A3 (2)	Feed efficiency	[125]
20: 71.65-71.80	0.00498	SRP	SLC9A3 (2), EXOC3 (3)	Feed efficiency	[125]
24: 49.90-49.94	0.00205	FNC	ACAA2 (1)	Milk content	[126]
24: 49.90-49.94	0.00205	FNC	ACAA2 (1)	RFI	[72]
26: 22.21-23.02	0.00021	SHF	ELOVL3 (1)	Milk content	[127]
26: 22.21-23.02	0.00021	SHF	NFKB2 (8)	Milk content	[128]

q-value: q-value of the most significant SNP within the significant genomic region
Breed: breed names are shown in abbreviated form (full names are in Table 1)
Candidate genes: candidate genes within significant genomic regions
RFI Residual feed intake
The full list of genes is in Additional file 2

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ISSN: 1297-9686

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