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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]
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]
CCND2 (4) Stature [78]
5: 9.30-9.56 0.00039 SMC PPP1R12A (1) Reproduction [109]
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]
RFI [72]
26: 22.21-23.02 0.00021 SHF ELOVL3 (1) Milk content [127]
NFKB2 (8) Milk content [128]
  1. q-value: q-value of the most significant SNP within the significant genomic region
  2. Breed: breed names are shown in abbreviated form (full names are in Table 1)
  3. Candidate genes: candidate genes within significant genomic regions
  4. RFI Residual feed intake
  5. The full list of genes is in Additional file 2
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Genetics Selection Evolution

ISSN: 1297-9686