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. 2017 Aug 16;7:8487. doi: 10.1038/s41598-017-09170-9

Table 2.

The SNPs associated with female fertility traits detected by validating candidate SNPs from Chinese Holsteins using Nordic Holstein data.

BTA Position1(bp) SNP Trait2 MAF3 Chinese Holsteins MAF3 Nordic Holsteins Genes5
P-value Effect size4(%) P-value Effect size4(%)
3 16,179,998 rs109155222 IFLc 0.40 4.33E-03 1.75 0.43 3.41E-05 0.30 IL6R
3 25,763,148 rs110094798 IFLc 0.24 3.30E-03 1.95 0.20 3.12E-05 0.35 FAM46C, MAN1A2
3 26,949,196 rs109368837 IFLc 0.22 2.78E-03 2.09 0.20 7.67E-05 0.31 CD58, ATP1A1
3 66,768,945 rs42361598 IFLc 0.42 3.94E-03 1.69 0.44 4.85E-05 0.31 PTGFR, GIPC2
4 47,737,653 rs110127380 CRh 0.47 4.40E-03 3.69 0.41 7.90E-05 0.37 NAMPT, PIK3CG
4 67,145,895 rs41589544 ICF 0.07 1.51E-04 0.85 0.12 5.19E-05 0.21 CHN2
6 87,600,892 rs109377247 IFLc 0.33 6.51E-04 2.31 0.33 8.67E-06 0.35 ENSBTAG00000007816, AMTN
10 29,538,245 rs42563243 ICF 0.44 2.62E-03 0.65 0.38 4.01E-05 0.32 ENSBTAG00000021414 ENSBTAG00000025634
10 83,435,322 rs43642952 CRc 0.16 3.07E-03 1.56 0.18 1.41E-05 0.29 ENSBTAG00000005395, ENSBTAG00000025385
11 83,938,054 rs29026760 ICF 0.26 3.70E-03 0.62 0.28 5.08E-05 0.28 FAM84A, ENSBTAG00000019284
11 85,906,433 rs110195627 ICF 0.23 2.90E-03 0.66 0.26 1.35E-05 0.31 TRIB2, LPIN1
13 30,713,329 rs109193608 IFLc 0.35 2.68E-03 1.89 0.42 7.55E-06 0.33 FAM188A, PTER
13 31,364,982 rs110068451 ICF, IFLc 0.34 3.44E-03, 9.21E-04 0.58, 2.18 0.41 6.70E-11, 1.33E-06 0.69, 1.12 RSU1
13 31,416,451 rs109492780 IFLc 0.38 5.90E-04 2.53 0.43 8.11E-09 0.56 RSU1
13 31,524,626 rs41604666 IFLc 0.49 4.41E-04 2.64 0.48 4.37E-07 0.46 RSU1
13 32,802,426 rs41609782 IFLc 0.40 3.26E-03 1.82 0.41 1.69E-05 0.31 SLC39 A12, CACNB2
13 32,831,454 rs109983109 ICF, IFLc 0.41 8.03E-04, 3.11E-03 0.81, 1.86 0.45 6.64E-10, 4.95E-06 0.66, 0.34 SLC39A12, CACNB2
13 33,501,056 rs109621404 IFLc 0.46 3.90E-03 1.95 0.40 1.65E-08 0.60 EPC1
13 52,447,531 rs109573317 CRc 0.35 4.58E-03 1.37 0.30 4.07E-05 0.29 SLC4A11
15 27,235,378 rs110869861 ICF 0.27 4.94E-03 0.50 0.23 9.02E-06 0.42 CADM1, BUD13
16 53,070,045 rs41580862 ICF 0.27 4.14E-04 0.84 0.26 8.50E-05 0.30 SLC25A34
16 53,097,936 rs110199510 ICF 0.27 5.89E-04 0.79 0.26 8.50E-05 0.30 PLEKHM2
16 57,419,757 rs41581444 ICF 0.31 5.01E-04 0.87 0.36 3.89E-05 0.30 ENSBTAG00000027809, GPR52
17 67,245,920 rs41848120 CRh 0.48 1.28E-04 7.32 0.46 3.87E-05 0.41 PIWIL3
17 72,448,619 rs41634418 ICF 0.35 3.57E-03 0.59 0.34 5.79E-06 0.40 PISD
18 48,150,900 rs110543856 ICF, IFLc 0.15 2.60E-03, 2.99E-04 0.65, 2.80 0.13 5.84E-08, 3.96E-07 0.61, 0.50 SIPA1L3
21 41,383,298 rs29012716 ICF 0.16 4.96E-04 0.81 0.12 5.23E-05 0.40 PRKD1, G2E3
21 47,273,394 rs110964123 ICF 0.40 2.13E-03 0.63 0.38 7.52E-05 0.30 NKX2-8, PAX9
23 50,036,208 rs110076231 CRc 0.38 1.27E-03 1.95 0.45 1.31E-04 0.25 PRPF4B, PXDC1
23 51,938,161 rs29027634 IFLc, CRc 0.36 3.25E-03, 4.73E-03 1.84, 1.45 0.37 8.89E-05,1.26E-04 0.27, 0.26 EXOC2
24 30,468,614 rs109722348 ICF 0.39 2.98E-03 0.66 0.38 6.27E-05 0.31 AQP4, KCTD1
24 30,513,490 rs110839120 ICF 0.39 2.65E-03 0.68 0.38 1.07E-04 0.28 AQP4, KCTD1
24 33,624,891 rs109629413 ICF 0.48 2.35E-03 0.62 0.47 7.81E-05 0.30 TMEM241

1The base pair position in the BTA (Bos taurus autosome).

2CRh = conception rate at first insemination in heifers; ICF = interval from calving to first insemination; IFLc = interval from first to last insemination in cows; CRc = conception rate at first insemination in cows.

3Minor allele frequency of the validated SNP.

4The percentage of genetic variance explained by the most significant SNP.

5Genes harbor or closest to the significant SNP.