TABLE 4.
Significant single-nucleotide polymorphism (SNP) and nearby genes of the genetic effects of service sire on five reproductive traits carried out by genome-wide association studies in Holstein cattle.
| Trait | SNP | BTA | Position (bp) | P-value | MAF | Effect | FDR | Genesa |
| CR | rs29011049 | 1 | 97,448,665 | 1.21 × 10–6 | 0.38 | 0.006 | 0.018 | LRRC34, ACTRT3, MYNN, PHC3, SAMD7, SEC62, GPR160 |
| rs133215257 | 3 | 79,272,169 | 6.96 × 10–6 | 0.26 | −0.006 | 0.040 | PDE4B, MGC137454 | |
| rs43370565 | 3 | 115,520,121 | 3.81 × 10–6 | 0.10 | 0.005 | 0.026 | ASB18, GBX2, AGAP1 | |
| rs42882387 | 4 | 89,316,398 | 1.63 × 10–6 | 0.24 | 0.004 | 0.018 | POT1 | |
| rs137141507 | 6 | 3,362,250 | 1.32 × 10–6 | 0.09 | 0.006 | 0.018 | EXOSC9, CCNA2, BBS7, ANXA5 | |
| rs42487799 | 7 | 37,625,102 | 1.32 × 10–9 | 0.32 | 0.005 | <0.001 | COMMD10, SEMA6A | |
| rs109487947 | 7 | 54,827,253 | 1.07 × 10–6 | 0.08 | −0.005 | 0.018 | ||
| rs110233258 | 7 | 58,460,338 | 3.50 × 10–8 | 0.15 | −0.005 | 0.001 | STK32A, PPP2R2B, DPYSL3 | |
| rs109461455 | 9 | 37,700,129 | 1.92 × 10–6 | 0.15 | −0.003 | 0.018 | ||
| rs42864672 | 9 | 63,416,140 | 4.60 × 10–8 | 0.37 | −0.004 | 0.001 | ||
| rs136069526 | 9 | 67,796,936 | 1.04 × 10–5 | 0.48 | −0.003 | 0.050 | ARHGAP18 | |
| rs109859987 | 11 | 53,890,637 | 9.83 × 10–6 | 0.49 | −0.002 | 0.050 | ||
| rs109992118 | 13 | 21,561,365 | 1.97 × 10–6 | 0.21 | −0.003 | 0.018 | PLXDC2 | |
| rs109632400 | 13 | 58,602,292 | 1.73 × 10–6 | 0.35 | −0.003 | 0.018 | PCK1, RBM38, RAE1, ZBP1, CTCFL, PMEPA1 | |
| rs41751511 | 15 | 8,668,231 | 4.63 × 10–7 | 0.49 | 0.003 | 0.010 | CNTN5 | |
| rs43713533 | 15 | 28,453,282 | 2.87 × 10–6 | 0.29 | −0.003 | 0.022 | TMPRSS13, FXYD2, FXYD6 | |
| rs42402130 | 16 | 32,852,344 | 2.86 × 10–8 | 0.23 | 0.005 | 0.001 | ADSS2, C16H1orf100 | |
| rs41750173 | 16 | 57,750,820 | 4.74 × 10–6 | 0.18 | −0.004 | 0.029 | PAPPA2 | |
| rs29019796 | 17 | 25,645,239 | 4.84 × 10–6 | 0.05 | 0.007 | 0.029 | ||
| rs110578750 | 18 | 2,907,599 | 1.05 × 10–5 | 0.14 | −0.004 | 0.050 | GABARAPL2, CFDP2, CFDP1, TMEM170A, TMEM231, ADAT1, KARS1, TERF2IP, BCNT2, CHST6 | |
| rs110228250 | 20 | 40,015,842 | 3.52 × 10–6 | 0.05 | −0.006 | 0.026 | ADAMTS12, SLC45A2, RXFP3 | |
| rs41568642 | 21 | 12,166,884 | 2.40 × 10–6 | 0.17 | 0.004 | 0.020 | ||
| rs110340891 | 22 | 37,375,611 | 9.41 × 10–6 | 0.19 | 0.003 | 0.050 | ATXN7, PSMD6, PRICKLE2 | |
| NRR56 | rs43587839 | 1 | 155,197,244 | 1.91 × 10–7 | 0.09 | −0.003 | 0.003 | |
| rs134652568 | 2 | 74,743,823 | 4.21 × 10–6 | 0.15 | 0.003 | 0.024 | ||
| rs110190075 | 2 | 103,750,400 | 7.13 × 10–7 | 0.28 | 0.005 | 0.009 | ||
| rs43354413 | 3 | 92,138,083 | 7.02 × 10–6 | 0.30 | 0.002 | 0.036 | HSPB11, TMEM59, TCEANC2, MRPL37, SSBP3, LRRC42, CDCP2, CYB5RL, LDLRAD1, YIPF1 | |
| rs43371984 | 3 | 116,894,699 | 9.45 × 10–6 | 0.42 | −0.004 | 0.043 | MLPH, LRRFIP1, PRLH, RAB17, COL6A3 | |
| rs43386888 | 4 | 49,509,741 | 2.41 × 10–6 | 0.12 | −0.003 | 0.021 | NRCAM, NME8, PNPLA8 | |
| rs42766762 | 6 | 108,074,935 | 3.04 × 10–6 | 0.37 | −0.005 | 0.021 | ||
| rs110658771 | 8 | 19,488,876 | 3.48 × 10–6 | 0.17 | 0.003 | 0.022 | IZUMO3 | |
| rs109087862 | 8 | 63,729,696 | 7.17 × 10–8 | 0.46 | −0.003 | 0.003 | ANKS6, GALNT12, GABBR2 | |
| rs110409952 | 9 | 87,035,097 | 2.88 × 10–6 | 0.39 | 0.002 | 0.021 | NUP43, PCMT1, LATS1, ULBP17, LRP11, KATNA1, ULBP21 | |
| rs133014180 | 10 | 66,613,339 | 1.56 × 10–7 | 0.11 | 0.004 | 0.003 | BMP4 | |
| rs41667346 | 11 | 23,497,697 | 5.49 × 10–6 | 0.33 | −0.003 | 0.030 | ||
| rs110387293 | 11 | 73,919,337 | 3.11 × 10–7 | 0.21 | 0.003 | 0.004 | POMC, DTNB, DNMT3A | |
| rs41633184 | 13 | 13,837,771 | 4.25 × 10–6 | 0.09 | 0.005 | 0.024 | ||
| rs43709749 | 14 | 28,478,462 | 1.08 × 10–6 | 0.44 | 0.002 | 0.011 | ||
| rs41616446 | 15 | 13,400,749 | 9.97 × 10–9 | 0.26 | −0.004 | 0.001 | ||
| rs110815341 | 15 | 63,461,312 | 7.26 × 10–6 | 0.32 | −0.003 | 0.036 | EIF3M, QSER1, PRRG4, DEPDC7 | |
| rs42427669 | 17 | 66,079,314 | 3.04 × 10–7 | 0.07 | 0.003 | 0.004 | SEZ6L, TPST2, SRRD, TFIP11, HPS4, CRYBB1, CRYBA4, ASPHD2 | |
| rs133424642 | 18 | 13,506,620 | 1.02 × 10–6 | 0.49 | −0.003 | 0.011 | SLC7A5, CA5A, BANP | |
| rs110863925 | 24 | 7,065,050 | 1.59 × 10–7 | 0.45 | −0.003 | 0.003 | RTTN, SOCS6 | |
| rs135757150 | 24 | 54,887,194 | 3.08 × 10–6 | 0.45 | 0.003 | 0.021 | TCF4 | |
| rs109715869 | 25 | 25,154,075 | 7.91 × 10–6 | 0.44 | 0.002 | 0.037 | GSG1L, GTF3C1, KATNIP, IL21R | |
| rs136986771 | 30 | 133,828,729 | 2.61 × 10–6 | 0.14 | 0.003 | 0.021 | ||
| rs134555078 | 30 | 137,676,697 | 3.10 × 10–8 | 0.36 | −0.004 | 0.002 | ||
| CE | rs29016910 | 2 | 41,127,106 | 4.83 × 10–7 | 0.42 | 0.001 | 0.007 | KCNJ3 |
| rs43715311 | 3 | 114,365,299 | 5.28 × 10–6 | 0.44 | 0.001 | 0.034 | SH3BP4 | |
| rs43427376 | 5 | 7,184,325 | 1.41 × 10–6 | 0.28 | 0.001 | 0.015 | NAV3 | |
| rs133310180 | 5 | 90,520,626 | 2.21 × 10–6 | 0.35 | 0.001 | 0.019 | AEBP2, PLEKHA5 | |
| rs133412722 | 7 | 68,637,147 | 7.25 × 10–6 | 0.48 | 0.001 | 0.044 | HAVCR2, MED7 | |
| rs110471321 | 9 | 7,979,325 | 2.22 × 10–7 | 0.24 | −0.001 | 0.005 | ADGRB3 | |
| rs108984322 | 10 | 8,009,471 | 2.40 × 10–6 | 0.18 | −0.001 | 0.019 | IQGAP2, F2RL2, F2R, S100Z, CRHBP, AGGF1, F2RL1 | |
| rs29017584 | 10 | 33,364,541 | 2.50 × 10–6 | 0.49 | 0.002 | 0.019 | ||
| rs42568446 | 11 | 18,452,325 | 5.33 × 10–7 | 0.25 | 0.001 | 0.007 | ||
| rs42583510 | 11 | 30,305,738 | 2.78 × 10–6 | 0.22 | 0.002 | 0.020 | MSH6, FBXO11 | |
| rs41628019 | 14 | 28,529,843 | 3.23 × 10–7 | 0.37 | 0.001 | 0.006 | ||
| rs109928489 | 14 | 81,472,215 | 5.62 × 10–7 | 0.41 | 0.001 | 0.007 | COL14A1, DSCC1, DEPTOR | |
| rs41824124 | 16 | 70,244,076 | 3.87 × 10–6 | 0.19 | 0.001 | 0.026 | RPS6KC1 | |
| rs41635371 | 16 | 78,603,871 | 1.52 × 10–6 | 0.40 | −0.001 | 0.015 | ||
| rs42813960 | 18 | 64,728,827 | 1.32 × 10–7 | 0.35 | −0.001 | 0.004 | ZNF550, ZNF419, ZNF548 | |
| rs136257872 | 19 | 8,172,407 | 3.10 × 10–10 | 0.37 | 0.002 | <0.001 | MSI2 | |
| rs108970271 | 22 | 26,765,132 | 5.86 × 10–8 | 0.30 | −0.001 | 0.002 | ||
| rs42070292 | 25 | 29,175,853 | 8.31 × 10–10 | 0.12 | 0.002 | <0.001 | GALNT17, CALN1 | |
| SB | rs41594258 | 1 | 34,978,818 | 1.06 × 10–6 | 0.09 | −0.004 | 0.019 | VGLL3 |
| rs109309140 | 2 | 4,981,764 | 1.42 × 10–6 | 0.46 | 0.002 | 0.022 | PROC, SFT2D3, WDR33, GPR17, LIMS2, IWS1, MYO7B | |
| rs137754398 | 2 | 101,961,755 | 2.82 × 10–9 | 0.40 | −0.005 | <0.001 | ||
| rs43353437 | 3 | 83,295,309 | 5.81 × 10–6 | 0.25 | −0.003 | 0.039 | KANK4, DOCK7, USP1 | |
| rs43386788 | 4 | 27,127,668 | 3.98 × 10–6 | 0.09 | −0.005 | 0.036 | HDAC9 | |
| rs43424011 | 5 | 7,320,087 | 6.04 × 10–6 | 0.31 | −0.003 | 0.039 | NAV3 | |
| rs137802315 | 6 | 92,046,444 | 3.27 × 10–6 | 0.45 | 0.003 | 0.036 | CCNI, SEPTIN11, CCNG2 | |
| rs41630520 | 9 | 19,561,418 | 6.43 × 10–6 | 0.23 | −0.002 | 0.039 | TTK, ELOVL4 | |
| rs109624175 | 9 | 56,241,273 | 4.99 × 10–8 | 0.24 | 0.003 | 0.001 | ||
| rs109920124 | 11 | 44,744,209 | 4.96 × 10–6 | 0.38 | −0.003 | 0.039 | RANBP2, CCDC138, SULT1C3, LIMS1, GCC2, EDAR, SULT1C4, SULT1C2 | |
| rs135416382 | 12 | 24,302,230 | 3.62 × 10–6 | 0.27 | −0.003 | 0.036 | TRPC4, POSTN | |
| rs134002839 | 13 | 71,259,389 | 3.58 × 10–8 | 0.18 | −0.004 | 0.001 | PTPRT | |
| rs135791311 | 14 | 71,330,255 | 1.44 × 10–9 | 0.09 | 0.006 | <0.001 | TRIQK | |
| rs43168517 | 16 | 10,976,232 | 5.53 × 10–6 | 0.10 | 0.004 | 0.039 | ||
| rs108992403 | 19 | 16,143,462 | 4.99 × 10–6 | 0.20 | −0.002 | 0.039 | ASIC2 | |
| rs134228482 | 22 | 13,014,212 | 3.13 × 10–6 | 0.41 | −0.002 | 0.036 | MYRIP, EIF1B | |
| rs41588424 | 28 | 12,833,134 | 3.37 × 10–8 | 0.17 | −0.004 | 0.001 | CHRM3 | |
| rs42492371 | 29 | 1,952,181 | 1.88 × 10–6 | 0.50 | −0.003 | 0.026 | FAT3, MTNR1B | |
| GL | rs42630203 | 1 | 18,608,496 | 1.18 × 10–6 | 0.30 | −0.184 | 0.018 | CHODL, TMPRSS15 |
| rs110604162 | 1 | 112,217,694 | 2.99 × 10–6 | 0.42 | 0.162 | 0.027 | PLCH1 | |
| rs43271952 | 1 | 134,240,312 | 4.60 × 10–6 | 0.30 | 0.174 | 0.033 | EPHB1 | |
| rs43354413 | 3 | 92,138,083 | 2.94 × 10–6 | 0.30 | 0.179 | 0.027 | HSPB11, TMEM59, TCEANC2, MRPL37, SSBP3, LRRC42, CDCP2, CYB5RL, LDLRAD1, YIPF1 | |
| rs134191168 | 4 | 66,013,467 | 6.18 × 10–8 | 0.36 | 0.175 | 0.002 | ZNRF2, GGCT, NOD1, MTURN | |
| rs108993952 | 7 | 48,852,799 | 1.00 × 10–6 | 0.39 | −0.203 | 0.018 | SPOCK1 | |
| rs136460053 | 7 | 61,263,431 | 4.91 × 10–6 | 0.48 | 0.207 | 0.033 | HMGXB3, CSF1R, PPARGC1B, PDE6A, SLC26A2 | |
| rs109807989 | 8 | 88,740,000 | 1.92 × 10–6 | 0.28 | −0.254 | 0.021 | CKS2, SECISBP2, SEMA4D, SHC3 | |
| rs109727604 | 14 | 39,463,590 | 3.57 × 10–6 | 0.43 | −0.155 | 0.028 | ||
| rs136577145 | 16 | 30,791,818 | 1.73 × 10–6 | 0.37 | −0.202 | 0.021 | TFB2M, CNST, SCCPDH, H3-5, SMYD3 | |
| rs41619483 | 18 | 6,140,925 | 3.40 × 10–6 | 0.29 | 0.152 | 0.028 | WWOX | |
| rs110402487 | 18 | 64,444,876 | 2.27 × 10–8 | 0.29 | −0.228 | 0.001 | AURKC, ZNF304, ZNF805, ZNF548, ZIM3 | |
| rs109173977 | 21 | 41,990,869 | 3.80 × 10–7 | 0.35 | −0.328 | 0.010 | GPR33, HEATR5A, NUBPL | |
| rs110148531 | 23 | 39,148,251 | 1.09 × 10–6 | 0.19 | −0.175 | 0.018 | RNF144B | |
| rs137469593 | 27 | 19,456,244 | 1.74 × 10–6 | 0.37 | −0.170 | 0.021 | PDGFRL, PCM1, FGL1, MTUS1 | |
| rs135655219 | 28 | 5,171,795 | 1.79 × 10–8 | 0.26 | 0.236 | 0.001 | SIPA1L2 | |
| rs42178394 | 29 | 33,061,591 | 7.27 × 10–6 | 0.17 | −0.168 | 0.047 | JAM3, IGSF9B, SPATA19 |
CR, conception rate; NRR56, 56-day non-return rate; CE, calving ease; SB, stillbirth; GL, gestation length; MAF, minor allele frequency. aThe important candidate genes for each trait are shown in bold face.