TABLE 5.
Significant single-nucleotide polymorphism (SNP) and near-by genes of the genetic effects of dam 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 | rs110588394 | 1 | 157,046,373 | 8.55 × 10–9 | 0.19 | 0.008 | 0.001 | PP2D1, EFHB, RAB5A |
| rs135745940 | 2 | 86,206,807 | 5.58 × 10–8 | 0.23 | 0.006 | 0.002 | MARS2, COQ10B, PLCL1, RFTN2, HSPD1, HSPE1, MOB4, BOLL | |
| rs41625668 | 3 | 2,131,858 | 7.13 × 10–7 | 0.44 | 0.005 | 0.010 | TADA1, POGK, ILDR2 | |
| rs110992111 | 3 | 63,079,015 | 1.70 × 10–6 | 0.45 | −0.004 | 0.017 | ADGRL2 | |
| rs41657989 | 7 | 24,218,169 | 1.10 × 10–7 | 0.40 | −0.005 | 0.003 | CHSY3, ADAMTS19, MINAR2 | |
| rs41592654 | 9 | 32,237,919 | 1.38 × 10–7 | 0.21 | −0.005 | 0.003 | ASF1A, MCM9, CEP85L, PLN, FAM184A | |
| rs42557707 | 12 | 45,131,104 | 5.35 × 10–7 | 0.08 | −0.008 | 0.008 | ||
| rs110113735 | 12 | 75,616,202 | 2.53 × 10–6 | 0.17 | 0.004 | 0.021 | FARP1, SLC15A1, DOCK9, STK24 | |
| rs137128437 | 14 | 73,073,273 | 5.01 × 10–7 | 0.41 | −0.005 | 0.008 | SLC26A7 | |
| rs43713566 | 15 | 29,560,389 | 9.42 × 10–7 | 0.20 | 0.006 | 0.011 | BCL9L, VPS11, HMBS, DPAGT1, TRAPPC4, SLC37A4, DDX6, HYOU1, ABCG4, UPK2, FOXR1, C2CD2L, HINFP, CENATAC, RPS25, NLRX1, CXCR5 | |
| rs136206713 | 15 | 81,820,622 | 2.82 × 10–8 | 0.41 | 0.006 | 0.002 | CNTF, LPXN | |
| rs132777210 | 21 | 69,731,178 | 2.35 × 10–6 | 0.34 | 0.005 | 0.021 | BTBD6, BRF1, TMEM121, PACS2, TEDC1, CRIP1, NUDT14 | |
| rs109776480 | 22 | 57,040,932 | 1.13 × 10–6 | 0.43 | −0.005 | 0.012 | MRPS25, RBSN, SYN2, TIMP4 | |
| NRR56 | rs42827552 | 6 | 23,199,236 | 3.74 × 10–6 | 0.35 | −0.005 | 0.041 | BANK1 |
| rs41575824 | 9 | 53,639,845 | 3.48 × 10–6 | 0.12 | 0.007 | 0.041 | FUT9 | |
| rs136204465 | 14 | 9,422,558 | 2.62 × 10–7 | 0.15 | −0.005 | 0.005 | ||
| rs134979761 | 17 | 9,110,531 | 2.75 × 10–8 | 0.41 | 0.006 | 0.002 | ||
| rs109533406 | 17 | 57,716,043 | 2.82 × 10–7 | 0.39 | 0.006 | 0.005 | NOS1, FBXO21, KSR2 | |
| rs135974611 | 18 | 31,152,142 | 2.34 × 10–6 | 0.27 | −0.006 | 0.032 | ||
| rs41606596 | 18 | 45,936,015 | 1.35 × 10–7 | 0.07 | −0.006 | 0.004 | FAM187B, GRAMD1A, SCN1B, HPN, FFAR2, CD22, FFAR3, LSR, USF2, HAMP, MAG, LGI4, FXYD1, FXYD7, FXYD5, FFAR1 | |
| rs110401168 | 19 | 57,629,224 | 3.60 × 10–9 | 0.35 | 0.008 | <0.001 | ||
| rs42428874 | 21 | 36,656,375 | 4.58 × 10–6 | 0.19 | −0.005 | 0.042 | NOVA1 | |
| rs136876790 | 22 | 34,075,088 | 4.90 × 10–8 | 0.47 | 0.005 | 0.002 | SUCLG2 | |
| rs110534364 | 24 | 50,494,672 | 4.31 × 10–6 | 0.11 | 0.007 | 0.042 | ELAC1, SMAD4, MEX3C, ME2, MRO | |
| rs109783875 | 26 | 27,091,833 | 1.71 × 10–6 | 0.36 | −0.004 | 0.027 | ||
| CE | rs110752117 | 7 | 51,418,311 | 1.21 × 10–6 | 0.08 | −0.007 | 0.019 | PURA, NRG2, CYSTM1, HBEGF, SLC4A9, IGIP, PFDN1 |
| rs110761813 | 10 | 16,708,640 | 1.63 × 10–6 | 0.37 | −0.005 | 0.022 | ||
| rs109942798 | 12 | 18,661,493 | 1.07 × 10–6 | 0.08 | 0.005 | 0.019 | MLNR, FNDC3A | |
| rs109156982 | 13 | 47,716,129 | 6.75 × 10–8 | 0.28 | 0.005 | 0.002 | GPCPD1, PROKR2 | |
| rs110115548 | 13 | 67,003,397 | 3.93 × 10–6 | 0.20 | 0.005 | 0.048 | TTI1, VSTM2L, RPRD1B, BPI, TGM2, KIAA1755 | |
| rs109493014 | 15 | 72,384,357 | 1.12 × 10–9 | 0.43 | 0.005 | <0.001 | ||
| rs41578821 | 16 | 30,855,245 | 9.26 × 10–8 | 0.10 | −0.005 | 0.003 | TFB2M, CNST, H3-5, SMYD3 | |
| rs42949634 | 18 | 39,542,279 | 4.32 × 10–7 | 0.25 | 0.004 | 0.009 | CALB2, TAT, AP1G1, MARVELD3, PHLPP2, CHST4, ZNF19, ZNF23 | |
| rs42534666 | 26 | 5,084,073 | 6.45 × 10–9 | 0.14 | 0.008 | <0.001 | PCDH15 | |
| SB | rs135087719 | 4 | 69,282,296 | 4.09 × 10–7 | 0.18 | −0.001 | 0.004 | SKAP2 |
| rs135473218 | 7 | 95,890,433 | 8.29 × 10–7 | 0.23 | 0.001 | 0.008 | CAST, PCSK1 | |
| rs43546352 | 8 | 31,779,503 | 1.34 × 10–10 | 0.25 | −0.002 | <0.001 | TYRP1 | |
| rs134655277 | 9 | 4,579,294 | 1.88 × 10–6 | 0.45 | 0.001 | 0.015 | ||
| rs135323642 | 9 | 67,192,772 | 2.79 × 10–6 | 0.38 | 0.002 | 0.020 | LAMA2 | |
| rs41595401 | 10 | 38,651,279 | 9.51 × 10–7 | 0.33 | 0.001 | 0.008 | ||
| rs110003547 | 11 | 47,431,717 | 4.84 × 10–9 | 0.07 | 0.001 | <0.001 | EIF2AK3, RPIA, TEX37, FOXI3 | |
| rs42337856 | 11 | 58,828,979 | 2.61 × 10–7 | 0.27 | −0.001 | 0.003 | ||
| rs133162533 | 15 | 3,989,919 | 5.61 × 10–6 | 0.48 | 0.001 | 0.036 | ||
| rs41790653 | 16 | 9,685,690 | 1.47 × 10–7 | 0.47 | 0.001 | 0.003 | ||
| rs133390427 | 17 | 60,309,111 | 3.61 × 10–6 | 0.33 | 0.001 | 0.025 | TBX5 | |
| rs110008365 | 18 | 5,593,593 | 2.74 × 10–7 | 0.28 | −0.001 | 0.003 | WWOX | |
| rs109395549 | 20 | 523,765 | 4.10 × 10–7 | 0.42 | 0.001 | 0.004 | PANK3, SLIT3 | |
| rs110695662 | 21 | 44,838,064 | 1.22 × 10–9 | 0.17 | 0.001 | <0.001 | EAPP, SNX6, SPTSSA | |
| rs42566616 | 22 | 40,247,823 | 1.65 × 10–10 | 0.36 | 0.001 | <0.001 | ||
| rs137494875 | 22 | 47,178,548 | 1.88 × 10–7 | 0.21 | −0.001 | 0.003 | CACNA1D, CHDH, IL17RB, ACTR8, SELENOK | |
| rs109564594 | 26 | 1,419,659 | 8.41 × 10–8 | 0.20 | −0.001 | 0.002 | ||
| GL | rs43747887 | 1 | 88,621,323 | 2.52 × 10–6 | 0.49 | 0.183 | 0.031 | |
| rs135396670 | 2 | 130,043,555 | 2.25 × 10–6 | 0.32 | −0.172 | 0.031 | C1QA, C1QC, C1QB, EPHA8, LACTBL1, EPHB2, TEX46 | |
| rs42760413 | 6 | 90,933,892 | 5.91 × 10–7 | 0.17 | −0.168 | 0.013 | CXCL10, CXCL11, SDAD1, ART3, NUP54, SCARB2, PPEF2, NAAA, CXCL9 | |
| rs43482393 | 6 | 93,053,914 | 1.09 × 10–9 | 0.34 | −0.349 | <0.001 | FRAS1 | |
| rs109176316 | 7 | 52,159,740 | 1.67 × 10–6 | 0.31 | −0.175 | 0.026 | PCDHA13, PCDHB1, PCDHAC2 | |
| rs136804356 | 14 | 28,876,699 | 4.75 × 10–6 | 0.33 | 0.158 | 0.047 | ||
| rs136577145 | 16 | 30,791,818 | 3.97 × 10–10 | 0.39 | −0.244 | <0.001 | TFB2M, CNST, SCCPDH, H3-5, SMYD3 | |
| rs109102279 | 20 | 19,138,824 | 6.01 × 10–8 | 0.12 | 0.250 | 0.002 | ||
| rs42406702 | 20 | 55,193,435 | 3.00 × 10–6 | 0.12 | −0.229 | 0.033 | ||
| rs110072536 | 25 | 40,344,012 | 8.43 × 10–7 | 0.31 | −0.170 | 0.015 | CARD11 | |
| rs109960049 | 26 | 17,360,622 | 4.05 × 10–8 | 0.48 | −0.326 | 0.001 | ENTPD1, ZNF518A, BLNK, CCNJ |
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.