Table 2.
Significant SNPs and candidate genes from multiple-trait analysis for six heifer fertility and reproduction traits
| Chr |
Position (bp) |
P values | Genomic location |
Candidate genes (within ± 100 kb)a |
N of QTLb |
|---|---|---|---|---|---|
| BTA2 | 70,633,250 | 1.7755e-06 | Intergenic | EN1 | 0 |
| 80,773,959 | 8.2906e-06 | Intron | TMEFF2 | 0 | |
| 98,894,327 | 1.703e-05 | Intergenic | — | 0 | |
| BTA3 | 83,818,837 | 9.9389e-06 | Exon | PATJ | 0 |
| 89,878,033 | 1.2513e-06 | Intergenic | — | 98 | |
| BTA4 | 2,476,516 | 1.0209e-05 | Intergenic | — | 0 |
| 17,304,670 | 2.5726e-06 | Intergenic | — | 0 | |
| 36,768,135 | 2.6301e-05 | Intergenic | ENSBTAG00000053333* | 0 | |
| 77,892,378 | 2.4934e-05 | Intergenic | HECW1 | 0 | |
| BTA6 | 31,807,526 | 1.248e-05 | Intergenic | — | 2 |
| 54,108,303 | 9.9442e-06 | Intergenic | — | 1 | |
| BTA7 | 6,177,026 | 5.1964e-06 | Intron | CPAMD8, F2RL3, SIN3B, NWD1 | 1 |
| 8,193,333 | 2.7732e-05 | Exon | CASP14, CCDC105, SLC1A6, ENSBTAG00000053903, OR7C19, OR7A85, ENSBTAG00000051946 | 0 | |
| 62,865,717 | 8.3985e-06 | Intergenic | FAT2, SPARC, ENSBTAG00000054940, ATOX1 | 0 | |
| 97,438,333 | 1.6934e-05 | Intergenic | — | 0 | |
| 100,189,059 | 2.344e-05 | Intergenic | ST8SIA4 | 2 | |
| BTA9 | 21,350,462 | 1.1343e-05 | Intergenic | — | 0 |
| 71,191,104 | 1.5112e-05 | Intergenic | — | 0 | |
| 95,975,870 | 2.4538e-05 | Intergenic | ENSBTAG00000052316, SOD2, WTAP, ACAT2, TCP1, MRPL18, PNLDC1 | 5 | |
| BTA10 | 41,323,422 | 2.7906e-05 | Intergenic | — | 0 |
| 81,606,975 | 1.5652e-05 | Intron | SLC10A1, SMOC1 | 1 | |
| BTA12 | 45,686,110 | 1.8064e-05 | Intergenic | — | 0 |
| 45,712,972 | 2.0906e-05 | Intergenic | |||
| 69,768,461 | 1.8444e-05 | Intergenic | — | 0 | |
| 77,682,412 | 2.495e-05 | Intron | NALCN | 4 | |
| BTA13 | 3,327,860 | 1.1246e-05 | Intergenic | ANKEF1 | 0 |
| 42,023,779 | 3.7745e-05 | Downstream | NXT1, GZF1, NAPB, ENSBTAG00000027420, MGC133636, CST8, ENSBTAG00000015949 | 0 | |
| 42,049,979 | 3.7745e-05 | Intron | |||
| BTA14 | 18,883,604 | 1.0029e-05 | Intergenic | — | 3 |
| 54,326,109 | 7.0163e-06 | Intergenic | — | 1 | |
| 61,221,242 | 3.2749e-05 | Intergenic | CTHRC1, FZD6, BAALC | 3 | |
| 67,859,596 | 1.5109e-05 | Intergenic | PTDSS1 | 0 | |
| BTA15 | 45,999,990 | 2.9729e-05 | Intergenic | OR6A2, OR6B18, ENSBTAG00000027525, OR6B17, ENSBTAG00000037603, OR2D4, OR2D3G, OR2AG1E, OR2AG1G, OR2AG1, OR2AG2 | 0 |
| BTA18 | 39,676,071 | 1.3142e-05 | Intron | ZNF19, ZNF23, ENSBTAG00000053994*, CALB2, CMTR2, ENSBTAG00000051512 | 0 |
| 39,750,065 | 2.1267e-05 | Intergenic | |||
| 39,767,356 | 8.5276e-06 | Exon | |||
| 39,797,494 | 1.8113e-07 | Downstream | |||
| 39,854,578 | 9.5369e-06 | Upstream | |||
| 39,905,828 | 2.4327e-05 | Intron | |||
| 41,105,349 | 4.5111e-05 | Intron | ZNF536 | 2 | |
| 41,112,039 | 2.5866e-05 | Intron | |||
| BTA19 | 39,685,286 | 4.588e-05 | Exon | PLXDC1, CACNB1, RPL19, ENSBTAG00000050597, STAC2, ENSBTAG00000008368, FBXL20 | 0 |
| 46,856,509 | 2.2533e-05 | Intron | EFCAB3, METTL2A, TLK2 | 2 | |
| 53,776,030 | 3.7096e-06 | Intron | DNAH17, PGS1, SOCS3 | 0 | |
| 53,779,550 | 2.1366e-06 | Intron | |||
| BTA20 | 12,849,264 | 2.7392e-05 | Intron | ENSBTAG00000049964 | 0 |
| 15,673,813 | 3.5073e-06 | Intergenic | HTR1A | 0 | |
| 15,788,934 | 4.5398e-07 | Intergenic | |||
| 15,839,035 | 3.8454e-05 | Intergenic | |||
| 29,868,266 | 8.7288e-06 | Intergenic | ENSBTAG00000054476 | 0 | |
| 29,957,655 | 1.2013e-06 | Intergenic | |||
| 29,957,766 | 3.1125e-05 | Intergenic | |||
| 29,959,061 | 1.8094e-05 | Intergenic | |||
| 51,156,345 | 1.4415e-05 | Intron | CDH12 | 0 | |
| 62,043,263 | 3.4353e-05 | Intron | CTNND2 | 0 | |
| 62,043,442 | 3.5997e-05 | Intron | |||
| BTA21 | 17,250,280 | 2.0376e-05 | Intron | AGBL1 | 0 |
| BTA22 | 2,072,527 | 1.8504e-05 | Intergenic | EOMES | 0 |
| 5,159,344 | 4.422e-05 | Intron | TGFBR2, GADL1 | 1 | |
| 9,601,560 | 4.4335e-05 | Intergenic | ARPP21 | 0 | |
| 9,634,144 | 1.8949e-05 | Intergenic | |||
| 11,393,650 | 1.341e-05 | Intron | CTDSPL, VILL, PLCD1, DLEC1 | 0 | |
| 11,701,385 | 2.9746e-05 | Intron | ACAA1, ENSBTAG00000054286, MYD88, OXSR1, ENSBTAG00000050531*, SLC22A14, XYLB, ACVR2B | 0 | |
| 11,737,948 | 4.1052e-06 | Downstream | |||
| 35,777,156 | 2.4904e-05 | Intron | MAGI1 | 0 | |
| 51,337,027 | 3.512e-05 | Intron | CELSR3, SLC26A6, TMEM89, UQCRC1, ENSBTAG00000049917*, ENSBTAG00000052088*, ENSBTAG00000049028*, UCN2, PFKFB4, SHISA5, ENSBTAG00000048942, TREX1, ATRIP, TMA7, CCDC51 | 2 | |
| 55,900,928 | 4.9063e-05 | Intergenic | TAMM41, TRH, TMCC1 | 1 | |
| BTA23 | 5,726,221 | 2.9329e-05 | Intergenic | — | 0 |
| 25,235,958 | 5.2155e-05 | Intron | GSTA1, GSTA5, GSTA3, GSTA4, CILK1, FBXO9, GCM1 | 0 | |
| 25,819,703 | 4.2745e-05 | Intergenic | ENSBTAG00000013919, ENSBTAG00000048364, ENSBTAG00000038397, ENSBTAG00000015565, BOLA-DRA, BTNL2, ENSBTAG00000034945, ENSBTAG00000007618 | 0 | |
| 26,689,257 | 1.4214e-05 | Intergenic | — | 0 | |
| 28,036,775 | 4.1923e-06 | Intron | ENSBTAG00000051047, ENSBTAG00000007075, ENSBTAG00000053433, POU5F1, TCF19, CCHCR1, PSORS1C2, CDSN, C23H6orf15 | 1 | |
| 28,634,425 | 3.1365e-05 | Intergenic | BOLA-NC1, JSP.1, ENSBTAG00000037421, BOLA | 0 | |
| 30,058,286 | 2.9988e-05 | Intron | ZNF311, ENSBTAG00000052294*, TRIM27, ENSBTAG00000053198 | 0 | |
| 34,904,897 | 1.9645e-05 | Intergenic | GHE4, PRP2, PRP14, PRP9 | 0 | |
| 34,928,894 | 5.2141e-05 | Intron | |||
| BTA24 | 13,978,039 | 3.8859e-05 | Intron | PIK3C3 | 0 |
| 58,070,140 | 2.9176e-05 | Intron | ZNF532, ENSBTAG00000022829, SEC11C | 0 | |
| BTA25 | 38,933,869 | 4.7617e-05 | Intron | FBXL18, ENSBTAG00000050734*, TNRC18, SLC29A4, WIPI2 | 3 |
| BTA27 | 13,585,281 | 3.5455e-05 | Intron | TENM3 | 1 |
| 23,857,214 | 4.66e-05 | Intron | DLC1 | 0 | |
| 30,435,395 | 1.768e-05 | Intergenic | — | 0 | |
| 34,758,502 | 1.2659e-05 | Intron | ADAM2, ADAM3A | 3 | |
| BTA28 | 10,602,903 | 3.7999e-05 | Intergenic | RYR2, ZP4 | 1 |
| 24,802,568 | 6.4777e-05 | Intron | PBLD, HNRNPH3, RUFY2, DNA2, SLC25A16 | 0 | |
| 39,062,420 | 5.1602e-05 | Intergenic | GHITM, C10orf99, CDHR1 | 0 | |
| BTA29 | 27,630,533 | 1.1083e-05 | Intergenic | OR8G5, OR8G47, OR8D2, OR8B1U, OR8B1S, OR8B1AE, ENSBTAG00000051999, OR8B3G, ENSBTAG00000050103, OR8B3 | 0 |
aCandidate genes are represented by gene symbol when available, otherwise by the Ensembl gene ID. The long noncoding RNA genes are marked by asterisk (*). The genes directly linked to SNPs are further denoted in bold
bThe number of known and reproduction-associated QTL found in Cattle QTL Database v43 (www.animalgenome.org)