Table 5 Location of the most significant QTL, limited to the top 5 per breed, which were associated with width of withers, and the genes located within these QTL within each breed
From: Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds
Breed | Chr | Start | End | Number of suggestive and significant SNPs | Most significant SNP | P-value | Allele frequency of + allele | Candidate genes within this QTL | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
AA | CH | HE | LM | SI | ||||||||
AA | 1 | 40642399 | 41670931 | 3 | 41142399b | 2.49 × 10−6 | 0.997 | 0.998 | 0.009 | 0.991 | 0.000 | EPHA6d |
|  | 6 | 90992982 | 92064889 | 10 | 91513217a | 2.34 × 10−9 | 0.008 | 0.019 | 0.009 | 0.995 | 0.005 | EREG, AREG, RCHY1 |
|  | 14 | 9414135 | 10414890 | 9 | 9914135b | 3.85 × 10−6 | 0.016 | 0.936 | 0.144 | 0.969 | 0.951 | TG, KCNQ3d |
|  | 14 | 17744843 | 18889304 | 16 | 18244843b | 1.59 × 10−6 | 0.957 | 0.007 | 0.977 | 0.000 | 0.977 | ANXA13, KLHL38, FBXO32 |
|  | 15 | 66035436 | 67113172 | 4 | 66535436b | 3.42 × 10−7 | 0.004 | 0.996 | 0.930 | 0.003 | 0.992 | APIP, PDHX |
CH | 2 | 218127 | 8714844 | 1227 | 6808074a | 2.02 × 10−21 | 0.000 | 0.079 | 0.000 | 0.028 | 0.004 | WDR75e, ASNSD1d, NAB1e, MFSD6e, MSTNe, PMS1e, ORMDL1, COL3A1e, COL5A2e, ANKARe, SLC40A1e |
|  | 4 | 63740415 | 65180447 | 6 | 64680447a | 3.32 × 10−7 | 0.000 | 0.003 | 0.000 | 0.000 | 0.991 | NT5C3A, KBTBD2 |
|  | 14 | 67870173 | 68870239 | 7 | 68370173a | 2.98 × 10−7 | 0.028 | 0.060 | 0.965 | 0.053 | 0.024 | STK3, KCNS2, POP1, RPL30, MATN2 |
|  | 28 | 15669176 | 17454059 | 6 | 16943776a | 1.52 × 10−8 | 0.640 | 0.868 | 0.525 | 0.690 | 0.729 | ANK3, CDK1, RHOBTB1 |
|  | 28 | 31765108 | 33148059 | 7 | 32634467a | 1.61 × 10−7 | 0.367 | 0.889 | 0.664 | 0.511 | 0.468 | KCNMA1 |
HE | 7 | 63750754 | 64814905 | 15 | 64309256b | 1.46 × 10−7 | 0.022 | 0.949 | 0.008 | 0.011 | 0.009 | RPS14, MYOZ3, ZNF300, GPX3d, ANXA6 |
|  | 11 | 89579990 | 90599173 | 5 | 90079990a | 5.13 × 10−6 | 0.664 | 0.280 | 0.163 | 0.800 | 0.217 | RNF144A, RSAD2 |
|  | 18 | 11547513 | 12549350 | 5 | 12047513a | 4.85 × 10−6 | 0.479 | 0.565 | 0.507 | 0.532 | 0.446 | GSE1, IRF8, FOXC2 |
|  | 20 | 25429449 | 27124758 | 9 | 25929649a | 3.38 × 10−6 | 0.532 | 0.000 | 0.559 | 0.000 | 0.480 | FST |
|  | 26 | 32810942 | 33810987 | 3 | 33310942b | 2.78 × 10−6 | 0.000 | 0.000 | 0.998 | 0.000 | 0.000 | GPAM, ACSL5 |
LM | 2 | 5547713 | 8495179 | 725 | 6622189a | 8.77 × 10−12 | 0.490 | 0.447 | 0.250 | 0.043 | 0.800 | WDR75, ASNSD1d, NAB1, MFSD6, MSTN, PMS1d, ORMDL1, COL3A1, COL5A2e, ANKARd, SLC40A1e |
|  | 2 | 9053737 | 10527711 | 26 | 9559686a | 1.53 × 10−6 | 0.464 | 0.504 | 0.213 | 0.127 | 0.456 | ITGAV, ZC3H15 |
|  | 2 | 13916060 | 14957655 | 68 | 14450953b | 6.10 × 10−8 | 0.433 | 0.564 | 0.626 | 0.394 | 0.479 | PDE1Ad, PPP1R1C, NEUROD1 |
|  | 2 | 20539841 | 21539862 | 3 | 21039862a | 6.85 × 10−10 | 0.000 | 0.000 | 0.000 | 0.998 | 0.000 | HOXD1, HOXD3, HOXD4, HOXD9, HOXD10, HOXD11, HOXD12, HOXD13 |
|  | 6 | 19014612 | 21121181 | 13 | 19817910a | 8.15 × 10−9 | 0.000 | 0.000 | 0.008 | 0.995 | 0.000 | NPNT, GSTCDd |
SI | 1 | 79028842 | 80104503 | 3 | 79604503b | 3.81 × 10−7 | 0.022 | 0.040 | 0.000 | 0.964 | 0.004 | LPPd |
|  | 4 | 57566849 | 58584434 | 5 | 58084434d | 6.35 × 10−8 | 0.902 | 0.261 | 0.457 | 0.248 | 0.229 | IMMP2Ld, LRRN3 |
|  | 9 | 32996000 | 34471196 | 16 | 33604527b | 5.67 × 10−8 | 0.969 | 0.979 | 0.019 | 0.985 | 0.019 | NEPN, GOPCd |
|  | 12 | 28061051 | 29073791 | 3 | 28561051d | 7.49 × 10−7 | 0.008 | 0.020 | 0.084 | 0.016 | 0.998 | PDS5B |
|  | 20 | 65137216 | 66168943 | 4 | 65668943a | 1.76 × 10−7 | 0.000 | 0.009 | 0.000 | 0.977 | 0.007 | FASTKD3, ADCY2d |