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. 2020 Feb 4;11:20. doi: 10.3389/fgene.2020.00020

TABLE 1.

The location of the most significant QTLs, limited to the top 5, which were associated with wither height or stature, and the genes located within these QTLs within each breed.

No of suggestive and significant SNPs Most significant SNP Allele frequency of positive allele
Breed Chr Start End P-Value AA CH HE LM SI HF Candidate genes within this QTL
Angus 6 37859028 40529961 96 39955422a 7.31 × 10–9 0.114 0.000 0.000 0.064 0.000 0.042 ABCG2, PKD2, SPP1, MEPE, LAP3, NCAPG*, LCORL*
6 40760106 41784760 14 41276346b 2.74 × 10–7 0.445 0.000 0.372 0.522 0.000 0.784 SLIT2*, PACRGL, KCNIP4
16 72342264 73978632 25 72877647a 1.46 × 10–7 0.995 0.002 0.003 0.000 0.996 0.996 RPS6KC1, BATF3, PPP2R5A*
20 46866355 47884741 51 47372538a 7.48 × 10–7 0.161 0.310 0.523 0.768 0.822 0.834 ENSBTAG00000048105
26 40278450 41826296 23 41323903c 2.21 × 10–7 0.993 0.980 0.982 0.017 0.983 0.000 WDR11*, PTPRG, FHIT
Charolais 2 5346602 6349651 2 5846602a 6.02 × 10–8 0.690 0.585 0.703 0.000 0.586 0.390 NAB1, MSTN, MFSD6
5 40455760 41765149 12 40955760a 5.68 × 10–8 0.000 0.038 0.987 0.000 0.016 0.010 SLC2A13*, ABCD2
6 33942529 35471763 9 34442529a 7.78 × 10–6 0.998 0.011 0.000 0.003 0.000 0.000 CCSER1
27 11896148 12929004 15 12428578a 7.97 × 10–7 0.295 0.464 0.000 0.513 0.501 0.344 TENM3, DCTD
28 11615130 12630615 8 12127037a 6.97 × 10–7 0.758 0.975 0.273 0.138 0.153 0.146
Hereford 3 74681893 76225687 5 75725687b 5.73 × 10–7 0.005 0.003 0.976 0.000 0.995 0.390 CTH, LRRC7*, LRRC40
5 79055337 80113473 8 79564409a 3.32 × 10–7 0.536 0.606 0.975 0.487 0.403 0.900 SINHCAF
7 81624551 82816882 4 82124551a 1.88 × 10–7 0.994 0.003 0.995 0.000 0.003 0.991 TENM2, WWC1
20 19842459 20942794 51 20401686a 2.44 × 10–7 0.043 0.098 0.266 0.271 0.198 0.146 PDE4D, RAB3C
23 50140690 51876442 10 51357892b 8.96 × 10–7 0.277 0.755 0.229 0.786 0.184 0.582 SLC22A23, RIPK1, NQO2, GMDS*
Limousin 4 57644495 58664115 9 58148365a 5.52 × 10–7 0.974 0.053 0.932 0.092 0.953 0.335 IMMPL2
6 31747431 35203508 1588 33609037a 1.17 × 10–18 0.249 0.879 0.415 0.151 0.260 0.812 SMARCAD1, ATOH1, CCSER1
6 36934944 41871562 663 38035891d 1.45 × 10–16 0.086 0.000 0.000 0.128 0.636 0.007 PPM1K^, ABCG2^, PKD2^, SPP1^, MEPE*, LAP3, NCAPG^, LCORL^
6 42312608 43680601 17 42990479b 1.48 × 10–7 0.000 0.006 0.000 0.029 0.000 0.000 ADGRA3, KCNIP4*
11 104805923 105866536 3 105366536b 1.04 × 10–7 0.032 0.979 0.008 0.010 0.983 0.035 BRD3, WDR5, CACNA1B*
Simmental 8 82805400 83805881 3 83305881a 1.67 × 10–6 0.367 0.688 0.693 0.540 0.279 0.675 FANCC
8 106857510 107869952 3 107357510b 8.48 × 10–7 0.990 0.073 0.928 0.093 0.859 0.878 PAPPA*, TRIM32
12 55018060 56018149 3 55518060a 2.66 × 10–7 0.000 0.955 0.004 0.967 0.005 0.000 SPRY2
12 89258864 90269817 3 89758864a 2.78 × 10–6 0.015 0.988 0.992 0.028 0.950 0.982 ANKRD10, ING1, SOX1, TUBGCP3
22 1921471 3018467 32 2517667a 4.87 × 10–7 0.000 0.000 0.000 0.000 0.003 0.000 CMC1, AZI2
Holstein Friesian 4 108676456 109728131 8 109185322a 1.49 × 10–6 0.096 0.203 0.081 0.775 0.365 0.794 TPK1
5 59814571 62558882 76 60701477a 4.28 × 10–8 0.257 0.900 0.953 0.874 0.949 0.894 NEUROD4, TSPA1, NTN4*, SNRPF*, AMDHD1*, LTA4H*, CDK17*, NEDD1
5 104934097 106783101 135 106283101a 3.77 × 10–8 0.096 0.679 0.437 0.000 0.802 0.475 ANO2, NTF3, KCNA1, NDUFA9, FGF6*, FGF23*, TIGAR*
6 60485248 61489096 26 60985248d 1.94 × 10–6 0.965 0.903 0.148 0.000 0.904 0.973 UBE2K, N4BP2, RHOH, CHRNA9*, RBM47
7 23221527 24809431 46 23789810b 1.24 × 10–7 0.110 0.834 0.952 0.000 0.031 0.903 IRF1, PDLIM4, P4HA2, IL3, ACSL6, FNIP1*, HINT1

AA, Angus; CH, Charolais; HE, Hereford; LM, Limousin; SE, Simmental; HF, Holstein-Friesian. Superscript denotes SNP classification:aintergenic, bintron, cupstream gene variant, ddownstream gene variant. Symbols denote the significance of SNPs within genes: * gene contained at least one suggestive (p ≤ 1 × 10–5) SNP ^ gene contained at least one significant (p ≤ 1 × 10–8) SNP.