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

TABLE 3.

The location of the most significant QTLs, limited to the top 5, which were associated with hip width or rump width, 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 4 115417450 116432669 15 115922671b 6.53 × 10–7 0.031 0.925 0.109 0.840 0.788 0.268 KMT2C, ACTR3B*,XRCC2, CCT8L2
5 30902961 31924821 5 31402961a 2.79 × 10–7 0.002 0.992 0.978 0.006 0.002 0.990 RHEBL1, PRKAG1, WNT1, WNT10B, CCDC65
11 81485390 82623280 5 81985390b 1.09 × 10–6 0.004 0.000 0.000 0.996 0.994 0.000 FAM49A*
20 13855925 14889348 17 14374205a 1.16 × 10–6 0.004 0.021 0.013 0.000 0.016 0.002 TRIM23, ADAMTS6
25 15156974 16246007 4 15656974a 5.63 × 10–7 0.003 0.983 0.011 0.973 0.974 0.000 XYLT1
Charolais 2 30205997 31264765 30 30705997a 2.83 × 10–8 0.978 0.993 0.995 0.008 0.007 0.267 GALNT3*, SCN1A, SCN2A, SCN3A, TTC21B, CSRNP3
8 4328030 5328051 4 4828030b 1.09 × 10–6 0.000 0.005 0.004 0.028 0.026 0.997 GALNTL6*
9 12598999 13731582 8 13113448a 6.49 × 10–7 0.990 0.024 0.010 0.009 0.011 0.027 MTO1, EEF1A1
15 7774063 8881109 3 8274063b 2.59 × 10–7 0.000 0.004 0.000 0.005 0.998 0.000 ARHGAP42*
28 5674318 6741712 5 6241712c 1.09 × 10–6 0.002 0.004 0.996 0.000 0.006 0.000 PCNX2*
Hereford 4 105760789 106772084 113 106265147a 2.78 × 10–7 0.596 0.432 0.695 0.000 0.572 0.521 TAS2R3, TAS2R4, TAS2R38
8 4170402 5731161 6 4670402b 3.39 × 10–6 0.000 0.989 0.997 0.000 0.000 0.000 GALNTL6*, GALNT7
13 53374292 54375561 4 53874292a 2.94 × 10–6 0.784 0.292 0.690 0.727 0.309 0.880 STK35, PDYN, SIRPA
14 5352193 6396755 6 5852193a 4.29 × 10–6 0.000 0.000 0.986 0.000 0.000 0.000 COL22A1, FAM135B
18 21513927 22756651 3 22256651b 3.63 × 10–6 0.983 0.006 0.008 0.993 0.991 0.040 CHD9, RBL2, RPGRIP1L*, FTO*, IRX3
Limousin 5 16612583 17626967 5 17112583a 4.66 × 10–7 0.030 0.000 0.008 0.983 0.994 0.066
6 32350666 34490506 812 33611754a 1.95 × 10–9 0.246 0.880 0.366 0.150 0.232 0.819
6 37341111 40835172 153 38030341b 1.55 × 10–9 0.084 0.000 0.000 0.126 0.366 0.006 ABCG2^, PKD2^, SPP1*, MEPE, LAP3, NCAPG*, LCORL*
13 76534127 77546426 23 77045666d 4.01 × 10–6 0.962 0.000 0.988 0.041 0.023 0.101 NCOA3, SULF2
21 38149733 39222453 23 38702258a 3.41 × 10–7 0.000 0.940 0.003 0.002 0.997 0.000
Simmental 1 79028842 80104503 3 79590057b 1.77 × 10–7 0.022 0.040 0.000 0.040 0.005 0.027 LPP*
10 86379935 87382277 3 86879935c 1.13 × 10–6 0.009 0.988 0.000 0.000 0.995 0.000 YLPM1, PGF, EIF2B2, MLH3, ACYP1, ZC2HC1C, NEK9, TMED10
11 24184879 25302455 4 24684879a 1.36 × 10–6 0.000 0.000 0.000 0.000 0.998 0.006 PKDCC
18 9064056 10795231 11 10281382a 3.42 × 10–7 0.000 0.000 0.000 0.000 0.986 0.040 CDH13*, OSGIN1, MBTPS1, DNAAF1, TAF1C
22 25717794 30456249 16 29136317a 1.11 × 10–6 0.000 0.030 0.000 0.987 0.997 0.000 CHL1*, CNTN3, PDZRN3, GXYLT2
Holstein Friesian 1 8144528 9875908 27 9335614a 1.37 × 10–6 0.097 0.209 0.206 0.000 0.783 0.226 ADAMTS1, ADAMTS5, APP
9 31692809 33191394 7 32273403a 3.55 × 10–6 0.005 0.021 0.006 0.973 0.030 0.995 MAN1A1*, ASF1A, CEP85L, PLN, SLC35F1
13 78476376 79544490 4 78976376a 1.23 × 10–6 0.862 0.640 0.923 0.629 0.701 0.230 SNAI1, UBE2V1, PTPN1
20 63192522 64260191 3 63722163a 2.03 × 10–7 0.003 0.025 0.000 0.023 0.995 0.995 TAS2R1, SEMA5A
24 49503031 50528738 3 50024697b 5.55 × 10–7 0.081 0.901 0.938 0.066 0.023 0.936 ACAA2, MYO5B*, MBD1, CXXC1

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.