Table 2 Location of the most significant QTL, limited to the top 5 per breed which were associated with development of loin, 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 | 39155170 | 40155196 | 3 | 39655188a | 1.06 × 10−6 | 0.003 | 0.015 | 0.000 | 0.967 | 0.976 |  |
|  | 10 | 5741208 | 6752759 | 54 | 6241208a | 3.45 × 10−6 | 0.181 | 0.105 | 0.090 | 0.773 | 0.872 | GCNT4, HMGCR |
|  | 11 | 21539414 | 22560915 | 4 | 22049725c | 6.26 × 10−6 | 0.032 | 0.928 | 0.904 | 0.000 | 0.068 | CDKL8, MAP4K3 |
|  | 15 | 53716499 | 55635294 | 27 | 55096343a | 1.43 × 10−6 | 0.993 | 0.000 | 0.000 | 0.000 | 0.996 | RAB6A, MRPL48, UCP2, UCP3d, PPME1, NEU3 |
|  | 19 | 12894306 | 13934964 | 9 | 13430257a | 2.23 × 10−6 | 0.045 | 0.088 | 0.969 | 0.102 | 0.044 | USP32, MYO19, ACACA |
CH | 1 | 142705947 | 143712126 | 78 | 143205947c | 3.50 × 10−6 | 0.000 | 0.010 | 0.005 | 0.972 | 0.993 | BACE2, RIPK4, PRDM15, C2CD2 |
|  | 2 | 37387 | 8714844 | 1728 | 6808074a | 1.19 × 10−26 | 0.000 | 0.079 | 0.000 | 0.028 | 0.004 | WDR75e, ASNSD1e, MFSD6e, MSTNe, PMS1e, ORMDL1, COL3A1e, COL5A2e, ANKARe, SLC40A1e |
|  | 10 | 84923776 | 85960329 | 2 | 85423776a | 4.45 × 10−7 | 0.000 | 0.007 | 0.000 | 0.000 | 0.024 | PSEN1, ACOT2, ACOT4, DNAL1, ZNF410, FAM161B, COQ6 |
|  | 16 | 32025893 | 33120555 | 127 | 32558878a | 4.12 × 10−7 | 0.975 | 0.884 | 0.135 | 0.898 | 0.093 | SMYD3, KIF26B, EFCAB2 |
|  | 24 | 45933369 | 46937392 | 5 | 46437392b | 1.20 × 10−6 | 0.000 | 0.006 | 0.012 | 0.000 | 0.019 | PSTPIP2, ST8SIA5 |
HE | 2 | 79648265 | 81037622 | 15 | 80168803b | 1.42 × 10−6 | 0.000 | 0.994 | 0.996 | 0.987 | 0.997 | STAT1, MYO1Bd, NABP1 |
|  | 4 | 3339555 | 4351559 | 4 | 3851559a | 1.16 × 10−7 | 0.014 | 0.034 | 0.025 | 0.884 | 0.952 | ENSBTAG00000044810 |
|  | 11 | 17934758 | 18942324 | 3 | 18442324a | 1.11 × 10−6 | 0.876 | 0.011 | 0.011 | 0.964 | 0.988 | CRIM1 |
|  | 16 | 75812761 | 76823259 | 3 | 76312761a | 1.94 × 10−6 | 0.911 | 0.000 | 0.030 | 0.000 | 0.937 | ENSBTAG00000044497 |
|  | 29 | 9233633 | 10275049 | 26 | 9733633a | 1.80 × 10−6 | 0.650 | 0.417 | 0.304 | 0.378 | 0.801 | EED, SYTL2, CREBZF, TMEM126A, TMEM126B |
LM | 2 | 5545383 | 8287013 | 748 | 6747317a | 6.69 × 10−10 | 0.198 | 0.409 | 0.617 | 0.073 | 0.511 | WDR75d, ASNSD1d, MFSD6, MSTNd, PMS1d, ORMDL1, COL3A1, COL5A2d, ANKARe, SLC40A1d |
|  | 3 | 99009887 | 100073842 | 5 | 99509887b | 5.78 × 10−7 | 0.041 | 0.000 | 0.047 | 0.934 | 0.883 | CYP4X1, CYP4A22 |
|  | 5 | 71738658 | 72751064 | 6 | 72238658b | 2.70 × 10−6 | 0.000 | 0.819 | 0.163 | 0.251 | 0.830 | SYN3, TIMP3, MGC137211, MGC137014, LARGE1d |
|  | 6 | 110629080 | 112106706 | 11 | 111176155a | 3.30 × 10−7 | 0.126 | 0.868 | 0.898 | 0.830 | 0.211 | HS3ST1 |
|  | 12 | 32803688 | 33961156 | 7 | 33461156b | 5.12 × 10−7 | 0.000 | 0.000 | 0.000 | 0.997 | 0.975 | USP12, SHISA2 |
SI | 7 | 58665425 | 60243933 | 10 | 59590500a | 3.37 × 10−7 | 0.002 | 0.016 | 0.046 | 0.000 | 0.990 | SH3RF2d |
|  | 8 | 90813081 | 91857894 | 14 | 91313081a | 5.24 × 10−7 | 0.957 | 0.627 | 0.064 | 0.346 | 0.291 | SPIN1, FBXW12 |
|  | 14 | 79527472 | 81070931 | 18 | 80091780b | 3.45 × 10−7 | 0.908 | 0.052 | 0.981 | 0.114 | 0.070 | E2F5 |
|  | 17 | 69082585 | 70268366 | 4 | 69646862b | 1.04 × 10−7 | 0.975 | 0.010 | 0.987 | 0.992 | 0.003 | PITPNBd |
|  | 22 | 33231032 | 34644069 | 14 | 34044822b | 9.77 × 10−9 | 0.000 | 0.960 | 0.946 | 0.000 | 0.004 | FAM19A1, SUCLG2e, KBTBD8 |