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Table 4 Significant SNP based on false discovery rate (FDR) q threshold of 0.05 for beef carcass traits using single locus regression model

From: Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Trait1 Gene ID2 BTA3 Ref. SNP4 BPPos5 MAF6 n7 Estimate ± SE8 P-value*
LR 539020 1 rs43246339 81372644 0.165 664 1.151 ± 0.266 0.00002
IFR 539020 1 rs43246339 81372644 0.167 687 -0.622 ± 0.172 0.0003
IFR 614882 2 rs43287969 1280728 0.329 648 0.404 ± 0.143 0.005
F3 532545 2 rs43307594 43392336 0.379 847 0.473 ± 0.15 0.0016
IFR 538378 2 rs42315485 58475918 0.035 687 -0.968 ± 0.355 0.0065
Marbling 522946 3 ss914082840 2555332 0.445 851 -0.097 ± 0.028 0.00066
Marbling 522946 3 ss914082841 2557106 0.379 837 -0.092 ± 0.031 0.003
LMA 532836 4 rs41599809 96565402 0.107 848 3.08 ± 0.975 0.0016
LMA 532836 4 ss914082853 96570062 0.37 848 -1.807 ± 0.617 0.0035
Marbling 538086 5 ss914082862 50301829 0.414 851 -0.091 ± 0.03 0.0025
IFR 503621 6 ss914082876 32016672 0.131 687 0.625 ± 0.191 0.001
HCW 616908 6 rs41574929 36099801 0.397 949 5.277 ± 1.916 0.006
Marbling 540329 6 ss914082878 37288379 0.166 851 -0.117 ± 0.038 0.002
IFR 540329 6 ss914082878 37288379 0.14 687 -0.535 ± 0.178 0.0028
HCW 540329 6 ss914082878 37288379 0.162 959 7.16 ± 2.468 0.0038
Marbling 536203 6 ss914082880 37386084 0.174 850 -0.121 ± 0.037 0.001
IFR 536203 6 ss914082880 37386084 0.152 685 -0.511 ± 0.172 0.003
HCW 530393 6 rs29010894 37433382 0.124 958 -7.542 ± 2.706 0.005
IFR 530393 6 rs43702346 37439120 0.276 684 -0.393 ± 0.14 0.005
SQF 616568 7 ss914082884 10135670 0.129 928 -0.022 ± 0.008 0.004
GRF 616568 7 ss914082884 10135670 0.13 819 -0.572 ± 0.206 0.0056
Fat3 541122 9 rs43013785 33837458 0.487 841 0.431 ± 0.148 0.004
IFR 529759 11 ss914082698 80982741 0.066 687 0.928 ± 0.28 0.00097
Marbling 537649 12 ss914082709 13011713 0.294 851 0.125 ± 0.033 0.0002
F3 537649 12 ss914082709 13011713 0.293 847 0.443 ± 0.171 0.0097
IFR 535653 12 rs43694364 15748029 0.483 687 0.379 ± 0.131 0.0039
GRF 509602 12 ss914082715 76885563 0.411 845 0.409 ± 0.137 0.0029
LR 509602 12 ss914082715 76885563 0.425 663 -0.584 ± 0.201 0.0037
F3 509602 12 ss914082715 76885563 0.411 846 0.431 ± 0.15 0.004
IFR 509602 12 ss914082716 76889667 0.413 686 -0.503 ± 0.135 0.0002
LYR 509602 12 ss914082716 76889667 0.413 663 0.748 ± 0.208 0.0003
SQFR 509602 12 ss914082716 76889667 0.414 684 -0.355 ± 0.119 0.003
F3 509602 12 ss914082716 76889667 0.417 846 -0.439 ± 0.153 0.004
GRF 509602 12 ss914082716 76889667 0.418 845 -0.381 ± 0.14 0.0065
F3 512287 15 ss914082741 4101726 0.099 843 0.865 ± 0.254 0.00068
Fat1 521326 16 rs41821600 64875340 0.038 849 -2.099 ± 0.627 0.00085
Marbling 540672 20 rs43006895 54577104 0.479 851 0.1 ± 0.029 0.0006
F2 540672 20 rs43006895 54577104 0.478 850 0.904 ± 0.287 0.0017
BFR 534312 21 rs41980260 33909131 0.282 683 -0.162 ± 0.057 0.0049
BFR 534312 21 rs41980261 33909583 0.282 684 -0.151 ± 0.057 0.008
LMA 512725 23 ss914082809 32192762 0.488 848 1.609 ± 0.611 0.0086
LMA 512725 23 ss914082812 32207295 0.283 848 1.84 ± 0.703 0.009
LMA 504741 24 rs42047790 36412358 0.445 848 2.087 ± 0.625 0.0009
LMA 540050 26 rs42106947 37495213 0.488 848 -1.766 ± 0.611 0.004
BFR 518905 27 ss914082824 39712547 0.015 684 0.714 ± 0.231 0.002
IFR 515895 27 ss914082827 39798548 0.076 687 0.654 ± 0.237 0.006
SQFR 515895 27 ss914082827 39798548 0.077 685 0.569 ± 0.208 0.006
  1. 1F1, subcutaneous fat depth between the 1st and 2nd quarter of the longissimus; F2, subcutaneous fat depth between 2nd and 3rd quarter of the longissimus; F3, subcutaneous fat depth between the 3rd and 4th quarter of the longissimus; Marbling was scored as ≤ 3.0 = devoid; 3.1 to 4.0 = traces; 4.1 to 5.9 = slight; 6.0 to 7.0 = small to moderate; and ≥ 7.0 = slightly abundant to abundant; HCW = Hot carcass weight (kg); LMA = longissimus dorsi muscle area (cm2); LR = lean meat within the rib section (%); LY = Lean yield grade (%); GRF = Grade fat (mm); IFR = Intermuscular fat (%); BFR = Body cavity fat within the rib section (%); SQFR = Proportion of subcutaneous fat from the rib section (%); *is a significant SNP after adjusting for chromosome-wise 5% false discovery rate.
  2. Gene ID2 = Entrez gene identifier; BTA3 = Bos taurus autosome; Ref. SNP4 = (rs#) is a reference SNP ID number and (ss#) ID is the National Center for Biotechnology Information (NCBI) assay ID number assigned by NCBI to submitted SNPs for discovered SNPs using RNA-Seq.
  3. BPPos5 = the SNP’s position in a base pair; MAF6 = minor allele frequency; n7 = Number of animals’ phenotypes and genotypes for testing the association; Estimate ± SE8 = allele substitution effect ± standard error, the minor allele which the phenotypes regressed on its number (0, 1, and 2).