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Table 3 Significant and suggestive SNP based on false discovery rate (FDR) q threshold of 0.05 and 0.2 for feed efficiency traits using single locus regression model (SLRM) on 339 SNPs

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

Trait1 Gene ID2 BTA3 Ref. SNP4 Pos. ( bp)5 MAF6 Alleles7 n8 Estimate ± SE9 P-value
ADG 523789 3 rs42417924 75523597 0.102 C/G 726 -0.062 ± 0.02 0.0104&
DMI 616055 5 ss914082855 119551668 0.37 A/G 726 -0.234 ± 0.08 0.0025*
DMI 616055 5 ss914082856 119557146 0.37 T/C 720 -0.237 ± 0.08 0.0023*
MMWT 616908 6 rs41574929 36099801 0.388 T/G 716 0.992 ± 0.40 0.0132&
ADG 616908 6 rs41574929 36099801 0.388 T/G 716 0.049 ± 0.01 0.0009*
MMWT 540329 6 ss914082878 37288379 0.152 T/C 726 1.342 ± 0.54 0.0128&
MMWT 536203 6 ss914082880 37386084 0.16 A/G 725 1.293 ± 0.53 0.0148&
MMWT 530393 6 rs43702346 37439120 0.272 T/G 723 1.421 ± 0.43 0.0009*
DMI 784720 8 ss914082889 10674426 0.041 A/G 726 0.620 ± 0.18 0.0006*
RFI 784720 8 ss914082889 10674426 0.041 A/G 726 0.483 ± 0.15 0.0017*
MMWT 282689 10 ss914082689 50256553 0.197 T/C 725 -1.210 ± 0.48 0.01&
MMWT 282689 10 ss914082690 50259055 0.046 A/G 726 2.184 ± 0.89 0.015&
MMWT 614507 10 ss914082694 79315960 0.364 T/C 718 0.933 ± 0.39 0.0176&
RFI 533166 15 rs41755948 30710940 0.207 T/C 726 -0.201 ± 0.07 0.007&
RFI 533166 15 ss914082737 30717928 0.207 T/C 726 -0.201 ± 0.07 0.007&
RFI 521326 16 rs41821600 64875340 0.037 A/T 726 0.496 ± 0.17 0.0033*
RFI 521326 16 rs41820824 64950387 0.012 A/G 726 0.785 ± 0.29 0.0064*
RFI 508025 18 ss914082760 17150858 0.365 T/C 723 0.191 ± 0.06 0.0028*
FCR 282411 19 rs41914675 37278418 0.072 A/G 726 0.278 ± 0.10 0.004&
RFI 282411 19 rs41914675 37278418 0.072 A/G 726 0.342 ± 0.12 0.004&
DMI 282411 19 rs41914675 37278418 0.072 A/G 726 0.462 ± 0.14 0.0008*
RFI 524684 21 rs43020736 29054823 0.371 T/C 726 -0.162 ± 0.07 0.016&
DMI 524684 21 rs43020736 29054823 0.371 T/C 726 -0.248 ± 0.08 0.0018*
RFI 524684 21 rs43020769 29060759 0.478 A/G 726 0.172 ± 0.07 0.009&
MMWT 532512 25 ss914082815 36278405 0.11 T/C 719 1.555 ± 0.63 0.014&
MMWT 532512 25 ss914082816 36279504 0.02 T/C 726 3.099 ± 1.31 0.018&
MMWT 515895 27 ss914082827 39798548 0.08 A/G 726 -2.298 ± 0.71 0.0013*
DMI 508697 28 ss914082834 7727734 0.426 A/G 726 -0.211 ± 0.08 0.0067*
RFI 508697 28 ss914082834 7727734 0.426 A/G 726 -0.183 ± 0.07 0.005*
RFI 780878 28 ss914082829 13580673 0.187 T/A 726 -0.208 ± 0.08 0.009*
  1. 1average daily gain (ADG), kg d-1, average daily dry matter intake (DMI), kg d-1, mid-point metabolic weight (MMWT), kg75, feed efficiency conversion ratio (FCR), kg gainkg-1 DM and residual feed intake (RFI) kg d-1.
  2. *is a significant SNP after adjusting for chromosome-wise 5% false discovery rate.
  3. & is a suggestive SNP after adjusting for chromosome-wise 20% false discovery rate.
  4. Gene ID2 = Entrez gene identifier.
  5. BTA3 = Bos taurus autosome.
  6. 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.
  7. Pos. (bp)5 = the SNP’s position in a base pair.
  8. MAF6 = minor allele frequency.
  9. Alleles7 = first allele/second allele, the second allele is the minor allele which the phenotypes regressed on its number (0, 1, and 2).
  10. n8 = Number of animals’ phenotypes and genotypes for testing the association.
  11. Estimate ± SE9 = allele substitution effect ± standard error.