Table 3.
Identity, position, and effects of significantly associated dominance SNPs obtained by single SNP regression mixed model for birth weight (BWT), weaning weight (WWT), pre-weaning daily gain (PDG), yearling weight (YWT) and marbling score (MBS) in beef cattle
| Traits | Groups | SNP reference | BTA | Position | MAF | p value | FDR (%) | Allele substitution effects | Dominance effects | Genes | Region |
|---|---|---|---|---|---|---|---|---|---|---|---|
| BWT (kg) | C | rs110704582 | 1 | 113,215,525 | 0.327 | 4.60e−07 | 5 | 0.404 | − 0.942 | U6atac | Intergenic |
| C | rs41596755 | 6 | 55,697,300 | 0.244 | 3.91e−06 | 10 | 0.552 | 1.012 | – | Intergenic | |
| WWT (kg) | P | rs42779004 | 21 | 36,186,103 | 0.196 | 2.74e−07 | 5 | − 4.016 | 6.994 | bta-mir-2888-1 | Intergenic |
| A | rs29027109 | 3 | 98,222,548 | 0.387 | 2.64e−07 | 5 | − 0.361 | 2.610 | AGBL4 | Intron | |
| PDG (kg/d) | P | rs42779004 | 21 | 36,186,103 | 0.196 | 1.89e−06 | 10 | − 0.019 | 0.037 | bta-mir-2888-1 | Intergenic |
| A | rs29027109 | 3 | 98,222,548 | 0.387 | 2.29e−06 | 10 | − 0.001 | 0.016 | AGBL4 | Intron | |
| YWT (kg) | C | rs109808526 | 4 | 113,614,764 | 0.318 | 1.18e−06 | 10 | − 1.562 | 6.316 | REPIN1 | Intergenic |
| MBS | A | rs110361335 | 4 | 17,230,513 | 0.182 | 6.47e−07 | 5 | 8.317 | 13.88 | ICA1 | Intron |
| A | rs110564527 | 4 | 17,657,399 | 0.207 | 1.20e−07 | 5 | − 8.023 | 15.37 | NXPH1 | Intergenic |
P = purebred sample included individuals with > 80% of Angus, Hereford and Charolais (n = 1467); C = crossbred sample included Kinsella composite, Beefbooster TX composite (www.beefbooster.com) and two and more way crosses involving Angus, Hereford, Charolais, Gelbvieh, Simmental, Limousin, and Piedmontese breeds (n = 5327); A = combined data of all individuals in the study (n = 6794)