Table 2.
BTA | BTA SNP and indel-id | positon (bp) _UMD3,1a | Q/q haplotype | Number of animals genotyped for the haplotype | Minor allele frequency | Heritability | Haplotype effect on total genetic varianceb | Haplotype substitution P-valued effectc | P-valued |
---|---|---|---|---|---|---|---|---|---|
2 | g. 48476925C>T and g.48476943_48476946insGGC | 48476925 and 48476943. 48476946 | T and GCC/C and (-) | 1433 | 0.39 | 0.02 | 0.1 | 0.02 | 0.017 |
aThe positions shown are based on the UMD3.1 assembly of the bovine genome.
bThe effects of the haplotype were estimated as the least-square means from GLM analysis. The statistical model for GLM analysis included the fixed variables of the farm, birth year, and haplotype. The genetic variance explained by the haplotype was calculated based on estimates of the haplotype effect and the haplotype frequency [55]. Total genetic variance was estimated using the MTDF-REML programs. The effect size of haplotype was estimated as the proportion of genetic variance explained by the haplotype.
cThe average ANAI4 values for QQ and qq were 0.69 and 0.65, respectively.
dResults were tested by a 1-way ANOVA, followed by the Tukey–Kramer test for multiple comparisons