Table 4. Summary of nuclear markers significantly associated/linked1 to growth traits and their annotations.
| SNP | MAF2 | HW3 | QTDT 4 stratification test | Statistical Test(s) | Annotation9 | Location/amino acid change |
| nuSNP7 | 0.106 | NA | NA | 5,6,7,8 | Glucose phosphate isomerase b | 5′UTR |
| nuSNP1 | 0.354 | 1.00E−03 | NA | 5 | Enolase 3-1 | ORF/SYN |
| nuSNP8 | 0,142 | NA | NA | 6 | ATP2A1 calcium ATPase 3 | ORF/SYN |
| nuSNP17 | 0.313 | 1.20E−03 | NA | 5 | Myosin binding protein C | ORF/SYN |
| nuSNP20 | 0.033 | NA | NA | 6 | Myosin binding protein C | ORF/SYN |
| nuSNP21 | 0.036 | NA | <0.01 | 6,7 | Myosin binding protein C | ORF/SYN |
| nuSNP25 | 0.232 | NA | NA | 6,7,8 | Fast myotomal muscle actin 2 | ORF/SYN |
| nuSNP22 | 0.199 | NA | NA | 5 | Troponin C | 3′UTR |
| nuSNP23 | 0.189 | NA | NA | 5 | Troponin C | 3′UTR |
| nuSNP24 | 0.199 | NA | NA | 5 | Troponin C | 3′UTR |
| nuSNP27 | 0.138 | NA | <0.05 | 5 | Fast myotomal muscle troponin-T-2 | ORF/N→K |
| nuSNP29 | 0.235 | NA | NA | 5 | Taxilin beta muscle-derived protein 77 | ORF/G→A |
| nuSNP9 | 0.189 | 7.20E−03 | <0.05 | 5 | 60 S ribosomal protein L4-A | ORF/SYN |
| nuSNP12 | 0.337 | NA | NA | 6,7 | Unknown | Unknown |
Body weight was recorded on each animal at approximately 7 (Weight2), 9 (Weight3) and 12 (Weight4) months post-hatching. A family-based sample that included 40 full-sib families each with 17 progeny were genotyped with 30 SNPs. Summary statistics were obtained with program PLINK version 1.07 [22].
SNPs minor allele frequency (MAF).
SNPs showing deviation from Hardy-Weinberg equilibrium. Exact P-value estimated using 20,000 permutations.
QTDT population stratification test.
t-statistic for regression of phenotype on allele count P is the asymptotic P-value for t-statistic, was estimated using 20,000 permutations.
Genome-wide association analysis with family data (GWAF) R package [23].
Family-based Measured Genotype and QTLD analysis was performed with software SOLAR version 4.0 [24] or QTDT quantitative trait disequilibrium test [21].
Family-based Bayesian quantitative trait nucleotide (BQTN) analysis was performed with software SOLAR version 4.0 [24].
SNP annotation; gene name and SNP location (ORF/5′UTR/3′UTR), SYN = Synonymous, NON-SYN = Non-synonymous.
NA indicates statistically insignificant estimate.