Summary of nuclear markers significantly associated/linked¹ to growth traits and their annotations.

1

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].

2

SNPs minor allele frequency (MAF).

3

SNPs showing deviation from Hardy-Weinberg equilibrium. Exact P-value estimated using 20,000 permutations.

4

QTDT population stratification test.

5

t-statistic for regression of phenotype on allele count P is the asymptotic P-value for t-statistic, was estimated using 20,000 permutations.

6

Genome-wide association analysis with family data (GWAF) R package [23].

7

Family-based Measured Genotype and QTLD analysis was performed with software SOLAR version 4.0 [24] or QTDT quantitative trait disequilibrium test [21].

8

Family-based Bayesian quantitative trait nucleotide (BQTN) analysis was performed with software SOLAR version 4.0 [24].

9

SNP annotation; gene name and SNP location (ORF/5′UTR/3′UTR), SYN = Synonymous, NON-SYN = Non-synonymous.

NA indicates statistically insignificant estimate.