Summary of nuclear markers significantly associated/linked<sup>1</sup> to growth traits and their annotations.

1<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036264#pone.0036264-Purcell1" target="_blank">[22]</a>.</p>2<p>SNPs minor allele frequency (MAF).</p>3<p>SNPs showing deviation from Hardy-Weinberg equilibrium. Exact <i>P</i>-value estimated using 20,000 permutations.</p>4<p>QTDT population stratification test.</p>5<p><i>t</i>-statistic for regression of phenotype on allele count P is the asymptotic <i>P</i>-value for <i>t</i>-statistic, was estimated using 20,000 permutations.</p>6<p>Genome-wide association analysis with family data (GWAF) R package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036264#pone.0036264-Chen1" target="_blank">[23]</a>.</p>7<p>Family-based Measured Genotype and QTLD analysis was performed with software SOLAR version 4.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036264#pone.0036264-Almasy1" target="_blank">[24]</a> or QTDT quantitative trait disequilibrium test <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036264#pone.0036264-Abecasis1" target="_blank">[21]</a>.</p>8<p>Family-based Bayesian quantitative trait nucleotide (BQTN) analysis was performed with software SOLAR version 4.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036264#pone.0036264-Almasy1" target="_blank">[24]</a>.</p>9<p>SNP annotation; gene name and SNP location (ORF/5′UTR/3′UTR), SYN = Synonymous, NON-SYN = Non-synonymous.</p><p>NA indicates statistically insignificant estimate.</p>