Location of SNP within the promoter and untranslated region of chicken Mx.

<p>galGal4 Mx promoter region starting 400 nt upstream of the RNA transcription initiation site through the first 140 nt of the RNA transcript (excluding 4,647 nt from intron 1) are shown above. The previously described ISRE (−52 to −63) as well as other potential functional elements (ISRE2, −282 to −293; SP1-like element, −135 to −142; TATA box-like element, −19 to −12) are underlined. The “GAAA” motif found repeated in many IFN regulated gene promoter regions are shown in bold. SNP found in the 9 elite lines that differ from galGal4 are shown under the reference sequence. Additionally, the RNA transcription initiation and Mx 5′UTR, comprised of exon 1 and the first 92 nt of exon 2, is shown in italics.</p

Location of SNP within the promoter and untranslated region of chicken Mx.

<p>galGal4 Mx promoter region starting 400 nt upstream of the RNA transcription initiation site through the first 140 nt of the RNA transcript (excluding 4,647 nt from intron 1) are shown above. The previously described ISRE (−52 to −63) as well as other potential functional elements (ISRE2, −282 to −293; SP1-like element, −135 to −142; TATA box-like element, −19 to −12) are underlined. The “GAAA” motif found repeated in many IFN regulated gene promoter regions are shown in bold. SNP found in the 9 elite lines that differ from galGal4 are shown under the reference sequence. Additionally, the RNA transcription initiation and Mx 5′UTR, comprised of exon 1 and the first 92 nt of exon 2, is shown in italics.</p

Evidence of sites within the chicken Mx under selection.

a<p>chicken Mx codons with evidence of diversifying selection (dNS > dS) or purifying selection (dS > dNS).</p>b<p>p-value, *significance ≤0.1.</p>c<p>Bayes factor, * significance >50 significant.</p>d<p>Posterior probability, *significance ≥0.9.</p>e<p>not significant.</p><p>Evidence of sites within the chicken Mx under selection.</p

Predicted chicken Mx structure.

<p>The chicken Mx sequences were each analyzed using the RaptorX protein structure prediction server. These results identified the crystal structure of human MxA (PDB ID: 3SZR) as the most closely related to the chicken Mx sequence. These results where then visualized using PolyMol, and the regions of the HsMxA (aa#s) and chicken Mx (aa#s) compared. As before the GTPase Domain is shown in orange, the bundle signaling elements are in red, the stalk region which is comprised of the central dyanmin region and the GTPase effector domain are shown in green and blue respectively. The conserved proline residue that forms the hinge between the G-domain and the second BSE is shown in black.</p

Mx haplotypes with significant effect.

1<p>First haplotype has the most favorable effect for each trait.</p>2<p>MM: mortality (%) due to MDV challenge; LM: mortality (%) during lay in commercial environments.</p>3<p>SM: sexual maturity (age at first egg), PD: production rate (%), AH: albumen height (mm), CO: shell color index, EW: egg weight (g), PS: shell resistance (N).</p><p>Mx haplotypes with significant effect.</p

Primers used for amplification and sequencing.

<p>Primers used for amplification and sequencing.</p

Amino acid alignment of the HsMxA and galGal4.

<p>The different Mx functional domains are represented in colored text (BSE  =  red, G-domain  =  orange, Middle stalk domain  =  green, GTPase effector domain  =  blue) with the N-terminal region not represented in shown in italics, and the loop regions that connect BSE2 to MD (L1^BS) and MD to GED (L4^S) in plain text. Positions in orange bold represent the conserved GTPase enzymatic domain and underlined orange text denotes the GTP binding site. Secondary structural elements as described by Gao et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108054#pone.0108054-Gao1" target="_blank">[23]</a> et al. are indicated above the HsMxA sequence. Alpha helices are represented by red and with stripped bars. Beta strands are represented by arrows. Amino acids with similar numbers above the alignment indicate positions described to interact during oligimerization. HsMxA positions labeled with “#” indicates amino acid with forms hydrogen bonds with the backbone of the α3^B, and “!” denote additional positions described to be involved in oligemerization. “+” above the hsMxA indicates amino acid described by Mitchell et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108054#pone.0108054-Mitchell1" target="_blank">[30]</a> as under diversifying selection among primate MxA sequences. Amino acid positions in the chMx associated with dNS changes are reflected by the alternate amino acid under the chMx sequence. Positions associated with dS nt changes are indicated by “∧”. chMx positions with evidence of diversifying (dNS) or purifying (dS) selection are indicated with “+” or “−” under the chMx sequence.</p

Mx SNP with a significant allele substitution effect, and allele with favorable effect by trait.

1<p>MM: mortality (%) due to MDV challenge; LM: mortality (%) during lay in commercial environments.</p>2<p>EN: number of eggs produced, PD: rate of lay (%), AH: albumen height (mm), CO: shell color index, EW: egg weight (g), PS: shell resistance (N), Def: external egg defects.</p><p>Mx SNP with a significant allele substitution effect, and allele with favorable effect by trait.</p

Mx haplotype frequency changes over time by line.

1<p>not significant.</p><p>Mx haplotype frequency changes over time by line.</p