MOESM1 of Effects of number of training generations on genomic prediction for various traits in a layer chicken population

Additional file 1: Table S1. Examples of experimental design for training (T) and validation (V) sets. Table S2. Description of the average number of individuals with own phenotypes and genotypes in each generation for early and late traits. Table S3. Mean accuracies (¹ SD) of genomic predictions over 5 replicates for different training sets and for the studied traits. In this analysis, G10 was used as the validation generation and training individuals were randomly sampled from G4 to G9. (1) eCO (early egg color); (2) eC3 (early color of first 3 eggs; (3) eE3 (early weight of first 3 eggs); (4) eSM (early age at sexual maturity); (5) eAH (early albumen height); (6) eYW (early yolk weight); (7) ePD (early egg production rate); (8) ePS (early egg puncture score); (9) lCO (late egge color); (10) lEW (late average weight of 3-5 eggs); (11) lBW (late body weight); (12) lAH (late albumen height); (13) lYW (late yolk weight); (14) lPD (late egg production rate); (15) lPS (late egg puncture score)

MOESM2 of Effects of number of training generations on genomic prediction for various traits in a layer chicken population

Additional file 2: Figure S1. Scatter plot of accuracies of genomic predictions across different validation sets over training generations for each trait. The blue line is the regression of the accuracy on the number of training generations. The red line indicates the optimal number of training generations. The R-squared of regression line is presented as r2

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

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

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

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

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

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

Primers used for amplification and sequencing.

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