Population Genomic Analyses Based on 1 Million SNPs in Commercial Egg Layers

<div><p>Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, F_ST, is a useful index for evaluation of genetic differentiation between populations. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise F_ST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for F_ST calculation. Averages of F_ST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were <i>NCOA1</i>, <i>SREBF2</i> and <i>RALGAPA1</i> associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including <i>POMC</i>, <i>PRKAB2</i>, <i>SPP1</i>, <i>IGF2</i>, <i>CAPN1</i>, <i>TGFb2</i> and <i>IGFBP2</i>. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection.</p></div

Result of ADMIXTURE structural analysis with null hypothesis of six breeds.

<p>Two rightmost individuals in OG are Gallus gallus gallus, and the third and fourth last individuals are Gallus gallus spadiceus.</p

Name, abbreviation, number of individuals and the egg color for each breed used in this study.

<p>Name, abbreviation, number of individuals and the egg color for each breed used in this study.</p

FST-values of overlapping windows for comparison between commercial layers and out-group.

<p>Red (blue) line indicates the upper (lower) 1% of FST distribution.</p

FST-values of overlapping windows for comparison between brown layers and white layers.

<p>Red (blue line) indicates the upper (lower) 1% of FST distribution.</p

Average F_ST values with standard deviation over all SNPs for all compression.

<p>Average F_ST values with standard deviation over all SNPs for all compression.</p

Genes associated to productive traits in both comparisons. ≠ symbol stands for difference between two group and = symbol stand for similarity between two groups.

<p>B and W stand for comparison between brown and white egg layers and L and G stand for comparison between commercial layers and out-group.</p

Score values for severity of organ lesions ± standard deviation in respiratory and other organs.

<p>Infection with IMT5155, IMT5155Δ<i>yqi</i> and IMT11327 at infection dose 10⁹ CFU. Differences in organ scores between IMT5155 and IMT5155Δ<i>yqi</i> and between IMT5155 and negative control IMT11327 were statistically significant for air sacs, lungs and liver with a <i>p</i><0.05^*.</p

Bacterial adhesion to chicken fibroblast cells 1.5 h and 3 h after infection with an MOI = 100.

<p>Differences between IMT5155 and IMT5155Δ<i>yqi</i> were statistically significant with a <i>p</i><0.005 at 1.5 h and <i>p</i><0.05 at 3 h (A). Bacterial adhesion to polarized Madin Darby canine kidney (MDCK-1) cells 3 h after infection with an MOI = 100. The difference between IMT5155Δ<i>yqi</i> and IMT5155Δ<i>yqi</i> (pDSK602:<i>yqi</i>) was significant with a <i>p</i><0.04 (B).</p

Smoothed curves of squared correlation coefficients <i>r</i>² (upper panel) and rS2 (lower panel), calculated for SNP pairs in genic regions (red lines) versus matching non-genic regions (blue lines) with confidence regions (shaded gray) in <i>A</i>. <i>thaliana</i>, <i>H</i>. <i>sapiens</i> and <i>G</i>. <i>g</i>. <i>domesticus</i>, plotted against the physical distance in kilo base pairs.

<p>Smoothed curves of squared correlation coefficients <i>r</i>² (upper panel) and <math><mrow><msubsup><mi>r</mi><mi>S</mi><mn>2</mn></msubsup></mrow></math> (lower panel), calculated for SNP pairs in genic regions (red lines) versus matching non-genic regions (blue lines) with confidence regions (shaded gray) in <i>A</i>. <i>thaliana</i>, <i>H</i>. <i>sapiens</i> and <i>G</i>. <i>g</i>. <i>domesticus</i>, plotted against the physical distance in kilo base pairs.</p