Signature of selection reveals large difference in selection traits
Selection on animals changes the population-wide frequency spectrum of genes related to the traits under selection. With the aid of single-nucleotide polymorphism (SNP) methods, it is possible to inspect for changes in allelic frequencies directly. In order to reveal the impact of recent selection on genetic variation, we compared the allele frequencies before and after three generations of selection on an index of three traits in two lines (F and M) sampled from commercial broiler chicken. Line M animals are from a sire line that was selected mainly for growth traits, and line F animals are from a dam line that was selected mainly for reproductive traits. Selection was performed by applying single-step Genomic Best Linear Unbiased Prediction (ssGBLUP). Genotypes were used in this study for allele frequency analysis. The M and F lines consisted of 4,922 and 4,904 genotyped animals, respectively.
After quality control, genotypes included information on 52,742 and 52,639 SNPs in line M and F, respectively. Selection was for an index consisting of body weight at 6 wk, ultrasound measurement of breast meat, and leg score. The average allele frequency change for both lines on autosomes was 0.049. Threshold value for detecting selected regions, where allele frequency changes exceeded expectations under drift were 0.140 and 0.136 for line M and F, respectively. There were 25 and 17 selection regions detected on line M and F, respectively, without any overlap of regions between the lines. Average 4heterozygosity change in line F was greater compared to line M (0.008 vs. 0.003, P<0.01). The putative selected regions between line M and F are different.
The results we present indicate that in newly selected populations, the genotype frequencies across chromosomes change differently according to the selection lines even if animals are selected for same traits.
Keywords: SNP, allele frequency change, genomic selection