Assessment the effect of genomic selection and detection of selective signature in broilers

Abstract

Due to high selection advances and shortened generation interval, genomic selection (GS) is now an effective animal breeding scheme. In broilers, many studies have compared the accuracy of different GS prediction methods, but few reports have demonstrated phenotypic or genetic changes using GS. In this study, the paternal chicken line B underwent continuous selection for 3 generations. The chicken 55 k SNP chip was used to estimate the genetic parameters and detect genomic response regions by selective sweep analysis. The heritability for body weight (BW), meat production, and abdominal fat traits were ranged from 0.12 to 0.38. A high genetic correlation was found between BW and meat production traits, while a low genetic correlation (<0.1) was found between meat production and abdominal fat traits. Selection resulted in an increase of about 516 g in BW and 140 g in breast muscle weight. Percentage of breast muscle and whole thigh were increased 0.8 to 1.5%. No change was observed in abdominal fat percentage. The genomic estimated breeding value advances was positive for BW and meat production (except whole thigh percentage), while negative for abdominal fat percentage. By selective sweep analysis, 39 common chromosomal regions and 102 protein coding genes were found to be influenced, including MYH1A, MYH1B, and MYH1D of the MYH gene family. Tight junction pathway as well as myosin complex related terms were enriched. This study demonstrates the effective use of GS for improvements in BW and meat production in chicken line B. Further, genomic regions, responsive to intensive genetic selection, were identified to contain genes of the MYH family.

Keywords: body weight; chicken; genomic selection; meat production traits; selective sweep.

Figure 1

The genetic changes in different generations. (A–G) The genetic changes from G4 to G7 for BW, BrW, ThW, AbFW, BrP, ThP, and AbFP, respectively. The vertical axis was shown as the ratio of mean GEBV to standard deviation.

Figure 2

Average LD decay with increased physical distance between paired SNPs in each generation. The different color indicated four generations and merged populations (G4567). The LD decay distance (reduced to 0.1) was gradually increased (G7 > G6 > G5 > G4).

Figure 3

Selected regions in each generation compared to G4. (A–C) Selected regions in G5, G6, and G7, respectively. The x-axis represented π in log2 scale, and y-axis represented Fst index. The blue bars indicated the frequency of different π in log2 scale, and the orange bar indicated the frequency of different Fst value. The red dots represented the regions under selection, the blue dots represented the selected regions among three comparisons, while the gray dots represented the unselected regions. The dotted line indicated the top 5% threshold of Fst index and genetic diversity. Some limitations on Fst value and π were shown in figures, the full results was shown as Table S4.