Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks

Abstract

Background: Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks.

Results: We measured 18 carcass traits in 639 Pekin ducks and performed genotyping using genotyping-by-sequencing (GBS). Loci-based association analysis detected 37 significant loci for the 17 traits. Thirty-seven identified candidate genes were involved in many biological processes. One single nucleotide polymorphism (SNP) (Chr1_140105435 A > T) located in the intron of the ATPase phospholipid transporting 11A gene (ATP11A) attained genome-wide significance associated with five weight traits. Eight SNPs were significantly associated with three body size traits, including the candidate gene plexin domain containing 2 (PLXDC2) associated with breast width and tensin 3 (TNS3) associated with fossil bone length. Only two SNPs were significantly associated with foot weight and four SNPs were significantly associated with heart weight. In the gene-based analysis, three genes (LOC101791418, TUBGCP3 (encoding tubulin gamma complex-associated protein 3), and ATP11A) were associated with four traits (42-day body weight, eviscerated weight, half-eviscerated weight, and leg muscle weight percentage). However, no loci were significantly associated with leg muscle weight in this study.

Conclusions: The novel results of this study improve our understanding of the genetic mechanisms regulating body growth in ducks and thus provide a genetic basis for breeding programs aimed at maximizing the economic potential of Pekin ducks.

Keywords: Body size; Carcass trait; Genome-wide association study; Pekin duck.

Fig. 1

Manhattan plots showing associations of all SNPs with five traits and quantile-quantile (Q-Q) plots of the GLM (black dots) for five traits (a. DW, b. EW, c. HEW, d. BW42, e. WW). One SNP reached genome-wide significance for the five above traits. In Manhattan plots, SNPs are plotted on the x-axis according to their position on each chromosome, against association with these traits on the y-axis (shown as −log₁₀P-value). Blue solid line indicates suggestive significance association (P = 3.48E− 05), and red solid line shows genome-wide significance with a P-value threshold of 1.74E− 06. In Q-Q plots, expected P-values under the null hypothesis are plotted on the x-axis and observed P-values on the y-axis. The estimated genomic inflation factor λ ranged from 1.03–1.06

Fig. 2

Region of significant loci for DW (a), EW (b), HEW (c), BW42 (d), and WW (e). Blue curve represents the minor allele frequency; dot color represents the linkage coefficient between the most significant locus and other loci (red highest)