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

• Published in: BMC genomics Vol. 20; no. 1; p. 1
• Main Authors: Deng, Meng-Ting, Zhu, Feng, Yang, Yu-Ze, Yang, Fang-Xi, Hao, Jin-Ping, Chen, Si-Rui, Hou, Zhuo-Cheng
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03.01.2019; BioMed Central; BMC
• Subjects: Adenosine triphosphatase; Aquatic birds; Association analysis; ATPases; Beef cattle; Bioinformatics; Biological activity; Body size; Body weight; Breeding; Carcass trait; Ducks; Gene expression; Gene polymorphism; Genes; Genetic aspects; Genetic polymorphisms; Genome-wide association studies; Genome-wide association study; Genomes; Genomics; Genotyping; Hogs; Leg; Muscles; Novels; Pekin duck; Phospholipids; Physiological aspects; Polymorphism; Poultry industry; Principal components analysis; Proteins; Quantitative genetics; Quantitative trait loci; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies; Tensin; Tubulin; Waterfowl; China; Pekin duck; Genome-wide association study; Carcass trait; Body size
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-018-5379-1

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. 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. 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.