Multi-Trait Genome-Wide Association Studies Identifies Genetic Variants and Candidate Genes for Longitudinal Body Weights in Chicken

This study aimed at revealing the genetic architecture underlying the dynamic body weight of hens along with the life circle. Here, we constructed the experiment population of 1,534 F2 hens derived from reciprocal crosses between White Leghorn (WL) and Dongxiang chickens (DX). We measured the body weight (BW) at thirty time points from hatching to 72 weeks of age, average daily gains (ADG) from fortnightly body weight. The best nonlinear model was chosen to describe the weight-age data, and the whole growth process was divided into three stages (Stage 1 :0-8 wks, Stage 2 :9-20 wks, Stage 3 :21-72 wks) at the growth inflection point and age at first egg. Three growth stages were mainly determined by variants in chromosome 1 (GGA1), chromosome 4 (GGA4) and chromosome 27 (GGA27). We identified a narrow region spanning from 75.4 to 76.2 Mb of chromosome 4 (GGA4) to be strongly associated with chicken growth during weeks 8-20. In addition, A total of nine annotated candidate genes had interesting biological functions related to bone development (RB1, BST1), muscle development (LDB2, LCORL), body size (NCAPG), skeletal muscle development (FOXO1), Copper transport (ATP7B), adipogenesis (NGFR, GIP). The rs318027552 (GGA1) with a candidate gene ATP7B was found to be significantly associated with the whole stage except BW0 and accounted for 4.61~9.05% of the phenotypic variance for Stage 1. Our study was the first analysis of longitudinal body weight data using multiple phenotypes. Identification of the promising region as well as potential candidate genes could be helpful to future marker-assisted selection and genomic selection in chickens.