Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken

Qiuxia Lei; Shuer Zhang; Jie Wang; Chao Qi; Jie Liu; Dingguo Cao; Fuwei Li; Haixia Han; Wei Liu; Dapeng Li; Cunwei Tang; Yan Zhou

doi:10.1016/j.psj.2024.103705

Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken

Poult Sci. 2024 Mar 31;103(6):103705. doi: 10.1016/j.psj.2024.103705. Online ahead of print.

Authors

Qiuxia Lei¹, Shuer Zhang², Jie Wang¹, Chao Qi², Jie Liu¹, Dingguo Cao¹, Fuwei Li¹, Haixia Han¹, Wei Liu¹, Dapeng Li¹, Cunwei Tang³, Yan Zhou⁴

Affiliations

¹ Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China.
² Shandong Animal Husbandry General Station, 250023, Ji'nan, China.
³ Fujian Sunnzer Biological Technology Development Co. Ltd., 354100, Guang'ze, China.
⁴ Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China.. Electronic address: sally7919@163.com.

PMID: 38598913
DOI: 10.1016/j.psj.2024.103705

Abstract

Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.

Keywords: chicken; egg production trait; genome-wide association study; whole genome sequencing.