Genome-Wide Association Study and Selective Sweep Analysis Reveal the Genetic Architecture of Body Weights in a Chicken F2 Resource Population

Shouzhi Wang; Yuxiang Wang; Yudong Li; Fan Xiao; Huaishun Guo; Haihe Gao; Ning Wang; Hui Zhang; Hui Li

doi:10.3389/fvets.2022.875454

Genome-Wide Association Study and Selective Sweep Analysis Reveal the Genetic Architecture of Body Weights in a Chicken F₂ Resource Population

Front Vet Sci. 2022 Jul 26:9:875454. doi: 10.3389/fvets.2022.875454. eCollection 2022.

Authors

Shouzhi Wang^{1

2

3}, Yuxiang Wang^{1

2

3}, Yudong Li^{1

2

3}, Fan Xiao⁴, Huaishun Guo⁴, Haihe Gao⁴, Ning Wang^{1

2

3}, Hui Zhang^{1

2

3}, Hui Li^{1

2

3}

Affiliations

¹ Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.
² Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.
³ College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.
⁴ Fujian Sunnzer Biotechnology Development Co., Ltd., Fujian, China.

Abstract

Rapid growth is one of the most important economic traits in broiler breeding programs. Identifying markers and genes for growth traits may not only benefit marker-assisted selection (MAS)/genomic selection (GS) but also provide important information for understanding the genetic architecture of growth traits in broilers. In the present study, an F₂ resource population derived from a cross between the broiler and Baier yellow chicken (a Chinese local breed) was used and body weights from 1 to 12 weeks of age [body weight (BW) 1-BW12)] were measured. A total of 519 F₂ birds were genome re-sequenced, and a combination of genome-wide association study (GWAS) and selective sweep analysis was carried out to characterize the genetic architecture affecting chicken body weight comprehensively. As a result, 1,539 SNPs with significant effects on body weights at different weeks of age were identified using a genome-wide efficient mixed-model association (GEMMA) package. These SNPs were distributed on chromosomes 1 and 4. Besides, windows under selection identified for BW1-BW12 varied from 1,581 to 2,265. A total of 42 genes were also identified with significant effects on BW1-BW12 based on both GWAS and selective sweep analysis. Among these genes, diacylglycerol kinase eta (DGKH), deleted in lymphocytic leukemia (DLEU7), forkhead box O17 (FOXO1), karyopherin subunit alpha 3 (KPNA3), calcium binding protein 39 like (CAB39L), potassium voltage-gated channel interacting protein 4 (KCNIP4), and slit guidance ligand 2 (SLIT2) were considered as important genes for broiler growth based on their basic functions. The results of this study may supply important information for understanding the genetic architecture of growth traits in broilers.

Keywords: GWAS; body weight; broiler; growth trait; selective sweep.