Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study

Suozhou Yang; Chao Ning; Cheng Yang; Wenqiang Li; Qin Zhang; Dan Wang; Hui Tang

doi:10.3390/vetsci11020076

Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study

Vet Sci. 2024 Feb 6;11(2):76. doi: 10.3390/vetsci11020076.

Authors

Suozhou Yang^{1

2}, Chao Ning^{1

2}, Cheng Yang^{1

2}, Wenqiang Li^{1

2}, Qin Zhang^{2

3}, Dan Wang^{1

2}, Hui Tang^{1

2}

Affiliations

¹ Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai'an 271018, China.
² Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an 271018, China.
³ College of Animal Science and Technology, China Agricultural University, Beijing 100083, China.

Abstract

Copy number variation (CNV), as an essential source of genetic variation, can have an impact on gene expression, genetic diversity, disease susceptibility, and species evolution in animals. To better understand the weight and egg quality traits of chickens, this paper aimed to detect CNVs in Wenshui green shell-laying chickens and conduct a copy number variation regions (CNVRs)-based genome-wide association study (GWAS) to identify variants and candidate genes associated with their weight and egg quality traits to support related breeding efforts. In our paper, we identified 11,035 CNVRs in Wenshui green shell-laying chickens, which collectively spanned a length of 13.1 Mb, representing approximately 1.4% of its autosomal genome. Out of these CNVRs, there were 10,446 loss types, 491 gain types, and 98 mixed types. Notably, two CNVRs showed significant correlations with egg quality, while four CNVRs exhibited significant associations with body weight. These significant CNVRs are located on chromosome 4. Further analysis identified potential candidate genes that influence weight and egg quality traits, including FAM184B, MED28, LAP3, ATOH8, ST3GAL5, LDB2, and SORCS2. In this paper, the CNV map of the Wenshui green shell-laying chicken genome was constructed for the first time through population genotyping. Additionally, CNVRs can be employed as molecular markers to genetically improve chickens' weight and egg quality traits.

Keywords: Wenshui green shell-laying chickens; copy number variation; genome-wide association study; weight and egg quality traits.

Grants and funding

This research was funded by the Agricultural Breeding Project of Shandong Province (2022LZGCQY016), the Shandong Modern Agricultural Industry and Technology System (SDAIT-11-02).