Whole-genome resequencing reveals aberrant autosomal SNPs affect chicken feathering rate

Abstract

Previous studies have shown that the feather growth rate of chicks is determined by two alleles located on the sex chromosome Z; however, in chicken production, feathering is usually not consistently controlled by the sex chromosome. To identify whether the feathering rate is related to autosomal inheritance, whole-genome resequencing was performed in eight chickens with slow- and fast-feathering rate. A total of 54,984 autosomal single nucleotide polymorphisms (SNPs) were identified, including 393 and 376 exonic SNPs in slow-feathering and fast-feathering chickens, respectively. Mutated genes were mainly involved in response to stimuli and growth and reproduction processes. Mutated genes related to slow-feathering rate were mainly involved in wingless-type MMTV integration site signaling pathway and mitogen-activated protein kinase signaling pathway, whereas mutated genes associated with fast-feathering rate were primarily enriched in autophagy, calcium signaling pathway, extracellular matrix-receptor interaction, and Focal adhesion processes. Importantly, two SNPs, involved in feather development, were found in the exonic regions of Wnt signaling genes. These results shed new light on the relationship between genetic mutation and feather growth rate from the perspective of autosomal inheritance and may have economic significance in chicken breeding.

Keywords:

• Fast feathering
• slow feathering
• whole-genome resequencing
• single nucleotide polymorphisms

Acknowledgments

The authors are grateful to Sichuan Animal Science Academy for its availability and support.

Data availability statement

We have deposited our data in National Center for Biotechnology Information (NCBI) (accession number PRJNA633754). The data supporting the results of this article are included in the article and supplementary information.

Ethical approval

All chick sampling procedures were carried out according to the guidelines of China legislation on ethical use and care of laboratory animals, and all protocols were approved by the Animal Care and Use Committee of the Sichuan Animal Science Academy.

Conflicts of interest

Authors Mohan Qiu, Chaowu Yang, Huarui Du, Qingyun Li, Zengrong Zhang, XiaXiong, Chunlin Yu, Xiaoyan Song, Chenming Hu, Bo Xia, Li Yang, Han Peng, Lan Liu, and Xiaosong Jiang.

Additional information

Funding

This study was supported by National modern agricultural technology system construction of China (No. CARS-41-G04); the Province Key Technologies R & D Program of Livestock and Poultry Breeding Programs of Sichuan Province (No. 2016NYZ0025, No. 2016NYZ0043 and No. 2016NZ0104); the Province Key Technologies R & D Program (No. 2020YFSY0048); and special fiscal funds from Sichuan Province (No. SASA2020CZYX002 and No. SASA2020CZYX007).