Genome-wide association studies and haplotype sharing analysis targeting the growth traits in Yandang partridge chickens

Abstract

The body size of a chicken is an economically important trait as it directly influences the benefits of the poultry industry, but the relevant genetic mechanisms have not yet been elucidated. In this study, we measured eight growth traits for 94 Yandang partridge chickens, then undertook genome-wide association studies (GWAS) for those traits in using a linear mixed model based on 10× whole genomic sequencing data to better understand the knowledge of the genetic architecture of growth traits. Ninety-four individuals and 7647883 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. The result showed that only one significant single-nucleotide polymorphisms (SNP) locates at 14852873 bp on SSC13 surpassed the genome-wide significance level for Keel length (KL). Through linkage disequilibrium analysis and haplotype sharing analysis, we identified one haplotype underlying the SSC13 significantly associated with KL, which could be selected as a potential candidate haplotype that is used in molecular breeding of Yandang partridge chicken. On the other hand, we have learned from a method called bootstrap testing to verify the reliability of GWAS with small experimental samples, which users can access at https://github.com/xuwenwu24/Bootstrap-test.

Keywords:

• GWAS
• haplotype
• growth traits
• Yandang partridge chickens

Disclosure statement

The authors declare that they have no competing interests.

Ethics approval and consent to participate

The animal care and use protocol were approved by the Institutional Animal Care and Use Committee of the Zhejiang Academy of Agricultural Sciences (Hangzhou China), which was in accordance with the Guidelines for Experimental Animals established by the Ministry of Science and Technology (Beijing, China).

Author contributions

LLZ, XWW conceived and designed the experiments. WCQ, XWW analyzed the data. DLY, GXD, GFB contributed to materials and analysis tools. XWW, WCQ wrote the manuscript. All authors read and approved the final manuscript.

Data availability statement

The genotypic data of the 94 Yandang partridge chickens used in this study can be found in the figshare Digital Repository (https://figshare.com/s/6762adae356a92963c19).

Additional information

Funding

This work was supported by the National Waterfowl Industry Technology System [CARS-43-02] and Zhejiang Major Scientific and Technological project of agricultural (livestock’s) breeding [2016C02054-12]. The founder LLZ had role in the design of this study.