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

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 10x 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.

Automated summary

This study measured and conducted genome-wide association studies on growth traits of Yandang partridge chickens. It identified a significant locus associated with Keel length and identified a potential candidate haplotype. Additionally, the study introduced a bootstrap testing method for verifying GWAS reliability with small experimental samples.