生物
全基因组关联研究
连锁不平衡
单倍型
单核苷酸多态性
遗传学
遗传关联
基因组
核苷酸多型性
SNP公司
特质
关联映射
遗传建筑学
数量性状位点
计算生物学
基因
等位基因
基因型
计算机科学
程序设计语言
作者
Chunqin Wu,Liyan Dong,Xiantong Gan,Fangben Gan,Wenwu Xu,Lizhi Liu
标识
DOI:10.1080/10495398.2022.2059491
摘要
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.
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