Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

文献类型： 外文期刊

第一作者： Bai, Hao

作者： Bai, Hao;Sun, Yanyan;Liu, Nian;Xue, Fuguang;Li, Yunlei;Xu, Songshan;Ye, Jianhua;Chen, Jilan;Zhang, Lei;Chen, Yu

作者机构：

关键词： Beijing-you chickens; Beak deformity; SNP; Pathway; GWAS

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2018 年 19 卷

页码：

收录情况： SCI

摘要： Background: Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs the birds' growth and welfare. Although previous studies shed some light on the genetic regulation of this complex trait, the genetic basis of this malformation remains incompletely understood. Results: In this study, single SNP- and pathway-based genome-wide association studies (GWASs) were performed using ROADTRIPS and SNP ratio test (SRI), respectively. A total of 48 birds with deformed beaks (case) and 48 normal birds (control) were genotyped using Affymetrix 600 K HD genotyping arrays. As a result, 95 individuals and 429,539 SNPs were obtained after quality control. The P-value was corrected by a Bonferroni adjustment based on linkage disequilibrium pruning. The single SNP-based association study identified one associated SNP with 5% genome-wide significance and seven suggestively associated SNPs. Four high-confidence genes, LOC421892, TDRD3, RET, and STMN1, were identified as the most promising candidate genes underlying this complex trait in view of their positions, functions, and overlaps with previous studies. The pathway-based association study highlighted the association of six pathways with beak deformity, including the calcium signaling pathway. Conclusions: Potentially useful candidate genes and pathways for beak deformity were identified, which should be the subject of further functional characterization.

分类号：

  • 相关文献
作者其他论文 更多>>

微信小程序