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

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

doi:10.1186/s12864-018-4882-8

Hao Bai, Lei Zhang + Show 8 more

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https://doi.org/10.1186/s12864-018-4882-8

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Abstract

BackgroundBeak 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.ResultsIn this study, single SNP- and pathway-based genome-wide association studies (GWASs) were performed using ROADTRIPS and SNP ratio test (SRT), 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.ConclusionsPotentially useful candidate genes and pathways for beak deformity were identified, which should be the subject of further functional characterization.

Highlights

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
We identified six associated pathways (PEMP < 0.05), including the ribosome pathway, the oocyte meiosis pathway, the pantothenate and CoA biosynthesis pathway, the pyruvate metabolism pathway, the glycine, serine, and threonine metabolism pathway, and the calcium signaling pathway (Table 4 and Fig. 7)
In the present study, based on the case-control design, the genotype data of 48 birds with deformed beaks and 48 normal chickens were used for the single SNP and pathway-based Genome-wide association study (GWAS) analyses

Summary

Introduction

Typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. In a similar way to lips and teeth in mammals, the beak functions in birds primarily for feeding and drinking. With the advance of high-throughput genotyping platforms and computing technology, molecular markers and genes related to complex traits or diseases have been identified using genome-wide association studies (GWASs) [20,21,22,23]. This approach is powerful to identify a single SNP with a notable effect, especially for phenotypes that are determined by a unique gene or mutation. Pathway-based GWAS [25, 26] is one of the strategies and statistical approaches that considers multiple genetic variants as SNPs or genes in a biological pathway to understand the genetic contributors of complex traits [27, 28]

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