Genetic architecture dissection by genome-wide association analysis reveals avian eggshell ultrastructure traits.

Zhongyi Duan,Congjiao Sun,Jiangxia Zheng,Guiyun Xu,Ning Yang,Kehua Wang,Manman Shen

doi:10.1038/srep28836

Zhongyi Duan, Congjiao Sun + Show 5 more

Open Access

https://doi.org/10.1038/srep28836

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Abstract

The ultrastructure of an eggshell is considered the major determinant of eggshell quality, which has biological and economic significance for the avian and poultry industries. However, the interrelationships and genome-wide architecture of eggshell ultrastructure remain to be elucidated. Herein, we measured eggshell thickness (EST), effective layer thickness (ET), mammillary layer thickness (MT), and mammillary density (MD) and conducted genome-wide association studies in 927 F2 hens. The SNP-based heritabilities of eggshell ultrastructure traits were estimated to be 0.39, 0.36, 0.17 and 0.19 for EST, ET, MT and MD, respectively, and a total of 719, 784, 1 and 10 genome-wide significant SNPs were associated with EST, ET, MT and MD, respectively. ABCC9, ITPR2, KCNJ8 and WNK1, which are involved in ion transport, were suggested to be the key genes regulating EST and ET. ITM2C and KNDC1 likely affect MT and MD, respectively. Additionally, there were linear relationships between the chromosome lengths and the variance explained per chromosome for EST (R2 = 0.57) and ET (R2 = 0.67). In conclusion, the interrelationships and genetic architecture of eggshell ultrastructure traits revealed in this study are valuable for our understanding of the avian eggshell and contribute to research on a variety of other calcified shells.

Highlights

Through candidate gene association analysis, Dunn et al found that the variations in ovalbumin, ovocleidin-116 and RARRES1 were associated with eggshell thickness and mammillary layer thickness[13]
Because the genes associated with eggshell thickness (EST) and effective layer thickness (ET) were numerous, we explored the interrelationships among these genes
We found that mammillary layers with denser mammillae tended to be thinner, but there was no obvious effect on EST or ET (Fig. 1C), which was inconsistent with previous studies[19,20]

Summary

Introduction

Jonchère et al.[7,8] and Brionne et al.[9] characterized the chicken uterus transcriptome in detail and identified a large number of genes that encode matrix proteins or uterine ion transporters. Through candidate gene association analysis, Dunn et al found that the variations in ovalbumin, ovocleidin-116 and RARRES1 were associated with eggshell thickness and mammillary layer thickness[13]. These discoveries were still far from providing an understanding of the genetic bases of eggshell ultrastructure at a genome-wide level. The aim of our work was to uncover the genetic architecture of eggshell ultrastructure and to identify candidate mutations, which may be valuable for the genetic improvement of eggshell quality and furthering our understanding of eggshell biomineralization

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