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. 2021 Nov 2;22(1):786.
doi: 10.1186/s12864-021-08103-1.

Genetic variations for the eggshell crystal structure revealed by genome-wide association study in chickens

Quanlin Li #  1 , Zhongyi Duan #  2 , Congjiao Sun  1 , Jiangxia Zheng  1 , Guiyun Xu  1 , Ning Yang  3
Affiliations

Genetic variations for the eggshell crystal structure revealed by genome-wide association study in chickens

Quanlin Li et al. BMC Genomics. .

Abstract

Background: Eggshell is a bio-ceramic material comprising columnar calcite (CaCO3) crystals and organic proteinaceous matrix. The size, shape and orientation of the CaCO3 crystals influence the microstructural properties of chicken eggshells. However, the genetic architecture underlying eggshell crystal polymorphism remains to be elucidated.

Results: The integral intensity of the nine major diffraction peaks, total integral intensity and degree of orientation of the crystals were measured followed by a genome-wide association study in 839 F2 hens. The results showed that the total integral intensity was positively correlated with the eggshell strength, eggshell thickness, eggshell weight, mammillary layer thickness and effective layer thickness. The SNP-based heritabilities of total integral intensity and degree of orientation were 0.23 and 0.06, respectively. The 621 SNPs located in the range from 55.6 to 69.1 Mb in GGA1 were significantly associated with TA. PLCZ1, ABCC9, ITPR2, KCNJ8, CACNA1C and IAPP, which are involved in the biological process of regulating cytosolic calcium ion concentration, can be suggested as key genes regulating the total integral intensity.

Conclusions: The findings greatly advance the understanding of the genetic basis underlying the crystal ultrastructure of eggshell quality and thus will have practical significance in breeding programs for improving eggshell quality.

Keywords: Chicken; Crystal structure; Eggshell; GWAS; X-ray diffraction.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The phenotypic correlations between the crystal structure and eggshell quality. Abbreviations: A1-A9 = integrate intensity of peaks of No. 1–9; TA = total intensity of all 9 peaks; OD = degree of orientation; ESS = eggshell strength; ESW = eggshell weight; EST = eggshell thickness; ET = effective layer thickness; MT = mammillary layer thickness; MD = mammillary density. Abs (Correlation) = Absolute Correlation
Fig. 2
Fig. 2
Manhattan plots (left) and quantile–quantile plots (right) of the observed P-values for TA. The Manhattan plots indicate -log10 (observed P-values) for genome-wide SNPs (y-axis) plotted against their respective positions on each chromosome (x-axis), and the horizontal gray and red lines depict the genome-wide suggestive (1.73 × 10− 5) and significant (8.64 × 10− 7) thresholds, respectively. For quantile-quantile plots, the x-axis shows the expected -log10-transformed P-values, and the y-axis represents the observed -log10-transformed P-values. The genomic inflation factors (λ) are shown on the top left in the QQ plot. TA represents the total integral intensity of all peaks
Fig. 3
Fig. 3
Conditional association analyses (A) and linkage disequilibrium (LD) analysis (B) for TA. The genotype of rs315989578 was added to the multivariate model as a covariate for the conditional analysis. The LD plot of significant SNPs with the total intensity of all peaks in the region ranged from 55.6 to 69.1 Mb. Haplotypes are indicated by sample symbols connected by a solid line. The color represents Hedrick’s multiallelic D’, which indicates the degree of LD between two blocks. TA represents the total integral intensity of all peaks
Fig. 4
Fig. 4
Boxplots of the SNP effects on the TA. The figure shows the genotypes of six representative SNPs (x-axis) versus the phenotypic values of the corresponding traits (y-axis). TA represents the total integral intensity of all peaks
See this image and copyright information in PMC

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