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. 2023 Nov 22;24(1):704.
doi: 10.1186/s12864-023-09632-7.

Genome-wide association study exploring the genetic architecture of eggshell speckles in laying hens

Xue Cheng  1 , Xinghua Li  1 , Mengyuan Yang  1 , Chuanwei Zheng  2 , Haiying Li  3 , Lujiang Qu  4 , Zhonghua Ning  5
Affiliations

Genome-wide association study exploring the genetic architecture of eggshell speckles in laying hens

Xue Cheng et al. BMC Genomics. .

Abstract

Background: Eggshell speckle phenotype is an important trait in poultry production because they affect eggshell quality. However, the genetic architecture of speckled eggshells remains unclear. In this study, we determined the heritability of eggshell speckles and conducted a genome-wide association study (GWAS) on purebred Rhode Island Red (RIR) hens at 28 weeks to detect potential genomic loci and candidate genes associated with eggshell speckles.

Results: The heritability of eggshell speckles was 0.35 at 28 weeks, and the speckle level is not related to other eggshell quality traits in terms of phenotypic correlation. We detected 311 SNPs (6 significantly, and 305 suggestively associated) and 39 candidate genes associated with eggshell speckles. Based on the pathway analysis, the 39 candidate genes were mainly involved in alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, GnRH signaling pathway, vascular smooth muscle contraction, and MAPK signaling pathway. Ultimately, ten genes, LOC423226, SPTBN5, EHD4, LOC77155, TYRO3, ITPKA, DLL4, PLA2G4B, PLA2G4EL5, and PLA2G4EL6 were considered the most promising genes associated with eggshell speckles that were implicated in immunoregulation, calcium transport, and phospholipid metabolism, while its function in laying hens requires further studies.

Conclusions: This study provides new insights into understanding the genetic basis of eggshell speckles and has practical application value for the genetic improvement of eggshell quality.

Keywords: Egg quality; Eggshell speckles; GWAS; Laying hens.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Recording eggshell speckles. Eggshell spot density increases from left to right, representing grades 1, 2, 3, and 4 [2, 4]
Fig. 2
Fig. 2
Genetic properties between eggshell speckles and quality. (a) Phenotypic correlations between eggshell speckle level and quality. (b) Genetic correlations between eggshell speckle level and quality. L*, a*, and b*: eggshell colour; ESI: egg shape index; EW: egg weight; ESS: eggshell strength; SL: speckle level. P values are in parentheses
Fig. 3
Fig. 3
GWAS results of eggshell speckling. (a) Manhattan plot; (b) QQ plots; (c) LD plot for significant SNPs. In the Manhattan plot, the X-axis represents the chromosomal position corresponding to each SNP (40 and 41 represent the Z and W chromosomes, respectively). The Y-axis represents -log10 (P values). The red and blue lines represent the genome-wide significant threshold (5.87 × 10− 7) and suggestive significant threshold (1.17 × 10− 5), respectively. The QQ plot shows the expected -log10-transformed p value against the observed -log10-transformed p value. The λ value (1.008) is marked in the upper left of the QQ plot. The top line represents the position of the significant SNPs.
See this image and copyright information in PMC

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