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

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

doi:10.1038/srep28836

Cited by 18 publications

(18 citation statements)

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“…For example, genetic variations of ovocleidin-116, ovotransferrin and secreted phosphoprotein 1 were linked to the decreased eggshell quality [ 16 ]. Matrix protein genes such as ovalbumin, ovocleidin-116 and ovocalyxin-32 were associated with shell thickness and mammillary layer thickness [ 17 ], while ABCC9, ITPR2, KCNJ8 and WNK1, which are involved in ion transport, were suggested to be the key genes modulating eggshell thickness and effective thickness [ 18 ]. Hence, deteriorations in eggshell ultrastructure and quality in the late phase of production were speculated to be associated with age-related dysregulation of gene expression in uterus.…”

Section: Introductionmentioning

confidence: 99%

Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens

Feng

Zhang

et al. 2020

BMC Genomics

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Background Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell formation is a highly complex process under precise regulation of genes and biological pathways in uterus of laying hens. Herein, we evaluated the physical, mechanical and ultrastructure properties of eggshell and conducted RNA sequencing to learn the transcriptomic differences in uterus between laying hens in the peak (young hens) and late phase (aged hens) of production. Results The declined breaking strength and fracture toughness of eggshell were observed in aged hen group compared to those in young hen group, accompanied with ultrastructure variations including the increased thickness of mammillary layer and the decreased incidence of early fusion. During the initial stage of eggshell formation, a total of 183 differentially expressed genes (DEGs; 125 upregulated and 58 downregulated) were identified in uterus of laying hens in the late phase in relative to those at peak production. The DEGs annotated to Gene Ontology terms related to antigen processing and presentation were downregulated in aged hens compared to young hens. The contents of proinflammatory cytokine IL-1β in uterus were higher in aged hens relative to those in young hens. Besides, the genes of some matrix proteins potentially involved in eggshell mineralization, such as ovalbumin, versican and glypican 3, were also differentially expressed between two groups. Conclusions Altered gene expression of matrix proteins along with the compromised immune function in uterus of laying hens in the late phase of production may conduce to age-related impairments of eggshell ultrastructure and mechanical properties. The current study enhances our understanding of the age-related deteriorations in eggshell ultrastructure and provides potential targets for improvement of eggshell quality in the late laying period.

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Section: Introductionmentioning

confidence: 99%

Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens

Feng

Zhang

et al. 2020

BMC Genomics

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“…In addition, two genes, ITPR2 and VIPR1, were identified in the putative selection signature regions, which are possibly related to layer reproductive traits . One recent GWAS study in chicken revealed that the ITPR2 gene was associated with eggshell ultrastructure [ 58 ]. On the other hand, the VIPR1 gene was found to be associated with broodiness [ 59 ], and egg number in chicken [ 60 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

et al. 2018

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BackgroundMeat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.ResultsA total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.ConclusionsIn this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4444-0) contains supplementary material, which is available to authorized users.

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“…For example, genetic variations of ovocleidin-116, ovotransferrin and secreted phosphoprotein 1 were linked to the decreased eggshell quality [16]. Matrix protein genes such as ovalbumin, ovocleidin-116 and ovocalyxin-32 were associated with shell thickness and mammillary layer thickness [17], while ABCC9, ITPR2, KCNJ8 and WNK1, which are involved in ion transport, were suggested to be the key genes modulating eggshell thickness and effective thickness [18]. Hence, deteriorations in eggshell ultrastructure and quality in the late phase of production were speculated to be associated with age-related disturbance in the regulation of gene expression in uterus.…”

Section: Introductionmentioning

confidence: 99%

Uterine Transcriptome Analysis Reveals Mechanism Underlying the Ultrastructure Differences of Eggshell in Young and Aged Laying Hens

Feng

Zhang

et al. 2020

Preprint

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Background: Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell mineralization is a highly complex process under precise regulation of genes and biological pathways in uterus of laying hens. Herein, we evaluated the physical, mechanical and ultrastructure properties of eggshell and conducted RNA sequencing to learn the transcriptomic differences in uterus between laying hens in the peak (young hens) and late phase (aged hens) of production.Results: The declined breaking strength and fracture toughness of eggshell were observed in aged hen group compared to those in young hen group, accompanied with ultrastructure variations including the increased thickness of mammillary layer and the decreased incidence of early fusion. During the initial stage of eggshell formation, a total of 183 differentially expressed genes (DEGs; 125 upregulated and 58 downregulated) were identified in uterus of laying hens in the late phase in relative to those at peak production. The DEGs annotated to Gene Ontology terms related to antigen processing and presentation were downregulated in aged hens compared to young hens. The contents of proinflammatory cytokine IL-1β in uterus were higher in aged hens relative to those in young hens. Besides, the genes of some matrix proteins potentially involved in eggshell mineralization, such as ovalbumin, versican and glypican 3, were also differentially expressed between two groups.Conclusions: Altered gene expression of matrix proteins along with the compromised immune function in uterus of laying hens in the late phase of production may conduce to age-related impairments of eggshell ultrastructure and mechanical properties. The current study enhances our understanding of the age-related deteriorations in eggshell ultrastructure and provides potential targets for improvement of eggshell quality in the late laying period.

show abstract

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

Cited by 18 publications

References 60 publications

Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens

Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

Uterine Transcriptome Analysis Reveals Mechanism Underlying the Ultrastructure Differences of Eggshell in Young and Aged Laying Hens

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