Integrating transcriptome, proteome and QTL data to discover functionally important genes for duck eggshell and albumen formation

Zhang, Fan; Yin, Zhong-Tao; Zhang, Jinfeng; Zhu, Feng; Hincke, Maxwell T.; Yang, Ning; Hou, Zhuocheng

doi:10.1016/j.ygeno.2020.04.015

Cited by 15 publications

(13 citation statements)

References 59 publications

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“…Also, we observed that serine protease inhibitor family B member 2 (SERPINB2) was higher (> 3-fold) in the magnum, and similar up-regulation of SERPINB3 expression in the magnum of laying hens was reported by Jeong et al [11]. Recently, Zhang et al [33] also reported the upregulation of SERPINF1 and SEPRINH1 when an egg was present in the magnum of duck. This suggests that the SERPIN family of protease inhibitors has an important role in regulating the secretory activity of magnum for egg-white formation.…”

Section: Proteases Associated With the Albumen Synthesis And Secretionssupporting

confidence: 86%

“…1371/journal.pone.0076784.s001 The datasets from Yin et al [18] are available at PRJNA492958 in NCBI (https://www.ncbi.nlm.nih.gov/bioproject/?term=prjna492958), and was obtained from https://www.sciencedirect.com/science/article/pii/S088875431 8305810?via%3Dihub#bi0005 The datasets from Lu et al [19] does not contain a repository name; however, the data were obtained from mrd23428-sup-0001-APPENDICES.xlsx. The datasets from Zhang et al [33] are available at GenBank Short Read Archive (SRA: PRJNA493510) and were obtained from https://www. sciencedirect.com/science/article/pii/S0888754320300033#s0075…”

Section: Supplementary Informationmentioning

confidence: 99%

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RNA sequencing-based analysis of the magnum tissues revealed the novel genes and biological pathways involved in the egg-white formation in the laying hen

et al. 2021

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Background The mechanism of egg formation in the oviduct of laying hens is tightly controlled; each segment of the oviduct contributes a unique component of the egg. Several genes/proteins are involved in the synthesis of a completely healthy egg. This implies a time- and tissue-specific expression of genes and proteins in the different oviductal segments. We used hens at different physiological stages and time points to understand the transcriptional regulation of egg-white (albumen) synthesis and secretion onto the eggs in the magnum of laying hens. This study used Next-Generation Sequencing and quantitative real-time PCR (qPCR) to detect the novel genes and the cognate biological pathways that regulate the major events during the albumen formation. Results Magnum tissues collected from laying (n = 5 each at 3 h post-ovulation, p.o. and 15–20 h p.o.), non-laying (n = 4), and molting (n = 5) hens were used for differential gene expression analyses. A total of 540 genes (152 upregulated and 388 down-regulated) were differentially expressed at 3 h p.o. in the magnum of laying hens. Kyoto Encyclopedia of Genes and Genomes pathways analysis of the 152 upregulated genes revealed that glycine, serine, and threonine metabolism was the most-enriched biological pathway. Furthermore, the top two most enriched keywords for the upregulated genes were amino-acid biosynthesis and proteases. Nine candidate genes associated with albumen formation were validated with qPCR to have differential expression in laying, non-laying, and molting hens. Proteases such as TMPRSS9, CAPN2, MMP1, and MMP9 (protein maturation, ECM degradation, and angiogenesis); enzymes such as PSPH, PHGDH, and PSAT1 (amino-acid biosynthesis); RLN3, ACE, and REN (albumen synthesis, secretion and egg transport); and AVD, AvBD11, and GPX3 (antimicrobial and antioxidants) were recognized as essential molecules linked to albumen deposition in the magnum. Conclusions This study revealed some novel genes that participate in the signaling pathways for egg-white synthesis and secretion along with some well-known functional genes. These findings help to understand the mechanisms involved in albumen biosynthesis.

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Section: Proteases Associated With the Albumen Synthesis And Secretionssupporting

confidence: 86%

Section: Supplementary Informationmentioning

confidence: 99%

RNA sequencing-based analysis of the magnum tissues revealed the novel genes and biological pathways involved in the egg-white formation in the laying hen

et al. 2021

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“…Thus, the potential exists that eggshell quality can be improved by optimizing beneficial eggshell microstructure traits through genetic assisted selection programs. There is not yet a clear linkage between eggshell quality QTLs and genes encoding specific matrix proteins; however, progress is being made [61]. It is intriguing that eggs laid by aged hens exhibit modifications in eggshell ultrastructure and microstructure characteristics (i.e., type of defects, mammillary density; size of calcite crystal units) [62][63][64].…”

Section: And 33mentioning

confidence: 99%

Avian eggshell biomineralization: an update on its structure, mineralogy and protein tool kit

Gautron

Stapane

Roy

et al. 2021

BMC Mol and Cell Biol

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Background The avian eggshell is a natural protective envelope that relies on the phenomenon of biomineralization for its formation. The shell is made of calcium carbonate in the form of calcite, which contains hundreds of proteins that interact with the mineral phase controlling its formation and structural organization, and thus determine the mechanical properties of the mature biomaterial. We describe its mineralogy, structure and the regulatory interactions that integrate the mineral and organic constituents during eggshell biomineralization. Main Body. We underline recent evidence for vesicular transfer of amorphous calcium carbonate (ACC), as a new pathway to ensure the active and continuous supply of the ions necessary for shell mineralization. Currently more than 900 proteins and thousands of upregulated transcripts have been identified during chicken eggshell formation. Bioinformatic predictions address their functionality during the biomineralization process. In addition, we describe matrix protein quantification to understand their role during the key spatially- and temporally- regulated events of shell mineralization. Finally, we propose an updated scheme with a global scenario encompassing the mechanisms of avian eggshell mineralization. Conclusion With this large dataset at hand, it should now be possible to determine specific motifs, domains or proteins and peptide sequences that perform a critical function during avian eggshell biomineralization. The integration of this insight with genomic data (non-synonymous single nucleotide polymorphisms) and precise phenotyping (shell biomechanical parameters) on pure selected lines will lead to consistently better-quality eggshell characteristics for improved food safety. This information will also address the question of how the evolutionary-optimized chicken eggshell matrix proteins affect and regulate calcium carbonate mineralization as a good example of biomimetic and bio-inspired material design.

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“…However, there are little reports on QTLs studies related to egg production traits in ducks. Based on this, a study incorporated transcriptome, proteome and QTL analyses to identify advantageously significant genes that contribute to eggshell and albumen formation in duck ( Zhang et al, 2020 ). In another study by Liu et al (2021b) , GWAS was utilized to reveal the genetic variations for egg internal quality in ducks.…”

Section: Qtl Gwas Selection Signature or Combination Of Approaches To...mentioning

confidence: 99%

The study of candidate genes in the improvement of egg production in ducks – a review

2022

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Integrating transcriptome, proteome and QTL data to discover functionally important genes for duck eggshell and albumen formation

Cited by 15 publications

References 59 publications

RNA sequencing-based analysis of the magnum tissues revealed the novel genes and biological pathways involved in the egg-white formation in the laying hen

RNA sequencing-based analysis of the magnum tissues revealed the novel genes and biological pathways involved in the egg-white formation in the laying hen

Avian eggshell biomineralization: an update on its structure, mineralogy and protein tool kit

The study of candidate genes in the improvement of egg production in ducks – a review

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