Transcriptional regulation of albumen biosynthesis in the magnum of broiler breeder hens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1259418 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33450341_1.fastq.gz | Fastqsanger.gz | |||
| SRR33450341_2.fastq.gz | Fastqsanger.gz | |||
| SRR33450342_1.fastq.gz | Fastqsanger.gz | |||
| SRR33450342_2.fastq.gz | Fastqsanger.gz | |||
| SRR33450343_1.fastq.gz | Fastqsanger.gz |
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Project description:Broiler chicken production is crucial to meet the increasing global food demand. Hyperphagic and obese broiler breeder hens have a short production cycle, which is challenged by age-associated egg quality and fertility decline, affecting hatchability. A fertilized egg is a comprehensive set of essential elements to nurture and develop a healthy chick. Egg albumin occupies most of the egg content, which is synthesized and secreted by the magnum. The genetic regulation of albumin biosynthesis in broiler breeder hens and its alteration with age might reveal the genetic marker that will produce quality eggs in subsequent generations. Hence, the objective of the study is to determine the differentially expressed genes (DEGs) and pathways involved in albumin biosynthesis in the magnum (young vs aged). The magnum tissues were collected from the broiler breeder hens at peak production, identified as the young group (35 weeks, N=30), and from the declined production, recognized as the aged group (50 weeks, N=30). Five samples from each group (n=5) were used for RNA sequencing and analyzed to get DEGs and associated pathways. The significantly upregulated genes with a putative function in quality egg formation were confirmed using qPCR. Seventy-five up-regulated and 52 down-regulated genes were determined. The top 20 most upregulated genes and top 20 most downregulated genes, based on their putative function, were categorized into five groups: egg white synthesizing (AMDHD1, FER, CTNNA3), molecular communication (VAPA), oviduct tissue regeneration (ADAM19, CFAP100, AMD1, TM4SF19, SLC39A13, VMO1), and defense (ZBTB46, STAM2, OVoDA3). “Post-translational protein phosphorylation” was the most significantly enriched Reactome pathway involving DNAJC3, PPP3CA, TF, SPARCL1, PDIA6, SGPP2, HSP90B1, and PNPLA2 genes. The study successfully identified DEGs, genetic networks, and pathways that can be used as genetic markers to select quality egg producing broiler breeder hens.
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2025-04-28 | GSE295785 | GEO
Project description:The egg production cycle of broiler breeder hens is comparatively shorter than laying hens, and as they age, their egg production and eggshell quality decline. The eggshell formation occurs in the shell glands, which are influenced by several factors, including aging. The objectives of the study were to 1) identify differentially expressed genes (DEGs) and biological pathways in the shell glands (young vs aged) and 2) determine the age-associated changes in eggshell quality. The shell glands tissues were collected from broiler breeder hens at peak-lay (35 weeks of age; termed as “young”) and late-lay phases (50 weeks of age; termed as “aged”) (n=30/group) at 10-15 hours post-ovulation (unclassified egg present in the shell glands). To delineate the genes and biological pathways associated with eggshell biomineralization, total RNAs extracted from the shell glands of young and aged hens (n=6/group) were analyzed using RNA sequencing and validated using real-time PCR. The ultrastructure quality of eggshells (n=10 eggs/group) was analyzed using a Scanning Electron Microscope (SEM), and the elemental composition of eggshells was measured using SEM-Energy Dispersive Spectrometry, and their variability was confirmed by t-test in RStudio. Eggshell strength, thickness, palisade layer, and mammillary width were significantly higher in the young, while mammillary knobs were wider in aged hens (p<0.05). The sulfur and potassium levels in eggshells were higher in young hens than aged ones. Although the young group had a higher calcium concentration in the eggshells, the difference was statistically insignificant (p>0.05). RNA-Seq data identified highly upregulated genes specific to eggshell biomineralization, such as SPP1 (binds to hydroxyapatite), OTOP2 (maintains high conc. of cytosolic Ca2+), PKD2 (helps in releasing Ca2+), SLC22A15 (transports organic ions), and STAB2 (binds to gram-positive and gram-negative bacteria). The DEGs showed significant enrichment for biological pathways (SLC6A6, KCNK7, UCP3, SCNN1A, PKD2, OTOP2) associated with the transport of monoatomic and inorganic cations across the cell membrane, molecular functions related to the transport of potassium ions and the activity of monoatomic cation channels (KCNK7, PKD2, OTOP2), and the cellular components involved in the luminal side of the endoplasmic reticulum membrane (CALR, PKD2). These findings suggest that the aging process downregulates the transcriptomes of the shell glands, negatively impacting the transportation of ions required for eggshell formation, resulting in poor eggshell quality.
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Project description:Overfeeding reduces laying performance in broiler breeder hens (Gallus gallus domesticus). To unravel the effect of feeding regimes on energy metabolism and egg production, high-throughput RNA sequencing was utilized to identify differentially expressed genes (DEGs) in ovary, liver and adipose tissues of broiler chickens under ad libitum and restricted feeding. The transcriptome analysis showed that 289, 388 and 204 DEGs were identified in the adipose tissue, liver and ovary, respectively, between ad libitum and restricted feeding groups. Bioinformatics analysis by STRING further revealed DEGs were significantly enriched in phagosome pathway, lipid transport and location biological process, and the molecular function of lipid transporter activity and nutrient reservoir activity in ovary; the pathways of “steroid hormone biosynthesis” and “metabolism of xenobiotics by cytochrome P450”, and the molecular function of nutrient reservoir activity in adipose tissue; the metabolic pathways, Jak-STAT signaling pathway and PPAR signaling pathway in liver.
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Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide varitey of tissues has discovered. The aim of this study are to perform transcriptome profiling (RNA-seq) of magnum to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Magnum mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least three-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 30.5 million reads from layers and 33.4 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 540 were differentially expressed between layer and non-layer hens. 152 DEGs were significantly up-regulated and 388 were significantly down-regulated in the laying hens when compared to the non-laying hens. Conclusions: Our study reports the expression of several pre-discovered and many novel genes that may be involved in the transport of precurosor molecules for biosynthesis and secretion of the egg-white proteins in the magnum. These genes can be used as quantitative basis of selecting hens with an improved egg quality.
2021-03-22 | GSE123588 | GEO
Project description:Heat stress (HS) can damage the integrity of the intestinal mucosal barrier, leading to decreased poultry productivity. This study aimed to identify candidate genes related to acute HS in breeder hens and provide insight into the molecular mechanisms underlying acute HS in gut health. Fifty 28-week-old breeder hens were divided into two groups (25 hens each) raised under thermoneutral zone (23 °C) and acute HS (36 °C, 6 hours) conditions. The heart rate and cloacal temperature were measured in all hens, and jejunal mucosa tissues were randomly collected from 12 hens per treatment for RNA-sequencing analysis. The results indicated a significant increase in the heart rate and cloacal temperature in hens exposed to acute HS (P < 0.05). Transcriptome analysis identified 138 differentially expressed genes (DEGs) in heat-stressed breeder hens, including 75 upregulated DEGs containing heat shock protein (HSP), energy homeostasis metabolism-related gene (PDK4), and fat metabolism-related genes (PPARA and CD36), and 63 downregulated DEGs containing the bile acid transporter gene (SLC10A2). Gene ontology analysis revealed significant enrichment in biological processes related to heat response and cholesterol biosynthesis. Kyoto Encyclopedia of Genes and Genomes analysis highlighted several significant pathways, including steroid biosynthesis, steroid hormone biosynthesis, protein processing in endoplasmic reticulum, the peroxisome proliferator-activated receptor (PPAR) signaling pathway, and the adipocytokine signaling pathway. Protein-protein interaction network analysis involving two large networks: one containing several upregulated HSPs and genes related to energy homeostasis and fat metabolism (PDK4, PPARA, and CD36) and glucose transporter (SLC2A5), and the other containing downregulated DEGs related to cholesterol biosynthesis. Overall, acute HS might affect energy metabolism, fat metabolism, and glucose transport in the jejunal mucosa of breeder hens. Heat-stressed hens could restore the nutritional function of the jejunal mucosa by increasing the expression of HSPs. These findings provide a theoretical framework for further investigation into the molecular regulatory mechanisms responsible for HS-induced changes in the gut health of poultry.
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Project description:Expression data from ad libitum or restricted fed 16-week old broiler breeder hens
| PRJNA763188 | ENA