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ABSTRACT:
PROVIDER: PRJNA1313457 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The intestinal mucosa is the main organ that exerts nutrient absorption, which will further influence laying performance and egg nutrition in hens. Previously, we have screened out three strains of Lactobacillus (L. sa., L. ag. and L. av.) from a native chicken breed in China. However, the optimal regulation of Lactobacillus combination on poultry products needs to be verified. In this study, a total of 120 HyLine hens (n = 30) at the period of laying peak were randomly divided into four groups: (1) control, (2) L. sa. + L. ag., (3) L. sa. + L. av. and (4) L. ag. + L. av. groups, which were fed with corresponding Lactobacillus (10e8 CFUs/hen/day) for 30 consecutive days. Compared with the control group, feeding of L. sa. + L. ag. could improve the laying rate, egg weight, especially for higher amino acids level in albumen. The mechanism study showed that, in the intestine lumen, feeding of L. sa. + L.ag. could up-regulate the Lactobacillus abundance and down-regulate the Escherichia coli abundance. Meanwhile, the tryptophan metabolism pathway was up-regulated, the primary bile acid biosynthesis pathway was down-regulated. In the crypt, up-regulated genes involved the oxidative phosphorylation pathway and the ROS level were appeared in L. sa. + L.ag. feeding group. Our study further proved that the amount of Paneth cells and the mRNA abundance of Wnt3a and Dll1 in the crypt were up-regulated upon L. sa. + L. ag. feeding. Correspondingly, the mRNA abundance of Lgr5, CCND1 and CDK2 in the crypt were enhanced upon L. sa. + L. ag. feeding. In conclusion, co-feeding of L. sa. and L. ag. in hens could improve the gut microflora and altered the microflora metabolism profile in the intestine. Further, promote the crypt’s local energy metabolism and enhancing ROS level in the crypt, thereby enhance the activity of Paneth cell and regulate the activity of ISCs. Ultimately, the intestinal mucosal renewal and the laying performance were improved.
2021-12-31 | GSE176247 | GEO
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:Liver tissues of Guangxi Ma chicken from 32-week old with m performance, 50-week old with high and low laying performance, and 72-week old with high and low laying performance were collected and sequenced in quadruplicate using RNA-seq. The sequences were double-ended sequenced on the DNBSEQ sequencing platform. The sequence reads were quality controlled and then aligned with genomic sequences using HISAT2 program, quantified by featureCounts program, and gene expression levels were verified by qRT-PCR with SYBR Green detection. The results will be helpful to explore the factors that affecting laying performance from the perspective of yolk synthesis and provide a theoretical basis for improving the egg production of Guangxi Ma chicken.
2022-10-08 | GSE193655 | GEO
Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide variety of tissues has been discovered. The aim of this study are to perform uterine transcriptome profiling (RNA-seq) 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: Uterine 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 two-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 32 million reads from layers and 28 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 616 were differentially expressed between layer and non-layer hens. 229 DEGs were significantly up-regulated and 286 were significantly down-regulated in the laying hens when compared to the non-laying hens. Twelve candiate genes, linked to calcium remodeling, were identified by gene function analysis and validated using qPCR. MEPE, CALCB, OTOP2, STC2 and ATP2C2 were confirmed to be highly expressed in laying hens as compared to molting and non-laying hens. RNA-seq and qPCR data for relative gene expression were highly correlated (R2 =0.99). Conclusions: Our study reports the expression of four novel genes that are speculated to transport calcium ions across the uterine epithellium for eggshell mineralization. These genes can be used as quantitative basis of selecting hens with an improved eggshell quality.
2018-12-06 | GSE114103 | GEO
Project description:Laying performance is a key factor affecting production efficiency in poultry farming, but its molecular mechanism is still unclear. In this study, Yaoshan chickens, a local breed in Guizhou, China, and commercial chickens (GYR) with higher egg yield after the three-line cross improvement hybridization of Yaoshan chickens were used as animal samples. To explore the regulatory mechanism of the differences in laying performance, RNA-seq and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC‒MS/MS) were used to portray the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens. At the transcriptional level, 288 differentially expressed genes were upregulated in Yaoshan chickens and 353 differentially expressed genes were upregulated in GYR chickens. In addition, GSEA revealed that ECM-receptor interactions and the TGF-β signalling pathway were inhibited, resulting in increased egg production in GYR chickens. Furthermore, the upregulation of thiamine and carnitine was identified by metabolomic analysis to promote the laying performance of chickens. Finally, comprehensive analyses of the transcriptome and metabolome found that thiamine and carnitine were negatively correlated with ECM-receptor interactions and the TGF-β signalling pathway, which jointly regulate the laying performance of Yaoshan chickens and GYR chickens. In conclusion, our study delineates differences in the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens during the peak egg production period and provides new hypotheses and clues for further research on poultry egg production performance and the improvement of economic benefits.
2022-12-10 | GSE218287 | 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.
2025-05-12 | GSE296109 | GEO
Project description:Calcium (Ca) and phosphorus (P) are essential micronutrients that are linked to a wide set of biological processes. In laying hens there is still uncertainty about the optimal Ca/P ratio in feed and further strategies for the reliable mineral restriction in poultry diets are required. The dataset is based on Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) laying hens sampled at peak performance. The experimental design comprises four dietary groups differed in Ca (recommended vs. 15 % reduction) and mineral P (adequate vs. 20 % reduction) levels; 1) control diet (Con; Ca=34.4g/kg, P=5.3 g/kg and Ca/P ratio=7.45), 2) Low Ca and P diet (LCaP), 3) low Ca diet (LCa), and low P diet (LP). Jejunal transcriptome profiles were assessed by mRNA sequencing in a total of 80 animals (10 hens per experimental group for each laying line) at sampling age of 31 weeks) to approximate the consequences of variable Ca and P supply.
2021-06-14 | E-MTAB-9109 | biostudies-arrayexpress
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.
2025-05-16 | GSE296459 | GEO