Genetic analysis of residual feed intake and its molecular pathways in coloured broiler chicken [liver]
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE116932 | GEO | 2018/07/12
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome analysis was performed in duodenum of high and low RFI chicks for finding out differentially expressing genes and molecular pathways for RFI in colored broiler chicken. The sample of 4 birds each from high and low RFI group from the whole lot of 225 broilers was taken for transcriptome analysis. The expression of genes influencing low and high feed efficiency and the pathways of these genes was studied out to examine the molecular mechanism influencing feed efficiency.
2018-07-12 | GSE116940 | GEO
Project description:Residual feed intake (RFI) is a measure of feed efficiency, where low RFI denotes high feed efficiency. Caloric restriction (CR) is associated with feed efficiency in livestock species and to human health benefits such as longevity and cancer prevention. We have developed pig lines that differ in RFI and are interested to identify the genes and pathways that underlie feed efficiency. Prepubertal Yorkshire gilts with low RFI (n=10) or high RFI (n=10) were fed ad libitum or at 80% of maintenance for eight days. We measured serum metabolites and generated transcriptional profiles of liver and subcutaneous adipose tissue. 6,114 genes in fat and 305 genes in liver were differentially expressed (DE) in response to CR and 311 in fat and 147 in liver were DE due to RFI differences. Pathway analyses of CR-induced DE genes indicated a switch to a conservation mode of energy by down-regulating lipogenesis and steroidogenesis in both liver and fat. Interestingly, CR in pigs altered expression of genes in immune and cell cycle/apoptotic pathways in fat, which may explain part of the CR-driven lifespan enhancement. In-silico analysis of transcription factors revealed ESR1 as a putative regulator of the adaptive response to CR and several targets of ESR1 in our DE fat genes were annotated as cell cycle/apoptosis genes. Lipid metabolic pathway was overrepresented by down-regulated genes due to both CR and low RFI. We propose a common energy conservation mechanism, which may be controlled by PPARA, PPARG, and/or CREB in both CR and feed efficient pigs. Prepubertal Yorkshire gilts with low RFI (n=10) or high RFI (n=10) were fed ad libitum or at 80% of maintenance for eight days in 2 x 2 complete factorial arrangement.
2010-01-10 | E-GEOD-18359 | biostudies-arrayexpress
Project description:Residual feed intake (RFI) is a measure of feed efficiency, where low RFI denotes high feed efficiency. Caloric restriction (CR) is associated with feed efficiency in livestock species and to human health benefits such as longevity and cancer prevention. We have developed pig lines that differ in RFI and are interested to identify the genes and pathways that underlie feed efficiency. Prepubertal Yorkshire gilts with low RFI (n=10) or high RFI (n=10) were fed ad libitum or at 80% of maintenance for eight days. We measured serum metabolites and generated transcriptional profiles of liver and subcutaneous adipose tissue. 6,114 genes in fat and 305 genes in liver were differentially expressed (DE) in response to CR and 311 in fat and 147 in liver were DE due to RFI differences. Pathway analyses of CR-induced DE genes indicated a switch to a conservation mode of energy by down-regulating lipogenesis and steroidogenesis in both liver and fat. Interestingly, CR in pigs altered expression of genes in immune and cell cycle/apoptotic pathways in fat, which may explain part of the CR-driven lifespan enhancement. In-silico analysis of transcription factors revealed ESR1 as a putative regulator of the adaptive response to CR and several targets of ESR1 in our DE fat genes were annotated as cell cycle/apoptosis genes. Lipid metabolic pathway was overrepresented by down-regulated genes due to both CR and low RFI. We propose a common energy conservation mechanism, which may be controlled by PPARA, PPARG, and/or CREB in both CR and feed efficient pigs.
2010-01-10 | GSE18359 | GEO
Project description:The knowledge of the genetic architecture behind feed efficiency would allow to breed more efficient animals maximizing farm profitability and reducing the environmental impact of animal production. This study analyzes high throughput gene expression data from milk samples to determine key genes and biological mechanisms associated to feed efficiency in dairy sheep.A detailed description of the sheep management practices and calculations for the feed efficiency index (FEI) are detailed in 10.3168/jds.2020-19061. For these analyses, we selected animals with divergent FEI values from a group of 40 lactating Assaf ewes. RNA-Seq was performed on milk somatic cell samples from 8 high feed efficiency sheep (H-FE), FEI = −0.29 (SD = 0.23), RFI = −0.16 (SD = 0.25), and 8 low feed efficiency sheep (L-FE), FEI = 0.81 (SD = 0.24), RFI = 0.19 (SD = 0.24)).
2023-02-14 | E-MTAB-12355 | biostudies-arrayexpress
Project description:Global gene expression profiles of peripheral blood of 35 to 42 day-old Yorkshire pigs with extremely low (more efficient) and high RFI (less efficient) values from two Iowa State University lines (the low RFI line, n = 15, and the high RFI line, n =16) that were divergently selected for RFI during the grow-finish phase were determined by Illumina RNA-seq (100 bp, paired-end) on the Hiseq2000 platform to explore the transcription biomarkers for feed efficiency in pigs.
2016-01-15 | E-MTAB-4179 | biostudies-arrayexpress
Project description:The objective of this study was to decipher the molecular basis of feed efficiency in meat-type chicken using duodenum tissues from a chicken population divergently selected for residual feed intake (RFI). Residual feed intake is the deviation of expected feed intake from actual feed intake. Chickens that consume less feed than expected are efficient (LRFI) and chickens that consume more feed than expected are inefficient (HRFI). A divergent selection for RFI was undertaken using an unselected random bred chicken population. RFI at day 35-42 was used as a criterion for selecting low (LRFI) and high (HRFI) RFI. Duodenum tissues were collected from 16 male chickens under sterile conditions experimentation. Tissues were collected from 4 males at days 35 and 42 in each line.
2012-08-02 | GSE39824 | GEO
Project description:Gene expression determination between breast muscle associated with the phenotypic expression of feed efficiency (FE) in a single male broiler line. Goal was to determine the changes of gene expression by feed efficiency (FE). Two-condition experiment, high feed efficiency vs. low feed efficiency. Biological replicates: breast muscles from 4 high feed efficiency male broiler, breast muscles from 4 low feed efficiency male broiler
2010-11-24 | E-GEOD-24963 | biostudies-arrayexpress
Project description:The objective of this study was to decipher the molecular basis of feed efficiency in meat-type chicken using duodenum tissues from a chicken population divergently selected for residual feed intake (RFI). Residual feed intake is the deviation of expected feed intake from actual feed intake. Chickens that consume less feed than expected are efficient (LRFI) and chickens that consume more feed than expected are inefficient (HRFI). A divergent selection for RFI was undertaken using an unselected random bred chicken population. RFI at day 35-42 was used as a criterion for selecting low (LRFI) and high (HRFI) RFI. Duodenum tissues were collected from 16 male chickens under sterile conditions experimentation. Tissues were collected from 4 males at days 35 and 42 in each line. Duodenum at 35 and 42 days from a chicken population divergently selected for residual feed intake were utilized for RNA extraction and hybridization on Affymetrix microarrays.
2012-08-01 | E-GEOD-39824 | biostudies-arrayexpress
Project description:An accumulation of over a decade of research in cattle has shown that genetic selection for decreased residual feed intake (RFI), defined as the difference between an animal’s actual feed intake and its expected feed intake, is a viable option for improving feed efficiency and reducing the feed requirements of herds, thereby improving the profitability of cattle producers. Hormonal regulation is one of the most important factors in feed intake. To determine the relationship between hormones and feed efficiency, we performed gene expression profiling of hormonal regulation in whole blood of Chinese Holstein cattle with low and high RFI coefficients. 857 differential expression genes (from 24683 genes) were found. Among these, 415 genes were up-regulated and 442 genes were down-regulated in the low RFI group. The gene ontology (GO) search revealed 6 significant terms and 64 genes associated with hormonal regulation, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) selected the adipocytokine signaling pathway, insulin signaling pathway. In conclusion, the study indicated that the molecular expression of genes associated with hormonal regulation differs in dairy cows, depending on their RFI coefficients, and that these differences may be related to the molecular regulation of the leptin-NPY and insulin signaling pathways.
2015-03-24 | GSE67176 | GEO
Project description:Improvement of feed efficiency would increase profitability of the poultry industries by decreasing the amount of feed required for production. Korat (KR) chicken is a new alternative meat-type chicken breed which its meat is recognized for its high protein, low fat and low purine content, whereas its low feed efficiency leads to high cost of production. Deeper understanding on how feed efficiency influences meat quality is poorly elucidated. To fulfill deeper understand molecular key that point the variation in feed efficiency and meat quality, the aim of this study was to investigate molecular pathways and genes involved in feed efficiency and meat quality in thigh of slow-growing KR chicken. A total of 75 males KR chicken were reared in individual cage until 10 weeks of age. Individual feed intake and body weight were collected weekly to calculate Feed Conversion Ratio (FCR) and Residual Feed Intake (RFI). Meat quality parameters were measured in thigh muscles such as ultimate pH (pHu), water-holding capacity (WHC), drip loss (DL), nucleotides content and several biomolecules (amide, …). Base on extreme values of FCR at 10 weeks of ages, 12 birds from the high FCR group (HFCR) and 9 birds from the low FCR group (LFCR) were selected for investigating their transcriptome using an 8×60K Agilent chicken microarray. In addition, a weighted gene coexpression network analysis was performed to detect the relationship between modules of co-expressed genes and feed efficiency, meat quality in thigh muscle. The result in this study indicated that selection on feed efficiency (FCR, RFI) would affect flavor precursor, lipid and protein content in thigh muscle. Based on WGCNA and functional enrichment analysis, results suggested that the key molecular pathways relate to FCR, RFI and meat quality (WHC, DL, IMP, AMP and inosine) in thigh muscle were the pathways of regulation of biological process, biological regulation and regulation of metabolic. Moreover, we revealed four genes there are assembly competence domain (ACD) gene, baculoviral IAP repeat containing 5 (BIRC5) gene, cytochrome c oxidase assembly factor 3 (COA3) gene and myosin light chain 9 (MYL9) gene that might be biomarker gene in feed efficiency and meat quality in thigh muscle. The hypothesis of the current study was alteration feed efficiency in slow-growing chicken will impact meat quality especially in term of texture and flavor.
2021-10-14 | GSE162848 | GEO