Similar Datasets
Project description:In this study, we investigated the molecular regulatory mechanisms of milk protein production in dairy cows by studying the miRNAomes of five key metabolic tissues involved in protein synthesis and metabolism from dairy cows fed high- and low-quality diets. In total, 340, 338, 337, 330, and 328 miRNAs were expressed in the rumen, duodenum, jejunum, liver, and mammary gland tissues, respectively. Some miRNAs were highly correlated with feed and nitrogen efficiency, with target genes involved in transportation and phosphorylation of amino acid (AA). Additionally, low-quality forage diets (corn stover and rice straw) influenced the expression of feed and nitrogen efficiency-associated miRNAs such as miR-99b in rumen, miR-2336 in duodenum, miR-652 in jejunum, miR-1 in liver, and miR-181a in mammary gland. Ruminal miR-21-3p and liver miR-2285f were predicted to regulate AA transportation by targeting ATP1A2 and SLC7A8, respectively. Furthermore, bovine-specific miRNAs regulated the proliferation and morphology of rumen epithelium, as well as the metabolism of liver lipids and branched-chain AAs, revealing bovine-specific mechanisms. Our results suggest that miRNAs expressed in these five tissues play roles in regulating transportation of AA for downstream milk production, which is an important mechanism that may be associated with low milk protein under lowquality forage feed.
2018-07-21 | GSE117441 | 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:We recently performed global gene expression in the breast muscles of modern broiler and foundation line chickens. In this study, we have peformed miRNA expression analyses in the same tissues to identify muscle specific miRNAs that could be regulatory factors for muscle growth and feed efficiency in chickens.
2018-09-07 | GSE119528 | 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: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).
2010-11-24 | GSE24963 | GEO
Project description:Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. Differential open chromatin regions identified by ATAC-seq were linked to genes involved in glycolytic and fatty acid processes. GWAS identified 211 significant single nucleotide polymorphisms associated with feed efficiency traits, with candidate genes PPP1R14C, TH, and CTSD. Integration of duodenal ATAC-seq data and GWAS data identified six key functional variants, particularly in the 1500985–1509676 region on chromosome 2. In those regions, CTSD was found to be highly expressed in the duodenal tissues of pigs with a high feed conversion ratio, suggesting its role as a potential target gene. Overall, the integration of multi-omics data provided insights into the genetic basis of feed efficiency, offering valuable information for breeding more efficient pig breeds.
2024-09-30 | GSE270124 | 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
Project description:MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle Results: Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs (miRBase v.19). Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378 and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (version 19). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle Conclusions: Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying residual feed intake in bovine
2015-11-27 | GSE63691 | GEO