Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency
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ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE269311 | GEO | 2024/09/13
REPOSITORIES: GEO
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Project description:The objective of this work was to investigate differential gene expression of Charolais (n=90) and Holstein Freisian (n=77) steers divergent in RFI. The primary goal was to uncover genes and pathways associated with feed efficiency. Cattle were subjected to three different 70 day dietary phases. Initally animals were offered a high concentrate phase, termed "High Concentrate 1". Following this phase animals were offered sero grazed grass for 70 days followed by another high concentrate phase known as "High Concentrate 2". Prior to each stage beginning a dietary adaption period was allowed. Liver biopsies were taken at the end of each dietary phase for animals deemed as either high or low in RFI. RNA was extracted and liver gene expression was investigated using RNA-Seq.
2019-01-16 | GSE111464 | GEO
Project description:The objective of this study was to identify differentially expressed genes in the liver of steers with divergent Residual Feed Intake (RFI). Methods:In total 50 purebred Angus, 48 purebred Charolais and 158 Kinsella Composite breed steers were tested for individual feed intake using the GrowSafe system for an average period of 70 to 73 days. During the feedlot test animals were fed at ad libitum with a finishing diet composed of 75% barley grain, 20% barley silage and 5% rumensin pellet. Body weight of each animal was measured at an interval of 28days and ADG for each animal was obtained from a linear regression of serial body weight (BW) measurements (Kgs) on time (days). MWT was calculated as midpoint BW0.75, where midpoint BW was computed as the sum of initial BW of the animal and the product of its ADG multiplied by half the number test days. DMI of each animal was calculated as the average daily feed intake of the animals for the time during the feedlot test (days). The expected DMI for each animal was predicted using the regression intercept and regression coefficients of ADG and MWT on actual DMI, and RFI was computed as the difference between the standardized daily DMI and the expected DMI. At the end of the test, animals were slaughtered and liver tissue was collected immediately after slaughter separately bagged in plastic bags, labeled and flash frozen in liquid nitrogen. The frozen samples were transferred to the laboratory on ice and stored at -80C until RNA extraction. From the frozen samples, 20 samples from each breed were selected for total RNA extraction including six samples with extreme high and six samples extreme low-RFI phenotypes for each breed. Complementary DNA (cDNA) libraries were constructed for each of the 60 animals and consequently single end sequenced using Illumina Hiseq 2500 sequencer. The raw reads were aligned and mapped to the bovine reference genome UMD 3.1 using Tophat2 aligner with default alignment parameters. Thereafter, reads aligned uniquely to each annotated transcript of gene in the bovine genome were counted using HTSeq-count package with default parameters. Read counts from HTSeq-count, sample information (sample id, sire, feed efficiency group and sequencing mode) and gene annotation table from ENSEMBL Biomart were used for differential expression analysis within each breed using the edgeR package in R for the six extreme low-RFI and six extreme high-RFI samples. Results: At a false discovery rate of 0.05 and fold change > 2 , we identified 72, 41 and 175 differentially expressed genes for Angus, Charolais and KC RFI divergent steers respectively.
2018-05-17 | GSE107477 | GEO
Project description:The selection of cattle with high feed efficiency is of paramount importance with regard to reducing feed costs in the beef industry. Developing predictive biological markers specifically for improved feed efficiency is an attractive alternative to direct measurement on large numbers of animals.Evidence is provided that, effects of RFI on gene expression in muscle of beef cattle are not consistent across breed type or dietary phase. These novel observations challenge the practicality of selecting and breeding for low RFI animals across different diets and stages of development. Perhaps, future research should be directed at utilising different diets to harness the full genetic potential of animal based on breed or stage of maturity. Further to this, evidence is provided from our own work and that of others that less efficient HF steers consuming zero grazed grass are under increased stress as demonstrated by an upregulation of immune function in these animals.
2023-06-07 | GSE113135 | GEO
Project description:The biological mechanisms associated with the residual feed intake in ruminants have been harnessed immensely via transcriptome analysis of liver and ruminal epithelium, however, this concept has not been fully explored using whole blood. We applied whole blood transcriptome analysis and gene set enrichment analysis to identify key pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261.3 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, weekly whole blood samples were collected three times from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.
2022-04-07 | GSE198068 | GEO
Project description:The objectives of the current study was to profile miRNA expression in the liver tissue of beef steers and consequently identify differentially expressed miRNAs between efficient and inefficient beef steers. Materials and Methods: In total 50 purebred Angus, 48 purebred Charolais and 158 Kinsella Composite breed steers were tested for individual feed intake using the GrowSafe system for an average period of 70 to 73 days. During the feedlot test animals were fed at ad libitum with a finishing diet composed of 75% barley grain, 20% barley silage and 5% rumensin pellet. Body weight of each animal was measured at an interval of 28days and ADG for each animal was obtained from a linear regression of serial body weight (BW) measurements (Kgs) on time (days). MWT was calculated as midpoint BW0.75, where midpoint BW was computed as the sum of initial BW of the animal and the product of its ADG multiplied by half the number test days. DMI of each animal was calculated as the average daily feed intake of the animals for the time during the feedlot test (days). The expected DMI for each animal was predicted using the regression intercept and regression coefficients of ADG and MWT on actual DMI, and RFI was computed as the difference between the standardized daily DMI and the expected DMI. At the end of the test, animals were slaughtered and liver tissue was collected immediately after slaughter separately bagged in plastic bags, labelled and flash frozen in liquid nitrogen. The frozen samples were transferred to the laboratory on ice and stored at -80C until RNA extraction. From the frozen samples, 20 samples (10 with positive and 10 with negative RFI phenotype values) of each breed were considered for total RNA extraction. Each of the selected liver tissue sample was pulverised into fine powder using liquid nitrogen and a pre-chilled mortar and pestle on dry ice. Total RNA containing small RNAs was then extracted using a Qiagen RNeasy Plus Universal Mini Kit (Qiagen, Toronto, ON). NanoDrop 2000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) was used to quantify the RNA. We obtained total RNA of an average concertation of 1851.8ng/µl per sample, and with absorbance ratios (A260/280) ranging between 1.8 and 2.0 which were considered of high purity for downstream analyses. RNA integrity was confirmed using a TapeStation-Agilent instrument (Agilent Technologies Canada, Mississauga, ON), RNA integrity number (RIN) values for all samples were higher than 8 which deemed them of high quality for cDNA library preparation. In total 60 cDNA libraries were prepared and sequenced at Clinical Genomics Centre (Toronto, ON, Canada). The libraries were prepared using the Illumina Truseq Small RNA Library Prep Kit (Illumina, San Diego, CA, USA) from 1µg of each of total RNA samples we submitted. Firstly, an RNA 3’ adapter was ligated to the 3’ end of the RNAs in the total RNA sample using T4 RNA Ligase 2 enzyme, thereafter an RNA 5’ adapter was added to the 5’ end of the 3’ adaptor-ligated-RNAs using T4 RNA Ligase. The RNA 3’ and RNA 5’ adapters are designed to specifically target miRNAs and other small RNAs resulting from similar biogenic processing. The 5’ and 3’ adapter ligated RNA was then Reverse transcribed using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific, San Jose, CA, USA) and the RNA RT primer to generate single stranded cDNA. The cDNA was then PCR amplified a common RNA PCR primer, and a second RNA PCR primer containing a six-nucleotide indexing sequence to allow multiplexed sequencing of multiple samples on the same flow cell lane. The cDNA libraries were purified via gel electrophoresis using a 6% PAGE Gel, and the 160bp and 145bp cDNA bands were used for sequencing. Four sequencing pools of 15 samples were constructed by pooling an average of 2nM cDNA of each sample. The pooled cDNA libraries were single end sequenced on two flow cells using the Illumina Hiseq 2500 sequencing platform under Rapid run mode, with expected read length of 50bp (1x50bp SR). After sequencing raw sequence data were demultiplexed into individual FASTQ file each sample using Illumina bcl2fastq-v2.17.1.14 conversion software (Illumina). Adaptors on the 3' end of the sequences were clipped of using Cutadapt version 1.16, and consquently filtered for other small RNA species using bowtie-1.1.1 short read aligner. Individual miRNA (including known and novel miRNAs) were profiled using the UMD3.1 bovine reference genome and the miRDeep2 package (version 2.0.0.8), Differential miRNA expression analyses within each breed was performed between six extreme low RFI and high RFI animals using edgeR package in R, at a threshold of P < 0.05 and Fold change > 1.5. We identified 588 miRNAs as expressed in the liver tissue of the studied animals of which 90% of these miRNAs were expressed in animals from all three breed populations. Ten previously identified (known) miRNAs including bta-miR-192, bta-miR-143, bta-miR-148a, bta-miR-26a, bta-miR-30a-5p, bta-miR-22-3p, bta-miR-27b, bta-let-7f, bta-miR-27a-3p, and bta-miR-101 showed exceptionally high expression in the liver tissue of all steers, accounting for over 78% of the aligned sequence reads. We also identified 241 novel bovine miRNAs, of which the majority (69%) were uniquely expressed in one of the three breed populations. We identified 12 (7 up- and 5 down- regulated in low-RFI animals), 18 (12 up- and 6 down- regulated in low-RFI animals), and 12 (8 up- and 4 down- regulated in low-RFI animals) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with only bta-miR-449a being differentially expressed in all three breeds.
2020-11-16 | GSE144432 | 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: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:RNA-seq from backfat tissues were obatained from 22 steers, including Angus (AN; n=8), Charolais (CH; n=6), and Kinsella composite (KC; n=8). In each breed, cattle were classified two groups, i.e. high residual feed intake adjusted for off-test backfat thickness (RFIfat, RFIfat >= 0.5) and low RFIfat (RFIfat <= -0.5). For gene analysis, 46, 39 and 177 differentially expressed (DE) genes were identified in AN, CH and KC, respectively. Among them, 4, 17, 74 genes were up-regulated in high RFIfat as compared to low RFIfat in AN, CH and KC, respectively. All DE genes were used for functional and upstream analysis in Ingenuity Pathway Analysis. Some DE genes were involved in reduction of carbohydrate metabolism in AN, and reduction of lipid metabolism in KC.
2021-11-01 | GSE107268 | GEO
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:Transcriptional profiling in skeletal muscle of 48 pigs (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients: low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated.
2017-03-14 | GSE84092 | GEO