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741 results for “chicken”
Data from: The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity
Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.
Baba Yaga's Hut on Chicken's legs
Source: Objaverse 1.0 / Sketchfab
FIGURES 1–5 in A new species of the genus Amyrsidea (Phthiraptera: Amblycera: Menoponidae) parasitizing domestic chickens in Saudi Arabia
FIGURES 1–5. Amyrsidea (Argimenopon) saudiensis n. sp.: 1, female habitus. 2, male habitus. 3, female head and prothorax. 4, male genitalia. 5, hypopharyngeal sclerites.
MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing
<p></p><h1>Data sources</h1><br>This dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174).<br><h1>Sequencing data QC and metagenomic assembly</h1><br>First, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed.<br><h1>MAGs recovery</h1><br>MAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness < 70% or contamination > 5% or N50 < 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).<br><h1>Non-redundant gene catalog</h1><br>Genes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.<br><h1>MSPs recovery</h1><br>A raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.<br><h1>MAGs and MSPs taxonomic annotation</h1><br>Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.<br><h1>Construction of the phylogenetic tree</h1><br>39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB38174 (cohort used in catalogue assembly) and PRJEB29033, PRJEB33338, PRJEB53667 (independent cohort not used in assembly).<p></p>
Fig. 2 in Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum
Fig. 2. Whole genome sequence phylogeny of MMM721T, ISU324, PIG517 and all publicly available genomes on the PATRIC genome database as of November 2020. The tree is rooted by Eggerthia catenaformis OT569. Only bootstrap values>50% are noted for branch nodes. The PATRIC genome IDs are noted in parentheses after the strain name.
Fig. 1 in Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum
Fig. 1. (a) Transmission electron microscope image of MMM721T cells. Bar, 1 Μm. (b) Scanning electron microscope image of MMM721T cells. Bar, 2 Μm. Cells were cultured in BHIGL for 24 h at 42 °C prior to fixation and visualization.
Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed Eimeria species
<p>Coccidiosis caused by the <em>Eimeria</em> species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of <em>Eimeria</em>-infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi). Based on the changes in gene expression patterns, we defined three groups of genes that showed differential expression. This enabled us to capture evidence of endoplasmic reticulum stress at the initial stage of <em>Eimeria</em> infection. Furthermore, we found that innate immune responses against the parasite were activated at the first exposure; they then showed gradual normalization. Although the cytokine-cytokine receptor interaction pathway was significantly operative at 4 dpi, its downregulation led to an anti-inflammatory effect. Additionally, the construction of gene co-expression networks enabled identification of immunoregulation hub genes and critical pattern recognition receptors after <em>Eimeria</em> infection. Our results provide a detailed understanding of the host-pathogen interaction between chicken and <em>Eimeria</em>. The clusters of genes defined in this study can be utilized to improve chickens for coccidiosis control.</p>
Differential seasonal avoidance of anthropogenic features and woody vegetation by Lesser Prairie-chickens
<p>The influence of seasonal variation in animal behavior and the corresponding response in habitat selection is a critical component of habitat selection analyses. To examine this relationship, we conducted multi-scale analyses of Lesser Prairie-chicken (<em>Tympanuchus pallidicinctus</em>) habitat selection in relation to anthropogenic infrastructure associated with oil and gas development, mesquite, and trees during the spring and summer at home range and lek area scales. We tracked 159 Lesser Prairie-chickens using VHF radiotelemetry or PTT-GPS transmitters in the sand shinnery oak prairie region of eastern New Mexico, USA. We used discrete choice models and logistic regression to assess seasonal patterns of habitat selection at home range and lek area scales, respectively. The static habitat features we examined allowed us to observe differential patterns of habitat selection between the two seasons, revealing an overall increase in the degree of avoidance following the spring season. Results of our home range scale analysis indicate that utility pole density, mesquite cover and proximity, distance to active well pads, and proximity to private roads have significant negative effects on habitat selection during both seasons. Avoidance of dense utility pole areas was significantly greater during the summer. Lek area habitat selection results were similar, but differences in sensitivity to features between seasons were stronger. Avoidance of high mesquite cover and utility pole and tree densities, in particular, was significantly greater in the summer. The effects of density and cover of these features, which have previously been understudied or overlooked in Lesser Prairie-chicken research, provide critical information for future conservation practices. Furthermore, our study highlights the importance of accounting for potential seasonal patterns of their study species to best examine habitat selection.</p>
Demographics for all four breeds of broiler chickens
<p><span>In 2018, over nine billion chickens were slaughtered in the United States. As the demand for chickens increases, so too have concerns regarding the welfare of the chickens in these systems and the damage such practices cause to the surrounding ecosystems. To address welfare concerns, there is large-scale interest in raising chickens on pasture and switching to slower-growing, higher-welfare breeds as soon as 2024. We created a box model of US chicken demographics to characterize aggregate broiler chicken welfare and land use consequences at the country scale for US shifts to slower-growing chickens, housing with outdoor access, and pasture management. The US produces roughly 20 million metric tons of chicken meat annually. Maintaining this level of consumption entirely with a slower-growing breed would require a 44.6%–86.8% larger population of chickens and a 19.2% – 27.2% higher annual slaughter rate, relative to the current demographics of primarily "Ross 308" chickens that are slaughtered at a rate of 9.25 billion per year. Generating this quantity of slower-growing breeds in conventional concentrated animal feeding operations (CAFO) would require 90,582-98,687 km2, an increase of 19.9-30.6% over the 75,577 km2 of land used for current production of Ross 308. Housing slower-growing breeds on pasture, the more individually welfare-friendly option, would require </span><span>108,642-121,019 km2, a 43.8-60.1% increase over current land use. Allowing slower-growing breeds occasional outdoor access is an intermediate approach that would require 90,691-98,811 km2, an increase of 20-30.7% of the current land use, a very minor increase of land relative to managing slower-growing breeds in CAFOs. In sum, without a drastic reduction in consumption, switching to alternative breeds will lead to a substantial increase in the number of individuals killed each year, an untenable increase in land use, and a possible decrease in aggregate chicken welfare at the country-level scale. Pasture-based management requires substantial additional land use. These results demonstrate constraints and trade-offs in animal welfare, environmental conservation, and food animal consumption, while highlighting opportunities for policies to mitigate impacts in an integrated manner using a One Health approach.</span></p>
Chicken Nugget
mcdonald's boot-shape chicken nugget Source: Objaverse 1.0 / Sketchfab
Dataset for broiler chicken trial_BW_FPD
<p>Dataset for broiler chicken trial - related to Deliverable 4.3 Report on the effect of feeding alternative proteins on productive traits, physiological indicators, gut health and product quality and safety in chickens and turkeys</p>
Pathogenic potential and the role of clones and plasmids in beta-lactamase-producing E. coli from chicken faeces in Vietnam
<p>Raw data used to present figures and tables in the manuscript.</p>
JAR_Onion Chicken Chicken Soup Seasoning
<p>This datasheet presents the consumer preferences against onion chicken soup seasoning towards the top four brands in Indonesia evaluated using 3 scales JAR method.</p>
Supplementary_Gene ontology defines pre-post- hatch energy dynamics in the complexus muscle of broiler chickens
Open the record for dataset details and reuse information.
Data from: Widespread introgression in Chinese indigenous chicken breeds from commercial broiler
Chinese indigenous chickens constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality, and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on Chinese indigenous chickens. Using the chicken 60K single-nucleotide polymorphism (SNP) chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations, and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all Chinese indigenous chickens. Approximately 15% of the genome, on average, of Chinese indigenous chickens was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to Chinese indigenous chickens at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of Chinese indigenous chickens.
Data from: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken
The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome-wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity-related genes or both. Here, we tested whether genome-wide heterozygosity (20 990 SNPs) and diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater's prairie-chicken (Tympanuchus cupido attwateri). We found that postrelease survival of captive-bred birds was related to alleles of the innate (Toll-like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome-wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome-wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations and that in some populations specific functional genes may be better predictors of fitness than genome-wide heterozygosity.
Effects of Application of Recycled Chicken Manure and Spent Mushroom Substrate on Organic Matter, Acidity, and Hydraulic Properties of Sandy Soils
<p>This study aimed at examining the effects of long-term application of<br> chicken manure (CM) and spent mushroom substrate (SMS) on organic matter accumulation, acidity,<br> and hydraulic properties of soil. Two podzol soils with sandy texture in Podlasie Region (Poland)<br> were enriched with recycled CM (10 Mg ha1) and SMS (20 Mg ha1), respectively, every 1–2 years<br> for 20 years. The application of CM and SMS increased soil organic matter content at the depths<br> of 0–20, 20–40, and 40–60 cm, especially at 0–20 cm (by 102–201%). The initial soil pH increased in<br> the CM- and SMS-amended soil by 1.7–2.0 units and 1.0–1.2 units, respectively. Soil bulk density at<br> comparable depths increased and decreased following the addition of CM and SMS, respectively.<br> The addition of CM increased field water capacity (at –100 hPa) in the range from 45.8 to 117.8%<br> depending on the depth within the 0–60 cm layer. In the case of the SMS addition, the value of the<br> parameter was in the range of 42.4–48.5% at two depths within 0–40 cm. Depending on the depth, CM<br> reduced the content of transmission pores (>50 m) in the range from 46.3 to 82.3% and increased the<br> level of residual pores (<0.5 m) by 91.0–198.6%. SMS increased the content of residual pores at the<br> successive depths by 121.8, 251.0, and 30.3% and decreased or increased the content of transmission<br> and storage pores. Additionally, it significantly reduced the saturated hydraulic conductivity at<br> two depths within 0–40 cm. The fitted unsaturated hydraulic conductivity at two depths within the<br> 0–40 cm layer increased and decreased in the CM- and SMS-amended soils, respectively. The results<br> provide a novel insight into the application of recycled organic materials to sequester soil organic<br> matter and improve crop productivity by increasing soil water retention capacity and decreasing<br> acidity. This is of particular importance in the case of the studied low-productivity sandy acidic soils<br> that have to be used in agriculture due to limited global land resources and rising food demand.</p>
Chicken Embryonic stem cells
<p>Some pictures of chicken embryonic stem cells</p>
The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size
<p></p><p>Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional ∼66.5 Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression level are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based GWAS identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size QTL located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.</p><p></p>
Greater Prairie-chicken data used in "Responses to land cover and grassland management vary across life-history stages for a grassland specialist"
<p>Grassland birds have exhibited dramatic and widespread declines since the mid-20th century. Greater Prairie-Chickens (<i>Tympanuchus cupido pinnatus</i>) are considered an umbrella species for grassland conservation and are frequent targets of management, but their responses to land use and management can be quite variable. We used data collected during 2007-2009 and 2014-2015 to investigate effects of land use and grassland management practices on habitat selection and survival rates of Greater Prairie-Chickens in central Wisconsin, USA. We examined habitat, nest-site, and brood-rearing site selection by hens and modeled effects of land cover and management on survival rates of hens, nests, and broods. Prairie-chickens consistently selected grassland over other cover types, but selection or avoidance of management practices varied among life-history stages. Hen, nest, and brood survival rates were influenced by different land cover types and management practices. At the landscape scale, hens selected areas where brush and trees had been removed during the previous year, which increased hen survival. Hens selected nest sites in hay fields and brood-rearing sites in burned areas, but prescribed fire had a negative influence on hen survival. Brood survival rates were positively associated with grazing and were highest when home ranges contained ≈15-20% shrub/tree cover. The effects of landscape composition on nest survival were ambiguous. Collectively, our results highlight the importance of evaluating responses to management efforts across a range of life history stages, and suggest that a variety of management practices are likely necessary to provide structurally heterogeneous, high-quality habitat for Greater Prairie-Chickens. Brush and tree removal, grazing, hay cultivation, and prescribed fire may be especially beneficial for prairie-chickens in central Wisconsin, but trade-offs among life-history stages and the timing of management practices must be considered carefully.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.