Expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in 7th and 18th days of embryonic stage
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE62445 | GEO | 2014/10/17
SECONDARY ACCESSION(S): PRJNA264100
REPOSITORIES: GEO
Similar Datasets
Project description:The expression of genes were analysed in 7th day of embryonic stage between Aseel, an indigenous slow-growing chicken, and control broiler, a fast-growing broiler chicken line. The whole embryo was collected in TRIZOL and total RNA was isolated. The expression profile of gene was determined in 64k Agilent chicken microarray chip. The Cy3 dye was used for detection. The fold change of expression was analysed in Aseel as compared to broiler chicken line.
2014-10-17 | GSE62443 | GEO
Project description:The expression of genes were analysed in muscle of 18th day of embryonic stage between Aseel, an indigenous slow-growing chicken, and control broiler, a fast-growing broiler chicken line. The whole embryo was collected in TRIZOL and total RNA was isolated. The expression profile of gene was determined in 64k Agilent chicken microarray chip. The Cy3 dye was used for detection. The fold change of expression was analysed in Aseel as compared to broiler chicken line.
2014-10-17 | GSE62444 | GEO
Project description:Chinese indigenous chickens (CICs) 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 CICs. Using the chicken 60 K single nucleotide polymorphism 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 CICs. Approximately 15% of the genome, on average, of CICs 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 CICs 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 CICs.
| S-EPMC6383742 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-03-16 | GSE128376 | GEO
Project description:BackgroundIn China, consumers often prefer indigenous broiler chickens over commercial breeds, as they have characteristic meat qualities requested within traditional culinary customs. However, the growth-rate of these indigenous breeds is slower than that of the commercial broilers, which means they have not yet reached their full economic value. Therefore, combining the valuable meat quality of the native chickens with the efficiency of the commercial broilers is of interest. In this study, we generated an F2 intercross between the slow growing native broiler breed, Huiyang Beard chicken, and the fast growing commercial broiler breed, High Quality chicken Line A, and used it to map loci explaining the difference in growth rate between these breeds.ResultsA genome scan to identify main-effect loci affecting 24 growth-related traits revealed nine distinct QTL on six chromosomes. Many QTL were pleiotropic and conformed to the correlation patterns observed between phenotypes. Most of the mapped QTL were found in locations where growth QTL have been reported in other populations, although the effects were greater in this population. A genome scan for pairs of interacting loci identified a number of additional QTL in 10 other genomic regions. The epistatic pairs explained 6-8% of the residual phenotypic variance. Seven of the 10 epistatic QTL mapped in regions containing candidate genes in the ubiquitin mediated proteolysis pathway, suggesting the importance of this pathway in the regulation of growth in this chicken population.ConclusionsThe main-effect QTL detected using a standard one-dimensional genome scan accounted for a significant fraction of the observed phenotypic variance in this population. Furthermore, genes in known pathways present interesting candidates for further exploration. This study has thus located several QTL regions as promising candidates for further study, which will increase our understanding of the genetic mechanisms underlying growth-related traits in chickens.
| S-EPMC3679733 | biostudies-literature
Project description:Gallus gallus breed:indigenous chicken Genome sequencing and assembly
| PRJNA482210 | ENA
Project description:Transcriptome analysis of bursa of Fabricius after saline and Salmonella typhimurium lipopolysaccharide treatment in young chickens
| PRJNA353102 | ENA
Project description:BACKGROUND:Genetically selected modern broiler chickens have acquired outstanding production efficiency through rapid growth and improved feed efficiency compared to unselected chicken breeds. Recently, we analyzed the transcriptome of breast muscle tissues obtained from modern pedigree male (PeM) broilers (rapid growth and higher efficiency) and foundational Barred Plymouth Rock (BPR) chickens (slow growth and poorer efficiency). This study was designed to investigate microRNAs that play role in rapid growth of the breast muscles in modern broiler chickens. RESULTS:In this study, differential abundance of microRNA (miRNA) was analyzed in breast muscle of PeM and BPR chickens and the results were integrated with differentially expressed (DE) mRNA in the same tissues. A total of 994 miRNA were identified in PeM and BPR chicken lines from the initial analysis of small RNA sequencing data. After filtering and statistical analyses, the results showed miR-2131-5p, miR-221-5p, miR-126-3p, miR-146b-5p, miR-10a-5p, let-7b, miR-125b-5p, and miR-146c-5p up-regulated whereas miR-206 down-regulated in PeM compared to BPR breast muscle. Based on inhibitory regulations of miRNAs on the mRNA abundance, our computational analysis using miRDB, an online software, predicated that 118 down-regulated mRNAs may be targeted by the up-regulated miRNAs, while 35 up-regulated mRNAs appear to be due to a down-regulated miRNA (i.e., miR-206). Functional network analyses of target genes of DE miRNAs showed their involvement in calcium signaling, axonal guidance signaling, and NRF2-mediated oxidative stress response pathways suggesting their involvement in breast muscle growth in chickens. CONCLUSION:From the integrated analyses of differentially expressed miRNA-mRNA data, we were able to identify breast muscle specific miRNAs and their target genes whose concerted actions can contribute to rapid growth and higher feed efficiency in modern broiler chickens. This study provides foundation data for elucidating molecular mechanisms that govern muscle growth in chickens.
| S-EPMC6142689 | biostudies-literature
Project description:Chicken plumage color is an inheritable phenotype that was naturally and artificially selected for during domestication. The Baicheng You chicken is an indigenous Chinese chicken breed presenting three main feather colors, lavender, black, and yellow plumages. To explore the genetic mechanisms underlying the pigmentation in Baicheng You chickens, we re-sequenced the whole genome of Baicheng You chicken with the three plumage colors. By analyzing the divergent regions of the genome among the chickens with different feather colors, we identified some candidate genomic regions associated with the feather colors in Baicheng You chickens. We found that EGR1, MLPH, RAB17, SOX5, and GRM5 genes were the potential genes for black, lavender, and yellow feathers. MLPH, GRM5, and SOX5 genes have been found to be related to plumage colors in birds. Our results showed that EGR1 is a most plausible candidate gene for black plumage, RAB17, MLPH, and SOX5 for lavender plumage, and GRM5 for yellow plumage in Baicheng You chicken.
| S-EPMC9720402 | biostudies-literature
Project description:This study was carried out to compare the impact of choline supplementation (available from two sources synthetic and natural) on various dosages in broilers. The mode of choline supplementation, via diet and additional sources, synthetic and natural, and the data of performance, carcass quality, blood parameters, and hepatic steatosis were compared. A total of 1050 day-old male Cobb 500 broiler chicks were randomly assigned to 10 treatments, using a completely randomized design model in a factorial scheme, with 6 replicates per treatment and 25 birds per replicate. Choline was supplemented using three sources: synthetic choline chloride 60% (CC), and two sources of natural choline A (NCA), and B (NCB). The Control treatment did not receive any choline supplementation. The diets were supplemented with low, intermediate and high doses of choline sources (400g/t, 800g/t, and 1200g/t of CC; 100g/t, 200g/t, and 300g/t of both NCA and NCB). Data analysis was performed using a factorial model to investigate the effects of choline supplementation (CC, NCA, NCB) and doses on the measured variables. Overall, the results indicated that the the performance of NCA was better than CC & NCB, specifically the dose of 100g/t of NCA outperformed MAR at 100g/t & CC at 400g/t, leading to a significant increase in body weight gain (85.66g & 168.84g respectively), and a noteworthy (9- & 12-point respectively) improvement in feed conversion ratio. Furthermore, NCA contributed to a reduction in steatosis when contrasted with various NCB & CC doses, likely due to the presence of curcumins and catechins in the natural choline source. These findings demonstrated that NCA supplementation yielded superior results compared to CC and NCB across both performance and liver health aspects in broilers aged 1 to 42 days. In conclusion, NCA can be used to replace the CC 60% without compromise on the zootechnical performance in broilers.
| S-EPMC10950236 | biostudies-literature