Single-cell RNA transcriptome reveals heterogeneity and dynamics of cells during skeletal muscle development in different chicken breeds
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ABSTRACT: Different chicken breeds exhibit distinct muscle phenotypes resulting from selective breeding, but little is known about the molecular mechanisms responsible for this phenotypic difference. Skeletal muscle is composed of a large number of heterogeneous cell populations. Differences in differentiation and interaction of cell populations play a key role in the difference of skeletal muscle phenotype. Here, skeletal muscle single-cell RNA sequencing in three developmental stages was performed on Daheng broiler (cultivated breed) and Tibetan chicken (native breed).
Project description:Copy number variation profiles comparing control female Dehong chicken blood DNA with 3 different chicken breeds (white Leghorn, Cobb broiler, and Dou chicken) blood DNA. Each test breed had one male and one female sample, for a total of 6 test DNA samples. The goal is to determine the global copy number variation profiles between chicken breeds.
Project description:Copy number variation profiles comparing control female Dehong chicken blood DNA with 3 different chicken breeds (white Leghorn, Cobb broiler, and Dou chicken) blood DNA. Each test breed had one male and one female sample, for a total of 6 test DNA samples. The goal is to determine the global copy number variation profiles between chicken breeds. Female Dehong chicken DNA as reference DNA vs. 6 test chicken DNA samples.
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome gene expression profiles in liver and muscle tissues of two chicken breeds.
Project description:Copy number variation profiles comparing control female Dehong chiken blood DNA with 11 different chicken breeds(Silkie, Tibetan Chicken, Gallus gallus spadiceus, Bearded Chicken, Jinhu Chicken, Anak Chicken, Beijing Fatty Chicken, Langshan Chicken, Qingyuan partridge Chicken, Shek-Ki Chicken, Wenchang Chicken) blood DNA. Each test breeds had one male and one female sample, totally 22 test DNA samples.Goal is to get the golbal copy number variation profile between chicken breeds.
Project description:Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear. Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues. These results highlight some possible candidate genes for porcine adipose deposition and muscle growth and provide some data on which to base further studies of the molecular basis of energy metabolism. The mRNA expression differences of eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates are measured.
Project description:In the modern chicken industry, fast-growing broilers have undergone strong artificial selection for muscle growth, which has led to remarkable phenotypic variations compared with slow-growing chickens. However, the molecular mechanism underlying these phenotypes differences remains unknown. In this study, a systematic identification of candidate genes and new pathways related to myofiber development and composition in chicken Soleus muscle has been made using gene expression profiles of two distinct breeds: Qingyuan partridge (QY), a slow-growing Chinese breed possessing high meat quality and Cobb 500 (CB), a commercial fast-growing broiler line. Agilent cDNA microarray analyses were conducted to determine gene expression profiles of soleus and extensor digitorum longus muscle sampled at sexual maturity age of QY (112 d) and CB (42 d).
Project description:Bacterial infections remain an important cause of morbidity in poultry production. The molecular characteristics and dynamic changes in immune cell populations after bacterial infection have yet to be fully understood. Beijing-You chicken and Cobb broiler, two broiler breeds with different disease resistance, were infected with Salmonella typhimurium, and inflammation models were constructed. We characterized chicken spleen CD45+ immune cells by single-cell RNA sequencing.
Project description:Adaptation to hypoxia is a complicated and important physiological course for organisms, but the genetic mechanism underlying the adaptation is not fully understood yet. Tibetan Chicken (T), an indigenous chicken breed in China which inhabit in high areas with an altitude above 2,900 meters. Shouguang Chicken(S) and Dwarf Recessive White Chicken (DRW), two lowland chicken breeds, were used as control groups. The heart was the first functional organ to develop during the embryonic development. Furthermore, the heart is an efficient energy converter utilizing the most appropriate fuel for a given environment. Therefore, GeneChip® Chicken Genome Array was employed to identify the differentially expressed genes in embryonic hearts of Tibetan Chicken and two lowland chicken breeds in both hypoxic and normoxic incubating environments with a genome wide profile. Experiment Overall Design: To obtain general expression profiles of embryonic hearts in Tibetan Chicken(T), Dwarf Recessive White Chicken (DRW)and Shouguang Chicken (S)in hypoxia and normoxia, the fertilized full sib eggs of all the three chicken breeds were incubated under two different conditions. The heart was isolated from all the three chicken breeds under the two different conditions for RNA extraction and hybridization on Affymetrix microarrays.
Project description:Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear. Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues. These results highlight some possible candidate genes for porcine adipose deposition and muscle growth and provide some data on which to base further studies of the molecular basis of energy metabolism.