Publications by authors named "Ruirui Jiang"

42 Publications

Use of transcriptomic analysis to identify microRNAs related to the effect of stress on thymus immune function in a chicken stress model.

Res Vet Sci 2021 Sep 10;140:233-241. Epub 2021 Sep 10.

College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China. Electronic address:

In modern poultry production, stress-induced immunosuppression leads to serious economic losses and harm to animals, but the molecular mechanisms governing the effects of stress on the chicken thymus have not been elucidated. In this study, we successfully constructed a stress model of 7-day-old Gushi chickens by adding exogenous corticosterone (CORT) to their diet and determined the microRNA (miRNA) expression profile of thymus tissues using RNA-seq technology. The results identified 51 differentially expressed miRNAs (DEMs), including 30 upregulated miRNAs and 21 downregulated miRNAs. A total of 164 target genes of the DEMs were predicted based on bioinformatic analysis methods, and Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of these target genes were performed. The results from the GO enrichment analysis of the target genes identified 349 significantly enriched terms, including terms associated with the stress response and immune function that are primarily involved in the negative regulation of phagocytosis, the response to stress and the cellular response to stimulus. The KEGG pathway analysis indicated that the enriched pathways related to immunity or stress included the MAPK signaling pathway, lysosomes, endocytosis, and the RIG-I-like receptor signaling pathway. Among these pathways, DEMs (such as gga-miR-2954, gga-miR-106-5p, and gga-miR-16-5p) and corresponding target genes (such as IL11Ra, SIKE1, and CX3CL1) might be strongly correlated with thymic immunity in chickens. The results of this study provide a reference for further research on the molecular regulatory mechanisms governing the effect of stress on the immune function of the chicken thymus.
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http://dx.doi.org/10.1016/j.rvsc.2021.09.004DOI Listing
September 2021

TMT-based quantitative proteomic analysis reveals the spleen regulatory network of dexamethasone-induced immune suppression in chicks.

J Proteomics 2021 Sep 18;248:104353. Epub 2021 Aug 18.

Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou 450046, China; College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China. Electronic address:

Stress-induced immunosuppression is one of the most widespread problems in the poultry industry. Understanding the molecular regulatory mechanism of immunosuppression induced by stress in the chicken spleen would provide a scientific foundation for the prevention of stress reactions and antistress molecular breeding in poultry. To assess the protein expression profile of spleen tissue in a stress-included immunosuppression model, we performed a TMT-based proteomic analysis of chicken spleen tissue in a Dex-induced immunosuppression model (group C) and a control group (group A). We identified 590 differentially abundant proteins (DAPs) in chicken spleen tissue. These DAPs were significantly enriched in the following functional categories: ECM-receptor interaction, DNA replication, p53 signaling pathway, PI3K-Akt signaling pathway and NF-kappa B signaling pathway. Integrative analysis of the proteome and our previous transcriptome data revealed 62 DAPs showing correlations with the expression of their encoding mRNAs. Complementary proteome- and transcriptome-level analyses revealed a complex molecular network of stress-included immunosuppression. DPP4 and ALDH1A3 were the most significantly upregulated DAPs. GBP and OASL were identified as important nodes in the network related to stress-induced immunosuppression. The candidate genes identified in this study may be useful for the marker-based breeding of new chicken varieties with reduced stress levels. SIGNIFICANCE: This study provides a large amount of new information about the spleen proteome of the Dex-induced immunosuppression in chicks, as well as the correlation of transcriptome and proteome. Analysis of this resource has enabled us to examine mechanism of protein and transcript diversification, which expands the understanding of the complexity of the mechanism of stress-induced immunosuppression.
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http://dx.doi.org/10.1016/j.jprot.2021.104353DOI Listing
September 2021

Recent Progress in the Development of Graphene Detector for Terahertz Detection.

Sensors (Basel) 2021 Jul 22;21(15). Epub 2021 Jul 22.

National Key Laboratory of Science and Technology on Vacuum Electronics, School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China.

Terahertz waves are expected to be used in next-generation communications, detection, and other fields due to their unique characteristics. As a basic part of the terahertz application system, the terahertz detector plays a key role in terahertz technology. Due to the two-dimensional structure, graphene has unique characteristics features, such as exceptionally high electron mobility, zero band-gap, and frequency-independent spectral absorption, particularly in the terahertz region, making it a suitable material for terahertz detectors. In this review, the recent progress of graphene terahertz detectors related to photovoltaic effect (PV), photothermoelectric effect (PTE), bolometric effect, and plasma wave resonance are introduced and discussed.
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http://dx.doi.org/10.3390/s21154987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8347591PMC
July 2021

The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size.

Mol Biol Evol 2021 Jul 30. Epub 2021 Jul 30.

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.

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.
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http://dx.doi.org/10.1093/molbev/msab231DOI Listing
July 2021

Identification of genes related to stress affecting thymus immune function in a chicken stress model using transcriptome analysis.

Res Vet Sci 2021 Sep 7;138:90-99. Epub 2021 Jun 7.

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China. Electronic address:

With the rapid development of the poultry breeding industry and highly intensive production management, the losses caused by stress responses are becoming increasingly serious. To screen candidate genes related to chicken stress and provide a basis for future research on the molecular mechanisms governing the effects of stress on chicken immune function, we successfully constructed a chicken stress model by exogenously introducing corticosterone (CORT). RNA-seq technology was used to identify and analyze the mRNA and enrichment pathways of the thymus in the stress model group and the control group. The results showed that there were 101 significantly differentially expressed genes (SDEGs) (Padj < 0.05, |log2fold changes| ≥ 1 and FPKM >1), of which 44 were upregulated genes, while 57 were downregulated genes. Gene Ontology (GO) enrichment analysis found that the terms related to immunity or stress mainly included antigen processing and presentation, positive regulation of T cell-mediated immunity, and immune effector process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the main pathways related to immunity or stress were the PPAR signaling pathway, NOD-like receptor signaling pathway, and intestinal immune network for IgA production. Among the SDEGs, XCL1, HSPA8, DMB1 and BAG3 are strongly related to immunity or stress and may be important genes involved in regulating stress affecting the immune function of chickens. The above results provide a theoretical reference for subsequent research on the molecular regulatory mechanisms by which stress affects the immune function of poultry.
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http://dx.doi.org/10.1016/j.rvsc.2021.06.006DOI Listing
September 2021

Comparative analysis of hypothalamus transcriptome between laying hens with different egg-laying rates.

Poult Sci 2021 Jul 11;100(7):101110. Epub 2021 Mar 11.

College of Animal Science, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China. Electronic address:

Egg-laying performance is one of the most important economic traits in the poultry industry. Commercial layers can lay one egg almost every day during their peak-laying period. However, many Chinese indigenous chicken breeds show a relatively low egg-laying rate, even during their peak-laying period. To understand what makes the difference in egg production, we compared the hypothalamus transcriptome profiles of Lushi blue-shelled-egg chickens (LBS), a Chinese indigenous breed with low egg-laying rate and Rhode Island Red chickens (RIR), a commercial layer with relatively high egg-laying rate using RNA-seq. A total of 753 differentially expressed genes (DEGs) were obtained. Of these DEGs, 38 genes were enriched in 2 Gene Ontology (GO) terms, namely reproduction term and the reproductive process term, and 6 KEGG pathways, namely Wnt signaling pathway, Oocyte meiosis, GnRH signaling pathway, Thyroid hormone signaling pathway, Thyroid hormone synthesis and MAPK signaling pathway, which have been long known to be involved in egg production regulation. To further determine the core genes from the 38 DEGs, protein-protein interaction (PPI) network, co-expression network and transcriptional regulatory network analyses were carried out. After integrated analysis and experimental validation, 4 core genes including RAC1, MRE11A, MAP7 and SOX5 were identified as the potential core genes that are responsible for the laying-rate difference between the 2 breeds. These findings paved the way for future investigating the mechanism of egg-laying regulation and enriched the chicken reproductive regulation theory.
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http://dx.doi.org/10.1016/j.psj.2021.101110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187251PMC
July 2021

Characteristics and expression profiles of circRNAs during abdominal adipose tissue development in Chinese Gushi chickens.

PLoS One 2021 15;16(4):e0249288. Epub 2021 Apr 15.

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China.

Circular RNAs (circRNAs) play important roles in adipogenesis. However, studies on circRNA expression profiles associated with the development of abdominal adipose tissue are lacking in chickens. In this study, 12 cDNA libraries were constructed from the abdominal adipose tissue of Chinese domestic Gushi chickens at 6, 14, 22, and 30 weeks. A total of 1,766 circRNAs were identified by Illumina HiSeq 2500 sequencing. These circRNAs were primarily distributed on chr1 through chr10 and sex chromosomes, and 84.95% of the circRNAs were from gene exons. Bioinformatic analysis showed that each circRNA has 35 miRNA binding sites on average, and 62.71% have internal ribosome entry site (IRES) elements. Meanwhile, these circRNAs were primarily concentrated in TPM < 0.1 and TPM > 60, and their numbers accounted for 18.90% and 80.51%, respectively, exhibiting specific expression patterns in chicken abdominal adipose tissue. In addition, 275 differentially expressed (DE) circRNAs were identified by comparison analysis. Functional enrichment analysis showed that the parental genes of DE circRNAs were primarily involved in biological processes and pathways related to lipid metabolism, such as regulation of fat cell differentiation, fatty acid homeostasis, and triglyceride homeostasis, as well as fatty acid biosynthesis, fatty acid metabolism, and glycerolipid metabolism. Furthermore, ceRNA regulatory networks related to abdominal adipose development were constructed. The results of this study indicated that circRNAs can regulate lipid metabolism, adipocyte proliferation and differentiation, and cell junctions during abdominal adipose tissue development in chickens through complex ceRNA networks between circRNAs, miRNAs, genes, and pathways. The results of this study may help to expand the number of known circRNAs in abdominal adipose tissue and provide a valuable resource for further research on the function of circRNAs in chicken abdominal adipose tissue.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0249288PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049301PMC
April 2021

Identification and expression analysis of MicroRNAs in chicken spleen in a corticosterone-induced stress model.

Res Vet Sci 2021 May 1;136:287-296. Epub 2021 Mar 1.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China. Electronic address:

For investigating the effects of stress on the immune response of chickens, we established a corticosterone (CORT)-induced stress model by exogenous intake of CORT. Control group was fed with a basal diet and the stress model group was fed with a 30 mg/Kg CORT-treated diet in ad libitum conditions for 7 days. Then, we used RNA-seq technology to identify the expression pattern of miRNAs, target genes, and relevant pathways in chicken spleen. Results showed that 71 differentially expressed miRNAs (DEMs) were determined, 9 of which were significantly differentially expressed miRNAs (SDEMs), and 241 target genes of DEMs were predicted. GO annotation and KEGG pathway analysis were carried out to understand the role of the DEMs. Out of 287 significantly enriched GO terms, 37 were stress- or immune-related, such as response to light stimulus, detection of oxidative stress, and immune response in mucosal-associated lymphoid tissue. Out of 85 KEGG pathways, 8 were related to stress or immunity, such as cytokine-cytokine receptor interaction, JAK-STAT signaling pathway, and RLR signaling pathway. We then constructed the interaction networks between target genes from immune-related pathways and their DEMs. The analysis results suggested that some DEMs (gga-miR-17 family, gga-miR-15/16 family, gga-miR-2954 and gga-miR-34b-5p) and target genes (SIKE1, CX3CL1, IL11Ra, PIGR, and CDKN1A) were core miRNAs and genes. This study revealed the dynamic miRNA transcriptome, target genes and related pathways in chicken spleen under CORT-induced stress model, which provided a basis for studying the molecular mechanism of stress affecting immune function.
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http://dx.doi.org/10.1016/j.rvsc.2021.02.023DOI Listing
May 2021

Analysis of miRNA and mRNA reveals core interaction networks and pathways of dexamethasone-induced immunosuppression in chicken bursa of Fabricius.

Mol Immunol 2021 06 10;134:34-47. Epub 2021 Mar 10.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China. Electronic address:

Stress-induced immunosuppression is a serious problem affecting the production value of poultry, but its specific molecular mechanism has not yet been elucidated. We selected 7-day-old Gushi cocks as test animals and successfully established a stress-induced immunosuppression model by injecting 2.0 mg/kg (body weight) dexamethasone (Dex). We then constructed six cDNA libraries and two small RNA libraries of Bursa of Fabricius from the control group and the Dex group. RNA-seq results revealed 21,028 transcripts including 3920 novel transcripts; 500 miRNAs including 68 novel miRNAs were identified. Correlation analysis of miRNA, target genes and mRNA results indicated that the gga-miR-15 family, gga-miR-103-3p, gga-miR-456-3p, and gga-miR-27b-3p, as core differentially expressed miRNAs, may potentially regulate multiple genes which are involved in immune-related pathways; and that the core genes Suppressor of IKBKE 1 (SIKE1) and high mobility group AT-hook 2 (HMGA2) are associated with the miR-17 family (gga-miR-20a-5p, gga-miR-20b-5p, gga-miR-106-5p, and gga-miR-17-5p) and gga-let -7 family (gga-let-7b, gga-let-7i, gga-let-7c-5p, and gga-let-7f-5p). The interaction networks of mRNAs of significantly enrichment pathways and PPI (protein-protein interaction) networks showed that IL6, IL1B, IL8L1, CCL5, SOCS3, SOCS1, ITGB5, GSTA3, SQLE, FDFT1, FN1, IL18, IL10, MAPK11 and MAPK12 are network core nodes and that most of them are strongly associated with immune response. One of the candidate miRNAs, gga-miR-20b-5p, may play an important role in stress-induced immunosuppression. Luciferase assay and over-expression experiments suggested that gga-miR-20b-5p negatively regulated the expression of target gene SIKE1. These results provide better understanding of the mechanism of stress-induced immunosuppression in Gushi chicken bursa, and provide novel targets for subsequent research to improve poultry anti-stress capability.
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http://dx.doi.org/10.1016/j.molimm.2021.02.022DOI Listing
June 2021

OsbHLH98 regulates leaf angle in rice through transcriptional repression of OsBUL1.

New Phytol 2021 06 27;230(5):1953-1966. Epub 2021 Mar 27.

State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.

Leaf angle is an important agronomic trait in cereals that helps determine plant yield by affecting planting density. However, the regulation mechanism of leaf angle remained elusive. Here, we show that OsbHLH98, a rice bHLH transcription factor, negatively regulates leaf angle. osbhlh98 mutant leaves formed a larger leaf angle, whereas transgenic plants overexpressing OsbHLH98 exhibited a slight reduction in leaf angle. We determined that the changes in leaf angle resulted from increased number and size of parenchyma cells on the adaxial side of the lamina joint in osbhlh98 mutants. Experiments using reporter constructs showed that OsbHLH98 is expressed on the adaxial side of lamina joints, consistent with its proposed function in regulating leaf angle. Furthermore, we established by chromatin immunoprecipitation and CUT&RUN that OsBUL1 is a direct downstream target of OsbHLH98. Transactivation assays and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis indicated that OsbHLH98 represses OsBUL1 transcription. Our results demonstrate that OsbHLH98 negatively regulates leaf angle by counteracting brassinosteroid-induced cell elongation via the repression of OsBUL1 transcription. The characterization of OsbHLH98 and its role in determining leaf angle will lay the foundation to develop the ideal plant architecture for adaptation to high planting density.
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http://dx.doi.org/10.1111/nph.17303DOI Listing
June 2021

Associations among Dietary Omega-3 Polyunsaturated Fatty Acids, the Gut Microbiota, and Intestinal Immunity.

Mediators Inflamm 2021 2;2021:8879227. Epub 2021 Jan 2.

Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China.

Omega-3 polyunsaturated fatty acids (omega-3 PUFAs), which are essential fatty acids that humans should obtain from diet, have potential benefits for human health. In addition to altering the structure and function of cell membranes, omega-3 PUFAs (docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), alpha-linolenic acid (ALA), and docosapentaenoic acid (DPA)) exert different effects on intestinal immune tolerance and gut microbiota maintenance. Firstly, we review the effect of omega-3 PUFAs on gut microbiota. And the effects of omega-3 PUFAs on intestinal immunity and inflammation were described. Furthermore, the important roles of omega-3 PUFAs in maintaining the balance between gut immunity and the gut microbiota were discussed. Additional factors, such as obesity and diseases (NAFLD, gastrointestinal malignancies or cancer, bacterial and viral infections), which are associated with variability in omega-3 PUFA metabolism, can influence omega-3 PUFAs-microbiome-immune system interactions in the intestinal tract and also play roles in regulating gut immunity. This review identifies several pathways by which the microbiota modulates the gut immune system through omega-3 PUFAs. Omega-3 supplementation can be targeted to specific pathways to prevent and alleviate intestinal diseases, which may help researchers identify innovative diagnostic methods.
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http://dx.doi.org/10.1155/2021/8879227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801035PMC
January 2021

Effect of the Pressure of Reaction Gases on the Growth of Single-Crystal Graphene on the Inner Surfaces of Copper Pockets.

Micromachines (Basel) 2020 Dec 14;11(12). Epub 2020 Dec 14.

Zhongshan Branch of State Key Laboratory of Electronic Thin Films and Integrated Devices, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan 528402, China.

Single-crystal graphene has attracted much attention due to its excellent electrical properties in recent years, and many growth methods have been proposed, including the copper pockets method. In the copper pockets method, a piece of copper foil is folded into a pocket and put into a chemical vapor deposition (CVD) system for the growth of graphene. The dynamic balance of evaporation and deposition of copper on the inner surfaces of the copper pockets avoids high surface roughness caused by the evaporation of copper in open space, such as the outer surfaces of copper pockets. Much lower partial pressure of methane in the copper pockets and lower surface roughness reduce the nucleation density of graphene and increase the size of single-crystal graphene. It is found that the growth pressure is closely related to the size of single-crystal graphene prepared by the copper pockets method; the higher the growth pressure, the larger the size of single-crystal graphene. It is also found that the growth pressure has an effect on the inner surface roughness of the copper pockets, but the effect is not significant. The main factor affecting the size of the single-crystal graphene is the change in the volume of the copper pockets caused by the change in the growth pressure, and the volume of the copper pockets determines the content of methane in the copper pockets. According to the above law, the size of single-crystal graphene prepared by the copper pockets method can be enlarged by increasing the growth pressure. The size of single-crystal graphene can be enlarged in a wide range as the growth pressure can be increased in a wide range. In our experiments, when the growth pressure reached 450 Pa, single-crystal graphene with a diameter of 450 μm was prepared.
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http://dx.doi.org/10.3390/mi11121101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764845PMC
December 2020

Maximizing the Field Emission Performance of Graphene Arrays.

Nanomaterials (Basel) 2020 Oct 11;10(10). Epub 2020 Oct 11.

Zhongshan Branch of State Key Laboratory of Electronic Thin Films and Integrated Devices, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan 528402, China.

To design efficient and powerful field emission cathodes, the screening effect is of great importance and should be traded off between screening and emitter number. It has long been found that to achieve maximum emission efficiency in an array, neighboring emitters are at two or three times their height from each other. However, this is only true for one-dimensional emitters, such as carbon nanotubes, but for graphene, a two-dimensional material, it is different. In this work, we found that to achieve maximum emission efficiency in an array of graphene, the separation of the emitter is four times the height, and it is insensitive to the anode voltage and the distance between the cathode and the anode.
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http://dx.doi.org/10.3390/nano10102003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7599458PMC
October 2020

Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F chicken population.

Heredity (Edinb) 2021 Feb 28;126(2):293-307. Epub 2020 Sep 28.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.

Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1-6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.
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http://dx.doi.org/10.1038/s41437-020-00365-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026619PMC
February 2021

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken.

BMC Genomics 2020 Jul 23;21(1):511. Epub 2020 Jul 23.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.

Background: Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype.

Results: Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis.

Conclusions: These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.
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http://dx.doi.org/10.1186/s12864-020-06900-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376702PMC
July 2020

Identification of genes related to effects of stress on immune function in the spleen in a chicken stress model using transcriptome analysis.

Mol Immunol 2020 08 24;124:180-189. Epub 2020 Jun 24.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450002, China.

Stress is a physiological manifestation of the body's defense against adverse effects of external environment, but the molecular regulatory mechanism of stress effects on immune function of poultry has not been fully clarified. In this study, 7-day-old Chinese local breed Gushi cocks were used as model animal, and the stress model was successfully constructed by adding corticosterone (CORT) 30 mg/kg basic diet for 7 days. The spleen transcriptomes of the control group (B_S group) and the stress model group (C_S group) was determined by high-throughput mRNA sequencing (RNA-Seq) technology, and a total of 269 significantly differentially expressed genes (SDEGs) were obtained (Padj < 0.05, |FC| ≥ 2 and FPKM > 1). Compared with B_S group, there were 140 significantly up-regulated genes and 129 significantly down-regulated genes in C_S group. The immune/stress-related Gene Ontology (GO) terms included positive regulation of T cell mediated immunity, chemokine-mediated signaling pathway, T cell mediated immunity and so on. The SDEGs such as IL8L1, HSPA8, HSPA2, RSAD2, CCR8L and DMB1 were involved in these GO terms. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the SDEGs participated in many immune-related signaling pathways. The immune-related genes HSPA2, HSPA8, HSP90AA1, HSPH1 and HERPUD1 were enriched in Protein processing in endoplasmic reticulum pathway, IL8L1, CXCL13L2, CCR6, LEPR, CCR9 and CCR8L were enriched in Cytokine-cytokine receptor interaction pathway. The protein-protein interactions (PPI) analysis showed HSPA8, HSPA2 and IL8L1 as key core nodes had 7 interactions and may play important roles in the regulation of CORT-induced stress effects on immune function. The data onto this study enriched the genomic study of stress effects on immune function, and provided unique insights into the molecular mechanism of stress effects on immune function, and the genes identified in this study can be candidates for future research on stress response.
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http://dx.doi.org/10.1016/j.molimm.2020.06.004DOI Listing
August 2020

Transcriptomic Analysis of Spleen Revealed Mechanism of Dexamethasone-Induced Immune Suppression in Chicks.

Genes (Basel) 2020 05 6;11(5). Epub 2020 May 6.

Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.

Stress-induced immunosuppression is a common problem in the poultry industry, but the specific mechanism of its effect on the immune function of chicken has not been clarified. In this study, 7-day-old Gushi cocks were selected as subjects, and a stress-induced immunosuppression model was successfully established via daily injection of 2.0 mg/kg (body weight) dexamethasone. We characterized the spleen transcriptome in the control (B_S) and model (D_S) groups, and 515 significant differentially expressed genes (SDEGs) (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) > 1, adjusted -value (padj) < 0.05 and Fold change (|FC|) ≥ 2) were identified. The cytokine-cytokine receptor interaction signaling pathway was identified as being highly activated during stress-induced immunosuppression, including the following SDEGs-, and . At the same time, immune-related SDEGs including , and were significantly enriched in the intestinal immune network for the IgA production signaling pathway. The SDEG protein-protein interaction module analysis showed that and may play an important role in stress-induced immunosuppression. These findings provide a background for further research on stress-induced immunosuppression. Thus, we can better understand the molecular genetic mechanism of chicken stress-induced immunosuppression.
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http://dx.doi.org/10.3390/genes11050513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288455PMC
May 2020

The Landscape of DNA Methylation Associated With the Transcriptomic Network of Intramuscular Adipocytes Generates Insight Into Intramuscular Fat Deposition in Chicken.

Front Cell Dev Biol 2020 2;8:206. Epub 2020 Apr 2.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.

Intramuscular fat (IMF), which regulated by genetics, nutrition and environment is an important factor that influencing meat quality. Up to now, the epigenetic regulation mechanism underlying poultry IMF deposition remains poorly understood. Here, we focused on the DNA methylation, which usually regulate genes in transcription level. To look into the essential role of DNA methylation on the IMF deposition, chicken intramuscular preadipocytes were isolated and cultured , and a model of intramuscular adipocyte differentiation was constructed. Combined the whole genome bisulfite sequencing (WGBS) and RNA-Seq technologies, we identified several methylated genes, which mainly affecting fatty acid metabolism and muscle development. Furthermore, we reported that DNA methylation regulate intramuscular adipogenesis by regulating the genes, such as collagen, type VI, alpha 1 () thus affecting IMF deposition. Overexpression of increases the lipid droplet and inhibits cell proliferation by regulating and in intramuscular adipocytes, while knockdown of shows the opposite effect. Taken together, our results reveal that DNA methylation plays an important role in poultry IMF deposition.
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http://dx.doi.org/10.3389/fcell.2020.00206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142253PMC
April 2020

Comprehensive Transcriptome Analysis of lncRNAs Reveals the Role of lncAD in Chicken Intramuscular and Abdominal Adipogenesis.

J Agric Food Chem 2020 Mar 9;68(11):3678-3688. Epub 2020 Mar 9.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China.

Adipose tissue-specific distribution and deposition speed are the main factors affecting the slaughter performance and meat quality in poultry. Previous studies suggested that different adipose tissues owned various biochemical characteristics and gene expression patterns. To investigate the functional role of long noncoding RNAs (lncRNAs) during chicken intramuscular and abdominal adipogenesis, we performed transcriptome analysis by Ribo-Zero RNA-Seq technology. A total of 11247 lncRNAs were observed in the adipocytes derived from IMF and AbF in chicken. Among them, we got 1624 differentiated expressed novel lncRNAs. A large amount of lncRNAs were involved in several lipid metabolism and adipogenesis-related signaling pathways. Of these, lncRNAs, lncAD is one of the most upregulated lncRNA and was coexpressed with several genes of the PPAR signaling pathway. Here, we report that knockdown of lncAD inhibited its upstream gene expression in a -regulation manner, thus to decrease intramuscular preadipocytes adipogenic differentiation and promoted cell proliferation. Our present study revealed huge lncRNAs profile differences between IMF- and AbF-derived preadipocyte adipogenesis. Collectively, our findings not only provide valuable evidence for the identification of adipogenic lncRNAs but also contribute to further studies about the post-transcriptional regulation mechanism underlying tissue-specific fat deposition in poultry.
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http://dx.doi.org/10.1021/acs.jafc.9b07405DOI Listing
March 2020

Characteristics of the fecal microbiota of high- and low-yield hens and effects of fecal microbiota transplantation on egg production performance.

Res Vet Sci 2020 Apr 30;129:164-173. Epub 2020 Jan 30.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China. Electronic address:

The microbiota that resides in the digestive tract plays pivotal role in maintaining intestinal environmental stability by promoting nutrition digestion and intestinal mucosal immunity. However, whether the intestinal microbiota in laying hens affects egg laying- performance is not known. In this study, 16S rDNA gene sequencing and fecal microbiota transplantation were used to determine the structure of the intestinal microbiota and the effect of the intestinal microbiota on egg production. The results revealed that Firmicutes were dominant in both the H (high egg laying rates) and L (low egg laying rates) groups, while Bacteroides, Actinobacteria and Proteobacteria were significantly enriched in the L group compared to the H group. The laying rates were weakly affected in H hens transplanted with the fecal microbiota from L hens, except for temporary fluctuation, while the egg laying rates were significantly increased in L hens transplanted with the fecal microbiota from H hens. Therefore, we concluded that the population structure of the intestinal microbiota varied between the H and L groups, and the intestinal microbiota of high-yield laying hens had significant effects on low-yield laying hens performance.
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http://dx.doi.org/10.1016/j.rvsc.2020.01.020DOI Listing
April 2020

Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients.

Sci Rep 2020 02 7;10(1):2070. Epub 2020 Feb 7.

Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.

Non-small cell lung cancer (NSCLC) is featured with complex genomic alterations. Molecular profiling of large cohort of NSCLC patients is thus a prerequisite for precision medicine. We first validated the detection performance of a next-generation sequencing (NGS) cancer hotspot panel, OncoAim, on formalin-fixed paraffin-embedded (FFPE) samples. We then utilized OncoAim to delineate the genomic aberrations in Chinese NSCLC patients. Overall detection performance was powerful for mutations with allele frequency (MAF) ≥ 5% at >500 × coverage depth, with >99% sensitivity, high specificity (positive predictive value > 99%), 94% accuracy and 96% repeatability. Profiling 422 NSCLC FFPE samples revealed that patient characteristics, including gender, age, lymphatic spread, histologic grade and histologic subtype were significantly associated with the mutation incidence of EGFR and TP53. Moreover, RTK signaling pathway activation was enriched in adenocarcinoma, while PI(3)K pathway activation, oxidative stress pathway activation, and TP53 pathway inhibition were more prevalent in squamous cell carcinoma. Additionally, novel co-existence (e.g., variants in BRAF and PTEN) and mutual-exclusiveness (e.g., alterations in EGFR and NFE2L2) were found. Finally, we revealed distinct mutation spectrum in TP53, as well as a previously undervalued PTEN aberration. Our findings could aid in improving diagnosis, prognosis and personalized therapeutic decisions of Chinese NSCLC patients.
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http://dx.doi.org/10.1038/s41598-020-58819-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005734PMC
February 2020

Sudden sensorineural hearing loss with end-stage renal disease: a report of 32 cases.

Acta Otolaryngol 2019 Nov 5;139(11):1004-1007. Epub 2019 Sep 5.

Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xin Jiang Medical University , Urumchi , China.

Patients with end-stage renal disease (ESRD) have a higher risk of suffering sudden sensorineural hearing loss (SSNHL), but little is known about this population. To investigate the clinical characteristics, treatment and recovery of SSNHL patients with ESRD. Records of 32 SSNHL patients with ESRD were reviewed, including clinical characteristics and hearing recovery. Patients were divided into intratympanic steroid (ITS) group and oral steroid (OS) group, and hearing recovery was compared between two groups. Twenty-six patients (81.3%) exhibited tinnitus, and 18 patients (56.3%) suffered vertigo. Mean pure-tone threshold at the initial presentation was 73.2 ± 19.4 dB, and the audiogram configuration was ascending in 9.4%, descending in 9.4%, flat in 34.4% and profound in 46.9% cases. At 3-month follow-up, percentages of patients in complete recovery, partial recovery, slight recovery, and no improvement were 18.8%, 31.3%, 21.9% and 28.1%, respectively. Furthermore, the overall recovery rate, complete recovery rate and hearing improvement were significantly higher in the ITS group than those in the OS group. SSNHL patient with ESRD often suffered a severe hearing loss with a high rate of accompanying tinnitus and vertigo. ITS may provide better audiological results for SSNHL with ESRD than OS.
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http://dx.doi.org/10.1080/00016489.2019.1659516DOI Listing
November 2019

gga-miRNA-18b-3p Inhibits Intramuscular Adipocytes Differentiation in Chicken by Targeting the Gene.

Cells 2019 06 7;8(6). Epub 2019 Jun 7.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.

Intramuscular fat (IMF) is the most important evaluating indicator of chicken meat quality, the content of which is positively correlated with tenderness, flavor, and succulence of the meat. Chicken IMF deposition process is regulated by many factors, including genetic, nutrition, and environment. Although large number of omics' studies focused on the IMF deposition process, the molecular mechanism of chicken IMF deposition is still poorly understood. In order to study the role of miRNAs in chicken intramuscular adipogenesis, the intramuscular adipocyte differentiation model (IMF-preadipocytes and IMF-adipocytes) was established and subject to miRNA-Seq. A total of 117 differentially expressed miRNAs between two groups were obtained. Target genes prediction and functional enrichment analysis revealed that eight pathways involved in lipid metabolism related processes, such as fatty acid metabolism and fatty acid elongation. Meanwhile a putative miRNA, gga-miR-18b-3p, was identified be served a function in the intramuscular adipocyte differentiation. Luciferase assay suggested that the gga-miR-18b-3p targeted to the 3'UTR of . Subsequent functional experiments demonstrated that gga-miR-18b-3p acted as an inhibitor of intramuscular adipocyte differentiation by targeting . Our findings laid a new theoretical foundation for the study of lipid metabolism, and also provided a potential target to improve the meat quality in the poultry industry.
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http://dx.doi.org/10.3390/cells8060556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627633PMC
June 2019

Transcriptome Analysis of the Breast Muscle of Xichuan Black-Bone Chickens Under Tyrosine Supplementation Revealed the Mechanism of Tyrosine-Induced Melanin Deposition.

Front Genet 2019 15;10:457. Epub 2019 May 15.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.

The Xichuan black-bone chicken, which is a rare local chicken species in China, is an important genetic resource of black-bone chickens. Tyrosine can affect melanin production, but the molecular mechanism underlying tyrosine-induced melanin deposition in Xichuan black-bone chickens is poorly understood. Here, the blackness degree and melanin content of the breast muscle of Xichuan black-bone chickens fed a basic diet with five levels of added tyrosine (i.e., 0.2, 0.4, 0.6, 0.8, and 1.0%; these groups were denoted test groups I-V, respectively) were assessed, and the results showed that 0.8% tyrosine was the optimal level of added tyrosine. Moreover, the effects of tyrosine supplementation on the proliferation and tyrosinase content of melanocytes in Xichuan black-bone chickens were evaluated. The results revealed a dose-dependent relationship between tyrosine supplementation and melanocyte proliferation. In addition, 417 differentially expressed genes (DEGs), including 160 upregulated genes and 257 downregulated genes, were identified in a comparative analysis of the transcriptome profiles constructed using the pooled total RNA from breast muscle tissues of the control group and test group IV, respectively (fold change ≥2.0, < 0.05). These DEGs were mainly involved in melanogenesis, the calcium signaling pathway, the Wnt signaling pathway, the mTOR signaling pathway, and vascular smooth muscle contraction. The pathway analysis of the DEGs identified some key genes associated with pigmentation, such as and . In summary, the melanin content of breast muscle could be markedly enhanced by adding an appropriate amount of tyrosine to the diet of Xichuan black-bone chickens, and the -mediated molecular regulatory network could play a key role in the biological process of tyrosine-induced melanin deposition. These results have deepened the understanding of the molecular regulatory mechanism of melanin deposition in black-bone chickens and provide a basis for the regulation of nutrition and genetic breeding associated with melanin deposition in Xichuan black-bone chickens.
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http://dx.doi.org/10.3389/fgene.2019.00457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6529781PMC
May 2019

Target gene identification and functional characterization of miR-1704 in chicken.

Anim Biotechnol 2020 Jun 30;31(3):229-236. Epub 2019 Apr 30.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China.

MiRNAs are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. SNPs in miRNA genes may lead to phenotypic variation by altering miRNA expression and their targets. In this study, miR-1704 expression profiles in nine tissues at 1 d, 6 weeks and 16 weeks old Gushi chickens were detected. MiR-1704 was widely expressed in the detection of tissues. The expression in 1 d and 6 weeks old was low abundance, while its expression at 16 weeks was very high. An rs14668705 (C > G) SNP was detected within the pre-miR-1704 in an F resource population of Gushi chicken crossed with Anka broiler. Bioinformatic analysis indicated that the C > G mutation could introduce a base-pair mismatch and cause the change of free energy. Experiments further revealed that the rs14668705 in precursor miR-1704 could significantly affect mature miR-1704 biogenesis and was significantly associated with body weight at the age of 0, 6, 8, 10, and 12 weeks, shank circumference at 4, 8, and 12 weeks, carcass weight, and semi-evisceration weight ( < 0.05). () gene, one of the potential targets of miR-1704 was identified and further confirmed. These data suggested that miR-1704 targeted and have an effect on body weight in chicken.
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http://dx.doi.org/10.1080/10495398.2019.1585365DOI Listing
June 2020

Integrative analysis of long noncoding RNA and mRNA reveals candidate lncRNAs responsible for meat quality at different physiological stages in Gushi chicken.

PLoS One 2019 9;14(4):e0215006. Epub 2019 Apr 9.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.

Long noncoding RNAs (lncRNAs) play important roles in transcriptional and posttranscriptional regulation. However, the effects of lncRNAs on the meat quality of chicken hasn't been elucidated clearly yet. Gushi chickens are popular in China because of their superior meat quality, particularly the tender flesh, and unique flavor. Gushi chickens are popular in China because of their superior meat quality, delicate flesh, and unique flavor. We performed RNA-Seq analysis of breast muscle from Gushi chicken at two physiological stages, including juvenile (G20W) and laying (G55W). In total, 186 lncRNAs and 881 mRNAs were differentially expressed between G20W and G55W (fold change ≥ 2.0, P < 0.05). Among them, 131 lncRNAs presented upregulated and 55 were downregulated. We identified the cis and trans target genes of the differentially expressed lncRNAs, and constructed lncRNA-mRNA interaction networks. The results showed that differentially expressed mRNAs and lncRNAs were mainly involved in ECM-receptor interaction, glycerophospholipid metabolism, ubiquitin-mediated proteolysis, and the biosynthesis of amino acids. In summary, our study utilized RNA-seq analysis to predict the functions of lncRNA on chicken meat quality. Furthermore, comprehensive analysis identified lncRNAs and their target genes, which may contribute to a better understanding of the molecular mechanisms underlying in poultry meat quality and provide a theoretical basis for further research.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215006PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456248PMC
December 2019

Analyses of MicroRNA and mRNA Expression Profiles Reveal the Crucial Interaction Networks and Pathways for Regulation of Chicken Breast Muscle Development.

Front Genet 2019 18;10:197. Epub 2019 Mar 18.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.

There is a lack of understanding surrounding the molecular mechanisms involved in the development of chicken skeletal muscle in the late postnatal stage, especially in the regulation of breast muscle development related genes, pathways, miRNAs and other factors. In this study, 12 cDNA libraries and 4 small RNA libraries were constructed from Gushi chicken breast muscle samples from 6, 14, 22, and 30 weeks. A total of 15,508 known transcripts, 25,718 novel transcripts, 388 known miRNAs and 31 novel miRNAs were identified by RNA-seq in breast muscle at the four developmental stages. Through correlation analysis of miRNA and mRNA expression profiles, it was found that 417, 370, 240, 1,418, 496, and 363 negatively correlated miRNA-mRNA pairs of vs. , vs. , vs. , vs. , vs. , and vs. comparisons, respectively. Based on the annotation analysis of these miRNA-mRNA pairs, we constructed the miRNA-mRNA interaction network related to biological processes, such as muscle cell differentiation, striated muscle tissue development and skeletal muscle cell differentiation. The interaction networks for signaling pathways related to five KEGG pathways (the focal adhesion, ECM-receptor interaction, FoxO signaling, cell cycle, and p53 signaling pathways) and PPI networks were also constructed. We found that , , , , , , , , , , , and , , , , , , and other genes were the key core nodes of these networks, most of which are targets of miRNAs. The FoxO signaling pathway was in the center of the five pathway-related networks. In the PPI network, there was a clear interaction among and , , , and , and , and genes. These results increase the understanding for the molecular mechanisms of chicken breast muscle development, and also provide a basis for studying the interactions between genes and miRNAs, as well as the functions of the pathways involved in postnatal developmental regulation of chicken breast muscle.
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http://dx.doi.org/10.3389/fgene.2019.00197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431651PMC
March 2019

Association Between the Methylation Statuses at CpG Sites in the Promoter Region of the , RNA Expression and Color Change in Blue Eggshells in Lushi Chickens.

Front Genet 2019 26;10:161. Epub 2019 Feb 26.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.

The formation mechanism underlying the blue eggshell characteristic has been discovered in birds, and is the key gene that regulates the blue eggshell color. Insertion of an endogenous retrovirus, EAV-HP, in the 5' flanking region promotes expression in the chicken shell gland, and this expression causes bile salts to enter the shell gland, where biliverdin is secreted into the eggshell, forming a blue shell. However, at different laying stages of the same group of chickens, the color of the eggshell can vary widely, and the molecular mechanism underlying the eggshell color change remains unknown. Therefore, to reveal the molecular mechanism of the blue eggshell color variations, we analyzed the change in the eggshell color during the laying period. The results indicated that the eggshell color in Lushi chickens can be divided into three stages: 20-25 weeks for dark blue, 26-45 weeks for medium blue, and 46-60 weeks for light blue. We further investigated the expression and methylation levels of the gene at eight different weeks, finding that the relative expression of was significantly higher at 25 and 30 weeks than at other laying weeks. Furthermore, the overall methylation rate of the gene in Lushi chickens increased gradually with increasing weeks of egg production, as shown by bisulfite sequencing PCR. Pearson correlation analysis showed that methylation of the promoter region of was significantly negatively correlated with both expression in the shell gland tissue and eggshell color. In addition, we predicted that CpG5 and CpG8 may be key sites for regulating gene transcription. Our findings show that as the level of methylation increases, methylation of the CpG5 and CpG8 sites hinders the binding of transcription factors to the promoter, reducing expression during the late period and resulting in a lighter eggshell color.
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http://dx.doi.org/10.3389/fgene.2019.00161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6399514PMC
February 2019

Transcriptome profile in bursa of Fabricius reveals potential mode for stress-influenced immune function in chicken stress model.

BMC Genomics 2018 Dec 13;19(1):918. Epub 2018 Dec 13.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.

Background: The molecular mechanisms underlying stress-influenced immune function of chicken (Gallus Gallus) are not clear. The stress models can be established effectively by feeding chickens corticosterone (CORT) hormone. The bursa of Fabricius is a unique central immune organ of birds. RNA-Seq technology was used to investigate differences in the expression profiles of immune-related genes and associated pathways in the bursa of Fabricius to clarify molecular mechanisms. The aim of this study was to broaden the understanding of the stress-influenced immune function in chickens.

Results: Differentially expressed genes (DEGs) in the bursa of Fabricius between experimental group (basal diet with added CORT 30 mg/kg; C_B group) and control group (basal diet; B_B group) were identified by using RNA-seq technology. In total, we found 1434 significant DEGs (SDEGs), which included 199 upregulated and 1235 downregulated genes in the C_B group compared with the B_B group. The immune system process GO term was the top significantly GO term, including MYD88, TLR4, IL15, VEGFA gene and so on. The cytokine-cytokine receptor interaction pathway and the Toll-like receptor signaling pathway were the key pathways affected by stress. The protein-protein interaction (PPI) analysis of the SDEGs showed that VEGFA, MyD88 and IL15 were hub genes and module analysis showed that MYD88, TLR4 and VEGFA play important roles in response to stress.

Conclusion: This study showed that the VEGFA and ILs (such as IL15) via the cytokine-cytokine receptor interaction pathway, MYD88 and TLR4 via the Toll-like receptor signaling pathway may play important roles in the regulation of immune function under stress condition with CORT administration. The results of this study provide a reference for further studies of the molecular mechanisms of stress-influenced immune function.
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http://dx.doi.org/10.1186/s12864-018-5333-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293626PMC
December 2018

Identification of a novel 43-bp insertion in the heparan sulfate 6-O-sulfotransferase 3 () gene and its associations with growth and carcass traits in chickens.

Anim Biotechnol 2019 Jul 24;30(3):252-259. Epub 2018 Nov 24.

a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , China.

Previous studies have revealed a significant association between SNPs found within the heparan sulfate 6-O-sulfotransferase 3 () gene and obesity. This study identified a novel 43-bp indel polymorphism in intron 1 of in 1963 chickens from nine different breeds, and three genotypes, designated II, ID and DD, were observed. The frequency of the 'I' (0.62-0.87) allele was higher than that of the 'D' (0.13-0.38) allele. A total of 777 individuals of the Gushi-Anka F resource population were used for the analysis of associations according to growth traits, carcass traits, serum variables and meat quality traits. The results showed that the 43-bp indel polymorphism was significantly associated with the body weight at 4 and 6 weeks of age, chest depth at 4 and 12 weeks of age and shank girth at 12 weeks of age ( < 0.05). In terms of the carcass traits, the indel polymorphism was significantly associated with breast muscle weight, heart weight and leg weight (P < 0.05). These findings suggested that this indel polymorphism has the potential to become a new target for the marker-assisted selection of chicken growth and carcass traits.
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http://dx.doi.org/10.1080/10495398.2018.1479712DOI Listing
July 2019
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