Publications by authors named "Ruili Han"

65 Publications

A 104-bp Structural Variation of the Gene Is Associated With Growth Traits in Chickens.

Front Genet 2021 26;12:691272. Epub 2021 Aug 26.

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

Analyzing marker-assisted breeding is an important method utilized in modern molecular breeding. Recent studies have determined that a large number of molecular markers appear to explain the impact of "lost heritability" on human height. Therefore, it is necessary to locate molecular marker sites in poultry and investigate the possible molecular mechanisms governing their effects. In this study, we found a 104-bp insertion/deletion polymorphism in the 5'UTR of the gene through resequencing. In cross-designed F resource groups, the indel was significantly associated with weight at 0, 2, 4, 6, and 10 weeks and a number of other traits [carcass weight (CW), semi-evisceration weight (SEW), evisceration weight (EW), claw weight (CLW), wings weight (DWW), gizzard weight (GW), pancreas weight (PW), chest muscle weight (CMW), leg weight (LW), leg muscle weight (LMW), shedding Weight (SW), liver rate (LR), and leg muscle rate (LMR)] ( < 0.05). In brief, the insertion-insertion (II) genotype was significantly associated with the greatest growth traits and meat quality traits, whereas the values associated with the insertion-deletion (ID) genotype were the lowest in the F reciprocal cross chickens. The mutation sites were genotyped in 4,526 individuals from 12 different chicken breeds and cross-designed F resource groups. The II genotype is the most important genotype in commercial broilers, and the I allele frequency observed in these breeds is relatively high. Deletion mutations tend to be fixed in commercial broilers. However, there is still considerable great potential for breeding in dual-purpose chickens and commercial laying hens. A luciferase reporter assay showed that the II genotype of the gene possessed 2.49-fold higher promoter activity than the DD genotype ( < 0.05). We hypothesized that this indel might affect the transcriptional activity of , thereby affecting the growth traits of chickens. These findings may help to elucidate the function of the gene and facilitate enhanced reproduction in the chicken industry.
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http://dx.doi.org/10.3389/fgene.2021.691272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8427608PMC
August 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

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 key miRNAs affecting broilers with valgus-varus deformity by RNA sequencing and analysis of miRNA-mRNA interactions.

Mol Omics 2021 Jun 24. Epub 2021 Jun 24.

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China. and Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.

Valgus-varus Deformity (VVD) leg disease often affects chickens raised in modern large-scale breeding operations. Losses due to VVD are costly to farmers, and the condition also causes significant suffering in affected birds. In this study, we profiled RNAs from the spleens of VVD (BS) and healthy (JS) broilers using high-throughput sequencing to identify miRNAs that might be involved in the development of the disease. Fifty differentially expressed miRNAs (DEMs) were found, of which 30 were up-regulated and 20 were down-regulated in VVD-affected birds (|log 2 Fold Change| ≥ 1 and q-value < 0.05). DEMs were matched with putative target genes and 864 target genes were found. Gene Ontology (GO) analyses of these target genes showed that they were significantly enriched in the "cytoplasm" term (q-value < 0.05), and most of the target genes were enriched in "cellular component". Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that they were significantly enriched in 11 signaling pathways (P-value < 0.05), including metabolic pathways, 2-oxocarboxylic acid metabolism, regulation of actin cytoskeleton, purine metabolism, endocytosis and so on. And we found that they were enriched in immune-related pathways in which MAPK, Notch, JAK-Stat, Toll-like receptor, p53 and other single pathways were involved in the development of skeletal diseases. Differentially expressed mRNAs obtained from our previous study were used to construct an interaction network consisting of 16 DEMs and 21 differentially expressed mRNAs (|log 2 Fold Change| ≥ 1 and q-value < 0.05). We found that miR-12247-5p, miR-15c-5p, miR-15b-5p, FKBP5 and HSP90AB1 were at the center of network interaction. This study provides a foundation for further investigations of the pathogenesis and genetic mechanisms underlying VVD.
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http://dx.doi.org/10.1039/d1mo00011jDOI Listing
June 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

Genome-wide identification evolution and expression of vestigial-like gene family in chicken.

Anim Biotechnol 2021 May 25:1-11. Epub 2021 May 25.

Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.

() genes are widespread in vertebrates and play an important role in muscle development. In this study, we used bioinformatics methods to systematically identify the chicken family in the whole genome and investigated its evolutionary history and gene structure features. Tissue expression spectra combined with real-time PCR data were used to analyze the organizational expression pattern of the genes. Based on the maximum likelihood method, a phylogenetic tree of the family was constructed, and 94 genes were identified in 24 breeds, among which four family genes were identified in the chicken genome. Ten motifs were detected in the genes, and the analysis of introns combined with gene structure revealed that the family was conserved during evolution. Tissue expression analysis suggested that the expression profiles of the family genes in 16 tissues differed between LU Shi and AA broilers. In addition, a single gene () showed increased expression in chickens at embryonic days 10-16 and was involved in the growth and development of skeletal muscle in chickens in the embryonic stage. In summary, genes are involved in chicken muscle growth and development, which provides useful information for subsequent functional studies of genes.
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http://dx.doi.org/10.1080/10495398.2021.1920425DOI Listing
May 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

LncRNAs and their regulatory networks in breast muscle tissue of Chinese Gushi chickens during late postnatal development.

BMC Genomics 2021 Jan 9;22(1):44. Epub 2021 Jan 9.

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

Background: Chicken skeletal muscle is an important economic product. The late stages of chicken development constitute the main period that affects meat production. LncRNAs play important roles in controlling the epigenetic process of growth and development. However, studies on the role of lncRNAs in the late stages of chicken breast muscle development are still lacking. In this study, to investigate the expression characteristics of lncRNAs during chicken muscle development, 12 cDNA libraries were constructed from Gushi chicken breast muscle samples from 6-, 14-, 22-, and 30-week-old chickens.

Results: A total of 1252 new lncRNAs and 1376 annotated lncRNAs were identified. Furthermore, 53, 61, 50, 153, 117, and 78 DE-lncRNAs were found in the W14 vs. W6, W22 vs. W14, W22 vs. W6, W30 vs. W6, W30 vs. W14, and W30 vs. W22 comparison groups, respectively. After GO enrichment analysis of the DE-lncRNAs, several muscle development-related GO terms were found in the W22 vs. W14 comparison group. Moreover, it was found that the MAPK signaling pathway was one of the most frequently enriched pathways in the different comparison groups. In addition, 12 common target DE-miRNAs of DE-lncRNAs were found in different comparison groups, some of which were muscle-specific miRNAs, such as gga-miR-206, gga-miR-1a-3p, and miR-133a-3p. Interestingly, the precursors of four newly identified miRNAs were found to be homologous to lncRNAs. Additionally, we found some ceRNA networks associated with muscle development-related GO terms. For example, the ceRNA networks contained the DYNLL2 gene with 12 lncRNAs that targeted 2 miRNAs. We also constructed PPI networks, such as IGF-I-EGF and FZD6-WNT11.

Conclusions: This study revealed, for the first time, the dynamic changes in lncRNA expression in Gushi chicken breast muscle at different periods and revealed that the MAPK signaling pathway plays a vital role in muscle development. Furthermore, MEF2C and its target lncRNA may be involved in muscle regulation through the MAPK signaling pathway. This research provided valuable resources for elucidating posttranscriptional regulatory mechanisms to promote the development of chicken breast muscles after hatching.
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http://dx.doi.org/10.1186/s12864-020-07356-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797159PMC
January 2021

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

Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity.

PLoS One 2020 24;15(9):e0239450. Epub 2020 Sep 24.

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

Background: Bone abnormality and leg disease in commercial broiler flocks are increasingly prominent, causing serious economic losses to the broiler breeding industry. Valgus-varus deformity (VVD) is a common deformity of the long bone in broilers that manifests as an outward or inward deviation of the tibiotarsus or tarsometatarsus. There is a paucity of studies on the molecular mechanisms of VVD.

Results: In this study, 6 cDNA libraries were constructed from spleen samples from VVD birds and normal birds. A total of 1951 annotated lncRNAs, 7943 novel lncRNAs and 30252 mRNAs were identified by RNA-sequencing. In addition, 420 differentially expressed (DE) mRNAs and 124 differentially expressed lncRNAs (adjusted P-value < 0.05) were obtained. A total of 16 dysregulated genes were confirmed by qPCR to be consistent with the results of the RNA-Seq. The functional lncRNA-mRNA co-expression network was constructed using differentially expressed mRNAs and target genes of the differentially expressed lncRNAs. 11 DE genes were obtained from the analysis. In order to gain insight into the interactions of genes, lncRNAs and pathways associated with VVD, we focused on the following pathways, which are involved in immunity and bone development: the Jak-stat signaling pathway, Toll-like receptor signaling pathway, Wnt-signaling pathway, mTOR signaling pathway, VEGF signaling pathway, Notch signaling pathway, TGF-beta signaling pathway and Fanconi anemia pathway. All together, 30 candidate DE genes were obtained from these pathways. We then analyzed the interaction between the DE genes and their corresponding lncRNAs. From these interaction network analyses we found that GARS, NFIC, PIK3R1, BMP6, NOTCH1, ACTB and CREBBP were the key core nodes of these networks.

Conclusion: This study showed that differentially expressed genes and signaling pathways were related to immunity or bone development. These results increase the understanding of the molecular mechanisms of VVD and provide some reference for the etiology and pathogenesis of VVD.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239450PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7514040PMC
November 2020

Antagonistic effects of IL-17 and Astragaloside IV on cortical neurogenesis and cognitive behavior after stroke in adult mice through Akt/GSK-3β pathway.

Cell Death Discov 2020 10;6:74. Epub 2020 Aug 10.

Department of Anesthesiology, The Second Affiliated Hospital of Air Force Medical University, 710038 Xi'an, Shaanxi Province China.

We aimed to investigate the exact effect of IL-17 on regulating neural stem cells (NSCs) stemness and adult neurogenesis in ischemic cortex after stroke, how Astragaloside IV(As-IV) regulated IL-17 expression and the underlying mechanism. Photochemical brain ischemia model was established and IL-17 protein expression was observed at different time after stroke in WT mice. At 3 days after stroke, when IL-17 expression peaked, IL-17 knock out (KO) mice were used to observe cell proliferation and neurogenesis in ischemic cortex. Then, As-IV was administered intravenously to assess cell apoptosis, proliferation, neurogenesis, and cognitive deficits by immunochemistry staining, western blots, and animal behavior tests in WT mice. Furthermore, IL-17 KO mice and As-IV were used simultaneously to evaluate the mechanism of cell apoptosis and proliferation after stroke in vivo. Besides, in vitro, As-IV and recombinant mouse IL-17A was administered, respectively, into NSCs culture, and then their diameters, viable cell proliferation and pathway relevant protein was assessed. The results showed knocking out IL-17 contributed to regulating PI3K/Akt pathway, promoting NSCs proliferation, and neurogenesis after ischemic stroke. Moreover, As-IV treatment helped inhibit neural apoptosis, promote the neurogenesis and eventually relieve mice anxiety after stroke. Unsurprisingly, IL-17 protein expression could be downregulated by As-IV in vivo and in vitro and they exerted antagonistic effect on neurogenesis by regulating Akt/GSK-3β pathway, with significant regulation for apoptosis. In conclusion, IL-17 exerts negative effect on promoting NSCs proliferation, neurogenesis and cognitive deficits after ischemic stroke, which could be reversed by As-IV.
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http://dx.doi.org/10.1038/s41420-020-00298-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7417740PMC
August 2020

Identification of a H6 Thioesterase Involved in Zearalenone Detoxification by Transcriptomic Analysis.

J Agric Food Chem 2020 Sep 1;68(37):10071-10080. Epub 2020 Sep 1.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China.

Zearalenone (ZEA), a nonsteroidal estrogenic mycotoxin produced by , induces hyperestrogenic responses in mammals and can cause reproductive disorders in farm animals. In this study, a transcriptome analysis of H6, which was previously identified as a ZEA-degrading bacterium, was conducted with high-throughput sequencing technology, and the differentially expressed genes were subjected to gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses. Among the 16 upregulated genes, BAMF_RS30125 was predicted to be the key gene responsible for ZEA degradation. The protein encoded by BAMF_RS30125 was then expressed in , and this recombinant protein (named ZTE138) significantly reduced the ZEA content, as determined by the enzyme-linked immunosorbent assay (ELISA) and high-performance liquid chromatography (HPLC), and decreased the proliferating activity of ZEA in MCF-7 cells. What is more, the liquid chromatography-tandem mass spectrometry (LC-MS/MS) results showed that the relative molecular mass and the structure of ZEA also changed. Sequence alignment of the ZTE138 protein showed that it is a protease that belongs to the YBGC/FADM family of coenzyme A thioesterases, and thus, the protein can presumably cleave the ZEA lactone bond and break down its macrolide ring.
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http://dx.doi.org/10.1021/acs.jafc.0c03954DOI Listing
September 2020

Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens.

Gene 2020 Nov 8;761:145046. Epub 2020 Aug 8.

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

Many studies have shown that the LDB2 gene plays a regulatory role in retinal development and the cell cycle, but its biological role remains unclear. In this study, a 31-bp indel in the LDB2 gene was found for the first time on the basis of 2797 individuals from 10 different breeds, which led to different genotypes among individuals (II, ID and DD). Among these genotypes, DD was the most dominant. Association analysis of an F resource population crossed with the Gushi (GS) chicken and Anka chicken showed that the DD genotype conferred a significantly greater semi-evisceration weight (SEW, 1108.665 g ± 6.263), evisceration weight (EW, 927.455 g ± 5.424), carcass weight (CW, 1197.306 g ± 6.443), breast muscle weight (BMW, 71.05 g ± 0.574), and leg muscle weight (LMW, 100.303 g ± 0.677) than the ID genotype (SEW, 1059.079 g ± 16.86; EW, 879.459 g ± 14.446; CW, 1141.821 g ± 17.176; BMW, 67.164 g ± 1.523; and LMW, 96.163 g ± 1.823). In addition, LDB2 gene expression in different breeds was significantly higher in the breast muscles and leg muscles than in other tissues. The expression level in the breast muscle differed significantly among stages of GS chicken development, with the highest expression observed at 6 weeks. The expression levels in the pectoral muscles differed significantly among Ross 308 genotypes. In summary, we studied the relationships between a 31-bp indel in the LDB2 gene and economic traits in chickens. The indel was significantly correlated with multiple growth and carcass traits in the F resource population and affected the expression of the LDB2 gene in muscle tissue. In short, our study revealed that the LDB2 gene 31-bp indel can be used as a potential genetic marker for molecular breeding.
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http://dx.doi.org/10.1016/j.gene.2020.145046DOI Listing
November 2020

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

Gut microbiota profiles of commercial laying hens infected with tumorigenic viruses.

BMC Vet Res 2020 Jun 29;16(1):218. Epub 2020 Jun 29.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000, China.

Background: Studies have shown that some viral infections cause structural changes in the intestinal microflora, but little is known about the effects of tumorigenic viral infection on the intestinal microflora of chickens.

Results: A 29-week commercial layer flock positive for avian leukosis virus-J (ALV-J), Marek's disease virus (MDV) and avian reticuloendotheliosis virus (REV) was selected, and fresh fecal samples were collected and examined for the composition of the gut microflora by Illumina sequencing of the V3-V4 region of the 16S rRNA gene. The operational taxonomic units (OTUs) of the fecal microbiota differentiated the chickens infected with only ALV-J and those coinfected with ALV-J and MDV or REV from infection-negative chickens. The enrichment and diversity of cloacal microflora in chickens infected with ALV-J alone were slightly different from those in the infection-negative chickens. However, the diversity of cloacal microflora was significantly increased in chickens coinfected with both ALV-J and MDV or REV.

Conclusions: The intestinal microbiota was more strongly disturbed in chickens after coinfection with ALV-J and MDV or REV than after infection with ALV-J alone, and there may be underlying mechanisms by which the capacity for the stabilization of the intestinal flora was impaired due to viral infection and tumorigenesis.
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http://dx.doi.org/10.1186/s12917-020-02430-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7324990PMC
June 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

Analysis of four complete linkage sequence variants within a novel lncRNA located in a growth QTL on chromosome 1 related to growth traits in chickens.

J Anim Sci 2020 May;98(5)

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

An increasing number of studies have shown that quantitative trait loci (QTLs) at the end of chromosome 1 identified in different chicken breeds and populations exert significant effects on growth traits in chickens. Nevertheless, the causal genes underlying the QTL effect remain poorly understood. Using an updated gene database, a novel lncRNA (named LncFAM) was found at the end of chromosome 1 and located in a growth and digestion QTL. This study showed that the expression level of LncFAM in pancreas tissues with a high weight was significantly higher than that in pancreas tissues with a low weight, which indicates that the expression level of LncFAM was positively correlated with various growth phenotype indexes, such as growth speed and body weight. A polymorphism screening identified four polymorphisms with strong linkage disequilibrium in LncFAM: a 5-bp indel in the second exon, an A/G base mutation, and 7-bp and 97-bp indels in the second intron. A study of a 97-bp insertion in the second intron using an F2 chicken resource population produced by Anka and Gushi chickens showed that the mutant individuals with genotype II had the highest values for body weight (BW) at 0 days and 2, 4, 6, 8, 10 and 12 weeks, shank girth (SG) at 4, 8 and 12 weeks, chest width (CW) at 4, 8 and 12 weeks, body slant length (BSL) at 8 and 12 weeks, and pelvic width (PW) at 4, 8 and 12 weeks, followed by ID and DD genotypes. The amplification and typing of 2,716 chickens from ten different breeds, namely, the F2 chicken resource population, dual-type chickens, including Xichuan black-bone chickens, Lushi green-shell layers, Dongxiang green-shell layers, Changshun green-shell layers, and Gushi chickens, and commercial broilers, including Ross 308, AA, Cobb and Hubbard broilers, revealed that II was the dominant genotype. Interestingly, only genotype II existed among the tested populations of commercial broilers. Moreover, the expression level in the pancreas tissue of Ross 308 chickens was significantly higher than that in the pancreas tissue of Gushi chickens (P < 0.001), which might be related to the conversion rates among different chickens. The prediction and verification of the target gene of LncFAM showed that LncFAM might regulate the expression of its target gene FAM48A through cis-expression. Our results provide useful information on the mutation of LncFAM, which can be used as a potential molecular breeding marker.
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http://dx.doi.org/10.1093/jas/skaa122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229885PMC
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

Identification of a Novel Lipid Metabolism-Associated Hepatic Gene Family Induced by Estrogen via ERα in Chicken ().

Front Genet 2020 31;11:271. Epub 2020 Mar 31.

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

Liver is the main organ of lipid metabolism in chicken, especially for laying hens. To explore the molecular mechanism of lipid metabolism in chicken, five novel genes discovered in chicken liver tissue were systematically studied. Bioinformatic analysis was used to analyze the gene characteristics. The expression patterns and regulatory molecular mechanism of the five genes were examined. Our results showed that all five novel genes contain a common NADP-binding site that belongs to the NADB-Rossmann superfamily, and the genes were designated 1-5. Phylogenetic tree of the gene family in different species suggested these five genes originated from the same ancestor. Tissue distributions showed that genes were highly expressed in lipid metabolism organs, including liver, kidney and duodenum, and that the gene was highly expressed in liver and kidney. The spatiotemporal expression indicated that the expression levels of genes in liver tissue were significantly greater in sexually mature hens than that of immature pullets (-value ≤ 0.05). The expression levels of were significantly induced by 17β-estradiol in primary cultured chicken embryo hepatocytes (-value ≤ 0.05), and 17β-estradiol regulated the expression of mediated by ERα. Individual assays verified that under induction of 17β-estradiol, the five novel genes were significantly upregulated, with subsequent alteration in serum TG, TC, and VLDLs in 10-week-old pullets. This study proved family mainly expressed in liver, kidney, and duodenum tissues. 17β-estradiol induces the expression of genes predominantly mediated via ERα. They likely involved in lipid metabolism in the liver of chicken.
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http://dx.doi.org/10.3389/fgene.2020.00271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7136477PMC
March 2020

Effects of remote ischemic preconditioning on prognosis in patients with lung injury: A meta-analysis.

J Clin Anesth 2020 08 21;63:109795. Epub 2020 Mar 21.

Department of Anesthesiology, Tangdu Hospital, Air Force Military Medical University, 710038 Xian, Shanxi Province, China. Electronic address:

Objective: A number of trials have shown that remote ischemic preconditioning (RIPC) could reduce lung injury of patients suffering cardiovascular surgery, pulmonary transplantation surgery and thoracic surgery with one-lung ventilation. However, there is still a controversy over the lung protection of RIPC in patients who suffers different types of surgery. We undertook meta-analysis of the randomized controlled trials to evaluate the effect of remote ischemic preconditioning on clinical outcomes of patients with lung injury.

Design: Systematic review and meta-analysis.

Setting: Perioperative care areas.

Patients: Adults and infants suffering cardiovascular surgery with lung injury.

Intervention: Remote ischemic preconditioning.

Measurements: The literatures were selected complying with the inclusive and exclusive criteria from the following databases as PubMed, Embase, Medline, Chinese Biomedical Literature and Journal Databases, Chinese Academic and VIP journal full-text Databases. Inclusion criteria includes: (1) Human clinical randomized and controlled trial; (2) the article we included is a clinical randomized controlled study; (3) the article discusses the effect of RIPC on lung injury of patients; (4) the primary evaluation indicators of the inclusive studies included postoperative intensive care unit stay time and mechanical ventilation time; (5) published in the form of full text, any language; (6) the type of operation is cardiovascular surgery; (7) there is no serious COPD, ARDS, respiratory failure and other lung diseases. Articles were excluded if they reported none of the outcomes as follows: postoperative intensive care unit stay time and mechanical ventilation time, human clinical controlled trails, pulmonary protection of RIPC, prospective clinical controlled trials. Two independent reviewers screened abstracts and titles, and selected records following full-text review. Software RevMan5.3 and STATA 12.0 were adopted to perform Meta-analysis.

Result: The search finally includes10 studies of 708 patients, 352 patients in RIPC group and 356 patients in control group. The baseline characteristics of patients are no differences in two groups (P > 0.05). Compared with control group, RIPC significantly reduced the duration of ICU (P < 0.05) and mechanical ventilation time (P < 0.05) in RIPC group. In addition, the serum TNF-α and MDA concentration 24 h after operation in RIPC group are significantly lower than control group (P < 0.05). However, there are no significant differences between RIPC group and control group in terms of serum IL-6, IL-8 concentrations, A-aDO, PaO/FiO and respiratory index 24 h after operation.

Conclusion: RIPC can decrease pulmonary inflammatory responses, reduce the duration of ICU and mechanical ventilation time, and improve the clinical outcomes of patients with lung injury.
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http://dx.doi.org/10.1016/j.jclinane.2020.109795DOI Listing
August 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

High-throughput transcriptome analysis reveals potentially important relationships between lncRNAs and genes in broilers affected by Valgus-varus Deformity (Gallus gallus).

Gene 2020 Jun 26;743:144511. Epub 2020 Feb 26.

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

Valgus-varus Deformity (VVD) is an outward or inward deviation of the tibiotarsus or tarsometatarsus, which results in physical distress of chickens and economic loss in poultry industry. While the etiology and pathogenesis of VVD at the molecular level are still not fully understood so far. Here, based on a case/control design with VVD birds and normal birds, we identified genes and lncRNAs which associated with VVD using RNA sequencing. Transcriptome analysis revealed 231 differentially expressed mRNAs and 23 differentially expressed lncRNAs between case and control of leg cartilage. We identified the cis- and trans-regulatory targets of the differentially expressed lncRNAs, and we constructed a functional lncRNA-mRNA co-expression network. Analysis of the network showed that the differentially expressed mRNAs and the target genes of the differentially expressed lncRNAs were enriched in the signaling pathways associated with bone development, including p53, MAPK, Toll-like receptor, Jak-STAT, Hedgehog, and PPAR. The expression levels of DENND4A, FGF10, FGF12 and BMP3 were also determined in cartilage and other six tissues. Overall, our study predicted the mRNAs and lncRNAs related with leg diseases by transcriptome analyses, which might contribute to understand the etiology and pathogenesis of VVD. It established the foundation for the further research on the function of -mRNAs and lncRNAs in skeleton development.
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http://dx.doi.org/10.1016/j.gene.2020.144511DOI Listing
June 2020

Detection of CNV in the SH3RF2 gene and its effects on growth and carcass traits in chickens.

BMC Genet 2020 02 28;21(1):22. Epub 2020 Feb 28.

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

Background: The SH3RF2 gene is a protein-coding gene located in a quantitative trait locus associated with body weight, and its deletion has been shown to be positively associated with body weight in chickens.

Results: In the present study, CNV in the SH3RF2 gene was detected in 4079 individuals from 17 populations, including the "Gushi ×Anka" F2 resource population and populations of Chinese native chickens, commercial layers, and commercial broilers. The F2 resource population was then used to investigate the genetic effects of the chicken SH3RF2 gene. The results showed that the local chickens and commercial layers were all homozygous for the wild-type allele. Deletion mutation individuals were detected in all of the commercial broiler breeds except Hubbard broiler. A total of, 798 individuals in the F2 resource group were used to analyze the effects of genotype (DD/ID/II) on chicken production traits. The results showed that CNV was associated with 2-, 6-, 10-, and 12-week body weight (P = 0.026, 0.042, 0.021 and 0.039 respectively) and significantly associated with 8-week breast bone length (P = 0.045). The mutation was significantly associated with 8-week body weight (P = 0.007) and 4-week breast bone length (P = 0.010). CNV was significantly associated with evisceration weight, leg muscle weight, carcass weight, breast muscle weight and gizzard weight (P = 0.032, 0.033, 0.045, 0.004 and 0.000, respectively).

Conclusions: CNV of the SH3RF2 gene contributed to variation in the growth and weight gain of chickens.
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http://dx.doi.org/10.1186/s12863-020-0831-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048116PMC
February 2020

Association of a new 99-bp indel of the CEL gene promoter region with phenotypic traits in chickens.

Sci Rep 2020 02 21;10(1):3215. Epub 2020 Feb 21.

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

Carboxyl ester lipase (CEL) encodes a cholesterol ester hydrolase that is secreted into the duodenum as a component of pancreatic juice. The objective of this study was to characterize the CEL gene, investigate the association between the CEL promoter variants and chicken phenotypic traits, and explore the CEL gene regulatory mechanism. An insertion/deletion (indel) caused by a 99-bp insertion fragment was shown for the first time in the chicken CEL promoter, and large differences in allelic frequency were found among commercial breeds, indigenous and feral birds. Association analysis demonstrated that this indel site had significant effects on shank length, shank girth, chest breadth at 8 weeks (p < 0.01), evisceration weight, sebum weight, breast muscle weight, and leg weight (p < 0.05). Tissue expression profiles showed extremely high levels of the CEL gene in pancreatic tissue. Moreover, the expression levels of the genes APOB, MTTP, APOV1 and SREBF1, which are involved in lipid transport, were significantly reduced by adding a 4% oxidized soybean oil diet treatment at the individual level and transfecting the embryonic primary hepatocytes with a CEL-overexpression vector. Interestingly, the results showed that the expression level of the II homozygous genotype was significantly higher than that of the ID and DD genotypes, while individuals with DD genotypes had higher phenotypic values. Therefore, these data suggested that the CEL gene might affect body growth by participating in hepatic lipoprotein metabolism and that the 99-bp indel polymorphism could be a potentially useful genetic marker for improving the economically important traits of chickens.
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http://dx.doi.org/10.1038/s41598-020-60168-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035288PMC
February 2020

Combined transcriptomics and proteomics forecast analysis for potential genes regulating the Columbian plumage color in chickens.

PLoS One 2019 6;14(11):e0210850. Epub 2019 Nov 6.

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

Background: Coloration is one of the most recognizable characteristics in chickens, and clarifying the coloration mechanisms will help us understand feather color formation. "Yufen I" is a commercial egg-laying chicken breed in China that was developed by a three-line cross using lines H, N and D. Columbian plumage is a typical feather character of the "Yufen I" H line. To elucidate the molecular mechanism underlying the pigmentation of Columbian plumage, this study utilizes high-throughput sequencing technology to compare the transcriptome and proteome differences in the follicular tissue of different feathers, including the dorsal neck with black and white striped feather follicles (Group A) and the ventral neck with white feather follicles (Group B) in the "Yufen I" H line.

Results: In this study, we identified a total of 21,306 genes and 5,203 proteins in chicken feather follicles. Among these, 209 genes and 382 proteins were differentially expressed in two locations, Group A and Group B, respectively. A total of 8 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) were found to be involved in the melanogenesis pathway. Additionally, a specifically expressed MED23 gene and a differentially expressed GNAQ protein were involved in melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis mapped 190 DEGs and 322 DEPs to 175 and 242 pathways, respectively, and there were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed that the following pathways were activated: melanogenesis, cardiomyocyte adrenergic, calcium and cGMP-PKG. The expression of DEGs was validated by real-time quantitative polymerase chain reaction (qRT-PCR) that produced results similar to those from RNA-seq. In addition, we found that the expression of the MED23, FZD10, WNT7B and WNT11 genes peaked at approximately 8 weeks in the "Yufen I" H line, which is consistent with the molting cycle. As both groups showed significant differences in terms of the expression of the studied genes, this work opens up avenues for research in the future to assess their exact function in determining plumage color.

Conclusion: Common DEGs and DEPs were enriched in the melanogenesis pathway. MED23 and GNAQ were also reported to play a crucial role in melanin synthesis. In addition, this study is the first to reveal gene and protein variations in in the "Yufen I" H line during Columbian feather color development and to discover principal genes and proteins that will aid in functional genomics studies in the future. The results of the present study provide a significant conceptual basis for the future breeding schemes with the "Yufen I" H line and provide a basis for research on the mechanisms of feather pigmentation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210850PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834273PMC
March 2020

MicroRNAs and their regulatory networks in Chinese Gushi chicken abdominal adipose tissue during postnatal late development.

BMC Genomics 2019 Oct 25;20(1):778. Epub 2019 Oct 25.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China.

Background: Abdominal fat is the major adipose tissue in chickens. The growth status of abdominal fat during postnatal late development ultimately affects meat yield and quality in chickens. MicroRNAs (miRNAs) are endogenous small noncoding RNAs that regulate gene expression at the post-transcriptional level. Studies have shown that miRNAs play an important role in the biological processes involved in adipose tissue development. However, few studies have investigated miRNA expression profiles and their interaction networks associated with the postnatal late development of abdominal adipose tissue in chickens.

Results: We constructed four small RNA libraries from abdominal adipose tissue obtained from Chinese domestic Gushi chickens at 6, 14, 22, and 30 weeks. A total of 507 known miRNAs and 53 novel miRNAs were identified based on the four small RNA libraries. Fifty-one significant differentially expressed (SDE) miRNAs were identified from six combinations by comparative analysis, and the expression patterns of these SDE miRNAs were divided into six subclusters by cluster analysis. Gene ontology enrichment analysis showed that the SDE miRNAs were primarily involved in the regulation of fat cell differentiation, regulation of lipid metabolism, regulation of fatty acid metabolism, and unsaturated fatty acid metabolism in the lipid metabolism- or deposition-related biological process categories. In addition, we constructed differentially expressed miRNA-mRNA interaction networks related to abdominal adipose development. The results showed that miRNA families, such as mir-30, mir-34, mir-199, mir-8, and mir-146, may have key roles in lipid metabolism, adipocyte proliferation and differentiation, and cell junctions during abdominal adipose tissue development in chickens.

Conclusions: This study determined the dynamic miRNA transcriptome and characterized the miRNA-mRNA interaction networks in Gushi chicken abdominal adipose tissue for the first time. The results expanded the number of known miRNAs in abdominal adipose tissue and provide novel insights and a valuable resource to elucidate post-transcriptional regulation mechanisms during postnatal late development of abdominal adipose tissue in chicken.
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http://dx.doi.org/10.1186/s12864-019-6094-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6815035PMC
October 2019

α7 Nicotinic Acetylcholine Receptor Mediates the Neuroprotection of Remote Ischemic Postconditioning in a Rat Model of Asphyxial Cardiac Arrest.

J Surg Res 2020 02 18;246:6-18. Epub 2019 Sep 18.

Department of Anesthesiology, The Second Affiliated Hospital of Air Force Medical University, Tangdu Hospital of Fourth Military Medical University, Xi'an, China. Electronic address:

Background: Remote ischemic postconditioning (RIPost) has been shown to reduce the ischemia-reperfusion injury of the heart and brain. However, the protection mechanisms have not yet been fully elucidated. We have observed that RIPost could alleviate the brain injury after cardiac arrest (CA). The aim of this study was to explore whether α7 nicotinic acetylcholine receptor (α7nAChR) mediates the neuroprotection of RIPost in a rat model of asphyxial CA.

Materials And Methods: Asphyxial CA model was induced by occlusion of the tracheal tube for 8 min and resuscitated later. RIPost produced by three cycles of 15-min occlusion and 15-min release of the right hind limb by a tourniquet was performed respectively at the moment and the third hour after restoration of spontaneous circulation. The α7nAChR agonist PHA-543613 and the antagonist methyllycaconitine (MLA) were used to investigate the role of α7nAChR in mediating neuroprotective effects.

Results: Results showed that α7nAChR was decreased in hippocampus and cortex after resuscitation, whereas RIPost could attenuate the reduction. The use of PHA-543613 provided neuroprotective effects against cerebral injury after CA. Furthermore, RIPost decreased the levels of neuron-specific enolase, inflammatory mediators, the number of apoptotic cells, and phosphorylation of nuclear factor-κB while increased the phosphorylation of signal transducer and activator of transcription-3. However, the above effects of RIPost were attenuated by α7nAChR antagonist methyllycaconitine.

Conclusions: Neuroprotection of RIPost was related with the activation of α7nAChR, which could suppress nuclear factor-κB and activate signal transducer and activator of transcription-3 in a rat asphyxial CA model.
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http://dx.doi.org/10.1016/j.jss.2019.07.091DOI Listing
February 2020

MicroRNA-15a Regulates the Differentiation of Intramuscular Preadipocytes by Targeting , and in Chickens.

Int J Mol Sci 2019 Aug 20;20(16). Epub 2019 Aug 20.

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

Our previous studies showed that microRNA-15a (miR-15a) was closely related to intramuscular fat (IMF) deposition in chickens; however, its regulatory mechanism remains unclear. Here, we evaluated the expression characteristics of miR-15a and its relationship with the expression of acetyl-CoA acyltransferase 1 (), acyl-CoA oxidase 1 () and sterol carrier protein 2 () by qPCR analysis in Gushi chicken breast muscle at 6, 14, 22, and 30 weeks old, where we performed transfection tests of miR-15a mimics in intramuscular preadipocytes and verified the target gene of miR-15a in chicken fibroblasts (DF1). The miR-15a expression level at 30 weeks increased 13.5, 4.5, and 2.7-fold compared with the expression levels at 6, 14, and 22 weeks, respectively. After 6 days of induction, miR-15a over-expression significantly promoted intramuscular adipogenic differentiation and increased cholesterol and triglyceride accumulation in adipocytes. Meanwhile, 48 h after transfection with miR-15a mimics, the expression levels of , and genes decreased by 56.52%, 31.18% and 37.14% at the mRNA level in intramuscular preadipocytes. In addition, the co-transfection of miR-15a mimics and , and 3'UTR (untranslated region) dual-luciferase vector significantly inhibited dual-luciferase activity in DF1 cells. Taken together, our data demonstrate that miR-15a can reduce fatty acid oxidation by targeting , , and , which subsequently indirectly promotes the differentiation of chicken intramuscular preadipocytes.
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http://dx.doi.org/10.3390/ijms20164063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6720712PMC
August 2019

Molecular characterization and an 80-bp indel polymorphism within the prolactin receptor () gene and its associations with chicken growth and carcass traits.

3 Biotech 2019 Aug 17;9(8):296. Epub 2019 Jul 17.

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

The prolactin receptor (), a type I cytokine receptor, must bind prolactin ( to act on target cells to mediate various physiological functions, including reproduction and lactation. This study identified an 80-bp insertion/deletion (indel) polymorphism in the 3'-untranslated region (3'-UTR) of the chicken gene in 3736 individuals from 15 breeds and analyzed its associations with growth and carcass traits in an F resource population. The results of the association analysis indicated that the 80-bp indel polymorphism was significantly ( < 0.05) or very significantly ( < 0.01) associated with multiple growth and carcass traits, such as body weight, leg weight, and shank length. In addition, we found that during the breeding process of commercial laying hens and commercial broilers, the 80-bp indel locus was artificially selected for the II genotype. Together, our findings reveal that this 80-bp indel polymorphism has potential as a new molecular marker for marker-assisted selection of chicken growth and carcass traits.
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http://dx.doi.org/10.1007/s13205-019-1827-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637161PMC
August 2019
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