Publications by authors named "Guirong Sun"

65 Publications

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

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

Anti-dsDNA, anti-nucleosome, anti-C1q, and anti-histone antibodies as markers of active lupus nephritis and systemic lupus erythematosus disease activity.

Immun Inflamm Dis 2021 Jun 20;9(2):407-418. Epub 2021 Jan 20.

Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China.

Introduction: Previous studies of anti-dsDNA, nucleosome (Nucl), histone (His), and C1q antibodies have revealed their clinical value in systemic lupus erythematosus (SLE). However, the correlation between four autoantibodies and SLE activity, lupus nephritis (LN) remains controversial, and data are insufficient on longitudinal monitoring. This study aimed at evaluating the value of these autoantibodies in active LN, and their performance on cross-sectional evaluating and longitudinal monitoring of SLE disease activity.

Methods: Serum levels of four autoantibodies in 114 SLE patients, 219 other autoimmune disease patients (OAD), and 59 healthy controls were assayed by a quantitative immunoassay. Sera of 38 inpatients were obtained again after treatment.

Results: We found that serum levels of four autoantibodies were significantly higher in SLE than OAD patients (p < 001), active LN than non-renal SLE patients (p < .05), and higher in SLE patients with moderate and severe disease activity than mild disease activity (p < .01). Horizontally, serum level of each autoantibody was correlated with SLE disease activity index (SLEDAI) (p < .05), and correlation coefficient of anti-dsDNA was the highest (r = .585). For longitudinal monitoring, the decreased levels of four autoantibodies were found following treatment (p < .001). Serum level variations of these antibodies were positively correlated with variations of SLEDAI (p < .05). The correlation coefficient of anti-Nucl was the highest (r = .629). Although the levels of C3 and C4 increased after treatment, the change was not related to the change of SLEDAI (p > .05).

Conclusions: Anti-C1q, anti-dsDNA, anti-Nucl, and anti-His perform well in diagnosing active LN and monitoring SLE disease activity. They could be indicators of active LN and SLE disease activity.
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http://dx.doi.org/10.1002/iid3.401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127563PMC
June 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

Effects of miR-125b-5p on Preadipocyte Proliferation and Differentiation in Chicken.

Mol Biol Rep 2021 Jan 4;48(1):491-502. Epub 2021 Jan 4.

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China.

Our previous studies have shown that miR-125b-5p was highly expressed and significantly upregulated during abdominal fat deposition in chickens. However, the role of miR-125b in the regulation of adipogenesis is not clear in chickens. Therefore, we evaluated the effects of miR-125b-5p on preadipocyte proliferation and differentiation and the interaction between miR-125b-5p and the acyl-CoA synthetase bubblegum family member 2 (ACSBG2) gene in adipogenesis in chicken abdominal adipose tissue. Here, transfection tests of miR-125b-5p mimic/inhibitor were performed in preadipocytes, and the effects of miR-125b-5p on preadipocytes proliferation and differentiation were analyzed. The target site of miR-125b-5p in the 3'UTR (untranslated region) of ACSBG2 were verified by a luciferase reporter assay. Our results showed that miR-125b-5p overexpression inhibited proliferation and reduced the number of cells in S phase and G2/M phase in preadipocytes; conversely, miR-125b-5p inhibition promoted the proliferation and increased the number of cells in S phase and G2/M phase. In adipocytes after induction, miR-125b-5p overexpression led to a notable increase in the accumulation of lipid droplets as well as in the concentration of triglycerides, while miR-125b-5p inhibition had the opposite effect. Furthermore, miR-125b-5p could directly bind to the 3'UTR of ACSBG2, and its overexpression could significantly repress the mRNA and protein expression of ACSBG2. These results indicate that miR-125b-5p can inhibit preadipocyte proliferation and can promote preadipocyte differentiation to affect adipogenesis in chicken abdominal adipose tissues, at least partially by downregulating ACSBG2.
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http://dx.doi.org/10.1007/s11033-020-06080-4DOI Listing
January 2021

Serum vitamin D level is related to disease progression in primary biliary cholangitis.

Scand J Gastroenterol 2020 Nov 6;55(11):1333-1340. Epub 2020 Oct 6.

Department of Clinical Laboratory, Key Laboratory of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.

Background And Aim: A nonskeletal role of vitamin D in primary biliary cholangitis (PBC) patients is not yet clear. The purpose of this study is to investigate the serum vitamin D level in patients with PBC and to explore whether serum vitamin D level is related to disease progression.

Methods: The serum levels of 25(OH)D were measured in 185 PBC patients and 141 healthy controls. The association with vitamin D levels and disease progression, particularly natural course, was assessed.

Results: Serum vitamin D levels were measured in 185 patients with PBC. The mean level of vitamin D in advanced stage patients was lower than that in early stage patients (9.15 ± 5.33 ng/ml vs. 13.68 ± 6.33 ng/ml,  = .000). In the follow-up patients, the vitamin D level in the taken calcitriol patients showed an upward trend, while the un-taken calcitriol patients was opposite. Besides, vitamin D levels were correlated with the changes of bilirubin, albumin (ALB) and APRI (<.05). PBC patients with vitamin D deficiency had higher bilirubin levels and lower ALB levels (<.05). Moreover, there were differences in serum vitamin D levels between taken calcitriol patients and un-taken calcitriol patients ( = .027).

Conclusions: Vitamin D deficiency is highly prevalent in PBC patients. The decrease of vitamin D levels may indicate disease progression in PBC. PBC patients need to be regularly measured for serum vitamin D level and take appropriate vitamin D supplementation.
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http://dx.doi.org/10.1080/00365521.2020.1829030DOI Listing
November 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

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

Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model.

Cancer Manag Res 2020 3;12:5353-5363. Epub 2020 Jul 3.

Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong, People's Republic of China.

Objective: The aim of this study was to explore the signatures of oral microbiome associated with OSCC using a random forest (RF) model.

Patients And Methods: A total of 24 patients with OSCC were enrolled in the study. The oral microbiome was assessed in cancerous lesions and matched paracancerous tissues from each patient using 16S rRNA gene sequencing. Signatures of mucosal microbiome in OSCC were identified using a RF model.

Results: Significant differences were found between OSCC lesions and matched paracancerous tissues with respect to the microbial profile and composition. Linear discriminant analysis effect size analyses (LEfSe) identified 15 bacteria genera associated with cancerous lesions. and were enriched. A classifier based on RF model identified a microbial signature comprising 12 bacteria, which was capable of distinguishing cancerous lesions and paracancerous tissues (AUC = 0.82). The network of the oral microbiome in cancerous lesions appeared to be simplified and fragmented. Functional analyses of oral microbiome showed altered functions in amino acid metabolism and increased capacity of glucose utilization in OSCC.

Conclusion: The identified microbial signatures may potentially be used as a biomarker for predicting OSCC or for clinical assessment of oral cancer risk.
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http://dx.doi.org/10.2147/CMAR.S251021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342497PMC
July 2020

Identification of genes related to dexamethasone-induced immunosuppression in chicken thymus using transcriptome analysis.

Res Vet Sci 2020 Oct 19;132:318-327. Epub 2020 Jul 19.

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:

The molecular mechanism of stress-induced immunosuppression (SIS) in certain poultry immune organs is not completely clear. In this study, we constructed a stress immunosuppression model by selecting 180 healthy 7-day-old Gushi chickens and dividing them randomly into two groups: a D_T group and a B_T group. The D_T group was given dexamethasone, and the B_T group was given normal saline, according to the treatment method established and reported in our previous study. Thymus samples were subsequently taken from both groups. RNA-seq was used to sequence the transcriptomes of the thymus samples from both groups, and 1278 significant differentially expressed genes (DEGs) were obtained, of which 845 genes were up-regulated and 433 genes were down-regulated (padj<0.05, |FC| ≥ 2, FPKM>1). We identified immune-related gene ontology (GO) terms including immune system processes, immune system process regulation, and T cell activation. The results of KEGG (http: //www.kegg.jp) analysis showed that the DEGs are involved in a variety of immune-related pathways, such as cytokine-cytokine receptor interactions, Jak-STAT signaling pathways, and cell adhesion molecules (CAMs). The cytokine-cytokine receptor interaction pathway involves the DEGs CCR6, CCR5, CD40LG and FAS. The DEGs in the Jak-STAT signaling pathway were SPRY2, BCL2L1. These DEGS play an important role in cell apoptosis. CD40L, CD8, among other genes, are involved in the CAMs pathway. The results of this study add to existing data on the genomic study of stress affecting immune function, and provide a basis for further studies of the molecular mechanisms of stress-influenced immune function.
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http://dx.doi.org/10.1016/j.rvsc.2020.07.002DOI Listing
October 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

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

MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens.

Animals (Basel) 2020 Mar 11;10(3). Epub 2020 Mar 11.

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

The excessive deposition of abdominal fat has become an important factor in restricting the production efficiency of chickens, so reducing abdominal fat deposition is important for improving growth rate. It has been proven that miRNAs play an important role in regulating many physiological processes of organisms. In this study, we constructed a model of adipogenesis by isolating preadipocytes (Ab-Pre) derived from abdominal adipose tissue and differentiated adipocytes (Ab-Ad) in vitro. Deep sequencing of miRNAs and mRNAs expressed in Ab-Pre and Ab-Ad groups was conducted to explore the effect of miRNAs and mRNAs on fat deposition. We identified 80 differentially expressed miRNAs (DEMs) candidates, 58 of which were up-regulated and 22 down-regulated. Furthermore, six miRNAs and six mRNAs were verified by qRT-PCR, and the results showed that the expression of the DEMs and differentially expressed genes (DEGs) in the two groups was consistent with our sequencing results. When target genes of miRNA were combined with mRNA transcriptome data, a total of 891 intersection genes were obtained, we predicted the signal pathways of cross genes enrichment to the MAPK signal pathway, insulin signal pathway, fatty acid metabolism, and ECM-receptor interaction. Meanwhile, we constructed miRNA and negatively correlated mRNA target networks, including 12 miRNA-mRNAs pairs, which showed a strong association with the abdominal adipocyte differentiation (miR-214-, , , , , , ; miR-148a-5p-; miR-10a-5p-; miR-146b-5p-; miR-6615-5p-; miR-1774-). Overall, these findings provide a background for further research on lipid metabolism. Thus, we can better understand the molecular genetic mechanism of chicken abdominal fat deposition.
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http://dx.doi.org/10.3390/ani10030468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143929PMC
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

HSPA1L rs1061581 polymorphism is associated with the risk of preeclampsia in Han Chinese women.

Biosci Rep 2020 02;40(2)

Medical Genetic Department, the Affiliated Hospital of Qingdao University, Qingdao, China.

Preeclampsia (PE) is an excessive systemic inflammation response with dysfunction of endothelial. As a stress protein, heat shock protein 70 (HSP70) plays a pivotal role in protecting cells against apoptosis, oxidative damage and genetic damage. In humans, three genes encode members of the HSP70 class: HSPA1A, HSPA1B and HSPA1L. Our study was to investigate the association between genetic variations of HSPA1L and the susceptibility for PE in Chinese Han population. The polymorphisms of rs2227956, rs1043618 and rs1061581 in HSPA1L were genotyped by TaqMan allelic discrimination real time polymerase chain reaction (PCR) in 929 PE patients and 1024 healthy pregnant women. Statistic difference of the genotypic and allelic frequencies were found in HSPA1L rs1061581 between PE patients and controls (χ2 = 29.863, P < 0.001 by genotype; χ2 = 27.298, P < 0.001, OR = 1.874, 95%CI 1.476-2.379 by allele) and HSPA1L rs1061581 A alleles occurred more frequently in PE patients compared with healthy controls (PE vs. controls 10.28% vs. 5.76%). Furthermore, we divided the PE cases into early-onset/late-onset PE and mild/severe PE subgroups and found statistical differences in genotypic and allelic frequencies of the HSPA1L rs1061581 between early-onset PE, late-onset PE, mild PE, severe PE and controls, respectively. Moreover, HSPA1L rs1061581 A alleles were more frequent in early-onset PE, late-onset PE, mild PE and severe PE than controls respectively. Therefore, we concluded that HSPA1L rs1061581 polymorphism is associated with the risk of PE in Han Chinese women and A alleles may play a role in the susceptibility for PE.
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http://dx.doi.org/10.1042/BSR20194307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048671PMC
February 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

Influence of cecotrophy on fat metabolism mediated by caecal microorganisms in New Zealand white rabbits.

J Anim Physiol Anim Nutr (Berl) 2020 Mar 14;104(2):749-757. Epub 2020 Jan 14.

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

Cecotrophy is a special behaviour of rabbits. Eating soft faeces can improve feed efficiency and maintain gut flora in rabbits. In our previous study, we found that fasting from soft faeces significantly reduced growth rate and total cholesterol (TC) in New Zealand white rabbits (NZW rabbits), thereby resulting in lower values for body weight and fat deposition in the soft faeces fasting group than in the control group. However, it has not been demonstrated whether cecotrophy by NZW rabbits can regulate lipid metabolism by changing the diversity of caecal microorganisms. In this study, thirty-six 28-day-old weaned NZW female rabbits were randomly divided into two groups (the soft faeces fasting group and the control group) and fed to 90 days. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their soft faeces. Then, the caecal contents of three rabbits from the soft faeces fasting group and three rabbits from the control group were collected for metagenomic sequencing. We found that the abundance of Bacteroides increased, while Ruminococcus decreased, compared with the control group after fasting from soft faeces. Relative abundance was depressed for genes related to metabolic pathways such as ascorbate and aldarate metabolism, riboflavin metabolism and bile secretion. Moreover, there was a general correlation between variation in microbial diversity and fat deposition. Bacteroides affects body weight and TC by participating in the riboflavin metabolism pathway. By investigating the effect of cecotrophy on caecal microorganisms of rabbits, we identified the key microorganisms that regulate the rapid growth performance of NZW rabbits, which may provide useful reference for the future research and development of microecological preparations for NZW rabbits.
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http://dx.doi.org/10.1111/jpn.13309DOI Listing
March 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

Transcriptome Analysis of the Effects of Fasting Caecotrophy on Hepatic Lipid Metabolism in New Zealand Rabbits.

Animals (Basel) 2019 Sep 3;9(9). Epub 2019 Sep 3.

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

In order to investigate the effects of fasting caecotrophy on hepatic lipid metabolism in rabbits, 12 weaned female New Zealand white rabbits were randomly divided into (n = 6/group) a control and fasting caecotrophy group. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their own soft feces for a 60-day period. Growth and blood biochemical indices, transcriptome sequencing and histology analysis of the liver were performed. Compared with the control group, final weight, weight gain, liver weight, growth rate and feed conversion ratio, all decreased in the experimental group (p < 0.05). RNA sequencing (RNA-seq) analysis revealed a total of 301.2 million raw reads (approximately 45.06 Gb of high-quality clean data) that were mapped to the rabbit genome. After a five-step filtering process, 14,964 genes were identified, including 444 differentially expressed genes (p < 0.05, foldchange ≥ 1). A number of differently expressed genes linked to lipid metabolism were further analyzed including , SREBP, , GPAM, CYP3A1, RBP RDH5. The KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation of the differentially expressed genes indicated that main pathways affected were pentose and glucuronide interactions, starch and sucrose metabolism, retinol metabolism and signaling. Overall, the present study revealed that preventing caecotrophy reduced growth and altered lipid metabolism, both of which will help guide the development of new approaches for rabbits' feeding and production. These data also provide a reference for studying the effects of soft feces in other small herbivores.
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http://dx.doi.org/10.3390/ani9090648DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769842PMC
September 2019

Risk factors for pelvic lymph node metastasis in endometrial cancer.

Arch Gynecol Obstet 2019 10 21;300(4):1007-1013. Epub 2019 Aug 21.

Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China.

Purpose: To evaluate the risk factors for pelvic lymph node metastasis (LNM) in endometrial cancer (EC).

Methods: Clinicopathological characteristics and preoperative laboratory results were retrospectively analyzed in 393 surgically staged patients with EC (January 2014-February 2019).

Results: Pelvic LNM was detected in 45 (11.5%) patients. Univariate analysis showed that increased preoperative levels of human epididymis protein 4 (HE4), carbohydrate antigen 125 (CA125), monocyte to lymphocyte ratio (MLR), platelet to lymphocyte ratio (PLR), and decreased absolute lymphocyte count (ALC), as well as non-endometrioid histology, grade 3 tumor, deep myometrial invasion, vaginal or para-uterine involvement, adnexal involvement, positive peritoneal cytology, and lymphovascular space invasion (LVSI) were risk factors for pelvic LNM (All p < 0.05). Multivariate analysis revealed that preoperative serum HE4 ≥ 132 pmol/L (odds ratio (OR) 4.25, 95% confidence interval (CI) 1.65-10.94, p = 0.003), serum CA 125 ≥ 27.6 U/mL (OR 6.10, 95% CI 2.31-16.07, p = 0.000), non-endometrioid histology (OR 16.64, 95% CI 5.96-46.47, p = 0.000), myometrial invasion ≥ 50% (OR 5.30, 95% CI 2.07-13.55, p = 0.001), positive peritoneal cytology (OR 4.70, 95% CI 1.21-18.27, p = 0.025), and LVSI (OR 3.11, 95% CI 1.09-8.92, p = 0.034) remained as independent risk factors for pelvic LNM in EC. With the increase of these independent risk factors, the rate of pelvic LNM was increased significantly.

Conclusions: Higher preoperative levels of serum HE4 and CA125, non-endometrioid histology, deep myometrial invasion, positive peritoneal cytology, and LVSI are independent risk factors for pelvic LNM in EC, which can provide scientific basis for lymphadenectomy.
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http://dx.doi.org/10.1007/s00404-019-05276-9DOI Listing
October 2019

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

MicroRNA Sequencing Reveals the Effect of Different Levels of Non-Fibrous Carbohydrate/Neutral Detergent Fiber on Rumen Development in Calves.

Animals (Basel) 2019 Jul 28;9(8). Epub 2019 Jul 28.

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

Rumen development in calves is affected by many factors, including dietary composition. MicroRNAs (miRNAs) are known to function in the development of the rumen in cattle, what is not known is how these miRNAs function in rumen development of calves fed with high and low ratios of non-fibrous carbohydrate (NFC)/neutral detergent fiber (NDF). A total of six healthy Charolais hybrids bull calves of similar weight were divided into two groups; three calves were fed a mixed diet with NFC/NDF = 1.35 (H group), and three were fed a mixed diet with NFC/NDF = 0.80 (L group). After 105 days on the diet, calves were sacrificed and rumen tissues were collected. Tissues were subjected to histological observation and miRNA expression analysis. Functional enrichment analysis was conducted on the target genes of the miRNAs. Targeting and regulatory relationships were verified by luciferase reporter assay and quantitative PCR (qPCR). We found that the length of rumen papilla in the L group was significantly greater than that in the H group, while the width of rumen papilla in H group was significantly greater than that that in L group. We identified 896 miRNAs; 540 known miRNAs, and 356 novel predicted miRNAs. After statistical testing, we identified 24 differentially expressed miRNAs (DEmiRNAs). miRNA-mRNA-cluster network analysis and literature reviews revealed that cell proliferation, differentiation, physical and nutrient stimuli processes participate in rumen development under different NFC/NDF levels. The regulatory relationships between three DEmiRNAs and five target genes were verified by examining the levels of expression. The binding sites on bta-miR-128 for the peroxisome proliferator activated receptor gamma () and solute carrier family 16 member 1 ( genes were investigated using a dual luciferase assay. The results of this study provide insight into the role of miRNAs in rumen development in calves under different NFC/NDF levels.
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http://dx.doi.org/10.3390/ani9080496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6720277PMC
July 2019
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