Publications by authors named "Zhuanjian Li"

64 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

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

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens.

BMC Genomics 2021 Jun 9;22(1):428. Epub 2021 Jun 9.

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

Background: Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken liver is poorly understood. To identify estrogen-responsive genes and estrogen functional sites on a genome-wide scale, we determined expression profiles of mRNAs, lncRNAs, and miRNAs in estrogen-treated ((17β-estradiol)) and control chicken livers using RNA-Sequencing (RNA-Seq) and studied the estrogen receptor α binding sites by ChIP-Sequencing (ChIP-Seq).

Results: We identified a total of 990 estrogen-responsive genes, including 962 protein-coding genes, 11 miRNAs, and 17 lncRNAs. Functional enrichment analyses showed that the estrogen-responsive genes were highly enriched in lipid metabolism and biological processes. Integrated analysis of the data of RNA-Seq and ChIP-Seq, identified 191 genes directly targeted by estrogen, including 185 protein-coding genes, 4 miRNAs, and 2 lncRNAs. In vivo and in vitro experiments showed that estrogen decreased the mRNA expression of PPARGC1B, which had been reported to be linked with lipid metabolism, by directly increasing the expression of miR-144-3p.

Conclusions: These results increase our understanding of the functional network of estrogen in chicken liver and also reveal aspects of the molecular mechanism of estrogen-related lipid metabolism.
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http://dx.doi.org/10.1186/s12864-021-07679-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190866PMC
June 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

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

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

Evolution, expression profile, and regulatory characteristics of ACSL gene family in chicken (Gallus gallus).

Gene 2021 Jan 26;764:145094. Epub 2020 Aug 26.

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

Long chain acyl-CoA synthetases (ACSLs), which drive the conversion of long chain fatty acid into acyl-CoA, an ingredient of lipid synthesis, have been well-acknowledged to exert an indispensable role in many metabolic processes in mammals, especially lipid metabolism. However, in chicken, the evolutionary characteristics, expression profiles and regulatory mechanisms of ACSL gene family are rarely understood. Here, we analyzed the genomic synteny, gene structure, evolutionary event and functional domains of the ACSL gene family members using bioinformatics methods. The spatiotemporal expression profiles of ACSL gene family, and their regulatory mechanism were investigated via bioinformatics analysis incorporated with in vivo and in vitro estrogen-treated experiments. Our results indicated that ACSL2 gene was indeed evolutionarily lost in the genome of chicken. Chicken ACSLs shared an AMP-binding functional domain, as well as highly conversed ATP/AMP and FACS signature motifs, and were clustered into two clades, ACSL1/5/6 and ACSL3/4, based on high sequence similarity, similar gene features and conversed motifs. Chicken ACSLs showed differential tissue expression distributions, wherein the significantly decreased expression level of ACSL1 and the significantly increased expression level of ACSL5 were found, respectively, the expression levels of the other ACSL members remained unchanged in the liver of peak-laying hens versus pre-laying hens. Moreover, the transcription activity of ACSL1, ACSL3 and ACSL4 was silenced and ACSL6 was activated by estrogen, but no response to ACSL5. In conclusion, though having highly conversed functional domains, chicken ACSL gene family is organized into two separate groups, ACSL1/5/6 and ACSL3/4, and exhibits varying expression profiles and estrogen effects. These results not only pave the way for better understanding the specific functions of ACSL genes in avian lipid metabolism, but also provide a valuable evidence for gene family characteristics.
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http://dx.doi.org/10.1016/j.gene.2020.145094DOI Listing
January 2021

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

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

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

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

Evolution, dynamic expression changes and regulatory characteristics of gene families involved in the glycerophosphate pathway of triglyceride synthesis in chicken (Gallus gallus).

Sci Rep 2019 09 4;9(1):12735. Epub 2019 Sep 4.

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

It is well documented that four gene families, including the glycerophosphate acyltransferases (GPATs), acylglycerophosphate acyltransferases (AGPATs), lipid phosphate phosphohydrolases (LPINs) and diacylglycerol acyltransferases (DGATs), are involved in the glycerophosphate pathway of de novo triglyceride (TG) biosynthesis in mammals. However, no systematic analysis has been conducted to characterize the gene families in poultry. In this study, the sequences of gene family members in the glycerophosphate pathway were obtained by screening the public databases. The phylogenetic tree, gene structures and conserved motifs of the corresponding proteins were evaluated. Dynamic expression changes of the genes at different developmental stages were analyzed by qRT-PCR. The regulatory characteristics of the genes were analyzed by in vivo experiments. The results showed that the GPAT, AGPAT and LPIN gene families have 2, 7 and 2 members, respectively, and they were classified into 2, 4 and 2 cluster respectively based on phylogenetic analysis. All of the genes except AGPAT1 were extensively expressed in various tissues. Estrogen induction upregulated the expression of GPAM and AGPAT2, downregulated the expression of AGPAT3, AGPAT9, LPIN1 and LPIN2, and had no effect on the expression of the other genes. These findings provide a valuable resource for further investigation of lipid metabolism in liver of chicken.
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http://dx.doi.org/10.1038/s41598-019-48893-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6726641PMC
September 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

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

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

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

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

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

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

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

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

Clinical assessment of growth performance, bone morphometry, bone quality, and serum indicators in broilers affected by valgus-varus deformity.

Poult Sci 2019 Oct;98(10):4433-4440

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

The large economic losses caused by leg disorders have raised concerns in the broiler industry. Several types of leg disorders in broilers have been identified, such as tibial dyschondroplasia (TD), femoral head necrosis (FHN), and valgus-varus deformity (VVD). In this study, phenotypic changes associated with VVD were examined using clinical diagnosis, anatomical examination, measured growth performance, bone traits, and serum indicators. The incidence of VVD among the chicken population at a commercial facility in Tangshan China was 1.75% (n = 52,000), distributed about 1:1 (n = 122), between females and males. A majority of chickens were characterized by a unilaterally abnormality, while appropriately 17.6% by bilateral abnormality. Approximately 97.9% of affected broilers were classified as the "valgus" type. Growth traits, including body weight, shank length, and shank girth, were significantly lower in chickens with VVD, while tibia and metatarsal bone indexes were about 1.3-fold higher in the affected birds than in the normal birds. Bone mineral density, bone breaking strength, and several serum indicators were significantly different between affected and normal broilers. Sparse and disarranged bony trabecular was observed in abnormal broilers by histological analysis. Generally, leg disorders are associated with compromised growth, bone quality, bone structure, and lipid metabolism. This study provides a reference for clinical diagnosis of VVD and lays a foundation for exploring its underlying mechanisms.
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http://dx.doi.org/10.3382/ps/pez269DOI Listing
October 2019

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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