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Hua Li
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, Foshan, People’s Republic of China

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Research article
Published: 16 August 2021 in Genetics Selection Evolution
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Background In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age. Results First, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism. Conclusions Our study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.

ACS Style

Huimin Kang; Di Zhao; Hai Xiang; Jing Li; Guiping Zhao; Hua Li. Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content. Genetics Selection Evolution 2021, 53, 1 -23.

AMA Style

Huimin Kang, Di Zhao, Hai Xiang, Jing Li, Guiping Zhao, Hua Li. Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content. Genetics Selection Evolution. 2021; 53 (1):1-23.

Chicago/Turabian Style

Huimin Kang; Di Zhao; Hai Xiang; Jing Li; Guiping Zhao; Hua Li. 2021. "Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content." Genetics Selection Evolution 53, no. 1: 1-23.

Journal article
Published: 20 July 2021 in Animals
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Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p< 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

ACS Style

Feilong Deng; Yushan Li; Yunjuan Peng; Xiaoyuan Wei; Xiaofan Wang; Samantha Howe; Hua Yang; Yingping Xiao; Hua Li; Jiangchao Zhao; Ying Li. The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs. Animals 2021, 11, 2139 .

AMA Style

Feilong Deng, Yushan Li, Yunjuan Peng, Xiaoyuan Wei, Xiaofan Wang, Samantha Howe, Hua Yang, Yingping Xiao, Hua Li, Jiangchao Zhao, Ying Li. The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs. Animals. 2021; 11 (7):2139.

Chicago/Turabian Style

Feilong Deng; Yushan Li; Yunjuan Peng; Xiaoyuan Wei; Xiaofan Wang; Samantha Howe; Hua Yang; Yingping Xiao; Hua Li; Jiangchao Zhao; Ying Li. 2021. "The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs." Animals 11, no. 7: 2139.

Journal article
Published: 25 May 2021 in Animals
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Long non-coding RNAs (lncRNAs) and mRNAs are temporally expressed during chicken follicle development. However, follicle transcriptome studies in chickens with timepoints relating to changes in luteinizing hormone (LH) levels are rare. In this study, gene expression in Rohman layers was investigated at three distinct stages of the ovulatory cycle: zeitgeber time 0 (ZT0, 9:00 a.m.), zeitgeber time 12 (ZT12, 9:00 p.m.), and zeitgeber time 20 (ZT20, 5:00 a.m.) representing the early, middle, and LH surge stages, respectively, of the ovulatory cycle. Gene expression profiles were explored during follicle development at ZT0, ZT12, and ZT20 using Ribo-Zero RNA sequencing. The three stages were separated into two major stages, including the pre-LH surge and the LH surge stages. A total of 12,479 mRNAs and 7528 lncRNAs were identified among the three stages, and 4531, 523 differentially expressed genes (DEGs) and 2367, 211 differentially expressed lncRNAs (DELs) were identified in the ZT20 vs. ZT12, and ZT12 vs. ZT0, comparisons. Functional enrichment analysis revealed that genes involved in cell proliferation and metabolism processes (lipid-related) were mainly enriched in the ZT0 and ZT12 stages, respectively, and genes related to oxidative stress, steroids regulation, and inflammatory process were enriched in the ZT20 stage. These findings provide the basis for further investigation of the specific genetic and molecular functions of follicle development in chickens.

ACS Style

Liang Li; Xun Deng; Silu Hu; Zhifu Cui; Zifan Ning; Taotao Gui; Xiaoling Zhao; Diyan Li; Yan Wang; Huadong Yin; Lin Ye; Yaofu Tian; Yao Zhang; Hua Li; Qing Zhu. Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells during the Hen Ovulatory Cycle. Animals 2021, 11, 1533 .

AMA Style

Liang Li, Xun Deng, Silu Hu, Zhifu Cui, Zifan Ning, Taotao Gui, Xiaoling Zhao, Diyan Li, Yan Wang, Huadong Yin, Lin Ye, Yaofu Tian, Yao Zhang, Hua Li, Qing Zhu. Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells during the Hen Ovulatory Cycle. Animals. 2021; 11 (6):1533.

Chicago/Turabian Style

Liang Li; Xun Deng; Silu Hu; Zhifu Cui; Zifan Ning; Taotao Gui; Xiaoling Zhao; Diyan Li; Yan Wang; Huadong Yin; Lin Ye; Yaofu Tian; Yao Zhang; Hua Li; Qing Zhu. 2021. "Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells during the Hen Ovulatory Cycle." Animals 11, no. 6: 1533.

Journal article
Published: 30 April 2021 in Viruses
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The hemorrhagic disease of grass carp (HDGC) caused by grass carp reovirus (GCRV) still poses a great threat to the grass carp industry. Isolation and identification of the GCRV genotype I (GCRV-I) has been rarely reported in the past decade. In this study, a new GCRV was isolated from diseased fish with severe symptoms of enteritis and mild hemorrhages on the body surface. The isolate was further identified by cell culture, transmission electron, indirect immunofluorescence, and SDS-PAGE electrophoretic pattern analysis of genomic RNA. The results were consistent with the new isolate as a GCRV-I member and tentatively named GCRV-GZ1208. Both grass carp and rare minnow infected by the GCRV-GZ1208 have no obvious hemorrhagic symptoms, and the final mortality rate was ≤10%, indicating that it may be a low virulent isolate. GZ1208 possessed highest genomic homology to 873/GCHV (GCRV-I) and golden shiner reovirus (GSRV). Additionally, it was found a 90.7–98.3% nucleotide identity, a 96.4–100% amino acid identity, and <50% identity with GCRV-II and III genotypes. Interestingly, the sequences of some segments of GZ1208 were similar to GCRV-8733/GCHV, whereas the remaining segments were more closely related to GSRV, suggesting that a recombination event had occurred. Bootscan analysis of the complete genomic sequence confirmed this hypothesis, and recombination events between 873/GCHV and other GSRV-like viruses were also accompanied by gene mutations.

ACS Style

Weiwei Zeng; Sven Bergmannc; Hanxu Dong; Ying Yang; Minglin Wu; Hong Liu; Yanfeng Chen; Hua Li. Identification, Virulence, and Molecular Characterization of a Recombinant Isolate of Grass Carp Reovirus Genotype I. Viruses 2021, 13, 807 .

AMA Style

Weiwei Zeng, Sven Bergmannc, Hanxu Dong, Ying Yang, Minglin Wu, Hong Liu, Yanfeng Chen, Hua Li. Identification, Virulence, and Molecular Characterization of a Recombinant Isolate of Grass Carp Reovirus Genotype I. Viruses. 2021; 13 (5):807.

Chicago/Turabian Style

Weiwei Zeng; Sven Bergmannc; Hanxu Dong; Ying Yang; Minglin Wu; Hong Liu; Yanfeng Chen; Hua Li. 2021. "Identification, Virulence, and Molecular Characterization of a Recombinant Isolate of Grass Carp Reovirus Genotype I." Viruses 13, no. 5: 807.

Journal article
Published: 18 March 2021 in The Journal of Steroid Biochemistry and Molecular Biology
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XX sex reversal, also called XX disorders of sex development (XX-DSD), is a condition affecting the development of the gonads or genitalia, and is relatively common in pigs. However, its genetic etiology and transcriptional regulation mechanism in the hypothalamic-pituitary-gonadal axis (HPGA) remain mostly unknown. XX-DSD (SRY-negative) pigs and normal sows were selected by external genitalia observation. The hypothalamus, which is the integrated center of the HPGA was sampled for whole-transcriptome RNA-seq. The role of DEmiRNA was validated by its overexpression and knockdown in vitro. A total of 1,258 lncRNAs, 1,086 mRNAs, and 61 microRNAs differentially expressed in XX-DSD pigs compared with normal female pigs. Genes in the hormone biosynthesis and secretion pathway significantly up-regulated, and the up-regulation of GNRH1, KISS1 and AVP may associate with the abnormal secretion of GnRH. We also predicted the lncRNA-miRNA-mRNA co-expression triplets and constructed three competing endogenous RNA (ceRNA) potentially associated with XX-DSD. Functional enrichment studies suggested that TCONS_00340886, TCONS_00000204 and miR-181a related to GnRH secretion. Further, miR-181a inhibitor up-regulated GNRH1, PAK6, and CAMK4 in the GT1-7 cells. Conversely, transfection of miR-181a mimics obtained the opposite trends. The expression levels of FSHR, LHR, ESR1 and ESR2 were significantly higher in XX-DSD gondas than those in normal sows. Taken together, we proposed that the balance of endocrine had broken in XX-DSD pigs. The current study is the first to examine the transcriptomic profile in the hypothalamus of XX-DSD pigs. It provides new insight into coding and non-coding RNAs that may be associated with DSD in pigs.

ACS Style

Shuwen Tan; Yi Zhou; Haiquan Zhao; Jinhua Wu; Hui Yu; Yin Yang; Yalan Yang; Huabin Zhao; Hua Li. Comprehensive transcriptome analysis of hypothalamus reveals genes associated with disorders of sex development in pigs. The Journal of Steroid Biochemistry and Molecular Biology 2021, 210, 105875 .

AMA Style

Shuwen Tan, Yi Zhou, Haiquan Zhao, Jinhua Wu, Hui Yu, Yin Yang, Yalan Yang, Huabin Zhao, Hua Li. Comprehensive transcriptome analysis of hypothalamus reveals genes associated with disorders of sex development in pigs. The Journal of Steroid Biochemistry and Molecular Biology. 2021; 210 ():105875.

Chicago/Turabian Style

Shuwen Tan; Yi Zhou; Haiquan Zhao; Jinhua Wu; Hui Yu; Yin Yang; Yalan Yang; Huabin Zhao; Hua Li. 2021. "Comprehensive transcriptome analysis of hypothalamus reveals genes associated with disorders of sex development in pigs." The Journal of Steroid Biochemistry and Molecular Biology 210, no. : 105875.

Preprint
Published: 23 February 2021
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Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n=76), Denmark (n=100), and France (n=100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P<0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

ACS Style

Feilong Deng; Yushan Li; Xiaoyuan Wei; Xiaofan Wang; Samantha Howe; Hua Li; Jiangchao Zhao; Ying Li. The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs. 2021, 1 .

AMA Style

Feilong Deng, Yushan Li, Xiaoyuan Wei, Xiaofan Wang, Samantha Howe, Hua Li, Jiangchao Zhao, Ying Li. The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs. . 2021; ():1.

Chicago/Turabian Style

Feilong Deng; Yushan Li; Xiaoyuan Wei; Xiaofan Wang; Samantha Howe; Hua Li; Jiangchao Zhao; Ying Li. 2021. "The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs." , no. : 1.

Journal article
Published: 25 January 2021 in Vaccines
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Tilapia lake virus (TiLV) is a newly emerging pathogen responsible for high mortality and economic losses in the global tilapia industry. Currently, no antiviral therapy or vaccines are available for the control of this disease. The goal of the present study was to evaluate the immunological effects and protective efficacy of formaldehyde- and β-propiolactone-inactivated vaccines against TiLV in the presence and absence of the Montanide IMS 1312 VG adjuvant in tilapia. We found that β-propiolactone inactivation of viral particles generated a vaccine with a higher protection efficacy against virus challenge than did formaldehyde. The relative percent survivals of vaccinated fish at doses of 108, 107, and 106 50% tissue culture infectious dose (TCID50)/mL were 42.9%, 28.5%, and 14.3% in the absence of the adjuvant and 85.7%, 64.3%, and 32.1% in its presence, respectively. The vaccine generated specific IgM and neutralizing antibodies against TiLV at 3 weeks following immunization that were significantly increased after a second booster immunization. The steady state mRNA levels of the genes tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interferon γ (IFN-γ), cluster of differentiation 4 (CD4), major histocompatibility complex (MHC)-Ia, and MHC-II were all increased and indicated successful immune stimulation against TiLV. The vaccine also significantly lowered the viral loads and resulted in significant increases in survival, indicating that the vaccine may also inhibit viral proliferation as well as stimulate a protective antibody response. The β-propiolactone-inactivated TiLV vaccine coupled with the adjuvant Montanide IMS 1312 VG and booster immunizations can provide a high level of protection from virus challenge in tilapia.

ACS Style

Weiwei Zeng; Yingying Wang; Huzi Hu; Qing Wang; Sven Bergmann; Yahui Wang; Bo Li; Yuefeng Lv; Hua Li; Jiyuan Yin; Yingying Li. Cell Culture-Derived Tilapia Lake Virus-Inactivated Vaccine Containing Montanide Adjuvant Provides High Protection against Viral Challenge for Tilapia. Vaccines 2021, 9, 86 .

AMA Style

Weiwei Zeng, Yingying Wang, Huzi Hu, Qing Wang, Sven Bergmann, Yahui Wang, Bo Li, Yuefeng Lv, Hua Li, Jiyuan Yin, Yingying Li. Cell Culture-Derived Tilapia Lake Virus-Inactivated Vaccine Containing Montanide Adjuvant Provides High Protection against Viral Challenge for Tilapia. Vaccines. 2021; 9 (2):86.

Chicago/Turabian Style

Weiwei Zeng; Yingying Wang; Huzi Hu; Qing Wang; Sven Bergmann; Yahui Wang; Bo Li; Yuefeng Lv; Hua Li; Jiyuan Yin; Yingying Li. 2021. "Cell Culture-Derived Tilapia Lake Virus-Inactivated Vaccine Containing Montanide Adjuvant Provides High Protection against Viral Challenge for Tilapia." Vaccines 9, no. 2: 86.

Original article
Published: 28 October 2020 in Journal of Animal Breeding and Genetics
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Qingyuan partridge chicken is an important indigenous chicken in China. In its breeding schemes, chickens are usually selected at the age of 105‐day‐old for five traits, including body weight (BW), shank length (SL), shank girth (SG), comb height (CH) and feather maturity (FM). At present, genetic parameters of the aforementioned traits have still not been studied in Qingyuan partridge chickens. The objectives of this study were the following: (1) to investigate whether the optimal statistical models of these traits need to consider maternal genetic and permanent environmental effects in late‐feathering Qingyuan partridge hens, and (2) to estimate genetic parameters for these traits based on the optimal models. The numbers of records for BW, SL, SG, CH and FM were 13,721, 13,671, 13,670, 13,669 and 13,672, respectively. Variance components were estimated using average information‐restricted maximum likelihood method, and the optimal model was determined based on Bayesian information criterion. More specifically, the optimal model for BW considered maternal genetic and permanent environmental effects in addition to direct additive genetic effect; SL, SG and FM considered direct and maternal genetic effects; and CH considered direct and maternal genetic effects, and the covariance between them. The direct heritabilities of these traits estimated using the optimal models were 0.21 ± 0.04, 0.30 ± 0.05, 0.40 ± 0.05, 0.59 ± 0.09 and 0.09 ± 0.04, respectively; the maternal heritabilities were 0.01 ± 0.04, 0.05 ± 0.05, 0.04 ± 0.05, 0.09 ± 0.09 and 0.03 ± 0.04, respectively. Maternal genetic effect evidently played an important part in FM and maternal heritability accounted for 30 per cent of total heritability. Furthermore, the direct and maternal genetic effects for CH were estimated to be negatively and moderately correlated (−0.51 ± 0.11). For all traits, neglecting existent maternal effects biased the estimation of direct heritability. Therefore, to implement optimum breeding strategies for improvement of these traits in Qingyuan partridge hens, maternal effects should be taken into consideration.

ACS Style

Huimin Kang; Shanshan Li; Hua Li; Jiankang Gan; Jieling Luo; Zhengfen Zhang; Xuqing Deng; Jindui Wei; Gen Li. Genetic parameters and direct and maternal effects for important traits in late‐feathering Qingyuan partridge hens in China. Journal of Animal Breeding and Genetics 2020, 138, 454 -462.

AMA Style

Huimin Kang, Shanshan Li, Hua Li, Jiankang Gan, Jieling Luo, Zhengfen Zhang, Xuqing Deng, Jindui Wei, Gen Li. Genetic parameters and direct and maternal effects for important traits in late‐feathering Qingyuan partridge hens in China. Journal of Animal Breeding and Genetics. 2020; 138 (4):454-462.

Chicago/Turabian Style

Huimin Kang; Shanshan Li; Hua Li; Jiankang Gan; Jieling Luo; Zhengfen Zhang; Xuqing Deng; Jindui Wei; Gen Li. 2020. "Genetic parameters and direct and maternal effects for important traits in late‐feathering Qingyuan partridge hens in China." Journal of Animal Breeding and Genetics 138, no. 4: 454-462.

Original study
Published: 14 July 2020 in Archives Animal Breeding
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A genome-wide association study (GWAS) was performed on a resource family consisting of white and colored chickens for identification of genes related to plumage coloration using the Fixed and random model Circulating Probability Unification (FarmCPU) package. GWAS identified three chromosomal single-nucleotide polymorphisms (SNPs), demonstrating the polygenic basis of plumage phenotypes. Herein, retinoic acid-induced protein 14 (RAI14), a developmentally regulated gene that encodes a protein containing many ankyrin repeats, was identified as a candidate gene involved in plumage color. In this study, mRNA expression profiles of chicken RAI14 were determined, indel (insertion–deletion) variants were identified, and their association was analyzed in white and colored chickens. RA114 mRNA was expressed in all tissues tested (brain, spleen, liver, heart, oviduct, kidney, lung, pituitary gland, ovary, muscle, feather bulb, and skin). A relatively high RAI14 expression in white feather bulb compared to colored feather bulb (P

ACS Style

Adeyinka Abiola Adetula; Xiaolei Liu; Liubin Yang; Chengchi Fang; Hui Yu; Hua Li; Shijun Li. RAI14 in the blood feather regulates chicken pigmentation. Archives Animal Breeding 2020, 63, 231 -239.

AMA Style

Adeyinka Abiola Adetula, Xiaolei Liu, Liubin Yang, Chengchi Fang, Hui Yu, Hua Li, Shijun Li. RAI14 in the blood feather regulates chicken pigmentation. Archives Animal Breeding. 2020; 63 (2):231-239.

Chicago/Turabian Style

Adeyinka Abiola Adetula; Xiaolei Liu; Liubin Yang; Chengchi Fang; Hui Yu; Hua Li; Shijun Li. 2020. "RAI14 in the blood feather regulates chicken pigmentation." Archives Animal Breeding 63, no. 2: 231-239.

Research paper
Published: 01 January 2020 in Virulence
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Avian leucosis (AL) is a disease characterized by tumors and is caused by the avian leukosis virus (ALV). Because of the high variability of viruses and complex pathogenic mechanisms, screening and breeding J subgroup of ALV (ALV-J) resistant avian breeds is one of the strategies for prevention and treatment of AL, thus screening of significant immune markers is needed to promote the development of disease-resistant breeds. In this study, data-independent acquisition (DIA) technology was used to detect the DEPs of three breeds of chicken according to different comparison to investigate the potential markers. Results showed special DEPs for spleen development of each breed were detected, such as PCNT, DDB2, and ZNF62. These DEPs were involved in intestinal immune network used in production of IgA signaling pathways and related to immune response which can be used as potential markers for spleen development in different breeds. The DEPs such as RAB44 and TPN involved in viral myocarditis, transcriptional misregulation in cancer, and tuberculosis can be used as potential markers of spleen immune response after ALV-J infection in chickens. Pair-wise analysis was performed for the three breeds after the infection of ALV-J. The proteins such as RFX1, TAF10, and VH1 were differently expressed between three breeds. These DEPs involved in antigen processing and expression, acute myelogenous leukemia, and viral carcinogenesis can be used as potential immune markers after ALV-J infection of different genetic backgrounds. The screening of potential markers at protein level provides a strong theoretical research basis for disease resistance breeding in poultry.

ACS Style

Fei Ye; Yan Wang; Qijian He; Zhaoshuo Wang; Enyue Ma; Shiliang Zhu; Heling Yu; Huadong Yin; Xiaoling Zhao; Diyan Li; Hengyong Xu; Hua Li; Qing Zhu. Screening of immune biomarkers in different breeds of chickens infected with J subgroup of avian leukemia virus by proteomic. Virulence 2020, 11, 1158 -1176.

AMA Style

Fei Ye, Yan Wang, Qijian He, Zhaoshuo Wang, Enyue Ma, Shiliang Zhu, Heling Yu, Huadong Yin, Xiaoling Zhao, Diyan Li, Hengyong Xu, Hua Li, Qing Zhu. Screening of immune biomarkers in different breeds of chickens infected with J subgroup of avian leukemia virus by proteomic. Virulence. 2020; 11 (1):1158-1176.

Chicago/Turabian Style

Fei Ye; Yan Wang; Qijian He; Zhaoshuo Wang; Enyue Ma; Shiliang Zhu; Heling Yu; Huadong Yin; Xiaoling Zhao; Diyan Li; Hengyong Xu; Hua Li; Qing Zhu. 2020. "Screening of immune biomarkers in different breeds of chickens infected with J subgroup of avian leukemia virus by proteomic." Virulence 11, no. 1: 1158-1176.

Journal article
Published: 13 December 2019 in Animals
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Bird beaks are important for biological purposes such as food intake, removing parasites, and defining phenotypic attributes. Cross-beaks are a threat to poultry health and are harmful to productivity, wasting some units in the poultry industry. However, there is still limited research on subtypes of cross-beaks and the genetic basis of cross-beaks as well. Here, we described the subtypes of cross-beaks in terms of left or right and upper or lower jaw bones. We evaluated the impact of cross-beaks on craniofacial bones and figured out the relationship between bone morphogenetic protein 4 (BMP4) and the development of craniofacial bones in Huiyang bearded chickens. We identified five typical subtypes of cross-beaks by morphological assessment and X-ray scanning. We found that cross-beaks caused certain changes in the facial bone morphology, including changes to the length and width of the bone around the ocular area (p < 0.05). The relative expressions of BMP4 in lacrimal, mandible, premaxilla, frontal, and parietal bones were significantly higher in the severe cross-beak group, followed by that of the medium cross-beak group, weak cross-beak group, and control group (p < 0.05). Overall, we constructed a generally applicable method to classify cross-beaks in term of the angle. The skeleton around the ocular area was affected by the cross-beak. The expression levels of BMP4 in craniofacial bones may provide insight to potential role of BMP4 in the development of cross-beaks.

ACS Style

Yuyu Hong; Yuchang Pang; Haiquan Zhao; Siyu Chen; Shuwen Tan; Hai Xiang; Hui Yu; Hua Li. The Morphology of Cross-Beaks and BMP4 Gene Expression in Huiyang Bearded Chickens. Animals 2019, 9, 1143 .

AMA Style

Yuyu Hong, Yuchang Pang, Haiquan Zhao, Siyu Chen, Shuwen Tan, Hai Xiang, Hui Yu, Hua Li. The Morphology of Cross-Beaks and BMP4 Gene Expression in Huiyang Bearded Chickens. Animals. 2019; 9 (12):1143.

Chicago/Turabian Style

Yuyu Hong; Yuchang Pang; Haiquan Zhao; Siyu Chen; Shuwen Tan; Hai Xiang; Hui Yu; Hua Li. 2019. "The Morphology of Cross-Beaks and BMP4 Gene Expression in Huiyang Bearded Chickens." Animals 9, no. 12: 1143.

Original article
Published: 16 August 2019 in 3 Biotech
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Immunosuppression caused by avian leukemia virus J subgroup (ALV-J) infection includes atrophy or regeneration disorders of the lymphoid organs, decreased immune response, and termination of B lymphocyte maturation process and inhibition of T-lymphocyte development. The regulatory mechanism of the related resistance genes and protein expression is not clear. While searching for a molecular marker for the immune response to ALV-J infection, we detected differentially expressed proteins (DEPs) of spleens from chicken infected by ALV-J at 15th day and 30th day by the data-independent acquisition technique. Approximately 220 DEPs from the spleens of chickens infected by ALV-J were detected. To find a relatively stable biomarker molecule, we summarized the DEPs at two timepoints and selected activating signal cointegrator 1 complex subunit 3 (ASCC3), TBC1 domain family member 2 (TBC1D2), MHC class II beta chain 1 (BLB2), ensconsin (MAP7), complement component 1 Q subcomponent B chain (C1QB), and Follistatin-like 1 (FSTL1) from both comparisons for protein interaction network analysis. ASCC3, BLB2, C1QB, and FSTL1 were potential biomarkers for the complex infection mechanism of ALV-J and the dynamic immune mechanism of the body.

ACS Style

Fei Ye; Qijian He; Yan Wang; Can Cui; Fuling Yang; Bin Luo; Huadong Yin; Xiaoling Zhao; Diyan Li; Hengyong Xu; Hua Li; Qing Zhu. Data-independent acquisition of the proteomics of spleens from chickens infected by avian leukosis virus. 3 Biotech 2019, 9, 1 -11.

AMA Style

Fei Ye, Qijian He, Yan Wang, Can Cui, Fuling Yang, Bin Luo, Huadong Yin, Xiaoling Zhao, Diyan Li, Hengyong Xu, Hua Li, Qing Zhu. Data-independent acquisition of the proteomics of spleens from chickens infected by avian leukosis virus. 3 Biotech. 2019; 9 (9):1-11.

Chicago/Turabian Style

Fei Ye; Qijian He; Yan Wang; Can Cui; Fuling Yang; Bin Luo; Huadong Yin; Xiaoling Zhao; Diyan Li; Hengyong Xu; Hua Li; Qing Zhu. 2019. "Data-independent acquisition of the proteomics of spleens from chickens infected by avian leukosis virus." 3 Biotech 9, no. 9: 1-11.

Journal article
Published: 01 August 2019 in Veterinary Medicine and Science
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The ban on the use of antibiotic in feed encouraged nutritionists to using alternatives to maintain growth performance and intestinal function of broilers. This study was conducted to evaluate the effects of Yupingfeng polysaccharides (YP) supplementation on growth performance and expression of SGLT1, GLUT2 and GLUT5 in Qingyuan partridge chicken. Experiment 1: a total of 540 chickens were randomly allocated to five groups with six replication. Dietary treatments were: (1) CON (control group), basal diet; (2) T1, CON + 0.5 g kg-1 YP; (3) T2, CON + 1 g kg-1 YP; (4) T3, CON + 2 g kg-1 YP; (5) T4, CON + 4 g kg-1 YP. Experiment 2, a total of 162 were randomly allocated to three groups with three replication. Dietary treatments were: (1) CON, basal diet; (2) T1, CON + 0.5 g kg-1 YP; (3) T2, CON + 1 g kg-1 YP. From days 1 to 14 and overall, chicken fed T1 diet had higher ADG. On day 42, there was increased villus height of jejunum in T1 group. On days 14 and 28, there was decreased villus height of duodenum and jejunum in T2 group. In duodenum, the expression of SGLT1 (days 21, 35 and 42), GLUT2 (days 7, 14, 21, 28, 35 and 42) and GLUT5 (days 7, 14, 21 and 28) was increased with YP supplementation. In jejunum, the expression of SGLT1 (days 7, 14, 21, 28 and 35), GLUT2 (days 14, 21, 28, 35 and 42) and GLUT5 (days 7, 14, 21, 28, 35 and 42) was increased with YP supplementation. In ileum, the expression of SGLT1 (days 7, 21, 35 and 42), GLUT2 (days 7, 14, 21 and 42) and GLUT5 (days 7, 14, 21, 28, 35 and 42) was increased with YP supplementation. Dietary YP supplementation improves growth performance and expression of SGLT1, GLUT2 and GLUT5 in intestine.

ACS Style

Fuquan Yin; Ruixia Lan; Zhengmin Wu; Zhijing Wang; Haohao Wu; Zhiming Li; Hui Yu; Zhihui Zhao; Hua Li. Yupingfeng polysaccharides enhances growth performance in Qingyuan partridge chicken by up‐regulating the mRNA expression of SGLT 1, GLUT 2 and GLUT5. Veterinary Medicine and Science 2019, 5, 451 -461.

AMA Style

Fuquan Yin, Ruixia Lan, Zhengmin Wu, Zhijing Wang, Haohao Wu, Zhiming Li, Hui Yu, Zhihui Zhao, Hua Li. Yupingfeng polysaccharides enhances growth performance in Qingyuan partridge chicken by up‐regulating the mRNA expression of SGLT 1, GLUT 2 and GLUT5. Veterinary Medicine and Science. 2019; 5 (3):451-461.

Chicago/Turabian Style

Fuquan Yin; Ruixia Lan; Zhengmin Wu; Zhijing Wang; Haohao Wu; Zhiming Li; Hui Yu; Zhihui Zhao; Hua Li. 2019. "Yupingfeng polysaccharides enhances growth performance in Qingyuan partridge chicken by up‐regulating the mRNA expression of SGLT 1, GLUT 2 and GLUT5." Veterinary Medicine and Science 5, no. 3: 451-461.

Short communications
Published: 20 February 2019 in British Poultry Science
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1. The goal of the current study was to evaluate the genetic effects of the vascular endothelial growth factor (VEGF) and its receptor (VEGFR-2) on feather maturity in the Qingyuan partridge chicken, Guangxi Sanjuana chicken and Princesss chicken. 2. Both SSCP-PCR and qPCR were employed to detect the polymorphism and gene expression of the VEGF and VEGFR-2 genes. 3. Four SNPs were identified in the VEGFR-2 gene. Exon10-A69G was associated with feather maturity (P<0.01). Princesss chickens with the genotype EF had higher feather maturity scores (P<0.01). Higher expression levels of VEGF and VEGFR-2 were detected in the immature feather group of Qingyuan partridge chickens, especially in the skin. 4. The VEGF and VEGFR-2 genes play critical roles in feather maturity. In addition, exon10-A69G and genotype EF in the Princesss chicken could potentially be utilised as genetic markers to improve efficiency in breeding.

ACS Style

Shu-Wen Tan; Pei-Zhou Li; Hua Li; Hui Yu; Z.-F Zhang; Zheng Zeng; De-Chun Huang. Genetic effects of vascular endothelial growth factor and its receptor 2 on feather maturity in three chicken breeds. British Poultry Science 2019, 60, 109 -114.

AMA Style

Shu-Wen Tan, Pei-Zhou Li, Hua Li, Hui Yu, Z.-F Zhang, Zheng Zeng, De-Chun Huang. Genetic effects of vascular endothelial growth factor and its receptor 2 on feather maturity in three chicken breeds. British Poultry Science. 2019; 60 (2):109-114.

Chicago/Turabian Style

Shu-Wen Tan; Pei-Zhou Li; Hua Li; Hui Yu; Z.-F Zhang; Zheng Zeng; De-Chun Huang. 2019. "Genetic effects of vascular endothelial growth factor and its receptor 2 on feather maturity in three chicken breeds." British Poultry Science 60, no. 2: 109-114.

Journal article
Published: 25 May 2018 in BMC Genomics
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Early feathering and late feathering in chickens are sex-linked phenotypes, which have commercial application in the poultry industry for sexing chicks at hatch and have important impacts on performance traits. However, the genetic mechanism controlling feather development and feathering patterns is unclear. Here, miRNA and mRNA expression profiles in chicken wing skin tissues were analysed through high-throughput transcriptomic sequencing, aiming to understand the biological process of follicle development and the formation of different feathering phenotypes. Compared to the N1 group with no primary feathers extending out, 2893 genes and 31 miRNAs displayed significantly different expression in the F1 group with primary feathers longer than primary-covert feathers, and 1802 genes and 11 miRNAs in the L2 group displayed primary feathers shorter than primary-covert feathers. Only 201 altered genes and 3 altered miRNAs were identified between the N1 and L2 groups (fold change > 2, q value < 0.01). Both sequencing and qPCR tests revealed that PRLR was significantly decreased in the F1 and L2 groups compared to the N1 group, whereas SPEF2 was significantly decreased in the F1 group compared to the N1 or L2 group. Functional analysis revealed that the altered genes or targets of altered miRNAs were involved in multiple biological processes and pathways related to feather growth and development, such as the Wnt signalling pathway, the TGF-beta signalling pathway, the MAPK signalling pathway, epithelial cell differentiation, and limb development. Integrated analysis of miRNA and mRNA showed that 14 pairs of miRNA-mRNA negatively interacted in the process of feather formation. Transcriptomic sequencing of wing skin tissues revealed large changes in F1 vs. N1 and L2 vs. N1, but few changes in F1 vs. L2 for both miRNA and mRNA expression. PRLR might only contribute to follicle development, while SPEF2 was highly related to the growth rate of primary feathers or primary-covert feathers and could be responsible for early and late feather formation. Interactions between miR-1574-5p/NR2F, miR-365-5p/JAK3 and miR-365-5p/CDK6 played important roles in hair or feather formation. In all, our results provide novel evidence to understand the molecular regulation of follicle development and feathering phenotype. The online version of this article (10.1186/s12864-018-4773-z) contains supplementary material, which is available to authorized users.

ACS Style

Guijun Fang; Xinzheng Jia; Hua Li; Shuwen Tan; Qinghua Nie; Hui Yu; Ying Yang. Characterization of microRNA and mRNA expression profiles in skin tissue between early-feathering and late-feathering chickens. BMC Genomics 2018, 19, 399 .

AMA Style

Guijun Fang, Xinzheng Jia, Hua Li, Shuwen Tan, Qinghua Nie, Hui Yu, Ying Yang. Characterization of microRNA and mRNA expression profiles in skin tissue between early-feathering and late-feathering chickens. BMC Genomics. 2018; 19 (1):399.

Chicago/Turabian Style

Guijun Fang; Xinzheng Jia; Hua Li; Shuwen Tan; Qinghua Nie; Hui Yu; Ying Yang. 2018. "Characterization of microRNA and mRNA expression profiles in skin tissue between early-feathering and late-feathering chickens." BMC Genomics 19, no. 1: 399.

Journal article
Published: 01 November 2016 in Fish & Shellfish Immunology
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Exposure to high temperature is an inherent feature of grass carp culture in southern China and juvenile grass carps are predisposed to infectious disease in this condition. To understand how high temperature impacts the immune response to pathogens in grass carp, the transcriptomic profiles of the spleens from immune injected grass carp groups undergoing heat stress and normal temperature were investigated. An average of 72 million clean reads per library was obtained, and approximate 80% of these genes were successfully mapped to the reference genome. A total of 2287 up-regulated and 1068 down-regulated genes were identified. 10 immune-related categories involving 90 differently expressed genes were scrutinized. Expression patterns of 18 differentially expressed genes involving in immune response were validated by quantitative real-time RT-PCR. These results provide further significant insights into the influence mechanism of high temperature to immune response in grass carp.

ACS Style

Ying Yang; Hui Yu; Hua Li; Anli Wang; Hai-Yi Yu. Effect of high temperature on immune response of grass carp (Ctenopharyngodon idellus) by transcriptome analysis. Fish & Shellfish Immunology 2016, 58, 89 -95.

AMA Style

Ying Yang, Hui Yu, Hua Li, Anli Wang, Hai-Yi Yu. Effect of high temperature on immune response of grass carp (Ctenopharyngodon idellus) by transcriptome analysis. Fish & Shellfish Immunology. 2016; 58 ():89-95.

Chicago/Turabian Style

Ying Yang; Hui Yu; Hua Li; Anli Wang; Hai-Yi Yu. 2016. "Effect of high temperature on immune response of grass carp (Ctenopharyngodon idellus) by transcriptome analysis." Fish & Shellfish Immunology 58, no. : 89-95.