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Zhanjiang Liu - One of the best experts on this subject based on the ideXlab platform.

  • Genomic Prediction of Columnaris Disease Resistance in Catfish.
    Marine biotechnology (New York N.Y.), 2020
    Co-Authors: Yaqun Zhang, Zhanjiang Liu
    Abstract:

    Catfish is an important aquaculture species in the USA. Columnaris disease is distributed worldwide, affecting a wide variety of fish species including catfish . It leads to huge economic losses each year to the US catfish industry. Channel catfish in general is highly resistant to the disease, while blue catfish is highly susceptible. Genomic selection is an effective and accurate way to predict the breeding values and thus was expected to improve the prediction veracity of Columnaris disease resistance in catfish effectively. In this study, two different methods, elastic net genomic best linear unbiased prediction (ENGBLUP) and genomic best linear unbiased prediction (GBLUP), were used to predict the Columnaris disease resistance evaluated by binary survival status. Cross-validation showed that the prediction accuracy of ENGBLUP and GBLUP was 0.7347 and 0.4868, respectively, showing that ENGBLUP had a high prediction accuracy. It was shown that fitting QTL and polygenic effect with different distribution will improve genomic prediction accuracy for binary traits. In this study, an accurate and effective genomic selection method was proposed to predict the Columnaris resistance in catfish, and its application should be beneficial to catfish breeding.

  • transcriptomic signatures of attachment nf κb suppression and ifn stimulation in the catfish gill following Columnaris bacterial infection
    Developmental and Comparative Immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value <0.001). Our results highlight several putative immune pathways and individual candidate genes deserving of further investigation in the context of development of therapeutic regimens and laying the foundation for selection of resistant catfish lines against Columnaris.

  • Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following Columnaris bacterial infection.
    Developmental and comparative immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value

Fanyue Sun - One of the best experts on this subject based on the ideXlab platform.

  • A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for Columnaris disease resistance.
    BMC genomics, 2015
    Co-Authors: Xin Geng, Jin Sha, Shikai Liu, Lisui Bao, Jiaren Zhang, Ruijia Wang, Jun Yao, Jianbin Feng, Fanyue Sun
    Abstract:

    Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in the United States, serves as a great model for the analysis of host resistance against Columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with Columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus). A genomic region on linkage group 7 was found to be significantly associated with Columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host. The GWAS revealed four QTLs associated with Columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for Columnaris resistance.

  • transcriptomic signatures of attachment nf κb suppression and ifn stimulation in the catfish gill following Columnaris bacterial infection
    Developmental and Comparative Immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value <0.001). Our results highlight several putative immune pathways and individual candidate genes deserving of further investigation in the context of development of therapeutic regimens and laying the foundation for selection of resistant catfish lines against Columnaris.

  • Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following Columnaris bacterial infection.
    Developmental and comparative immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value

Shikai Liu - One of the best experts on this subject based on the ideXlab platform.

  • Identification of NF-κB related genes in channel catfish and their expression profiles in mucosal tissues after Columnaris bacterial infection.
    Developmental and comparative immunology, 2017
    Co-Authors: Xiaozhu Wang, Shikai Liu, Yujia Yang, Ash Abebe, Zhanjian Liu
    Abstract:

    Interactions of NF-κB family, IκB family and IKK complex are the key components of NF-κB pathway that is essential for many biological processes including innate and adaptive immunity, inflammation and stress responses. In spite of their importance, systematic analysis of these genes in fish has been lacking. Here we report a systematic study of the NF-κB related genes in channel catfish. Five NF-κB family genes, five IκB family genes and three IKK complex genes were identified in the channel catfish genome. Annotation of these 13 NF-κB related genes was further confirmed by phylogenetic and syntenic analysis. Negative selection was found to play a crucial role in the adaptive evolution of these genes. Expression profiles of NF-κB related genes after Flavobacterium columnare (Columnaris) infection were determined by analysis of the existing RNA-Seq dataset. The majority of NF-κB related genes were significantly regulated in mucosal tissues of gill, skin and intestine after Columnaris infection, indicating their potential involvement in host defense responses. Distinct expression patterns of NF-κB related genes were observed in susceptible and resistant catfish in response to Columnaris infection, suggesting that expression of these genes may contribute to the variations in disease resistance/susceptibility of catfish.

  • A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for Columnaris disease resistance.
    BMC genomics, 2015
    Co-Authors: Xin Geng, Jin Sha, Shikai Liu, Lisui Bao, Jiaren Zhang, Ruijia Wang, Jun Yao, Jianbin Feng, Fanyue Sun
    Abstract:

    Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in the United States, serves as a great model for the analysis of host resistance against Columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with Columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus). A genomic region on linkage group 7 was found to be significantly associated with Columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host. The GWAS revealed four QTLs associated with Columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for Columnaris resistance.

  • transcriptomic signatures of attachment nf κb suppression and ifn stimulation in the catfish gill following Columnaris bacterial infection
    Developmental and Comparative Immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value <0.001). Our results highlight several putative immune pathways and individual candidate genes deserving of further investigation in the context of development of therapeutic regimens and laying the foundation for selection of resistant catfish lines against Columnaris.

  • Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following Columnaris bacterial infection.
    Developmental and comparative immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value

Eric Peatman - One of the best experts on this subject based on the ideXlab platform.

  • putative roles for a rhamnose binding lectin in flavobacterium columnare pathogenesis in channel catfish ictalurus punctatus
    Fish & Shellfish Immunology, 2012
    Co-Authors: Benjamin H. Beck, Bradley D. Farmer, David L. Straus, Eric Peatman
    Abstract:

    Columnaris disease, caused by the bacterial pathogen Flavobacterium columnare, continues to be a major problem worldwide and commonly leads to tremendous losses of both wild and cultured freshwater fish, particularly in intensively farmed aquaculture species such as channel catfish. Despite its ecologic and economic impacts, the fundamental molecular mechanisms of the host immune response to this pathogen remain unclear. While F. columnare can induce marked pathologic changes in numerous ectopic tissues, the adhesion of F. columnare to the gill in particular is strongly associated with pathogen virulence and host susceptibility. Recently, in this regard, using RNA-seq expression profiling we found that a rhamnose-binding lectin (RBL) was dramatically upregulated in the gill of fish infected with F. columnare (as compared to naive fish). Thus, in the present study we sought to further characterize and understand the RBL response in channel catfish (Ictalurus punctatus). We first identified two distinct catfish families with differential susceptibilities to Columnaris disease; one family was found to be completely resistant while the other was susceptible (0% mortality versus 18.3% respectively, P 120-fold; P < 0.05) in fish fasted for 7 d (as compared to fish fed to satiation daily), yet expression levels returned to those of satiated fish within 4 h after re-feeding. Collectively, these findings highlight putative roles for RBL in the context of Columnaris disease and reveal new aspects linking RBL regulation to feed availability.

  • transcriptomic signatures of attachment nf κb suppression and ifn stimulation in the catfish gill following Columnaris bacterial infection
    Developmental and Comparative Immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value <0.001). Our results highlight several putative immune pathways and individual candidate genes deserving of further investigation in the context of development of therapeutic regimens and laying the foundation for selection of resistant catfish lines against Columnaris.

  • Catfish hybrid Ictalurus punctatus × I. furcatus exhibits higher resistance to Columnaris disease than the parental species.
    Diseases of aquatic organisms, 2012
    Co-Authors: Covadonga R. Arias, Eric Peatman, Wenlong Cai, Stephen A Bullard
    Abstract:

    We present experimental data on susceptibility to Columnaris disease, caused by the bacterium Flavobacterium columnare, in hybrid catfish (female channel catfish Ictalurus puncta- tus × male blue catfish I. furcatus) (C×B). Under our experimental conditions, C×B hybrids were significantly more resistant to Columnaris disease caused by the highly virulent strain of F. columnare BGFS-27 (genomovar II) than channel catfish and blue catfish. Channel and blue catfish cumulative mortalities after immersion challenge were 74 and 87%, respectively, whereas mortality in the C×B hybrid was 31%. Susceptibility to the strain ARS-1 (genomovar I) was lower among all catfishes, although channel catfish was the least resistant species at 32% cumulative mortality. By contrast, C×B hybrid and blue catfishes were strongly resistant to the ARS-1 strain, with

  • catfish hybrid ictalurus punctatus i furcatus exhibits higher resistance to Columnaris disease than the parental species
    Diseases of Aquatic Organisms, 2012
    Co-Authors: Covadonga R. Arias, Eric Peatman, Wenlong Cai, Stephen A Bullard
    Abstract:

    We present experimental data on susceptibility to Columnaris disease, caused by the bacterium Flavobacterium columnare, in hybrid catfish (female channel catfish Ictalurus puncta- tus × male blue catfish I. furcatus) (C×B). Under our experimental conditions, C×B hybrids were significantly more resistant to Columnaris disease caused by the highly virulent strain of F. columnare BGFS-27 (genomovar II) than channel catfish and blue catfish. Channel and blue catfish cumulative mortalities after immersion challenge were 74 and 87%, respectively, whereas mortality in the C×B hybrid was 31%. Susceptibility to the strain ARS-1 (genomovar I) was lower among all catfishes, although channel catfish was the least resistant species at 32% cumulative mortality. By contrast, C×B hybrid and blue catfishes were strongly resistant to the ARS-1 strain, with <10% mortality. Our data suggest enhanced disease resistance of the C×B hybrid to colum- naris disease.

  • Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following Columnaris bacterial infection.
    Developmental and comparative immunology, 2012
    Co-Authors: Fanyue Sun, Shikai Liu, Eric Peatman, Yanliang Jiang, Zunchun Zhou, Zhanjiang Liu
    Abstract:

    Outbreaks of Columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to Columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to Columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value

Ekaterina D. Badaeva - One of the best experts on this subject based on the ideXlab platform.