Rex Dunham - Academia.edu (original) (raw)

Papers by Rex Dunham

Research paper thumbnail of Additional file 2: of The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish

Figure S1. Amino acid comparison of BCAR1 gene between XX and YY catfish. (JPG 1401 kb)

Research paper thumbnail of Full Paper Construction of a high-density, high-resolution

genetic map and its integration with BAC-based physical map in channel catfish

Research paper thumbnail of Growth and survival of crossbreeds between wild and domestic strains of Mekong Delta bighead catfish (Clarias macrocephalus Günther, 1864) cultured in tanks

Aquaculture, 2021

Abstract Crossbreeding between wild and domesticated strains of important aquaculture species to ... more Abstract Crossbreeding between wild and domesticated strains of important aquaculture species to determine potential for heterosis and heterobeltiosis is of interest to aquaculturists. The present study was aimed to evaluate broodstock strain effects and heterosis for growth and survival rates from larvae to grow out stages of bighead catfish (Clarias macrocephalus) crossed from one domesticated (Can Tho, CT) and two wild (Ca Mau, CM and Hau Giang, HG) populations. Nine crossbreeds were reared for 40 days at the larval stage in static tanks, 60 days for juveniles, and 90 days for grow out in recirculating systems. At harvest, pure CT exhibited the highest growth (final body weight BW = 154.1 ± 61.3 g), while HG × CT and HG × CM crossbreeds had the lowest (57.0 ± 17.0 g and 68.0 ± 28.5 g, respectively) and the other crossbreeds had intermediate values (mean BW ranged from 93.4 g to 113.1 g) (P = 0.01). The three stages showed consistently that the domestic CT strain grew faster than wild CM and HG strains. The growth performance of offspring was affected by dam strains, but not sire strains. Parental crosses generally had better growth rates compared to crossbreeds of the same dam source. However, crossbreeds did not differ in feed conversion ratios and survival rates from parental crosses. None of the crossbreeds had better growth than the better parent (heterobeltiosis), suggesting that crossbreeding among strains in the Mekong Delta may not be an effective genetic improvement program for bighead catfish.

Research paper thumbnail of Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish

Molecular genetics and genomics : MGG, Jan 2, 2018

Disease resistance is one of the most important traits for aquaculture industry. For catfish indu... more Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance. Three significant QTL, with two of located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified to be associated with ESC resistance. With a well-assembled- and -annotated reference genome sequence, genes around the involved QTL regions were identified. Among these genes, 37 genes had known functions in immunity, which may be involved in ESC resistance. Notably, nlrc3 and nlrp12 identified here were also found in QTL...

Research paper thumbnail of Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments

BMC genomics, Feb 13, 2018

Repetitive elements make up significant proportions of genomes. However, their roles in evolution... more Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. The enriched a...

Research paper thumbnail of Microinjection of CRISPR/Cas9 Protein into Channel Catfish, Ictalurus punctatus, Embryos for Gene Editing

Journal of visualized experiments : JoVE, Jan 20, 2018

The complete genome of the channel catfish, Ictalurus punctatus, has been sequenced, leading to g... more The complete genome of the channel catfish, Ictalurus punctatus, has been sequenced, leading to greater opportunities for studying channel catfish gene function. Gene knockout has been used to study these gene functions in vivo. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) system is a powerful tool used to edit genomic DNA sequences to alter gene function. While the traditional approach has been to introduce CRISPR/Cas9 mRNA into the single cell embryos through microinjection, this can be a slow and inefficient process in catfish. Here, a detailed protocol for microinjection of channel catfish embryos with CRISPR/Cas9 protein is described. Briefly, eggs and sperm were collected and then artificial fertilization performed. Fertilized eggs were transferred to a Petri dish containing Holtfreter's solution. Injection volume was calibrated and then guide RNAs/Cas9 targeting the toll/interleukin 1 receptor domain-containing ad...

Research paper thumbnail of JAK and STAT members in channel catfish: Identification, phylogenetic analysis and expression profiling after Edwardsiella ictaluri infection

Developmental and comparative immunology, Apr 22, 2017

The Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway ... more The Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway is one of the main pleiotropic cascades used to transmit information from extracellular receptors to the nucleus, which results in DNA transcription and expression of genes involved in immunity, proliferation, differentiation, migration, apoptosis, and cell survival. Members of JAK family and STAT family have been extensively studied in different mammalian species because of their important roles in innate and adaptive immune responses. However, they have not been systematically studied among teleost fish species. In this study, five JAK family members and eight STAT family members were identified and characterized from channel catfish. Phylogenetic analysis was conducted to properly annotate these genes. Syntenic analysis was also conducted to establish orthology, and confirm the results from phylogenetic analysis. Compared to mammals, more members of the JAK and STAT family were identi...

Research paper thumbnail of Effects of strain and body weight on low-oxygen tolerance of channel catfish (Ictalurus punctatus)

Aquaculture International, 2017

Low-oxygen tolerance is important for aquaculture species, because exposure to hypoxia can result... more Low-oxygen tolerance is important for aquaculture species, because exposure to hypoxia can result in heavy mortalities. This study evaluated the effects of strain, body weight, and gender on low-oxygen tolerance in channel catfish (Ictalurus punctatus) exposed to a lethal concentration of dissolved oxygen (0.1 mg/L). The variation in low-oxygen tolerance, assessed as the time to loss of equilibrium, of channel catfish from six strains (103KS, Kansas, KMix, Marion, Marion S, and Thompson) was examined. Catfish (15-179 g) showed a large variation in resistant time to hypoxia, ranging from 8 to 104 min, and both strain and body weight contributed significantly to this variation (P < 0.05). 103KS and Marion S strains had higher low-oxygen tolerance than the other strains, while the Marion strain had the poorest low-oxygen tolerance (P < 0.05). In addition to genetic background, body weight positively correlated with low-oxygen tolerance, but there were no significant differences between female and male catfish in low-oxygen tolerance. The results indicate that genetic background and body weight are important factors that contribute variations in low-oxygen tolerance.

Research paper thumbnail of A deletion in the Hermansky–Pudlak syndrome 4 (Hps4) gene appears to be responsible for albinism in channel catfish

Molecular Genetics and Genomics, 2017

Albinism is caused by a series of genetic abnormalities leading to reduction of melanin productio... more Albinism is caused by a series of genetic abnormalities leading to reduction of melanin production. Albinism is quite frequent in catfish, but the causative gene and the molecular basis were unknown. In this study, we conducted a genome-wide association study (GWAS) using the 250 K SNP array. The GWAS analysis allowed mapping of the albino phenotype in the Hermansky-Pudlak syndrome 4 (Hps4) gene, which is known to be involved in melanosome biosynthesis. Sequencing analysis revealed that a 99-bp deletion was present in all analyzed albino catfish at the intron 2 and exon 3 junction. This deletion led to the skipping of the entire exon 3 which was confirmed by RT-PCR. Therefore, Hps4 was determined to be the candidate gene of the catfish albinism.

Research paper thumbnail of Erratum to: Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

BMC genomics, Mar 16, 2017

Research paper thumbnail of Analysis of apolipoprotein genes and their involvement in disease response of channel catfish after bacterial infection

Developmental and comparative immunology, Feb 15, 2016

Apolipoproteins are protein component of plasma lipoproteins. They exert crucial roles in lipopro... more Apolipoproteins are protein component of plasma lipoproteins. They exert crucial roles in lipoprotein metabolism and serve as enzyme cofactors, receptor ligands, and lipid transfer carriers in mammals. In teleosts, apolipoproteins are also involved in diverse processes including embryonic and ontogenic development, liver and digestive system organogenesis, and innate immunity. In this study, we identified a set of 19 apolipoprotein genes in channel catfish (Ictalurus punctatus). Phylogenetic analysis and syntenic analysis were conducted to determine their identities and evolutionary relationships. The expression signatures of apolipoproteins in channel catfish were determined in healthy tissues and after infections with two major bacterial pathogens, Edwardsiella ictaluri and Flavobacterium columnare. In healthy channel catfish, most apolipoprotein genes exhibited tissue-specific expression patterns in channel catfish. After ESC and columnaris infections, 5 and 7 apolipoprotein gene...

Research paper thumbnail of Gene Mapping, Isolation and Genetic Improvement in Catfish

Aquatic Genomics, 2003

The catfish genetic improvement program at Auburn University utilizes an integrated approach of g... more The catfish genetic improvement program at Auburn University utilizes an integrated approach of genomics, gene isolation, selective breeding and gene transfer for the development of superior lines, crosses, hybrids and transgenics of catfish. A linkage map was recently completed that identified 44 linkage groups containing 607 AFLP markers. Analysis and placement of 100 microsatellite loci will soon be completed and added to this map as well as several quantitative trait loci. Additionally, 17 isozyme loci were mapped to 5 linkage groups. Selective genotyping has identified 3 microsatellites linked to feed conversion efficiency in channel catfish, Ictalurus punctatus, one microsatellite linked to growth and one microsatellite putatively linked to resistance to the bacterium, Edwardsiella ictaluri. F(ST) analysis indicated that nine of 13 isozyme loci examined in channel catfish were linked or associated with increased growth rate. Our laboratory has sequenced 7,000 EST clones from muscle, pituitary, brain, head kidney, skin and spleen of channel catfish representing 4,000 different genes.cDNA micro array analysis illustrated differential gene expression during hormone induced ovulation and in the muscles of different aged fish. Selection, intraspecific crossbreeding, interspecific hybridization and genetic engineering were all successful for improving production tr,aits in catfish. Growth hormone gene transfer and transfer of lytic peptides ,increased the growth and bacterial disease resistance, respectively, for channel catfish. Interspecific hybridization actually improved more traits in a single cross than any of the other breeding programs. However, mass selection combined with crossbreeding, mass selection combined with genetic engineering or strain selection combined with hybridization resulted in more genetic enhancement than any of the genetic improvement programs individually. The best aquaCUlture genotypes for the future will be developed by utilizing multiple breeding programs. The gene mapping data, QTL data, gene isolation and general genomics research will be utilized and integrated for marker-assisted selection, genetic engineering and in combination with multiple genetic improvement programs to maximize genetic potential of catfish for commercial catfish culture.

Research paper thumbnail of Gonadotropin alpha-subunit glycoprotein from channel catfish (Ictalurus punctatus) and its expression during hormone-induced ovulation

Molecular marine biology and biotechnology, 1997

Complementary DNA (cDNA) encoding the channel catfish (Ictalurus punctatus) gonadotropin (GTH) al... more Complementary DNA (cDNA) encoding the channel catfish (Ictalurus punctatus) gonadotropin (GTH) alpha-subunit glycoprotein was cloned by polymerase chain reaction (PCR) from a plasmid library made from pituitary RNA. Complete cDNA cloning was achieved by carrying out two PCR reactions: one with an upstream sense primer plus the universal sequencing primer, located downstream of the poly(A) sequence of the cDNA in the plasmid vector, to amplify the downstream portion of the cDNA; the other with a downstream antisense primer plus the reverse-sequencing primer, located upstream of the very 5' end of the cDNA sense strand in the plasmid vector, to amplify the upstream portion of the cDNA. The two amplified fragments overlapping about 70 bp. Nucleotide sequence analysis revealed that the catfish GTH alpha-subunit was 658 bp encoding 116 amino acids and harboring a 5' nontranslated region (NTR) of 42 bp and a 3' NTR of 265 bp. The deduced amino acid sequence of the catfish GTH ...

Research paper thumbnail of Sex-ratio-biasing constructs for the control of invasive lower vertebrates

Nature Biotechnology, 2014

volume 32 NumBeR 5 mAy 2014 nature biotechnology editors of the top-ranked biotechnology and appl... more volume 32 NumBeR 5 mAy 2014 nature biotechnology editors of the top-ranked biotechnology and applied microbiology journals who kindly gave us their opinion on synthetic biology and iGEM. We are indebted to

Research paper thumbnail of Gene transfer, expression and inheritance of PRSV-rainbow trout-GH cDNA in the common carp,Cyprinus carpio(Linnaeus)

Molecular Reproduction and Development, 1990

A recombinant plasmid containing the Rous sarcoma virus-long terminal repeat (RSV-LTR) promoter l... more A recombinant plasmid containing the Rous sarcoma virus-long terminal repeat (RSV-LTR) promoter linked to rainbow trout (Salmo gairdneri) growth hormone (GH) cDNA was microinjected into fertilized carp eggs. Genomic DNA extracted from pectoral fin of individual presumptive transgenic fish was analyzed by dot blot and Southern blot hybridization, using the RSV-LTR and/or the GH cDNA sequences as probes. Out of 365 presumptive transgenic fish analyzed, 20 individuals were found to contain pRSV-rtGH-cDNA sequence in the genomic DNA. Expression of the trout GH polypeptide was detected by immunobinding assay in the red blood cells of nine transgenic fish tested. The level of expression, however, varied among the transgenics and could not be correlated with exogenous DNA copy number. Although there was considerable variation in the sizes of the transgenic fish, those microinjected during the one-cell stage were (P less than 0.05) 22% larger, on the average, than their sibling controls. A randomly selected fraction of the progeny derived from crosses between transgenic males and non-transgenic females inherited the foreign DNA. These transgenic progeny grew faster (P less than 0.05) than their non-transgenic siblings.

Research paper thumbnail of Inheritance and usefulness of AFLP markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus), and their F1, F2, and backcross hybrids

Molecular and General Genetics MGG, 1998

Eight primer combinations were used to investigate the application of ampli®ed fragment length po... more Eight primer combinations were used to investigate the application of ampli®ed fragment length polymorphism (AFLP) markers in cat®sh for genetic analysis. Intraspeci®c polymorphism was low among channel cat®sh or blue cat®sh strains. Interspeci®c AFLP polymorphism was high between the channel cat®sh and blue cat®sh. Each primer combination generated from 70 to more than 200 bands, of which 38.6± 75.7% were polymorphic between channel cat®sh and blue cat®sh. On average, more than 20 polymorphic bands per primer combination were produced as quality markers suitable for genetic analysis. All AFLP markers were transmitted into channel cat®sh´blue cat®sh F1 hybrids, except rare markers that were heterozygous in the parents and therefore were segregating in F1 hybrids. The two reciprocal channel cat®sh´blue cat®sh F1 hybrids (channel cat®sh female´blue cat®sh male; blue cat®sh female´channel cat®sh male) produced identical AFLP pro®les. The AFLP markers were inherited and segregated in expected Mendelian ratios. At two loci, E8-b9 and E8-b2, markers were found at sig-ni®cantly lower frequencies than expected with F2 and backcross hybrids which had been selected for increased growth rates. The reproducibility of AFLP was excellent. These characteristics of the cat®sh AFLP markers make them highly useful for genetic analysis of cat®sh, especially for construction of genetic linkage and quantitative trait loci maps, and for marker-assisted selection.

Research paper thumbnail of Influence of Environmental Salinity on Messenger RNA Levels of Growth Hormone, Prolactin, and Somatolactin in Pituitary of the Channel Catfish (Ictalurus punctatus)

Marine Biotechnology, 2001

Pituitary growth hormone (GH), prolactin (PRL), and somatolactin (SL) messenger RNA levels in cha... more Pituitary growth hormone (GH), prolactin (PRL), and somatolactin (SL) messenger RNA levels in channel catfish (Ictalurus punctatus) were examined under various environmental and physiological conditions. Catfish were sampled following salinity challenge, during the winter (December) and spring or summer (April or July), and at different sizes (15-18 g, 620-664 g, and 956-1134 g). When catfish (956-1134 g) were transferred from freshwater to saline water containing 8 ppt NaCl, their plasma [Na(+)] increased significantly above values in the freshwater control group until they were transferred back to freshwater. Pituitary GH mRNA levels were low for the first 24 hours following transfer to saline water, but thereafter were significantly elevated above control values until the fish were transferred back to freshwater. Pituitary GH mRNA levels were highest in July and lowest in December. Growth hormone mRNA levels were also elevated in the size groups 15-18 g and 956-1134 g in July when compared with December values. Pituitary PRL mRNA levels increased for the first 24 hours following transfer to saline water (956-1134 g), but thereafter were significantly lower than control values until the fish were transferred back to freshwater. Pituitary PRL mRNA levels were highest in April and July and lowest in December, and were also elevated in the size groups 620-664 g and 956-1134 g. Pituitary SL mRNA levels were unaffected in catfish transferred to saline water; however, levels were significantly elevated in catfish of the 956-1134-g size group sampled in April when compared with December. These results suggest the involvement of GH in adaptation to brackish water and of PRL in adaptation to freshwater in the catfish, and seasonal and size-related differences in pituitary GH, PRL, and SL mRNA levels.

Research paper thumbnail of Molecular characterization and differential expression of the myostatin gene in channel catfish (Ictalurus punctatus)

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 2002

ABSTRACT Myostatin is a recently discovered gene that inhibits muscle growth. In the present stud... more ABSTRACT Myostatin is a recently discovered gene that inhibits muscle growth. In the present study, we characterized the myostatin locus and its expression in channel catfish (Ictalurus punctatus). The genomic DNA and cDNA encoding the channel catfish myostatin were cloned and sequenced. The myostatin gene has three exons encoding a protein of 389 amino acids. Comparison of the genomic sequences with those of the cDNA revealed that the myostatin cDNA was 1673 base pair (bp) long with a 5&#39;-untranslated region (UTR) and 3&#39;-UTR of 180 and 323 bp, respectively. The deduced amino acid sequences of the catfish myostatin is highly conserved with those of other organisms. The myostatin locus is highly polymorphic in channel catfish because of the presence of several microsatellites and single nucleotide polymorphic sites. The myostatin gene was expressed in various tissues and developmental stages at differential levels, suggesting complex regulation of this gene and perhaps roles for myostatin in addition to those originally suggested.

Research paper thumbnail of Diet fed to brood stock effects the growth of channel catfish (Ictalurus punctatus L) fry

Aquaculture Research, 2011

Research paper thumbnail of Economics of production of channel catfish,ictalurus punctatus,female x blue catfish,I.furcatus,male hybrid fingerlings and foodfish

Aquaculture Economics & Management, 2004

Tie profitability of the channel-blue hybrid catfish fingerlings and foodfish was compared to tha... more Tie profitability of the channel-blue hybrid catfish fingerlings and foodfish was compared to that of the channel catfish using enterprise budgets and sensitivity analyses. Average total costs of production were 15.0-22.5 per cent less for hybrids fingerlings, even if hybrid fry were bought at a price twice as high as that for channel catfish.

Research paper thumbnail of Additional file 2: of The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish

Figure S1. Amino acid comparison of BCAR1 gene between XX and YY catfish. (JPG 1401 kb)

Research paper thumbnail of Full Paper Construction of a high-density, high-resolution

genetic map and its integration with BAC-based physical map in channel catfish

Research paper thumbnail of Growth and survival of crossbreeds between wild and domestic strains of Mekong Delta bighead catfish (Clarias macrocephalus Günther, 1864) cultured in tanks

Aquaculture, 2021

Abstract Crossbreeding between wild and domesticated strains of important aquaculture species to ... more Abstract Crossbreeding between wild and domesticated strains of important aquaculture species to determine potential for heterosis and heterobeltiosis is of interest to aquaculturists. The present study was aimed to evaluate broodstock strain effects and heterosis for growth and survival rates from larvae to grow out stages of bighead catfish (Clarias macrocephalus) crossed from one domesticated (Can Tho, CT) and two wild (Ca Mau, CM and Hau Giang, HG) populations. Nine crossbreeds were reared for 40 days at the larval stage in static tanks, 60 days for juveniles, and 90 days for grow out in recirculating systems. At harvest, pure CT exhibited the highest growth (final body weight BW = 154.1 ± 61.3 g), while HG × CT and HG × CM crossbreeds had the lowest (57.0 ± 17.0 g and 68.0 ± 28.5 g, respectively) and the other crossbreeds had intermediate values (mean BW ranged from 93.4 g to 113.1 g) (P = 0.01). The three stages showed consistently that the domestic CT strain grew faster than wild CM and HG strains. The growth performance of offspring was affected by dam strains, but not sire strains. Parental crosses generally had better growth rates compared to crossbreeds of the same dam source. However, crossbreeds did not differ in feed conversion ratios and survival rates from parental crosses. None of the crossbreeds had better growth than the better parent (heterobeltiosis), suggesting that crossbreeding among strains in the Mekong Delta may not be an effective genetic improvement program for bighead catfish.

Research paper thumbnail of Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish

Molecular genetics and genomics : MGG, Jan 2, 2018

Disease resistance is one of the most important traits for aquaculture industry. For catfish indu... more Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance. Three significant QTL, with two of located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified to be associated with ESC resistance. With a well-assembled- and -annotated reference genome sequence, genes around the involved QTL regions were identified. Among these genes, 37 genes had known functions in immunity, which may be involved in ESC resistance. Notably, nlrc3 and nlrp12 identified here were also found in QTL...

Research paper thumbnail of Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments

BMC genomics, Feb 13, 2018

Repetitive elements make up significant proportions of genomes. However, their roles in evolution... more Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. The enriched a...

Research paper thumbnail of Microinjection of CRISPR/Cas9 Protein into Channel Catfish, Ictalurus punctatus, Embryos for Gene Editing

Journal of visualized experiments : JoVE, Jan 20, 2018

The complete genome of the channel catfish, Ictalurus punctatus, has been sequenced, leading to g... more The complete genome of the channel catfish, Ictalurus punctatus, has been sequenced, leading to greater opportunities for studying channel catfish gene function. Gene knockout has been used to study these gene functions in vivo. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) system is a powerful tool used to edit genomic DNA sequences to alter gene function. While the traditional approach has been to introduce CRISPR/Cas9 mRNA into the single cell embryos through microinjection, this can be a slow and inefficient process in catfish. Here, a detailed protocol for microinjection of channel catfish embryos with CRISPR/Cas9 protein is described. Briefly, eggs and sperm were collected and then artificial fertilization performed. Fertilized eggs were transferred to a Petri dish containing Holtfreter's solution. Injection volume was calibrated and then guide RNAs/Cas9 targeting the toll/interleukin 1 receptor domain-containing ad...

Research paper thumbnail of JAK and STAT members in channel catfish: Identification, phylogenetic analysis and expression profiling after Edwardsiella ictaluri infection

Developmental and comparative immunology, Apr 22, 2017

The Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway ... more The Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway is one of the main pleiotropic cascades used to transmit information from extracellular receptors to the nucleus, which results in DNA transcription and expression of genes involved in immunity, proliferation, differentiation, migration, apoptosis, and cell survival. Members of JAK family and STAT family have been extensively studied in different mammalian species because of their important roles in innate and adaptive immune responses. However, they have not been systematically studied among teleost fish species. In this study, five JAK family members and eight STAT family members were identified and characterized from channel catfish. Phylogenetic analysis was conducted to properly annotate these genes. Syntenic analysis was also conducted to establish orthology, and confirm the results from phylogenetic analysis. Compared to mammals, more members of the JAK and STAT family were identi...

Research paper thumbnail of Effects of strain and body weight on low-oxygen tolerance of channel catfish (Ictalurus punctatus)

Aquaculture International, 2017

Low-oxygen tolerance is important for aquaculture species, because exposure to hypoxia can result... more Low-oxygen tolerance is important for aquaculture species, because exposure to hypoxia can result in heavy mortalities. This study evaluated the effects of strain, body weight, and gender on low-oxygen tolerance in channel catfish (Ictalurus punctatus) exposed to a lethal concentration of dissolved oxygen (0.1 mg/L). The variation in low-oxygen tolerance, assessed as the time to loss of equilibrium, of channel catfish from six strains (103KS, Kansas, KMix, Marion, Marion S, and Thompson) was examined. Catfish (15-179 g) showed a large variation in resistant time to hypoxia, ranging from 8 to 104 min, and both strain and body weight contributed significantly to this variation (P < 0.05). 103KS and Marion S strains had higher low-oxygen tolerance than the other strains, while the Marion strain had the poorest low-oxygen tolerance (P < 0.05). In addition to genetic background, body weight positively correlated with low-oxygen tolerance, but there were no significant differences between female and male catfish in low-oxygen tolerance. The results indicate that genetic background and body weight are important factors that contribute variations in low-oxygen tolerance.

Research paper thumbnail of A deletion in the Hermansky–Pudlak syndrome 4 (Hps4) gene appears to be responsible for albinism in channel catfish

Molecular Genetics and Genomics, 2017

Albinism is caused by a series of genetic abnormalities leading to reduction of melanin productio... more Albinism is caused by a series of genetic abnormalities leading to reduction of melanin production. Albinism is quite frequent in catfish, but the causative gene and the molecular basis were unknown. In this study, we conducted a genome-wide association study (GWAS) using the 250 K SNP array. The GWAS analysis allowed mapping of the albino phenotype in the Hermansky-Pudlak syndrome 4 (Hps4) gene, which is known to be involved in melanosome biosynthesis. Sequencing analysis revealed that a 99-bp deletion was present in all analyzed albino catfish at the intron 2 and exon 3 junction. This deletion led to the skipping of the entire exon 3 which was confirmed by RT-PCR. Therefore, Hps4 was determined to be the candidate gene of the catfish albinism.

Research paper thumbnail of Erratum to: Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

BMC genomics, Mar 16, 2017

Research paper thumbnail of Analysis of apolipoprotein genes and their involvement in disease response of channel catfish after bacterial infection

Developmental and comparative immunology, Feb 15, 2016

Apolipoproteins are protein component of plasma lipoproteins. They exert crucial roles in lipopro... more Apolipoproteins are protein component of plasma lipoproteins. They exert crucial roles in lipoprotein metabolism and serve as enzyme cofactors, receptor ligands, and lipid transfer carriers in mammals. In teleosts, apolipoproteins are also involved in diverse processes including embryonic and ontogenic development, liver and digestive system organogenesis, and innate immunity. In this study, we identified a set of 19 apolipoprotein genes in channel catfish (Ictalurus punctatus). Phylogenetic analysis and syntenic analysis were conducted to determine their identities and evolutionary relationships. The expression signatures of apolipoproteins in channel catfish were determined in healthy tissues and after infections with two major bacterial pathogens, Edwardsiella ictaluri and Flavobacterium columnare. In healthy channel catfish, most apolipoprotein genes exhibited tissue-specific expression patterns in channel catfish. After ESC and columnaris infections, 5 and 7 apolipoprotein gene...

Research paper thumbnail of Gene Mapping, Isolation and Genetic Improvement in Catfish

Aquatic Genomics, 2003

The catfish genetic improvement program at Auburn University utilizes an integrated approach of g... more The catfish genetic improvement program at Auburn University utilizes an integrated approach of genomics, gene isolation, selective breeding and gene transfer for the development of superior lines, crosses, hybrids and transgenics of catfish. A linkage map was recently completed that identified 44 linkage groups containing 607 AFLP markers. Analysis and placement of 100 microsatellite loci will soon be completed and added to this map as well as several quantitative trait loci. Additionally, 17 isozyme loci were mapped to 5 linkage groups. Selective genotyping has identified 3 microsatellites linked to feed conversion efficiency in channel catfish, Ictalurus punctatus, one microsatellite linked to growth and one microsatellite putatively linked to resistance to the bacterium, Edwardsiella ictaluri. F(ST) analysis indicated that nine of 13 isozyme loci examined in channel catfish were linked or associated with increased growth rate. Our laboratory has sequenced 7,000 EST clones from muscle, pituitary, brain, head kidney, skin and spleen of channel catfish representing 4,000 different genes.cDNA micro array analysis illustrated differential gene expression during hormone induced ovulation and in the muscles of different aged fish. Selection, intraspecific crossbreeding, interspecific hybridization and genetic engineering were all successful for improving production tr,aits in catfish. Growth hormone gene transfer and transfer of lytic peptides ,increased the growth and bacterial disease resistance, respectively, for channel catfish. Interspecific hybridization actually improved more traits in a single cross than any of the other breeding programs. However, mass selection combined with crossbreeding, mass selection combined with genetic engineering or strain selection combined with hybridization resulted in more genetic enhancement than any of the genetic improvement programs individually. The best aquaCUlture genotypes for the future will be developed by utilizing multiple breeding programs. The gene mapping data, QTL data, gene isolation and general genomics research will be utilized and integrated for marker-assisted selection, genetic engineering and in combination with multiple genetic improvement programs to maximize genetic potential of catfish for commercial catfish culture.

Research paper thumbnail of Gonadotropin alpha-subunit glycoprotein from channel catfish (Ictalurus punctatus) and its expression during hormone-induced ovulation

Molecular marine biology and biotechnology, 1997

Complementary DNA (cDNA) encoding the channel catfish (Ictalurus punctatus) gonadotropin (GTH) al... more Complementary DNA (cDNA) encoding the channel catfish (Ictalurus punctatus) gonadotropin (GTH) alpha-subunit glycoprotein was cloned by polymerase chain reaction (PCR) from a plasmid library made from pituitary RNA. Complete cDNA cloning was achieved by carrying out two PCR reactions: one with an upstream sense primer plus the universal sequencing primer, located downstream of the poly(A) sequence of the cDNA in the plasmid vector, to amplify the downstream portion of the cDNA; the other with a downstream antisense primer plus the reverse-sequencing primer, located upstream of the very 5' end of the cDNA sense strand in the plasmid vector, to amplify the upstream portion of the cDNA. The two amplified fragments overlapping about 70 bp. Nucleotide sequence analysis revealed that the catfish GTH alpha-subunit was 658 bp encoding 116 amino acids and harboring a 5' nontranslated region (NTR) of 42 bp and a 3' NTR of 265 bp. The deduced amino acid sequence of the catfish GTH ...

Research paper thumbnail of Sex-ratio-biasing constructs for the control of invasive lower vertebrates

Nature Biotechnology, 2014

volume 32 NumBeR 5 mAy 2014 nature biotechnology editors of the top-ranked biotechnology and appl... more volume 32 NumBeR 5 mAy 2014 nature biotechnology editors of the top-ranked biotechnology and applied microbiology journals who kindly gave us their opinion on synthetic biology and iGEM. We are indebted to

Research paper thumbnail of Gene transfer, expression and inheritance of PRSV-rainbow trout-GH cDNA in the common carp,Cyprinus carpio(Linnaeus)

Molecular Reproduction and Development, 1990

A recombinant plasmid containing the Rous sarcoma virus-long terminal repeat (RSV-LTR) promoter l... more A recombinant plasmid containing the Rous sarcoma virus-long terminal repeat (RSV-LTR) promoter linked to rainbow trout (Salmo gairdneri) growth hormone (GH) cDNA was microinjected into fertilized carp eggs. Genomic DNA extracted from pectoral fin of individual presumptive transgenic fish was analyzed by dot blot and Southern blot hybridization, using the RSV-LTR and/or the GH cDNA sequences as probes. Out of 365 presumptive transgenic fish analyzed, 20 individuals were found to contain pRSV-rtGH-cDNA sequence in the genomic DNA. Expression of the trout GH polypeptide was detected by immunobinding assay in the red blood cells of nine transgenic fish tested. The level of expression, however, varied among the transgenics and could not be correlated with exogenous DNA copy number. Although there was considerable variation in the sizes of the transgenic fish, those microinjected during the one-cell stage were (P less than 0.05) 22% larger, on the average, than their sibling controls. A randomly selected fraction of the progeny derived from crosses between transgenic males and non-transgenic females inherited the foreign DNA. These transgenic progeny grew faster (P less than 0.05) than their non-transgenic siblings.

Research paper thumbnail of Inheritance and usefulness of AFLP markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus), and their F1, F2, and backcross hybrids

Molecular and General Genetics MGG, 1998

Eight primer combinations were used to investigate the application of ampli®ed fragment length po... more Eight primer combinations were used to investigate the application of ampli®ed fragment length polymorphism (AFLP) markers in cat®sh for genetic analysis. Intraspeci®c polymorphism was low among channel cat®sh or blue cat®sh strains. Interspeci®c AFLP polymorphism was high between the channel cat®sh and blue cat®sh. Each primer combination generated from 70 to more than 200 bands, of which 38.6± 75.7% were polymorphic between channel cat®sh and blue cat®sh. On average, more than 20 polymorphic bands per primer combination were produced as quality markers suitable for genetic analysis. All AFLP markers were transmitted into channel cat®sh´blue cat®sh F1 hybrids, except rare markers that were heterozygous in the parents and therefore were segregating in F1 hybrids. The two reciprocal channel cat®sh´blue cat®sh F1 hybrids (channel cat®sh female´blue cat®sh male; blue cat®sh female´channel cat®sh male) produced identical AFLP pro®les. The AFLP markers were inherited and segregated in expected Mendelian ratios. At two loci, E8-b9 and E8-b2, markers were found at sig-ni®cantly lower frequencies than expected with F2 and backcross hybrids which had been selected for increased growth rates. The reproducibility of AFLP was excellent. These characteristics of the cat®sh AFLP markers make them highly useful for genetic analysis of cat®sh, especially for construction of genetic linkage and quantitative trait loci maps, and for marker-assisted selection.

Research paper thumbnail of Influence of Environmental Salinity on Messenger RNA Levels of Growth Hormone, Prolactin, and Somatolactin in Pituitary of the Channel Catfish (Ictalurus punctatus)

Marine Biotechnology, 2001

Pituitary growth hormone (GH), prolactin (PRL), and somatolactin (SL) messenger RNA levels in cha... more Pituitary growth hormone (GH), prolactin (PRL), and somatolactin (SL) messenger RNA levels in channel catfish (Ictalurus punctatus) were examined under various environmental and physiological conditions. Catfish were sampled following salinity challenge, during the winter (December) and spring or summer (April or July), and at different sizes (15-18 g, 620-664 g, and 956-1134 g). When catfish (956-1134 g) were transferred from freshwater to saline water containing 8 ppt NaCl, their plasma [Na(+)] increased significantly above values in the freshwater control group until they were transferred back to freshwater. Pituitary GH mRNA levels were low for the first 24 hours following transfer to saline water, but thereafter were significantly elevated above control values until the fish were transferred back to freshwater. Pituitary GH mRNA levels were highest in July and lowest in December. Growth hormone mRNA levels were also elevated in the size groups 15-18 g and 956-1134 g in July when compared with December values. Pituitary PRL mRNA levels increased for the first 24 hours following transfer to saline water (956-1134 g), but thereafter were significantly lower than control values until the fish were transferred back to freshwater. Pituitary PRL mRNA levels were highest in April and July and lowest in December, and were also elevated in the size groups 620-664 g and 956-1134 g. Pituitary SL mRNA levels were unaffected in catfish transferred to saline water; however, levels were significantly elevated in catfish of the 956-1134-g size group sampled in April when compared with December. These results suggest the involvement of GH in adaptation to brackish water and of PRL in adaptation to freshwater in the catfish, and seasonal and size-related differences in pituitary GH, PRL, and SL mRNA levels.

Research paper thumbnail of Molecular characterization and differential expression of the myostatin gene in channel catfish (Ictalurus punctatus)

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 2002

ABSTRACT Myostatin is a recently discovered gene that inhibits muscle growth. In the present stud... more ABSTRACT Myostatin is a recently discovered gene that inhibits muscle growth. In the present study, we characterized the myostatin locus and its expression in channel catfish (Ictalurus punctatus). The genomic DNA and cDNA encoding the channel catfish myostatin were cloned and sequenced. The myostatin gene has three exons encoding a protein of 389 amino acids. Comparison of the genomic sequences with those of the cDNA revealed that the myostatin cDNA was 1673 base pair (bp) long with a 5&#39;-untranslated region (UTR) and 3&#39;-UTR of 180 and 323 bp, respectively. The deduced amino acid sequences of the catfish myostatin is highly conserved with those of other organisms. The myostatin locus is highly polymorphic in channel catfish because of the presence of several microsatellites and single nucleotide polymorphic sites. The myostatin gene was expressed in various tissues and developmental stages at differential levels, suggesting complex regulation of this gene and perhaps roles for myostatin in addition to those originally suggested.

Research paper thumbnail of Diet fed to brood stock effects the growth of channel catfish (Ictalurus punctatus L) fry

Aquaculture Research, 2011

Research paper thumbnail of Economics of production of channel catfish,ictalurus punctatus,female x blue catfish,I.furcatus,male hybrid fingerlings and foodfish

Aquaculture Economics & Management, 2004

Tie profitability of the channel-blue hybrid catfish fingerlings and foodfish was compared to tha... more Tie profitability of the channel-blue hybrid catfish fingerlings and foodfish was compared to that of the channel catfish using enterprise budgets and sensitivity analyses. Average total costs of production were 15.0-22.5 per cent less for hybrids fingerlings, even if hybrid fry were bought at a price twice as high as that for channel catfish.