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Shrimp from three major exporting countries – India, Vietnam, and Thailand – were identified to country of origin by elemental profiling. Concentrations of 23 elements, including essential macro- and micro-nutrients and non-essential trace elements, in headless shell on shrimp (HLSO) samples were analyzed by ICP-AES. Elemental concentrations in shrimp showed high variation. Multivariate statistics including principal component analysis, stepwise discriminant analysis, Kernel method, and canonical discriminant analysis demonstrated the validity of elemental profiling in distinguishing aquacultured shrimp from different countries. However, it was not possible to reach definitive conclusions about which elements are the best descriptors for each region. The method was also tested as a means of differentiating shrimp produced to area of origin for two areas in Thailand, three provinces in Vietnam and India. All the multivariate statistical analysis demonstrated that the separation on a smaller scale was not as reliable as on the country scale.

The rising atmospheric carbon dioxide (CO2) concentration is increasing the solubility of limestone, calcium silicate, and feldspars, resulting in greater total alkalinity concentration in inland waters. This phenomenon will result in inland waters having slightly greater alkalinity concentration (and buffering capacity), higher pH when at equilibrium with atmospheric CO2, and more available carbon for photosynthesis. However, the changes in water quality will be small. Fluctuations in CO2 concentration resulting from CO2 use in photosynthesis by aquatic plants and release of CO2 by respiration, acidity resulting from nitrification of ammonia nitrogen from feeding waste and fertilizer, and application of liming materials to ponds will continue to be the dominant factors affecting pH and alkalinity in waters of inland aquaculture systems.

Annual treatment of a water supply reservoir with agricultural limestone at the E. W. Shell Fisheries Center at Auburn University has roughly doubled conductivity and concentrations of total alkalinity, total hardness, and calcium hardness in the discharge water. It also has prevented pH values below 6.7. Concentrations of water quality variables decreased following some large rainfall events and during periods of prolonged rainfall. Calcium hardness concentrations were sometimes lower than recommended for hatchery water supplies intended for Channel Catfish Ictalurus punctatus. Nevertheless, liming has improved the quality of the reservoir discharge for use in both the hatchery and research ponds at the station.Received December 3, 2015; accepted May 9, 2016

The accuracy and precision of different methods for detecting the endpoint of the total alkalinity titration and the typical accuracy and precision obtained for alkalinity analyses by a large sample of laboratories were investigated. The optimum, endpoint for total alkalinity titrations decreased from pH 5.0 at 10 mg l − 1 alkalinity to pH 4.2 for 300 mg l − 1 alkalinity or more. The appropriate color changes for bromocresol green-methyl red (BG-MR) and methyl orange (MO) indicators also varied with the initial total alkalinity of samples. Despite differences in pHs at endpoints for samples of different alkalinities, when the best endpoint pH, best color of BG-MR and MO, or the endpoint of methyl purple were used in titrations of standard solutions, there were few differences between measured alkalinities and standard alkalinities — the accuracy was better than ± 3 mg l − 1 . Results of spike and recovery tests on aquaculture pond water samples also revealed that an accuracy of ± 3 mg l − 1 alkalinity could be achieved on either unfiltered or filtered samples by all four methods of acceptable endpoint detection. Although precision of measurements could not be consistently maintained below ± 1 mg l − 1 , coefficients of variation for repeated measurements usually were less than 3% for all methods of endpoint detection. Nevertheless, this degree of precision was adequate to achieve good accuracy that is the major concern in water analysis. Variations in alkalinity measurement that could result from improper selection of endpoint pH (or color) were rather small — usually not more than ± 5 mg l − 1 . In an interlaboratory comparison of alkalinity determinations on standard solutions, most laboratories reported inaccurate alkalinities. These inaccuracies were greater than possible endpoint variations. The most likely sources of error contributing to poor results by the different laboratories were improperly standardized acid for alkalinity titrations, reliance on burets or other titrating devices with coarse calibrations, and use of excessively small sample volumes. Moreover, it was clear that most of the participating laboratories did not have a satisfactory method of quality control. Statement of relevance Alkalinity is important as a source of carbon for photosynthesis, as a buffer, and as a general index of productivity. Thus, it is often measured, but by several different methods of endpoint detection. This study provides useful information of the reliability of alkalinity analyses and recommends how to maintain acceptable precision and accuracy of the procedure.

Total alkalinity and total hardness are familiar variables in aquatic animal production. Aquaculturists—both scientists and practitioners alike—have some understanding of the two variables and of methods for adjusting their concentrations. The chemistry and the biological effects of alkalinity and hardness, however, are more complex than generally realized or depicted in the aquaculture literature. Moreover, the discussions of alkalinity and hardness—alkalinity in particular—found in water chemistry texts are presented in a rigorous manner and without explanation of how the two variables relate to aquaculture. This review provides a thorough but less rigorous discussion of alkalinity and hardness specifically oriented toward aquaculture. Alkalinity and hardness are defined, their sources identified, and analytical methods explained. This is followed by a discussion of the roles of the two variables in aquaculture, including their relationships with carbon dioxide, pH, atmospheric pollution, ammonia, and other inorganic nitrogen compounds, phytoplankton communities, trace metals, animal physiology, and clay turbidity. Liming and other practices to manage alkalinity and hardness are explained. Changes in alkalinity and hardness concentrations that occur over time in aquaculture systems are discussed. Emphasis is placed on interactions among alkalinity, hardness, water quality, and aquacultural production.

Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ∼52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds.

To apply genome-based technologies for genetic improvements using marker-assisted selection, genome research involving genetic linkage mapping and physical mapping is required, and integration of genetic and linkage maps would significantly enhance the capacities for genome research. In catfish, the major aquaculture species in the United States, linkage and physical maps have been constructed. However, integration of genetic linkage and physical maps demands large-scale, genome-wide hybridizations, or genetic mapping of polymorphic markers derived from bacterial artificial chromosome (BAC) clones whose locations are known from the physical map. In this work, we identified a large number of microsatellites from BAC end sequences of channel catfish, characterized the microsatellites, tested their utility for linkage mapping in a resource family used for genetic mapping, and constructed a web-searchable database for BAC end sequences, their linked microsatellites, microsatellite primers, PCR conditions, and polymorphic information. A total of 3652 microsatellites in 2744 distinct BACs were identified. Of these, 1100 had sufficient and complex flanking sequences for PCR primer design. We have tested 500 primer pairs and found 211 (42.2%) were polymorphic and segregating in the resource family used for genetic mapping. These microsatellites represent a major fraction of co-dominant polymorphic markers identified to date in catfish, and should be a valuable resource for genetic mapping to increase linkage map resolution, and for integration of genetic linkage and physical maps.

The acute nature of disease outbreaks in aquaculture settings has served to emphasize the importance of the innate immune response of fish for survival and led to the recent identification and characterization of many of its components. Catfish, the predominant aquaculture species in the United States, is an important model for the study of the teleost immune system. However, transcriptomic-level studies of disease-related gene expression in catfish have only recently been initiated, and understanding of immune responses to pathogen infections is limited. Here, we have developed and utilized a 28K in situ oligonucleotide microarray composed of blue catfish (Ictalurus furcatus) and channel catfish (Ictalurus punctatus) transcripts. While channel catfish accounts for the majority of commercial production, the closely related blue catfish possesses several economically important phenotypic traits. Microarray analysis of gene expression changes in blue catfish liver after infection with Gram-negative bacterium Edwardsiella ictaluri indicated the strong upregulation of several pathways involved in the inflammatory immune response and potentially in innate disease resistance. A multifaceted response to infection could be observed, encompassing the complement cascade, iron regulation, inflammatory cell signaling, and antigen processing and presentation. The induction of several components of the MHC class I-related pathway following infection with an intracellular bacterium is reported here for the first time in fish. A comparison with previously published expression profiles in the channel catfish liver was also made and the microarray results extended by use of quantitative RT-PCR. Our results add to the understanding of the teleost immune responses and provide a solid foundation for future functional characterization, genetic mapping, and QTL analysis of immunity-related genes from catfish.

The acute phase response (APR) is a set of metabolic and physiological reactions occurring in the host in response to tissue infection or injury and is a crucial component of the larger innate immune response. The APR is best characterized by dramatic changes in the concentration of a group of plasma proteins known as acute phase proteins (APPs) which are synthesized in the liver and function in a wide range of immunity-related activities. Utilizing a new high-density in situ oligonucleotide microarray, we have evaluated the APR in channel catfish liver following infection with Edwardsiella ictaluri, a bacterial pathogen that causes enteric septicemia of catfish. Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely related blue catfish. The analysis of microarray results using a traditional 2-fold change in gene expression cutoff and a 10% false-discovery rate revealed a well-developed APR in catfish, with particularly high upregulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin). Other classical APP genes upregulated greater than 2-fold included coagulation factors, proteinase inhibitors, transport proteins, and complement components. Upregulation of the majority of the complement cascade was observed including the membrane attack complex components and complement inhibitors. A number of pathogen recognition receptors (PRRs) and chemokines were also differentially expressed in the liver following infection. Independent testing of a selection of differentially expressed genes with real-time RT-PCR confirmed microarray results.

Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize specific pathogen-associated molecular patterns and use conserved signaling pathways to activate proinflammatory cytokines and type-1 interferons to fight infection. TLR3 in mammals is best known for its recognition of dsRNA as ligand and its MyD88-independent signaling. TLR3, upon recognition of dsRNA, recruits and binds its adaptor protein TIR domain-containing adapter molecule (TICAM) 1. Here we report the genomic sequences and structures of TLR3 and a TICAM adaptor from channel catfish (Ictalurus punctatus). Whereas a partial TLR3 cDNA sequence has been reported from channel catfish, and complete TLR3 genes are known from other teleost fish species, a complete TICAM sequence has not been previously reported from a nonmammalian species. Analysis of catfish TLR3 and TICAM expression after infection with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC), suggested a conserved TLR3-TICAM receptor-adaptor relation in catfish. Comparison of TLR3 and TICAM expression profiles in channel catfish with those from the closely related blue catfish species (Ictalurus furcatus), which exhibits strong resistance to ESC, revealed a striking pattern of species-specific expression. A dramatic downregulation of TLR3 and TICAM gene expression was observed in blue catfish head kidney and spleen, which we speculate may be the result of maturation and migration of different cell types to and from the lymphoid tissues following infection.

Summary In the present study, 25 195 BAC ends for channel catfish (Ictalurus punctatus) were sequenced, generating 20 366 clean BAC-end sequences (BES), with an average read length of 557 bp after trimming. A total of 11 414 601 bp were generated, representing approximately 1.2% of the catfish genome. Based on this survey, the catfish genome was found to be highly AT-rich, with 60.7% A+T and 39.3% G+C. Approximately 12% of the catfish genome consisted of dispersed repetitive elements, with the Tc1/mariner transposons making up the largest percentage by base pair (4.57%). Microsatellites were detected in 17.5% of BES. Catfish BACs were anchored to the zebrafish and Tetraodon genome sequences by BLASTN, generating 16% and 8.2% significant hits (E

Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of 43,000 BAC end sequences and their applications for comparative genome analysis in catfish. Using these and the additional 20,000 existing BAC end sequences as a resource along with linkage mapping and existing physical map, conserved syntenic regions were identified between the catfish and zebrafish genomes. A total of 10,943 catfish BAC end sequences (17.3%) had significant BLAST hits to the zebrafish genome (cutoff value ≤ e-5), of which 3,221 were unique gene hits, providing a platform for comparative mapping based on locations of these genes in catfish and zebrafish. Genetic linkage mapping of microsatellites associated with contigs allowed identification of large conserved genomic segments and construction of super scaffolds. Conclusion BAC end sequences and their associated polymorphic markers are great resources for comparative genome analysis in catfish. Highly conserved chromosomal regions were identified to exist between catfish and zebrafish. However, it appears that the level of conservation at local genomic regions are high while a high level of chromosomal shuffling and rearrangements exist between catfish and zebrafish genomes. Orthologous regions established through comparative analysis should facilitate both structural and functional genome analysis in catfish.

A genetic linkage map of the channel catfish genome (N = 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3–18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.

BackgroundSNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large resource of ESTs is to become available in catfish allowing identification of large number of SNPs, but reliability of EST-derived SNPs are relatively low because of sequencing errors. This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs.Resultswo factors were found to be most significant for validation of EST-derived SNPs: the contig size (number of sequences in the contig) and the minor allele sequence frequency. The larger the contigs were, the greater the validation rate although the validation rate was reasonably high when the contigs contain four or more EST sequences with the minor allele sequence being represented at least twice in the contigs. Sequence quality surrounding the SNP under test is also crucially important. PCR extension appeared to be limited to a very short distance, prohibiting successful genotyping when an intron was present, a surprising finding.ConclusionStringent quality assessment measures should be used when working with EST-derived SNPs. In particular, contigs containing four or more ESTs should be used and the minor allele sequence should be represented at least twice. Genotyping primers should be designed from a single exon, completely avoiding introns. Application of such quality assessment measures, along with large resources of ESTs, should provide effective means for SNP identification in species where genome sequence resources are lacking.

Background EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish. Results A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing. Conclusion The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.

Twelve cDNA libraries from two species of catfish have been sequenced, resulting in the generation of nearly 500,000 ESTs., Background Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.