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At least 19 recordsLinked to original sources
USGS2020

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Yellow perch, Perca flavescens , is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene ( amhr2by ) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males ( amhr2by + ) from XX genetic females ( amhr2by − ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

Molecular Ecology Resources↗
USGS2010

Perspectives: Gene Expression in Fisheries Management

Functional genes and gene expression have been connected to physiological traits linked to effective production and broodstock selection in aquaculture, selective implications of commercial fish harvest, and adaptive changes reflected in non-commercial fish populations subject to human disturbance and climate change. Gene mapping using single nucleotide polymorphisms (SNPs) to identify functional genes, gene expression (analogue microarrays and real-time PCR), and digital sequencing technologies looking at RNA transcripts present new concepts and opportunities in support of effective and sustainable fisheries. Genomic tools have been rapidly growing in aquaculture research addressing aspects of fish health, toxicology, and early development. Genomic technologies linking effects in functional genes involved in growth, maturation and life history development have been tied to selection resulting from harvest practices. Incorporating new and ever-increasing knowledge of fish genomes is opening a different perspective on local adaptation that will prove invaluable in wild fish conservation and management. Conservation of fish stocks is rapidly incorporating research on critical adaptive responses directed at the effects of human disturbance and climate change through gene expression studies. Genomic studies of fish populations can be generally grouped into three broad categories: 1) evolutionary genomics and biodiversity; 2) adaptive physiological responses to a changing environment; and 3) adaptive behavioral genomics and life history diversity. We review current genomic research in fisheries focusing on those that use microarrays to explore differences in gene expression among phenotypes and within or across populations, information that is critically important to the conservation of fish and their relationship to humans.

Current Zoology↗
USGS1993

Monitoring of the in-river migration of smolts from two groups of spring chinook salmon, Oncorhynchus tshawytscha (Walbaum), with different profiles of Renibacterium salmoninarum infection

Broodstock segregation based on the measurement of maternal Renibacterium salmoninarum infection levels by the enzyme-linked immunosorbent assay (ELISA) and the membrane filtration-fluorescent antibody technique (MF-FAT) was previously shown to affect the prevalence and levels of bacterial kidney disease (BKD) in progeny of chinook salmon, Oncorhynchus tshawytscha (Walbaum), during hatchery rearing. Subgroups of fish from that study were marked with passive integrated transponder (PIT) tags, and monitored by PIT-tag detectors during the first 342km of their migration to the Pacific Ocean. Differences in the recovery of tagged fish were significant ( P ≤ 0·01) at each detection point and became more pronounced as the fish moved downstream. Cumulative recoveries of fish from the low-BKD group and the high-BKD group, respectively, were 31% and 28% after 116km, 44% and 37% after 176km, and 51% and 42% after 342km. There were no apparent differences in the migration timing of the two groups to the first detection point. The data suggested that in-river survival was higher in the progeny group from parents that had low R. salmoninarum infection levels or tested negative for R. salmoninarum (low-BKD group) than in the group female parents with high infection levels (high-BKD group).

Aquaculture Research↗
USGS2014

Effectiveness of eugenol sedation to reduce the metabolic rates of cool and warm water fish at high loading densities

Effects of eugenol (AQUI-S ® 20E, 10% active eugenol) sedation on cool water, yellow perch Perca flavescens (Mitchill), and warm water, Nile tilapia Oreochromis niloticus L. fish metabolic rates were assessed. Both species were exposed to 0, 10, 20 and 30 mg L −1 eugenol using static respirometry. In 17°C water and loading densities of 60, 120 and 240 g L −1 , yellow perch controls (0 mg L −1 eugenol) had metabolic rates of 329.6–400.0 mg O 2 kg −1 h −1 , while yellow perch exposed to 20 and 30 mg L −1 eugenol had significantly reduced metabolic rates of 258.4–325.6 and 189.1–271.0 mg O 2 kg −1 h −1 respectively. Nile tilapia exposed to 30 mg L −1 eugenol had a significantly reduced metabolic rate (424.5 ± 42.3 mg O 2 kg −1 h −1 ) relative to the 0 mg L −1 eugenol control (546.6 ± 53.5 mg O 2 kg −1 h −1 ) at a loading density of 120 g L −1 in 22°C water. No significant differences in metabolic rates for Nile tilapia were found at 240 or 360 g L −1 loading densities when exposed to eugenol. Results suggest that eugenol sedation may benefit yellow perch welfare at high densities (e.g. live transport) due to a reduction in metabolic rates, while further research is needed to assess the benefits of eugenol sedation on Nile tilapia at high loading densities.

Aquaculture Research↗
USGS2013

Depletion of florfenicol amine in tilapia (Oreochromis sp.) maintained in a recirculating aquaculture system following Aquaflor®-medicated feed therapy

Aquaflor ® [50% w w −1 florfenicol (FFC)], is approved for use in freshwater‐reared warmwater finfish which include tilapia Oreochromis spp. in the United States to control mortality from Streptococcus iniae . The depletion of florfenicol amine (FFA), the marker residue of FFC, was evaluated after feeding FFC‐medicated feed to deliver a nominal 20 mg FFC kg −1 BW d −1 dose (1.33× the label use of 15 mg FFC kg −1 BW d −1 ) to Nile tilapia O. niloticus and hybrid tilapia O. niloticus × O. aureus held in a recirculating aquaculture system (RAS) at production‐scale holding densities. Florfenicol amine concentrations were determined in fillets taken from 10 fish before dosing and from 20 fish at nine time points after dosing (from 1 to 240 h post‐dosing). Water samples were assayed for FFC before, during and after the dosing period. Parameters monitored included daily feed consumption and biofilter function (levels of ammonia, nitrite and nitrate). Mean fillet FFA concentration decreased from 13.77 μg g −1 at 1‐h post dosing to 0.39 μg g −1 at 240‐h post dosing. Water FFC concentration decreased from a maximum of 1400 ng mL −1 at 1 day post‐dosing to 847 ng mL −1 at 240 h post‐dosing. There were no adverse effects noted on fish, feed consumption or biofilter function associated with FFC‐medicated feed administration to tilapia.

Aquaculture Research↗
USGS2017

The effects of swimming exercise and dissolved oxygen on growth performance, fin condition and precocious maturation of early-rearing Atlantic salmon Salmo salar

Swimming exercise, typically measured in body-lengths per second (BL/s), and dissolved oxygen (DO), are important environmental variables in fish culture. While there is an obvious physiological association between these two parameters, their interaction has not been adequately studied in Atlantic salmon Salmo salar . Because exercise and DO are variables that can be easily manipulated in modern aquaculture systems, we sought to assess the impact of these parameters, alone and in combination, on the performance, health and welfare of juvenile Atlantic salmon. In our study, Atlantic salmon fry were stocked into 12 circular 0.5 m 3 tanks in a flow-through system and exposed to either high (1.5–2 BL/s) or low (<0.5 BL/s) swimming speeding and high (100% saturation) or low (70% saturation) DO while being raised from 10 g to approximately 350 g in weight. Throughout the study period, we assessed the impacts of exercise and DO concentration on growth, feed conversion, survival and fin condition. By study's end, both increased swimming speed and higher DO were independently associated with a statistically significant increase in growth performance ( p < .05); however, no significant differences were noted in survival and feed conversion. Caudal fin damage was associated with low DO, while right pectoral fin damage was associated with higher swimming speed. Finally, precocious male sexual maturation was associated with low swimming speed. These results suggest that providing exercise and dissolved oxygen at saturation during Atlantic salmon early rearing can result in improved growth performance and a lower incidence of precocious parr.

Aquaculture Research↗
USGS2018

Effects of formaldehyde on nitrification in biofilters of small‐scale recirculating systems

Florfenicol (Aquaflor®) is the only U.S. Food and Drug Administration (FDA) approved drug for treating diseased fish reared in recirculating aquaculture systems (RAS). Treating diseased fish in RAS is challenging because of the potential to damage nitrifying bacteria in the biofilters. Impaired nitrification can lead to concentrations of ammonia and nitrite that compromise fish welfare. The objective of this study was to determine the effects of a FDA‐approved parasiticide and fungicide, Parasite‐S ® (formalin), on biofilter nitrification. Stable biofilters were exposed once to 0, 9.25, 18.5, 37, or 55.5 mg/L formaldehyde. Total ammonia nitrogen (TAN) and nitrite nitrogen were monitored daily before and throughout the study to quantify biofilter function. Formaldehyde concentrations ≥37 mg/L increased TAN and nitrite nitrogen concentrations, and nitrification did not recover to pre‐exposure concentrations up to 8 day postexposure. On the basis of those results, a second trial was conducted. Stable biofilters were exposed once or on four consecutive days to 9.25 or 18.5 mg/L formaldehyde. Biofilters repeatedly exposed to formaldehyde showed signs of impairment and had variable recovery relative to single exposures. Results of this study may help identify formaldehyde concentrations that can be safely applied to RAS when treating diseased fish.

Aquaculture Research↗
USGS2022

Effects of formaldehyde (Parasite-S®) on biofilter nitrification from a cold- and a warm freshwater RAS

The effect of Parasite-S® (an aqueous formaldehyde solution) on the nitrification processes of biofilters was evaluated in two recirculating aquaculture systems (RASs). Rearing tanks in the warmwater RAS contained yellow perch ( Perca flavescens ) and grass carp ( Ctenopharyngodon idella ) with an initial weight of 166.8 kg and a mean density of 39.5 kg/m 3 . Rearing tanks in the coldwater RAS contained rainbow trout ( Oncorhynchus mykiss ) and lake trout ( Salvelinus namaycush ) with an initial weight of 1377.8 kg at a system density of 41.9 kg/m 3 . Parasite-S® was administered to the entire system on four consecutive days in both trials to achieve a nominal concentration of 14.8 mg/L formaldehyde (40 mg/L formalin) at the biofilter. Removal efficiencies for total ammonia nitrogen (TAN) and nitrite nitrogen were measured as indicators of biofilter nitrification processes. The active ingredient in Parasite-S®, formaldehyde, was measured until it was below the method detection limit of 0.8 mg/L. TAN volumetric removal rate was significantly decreased in both systems after formaldehyde addition and remained below pre-exposure efficiency in the coldwater RAS. Nitrite nitrogen volumetric removal rate was not significantly different, but the slope and intercepts were less after formaldehyde addition indicating an effect on the nitrifying bacteria. Although removal rates were decreased, no mortality occurred after four consecutive formaldehyde indefinite bath exposures in either system.

Aquaculture Research↗
USGS2008

Effects of selenium dietary enhancement on hatchery-reared coho salmon, Oncorhynchus kisutch (Walbaum), when compared with wild coho: hepatic enzymes and seawater adaptation evaluated.

Hatchery-reared coho salmon, Oncorhynchus kisutch (Walbaum), were fed elevated levels of selenium (as Na 2 SeO 3 ) to raise eviscerated body burdens to the level measured in wild counterparts. The goal was to find a dietary concentration that would achieve the desired effect without causing damage to growth and normal development. To measure some indices of health, the detoxifying enzymes chosen were hepatic glutathione peroxidase (GSH-Px) and hepatic superoxide dismutase (SOD). Eviscerated body selenium (Se) concentration, GSH-Px and SOD levels were measured during and at the end of the 9 month freshwater feeding trial. Selenium retention and enzyme activity were also measured during 6 months’residence in sea water (SW). Selenium supplements were added to a commercial ration to give final concentrations of 1.1, 8.6, 11.1, 13.6 μg g -1 Se in the four respective diets. The results indicated that a dietary concentration of 8.6 μg g -1 selenium was capable of inducing eviscerated body burdens similar to those found in wild fish. The elevated selenium levels persisted throughout the freshwater (FW) rearing phase, but declined when the fish were fed an unsupplemented ration upon SW entry. Superoxide dismutase levels did not increase above control levels. Glutathione peroxidase levels increased in fish fed the supplemented diets. GSH-Px activity declined in the higher supplemented dietary groups when all groups were reduced to the control group level of 1.1 μg g -1 . Cumulative mortality in SW was 20% in fish fed either the 1.1 or the 8.6 μg g -1 Se diets. The 8.6 μg g -1 Se supplemented diets did produce healthy coho, comparable to their wild counterparts.

Aquaculture Research↗
USGS2006

Effects of ascorbic acid enrichment by immersion of rainbow trout (Oncorhynchus mykiss, Walbaum 1792) eggs and embryos

This study was conducted to examine the effects of different forms and concentrations of ascorbic acid (vitamin C), and different enrichment times (24 and 48 h post ovulation) on egg, embryo and alevin ascorbate concentrations and survival of rainbow trout (enrichment was at the ova stage). In experiments 1 and 2, fertilized eggs were immersed in water containing ascorbate at 0 (control), 100, 1000 mg L-1 l-ascorbic acid (AA) and 2000 mg L -1 l-ascorbyl monophosphate (AP). In experiment 3, 0 (control), 500 and 1000 mg L-1 AA neutralized (N) with NaOH, 1000 mg L-1 AA non-neutralized (NN), 1000 and 2000 mg L-1 AP immersions were used. The mean total ascorbic acid (TAA) and dehydroascorbic acid (DHA) concentrations were measured before fertilization, at 3 and 24 h after fertilization, at the eyed stage, and in hatched alevins. We observed significant differences in TAA concentration at different immersion levels at 3 and 24 h after fertilization. Survival decreased significantly depending on the level of vitamin C, pH of the solutions and immersion time. We suggest that when broodstock rainbow trout do not have enough vitamin C in their ovaries, immersion of eggs in 1000 mg L-1 of neutralized AA may be useful. ?? 2006 Blackwell Publishing Ltd.

Aquaculture Research↗
USGS2024

Evaluation of larval sea lamprey Petromyzon marinus growth in the laboratory: Influence of temperature and diet

Conservation aquaculture provides a means for promoting environmental stewardship, useful both in the context of restoring native species and limiting the production of invasive species. Aquaculture of lampreys is a relatively recent endeavor aimed primarily at producing animals to support the restoration of declining native populations. However, in the Laurentian Great Lakes, where sea lamprey Petromyzon marinus are invasive, the ability to acquire a reliable source of certain life stages would be a significant benefit to those controlling their populations and studying the species. Here, we apply methodologies developed for Pacific lamprey Entosphenus tridentatus restoration to investigate the feasibility of rearing larval sea lamprey under laboratory conditions. In two experiments lasting 3 and 9 months, we tested the effects of different dietary sources and water temperature (ambient and controlled) on the survival and growth of wild-caught larvae. Rearing conditions had no effect on mortality, as larval survival was 100% in both experiments. Growth was significantly affected by water temperature, with the highest average daily growth rates observed at 22 and 15°C (0.14 mm day −1 ) and lowest at 8°C (0.06 mm day −1 ). Diets of yeast alone (0.19 and 0.21 g L −1 ) performed better than those comprising a mixture of yeast and other material when fed 3 times weekly (rice flour, wheat flour, fish meal; 0.19 and 0.32 g L −1 ). Averaged across the three constant temperatures (8, 15, and 22°C), larvae fed on yeast grew 0.13 mm day −1 and 0.01 g day −1 , whereas on yeast + fish meal, they grew 0.09 mm day −1 and 0.01 g day −1 . At ambient temperature (4–20°C), larvae fed on yeast grew 0.15 mm day −1 and 0.01 g day −1 , whereas those fed on yeast + wheat flour grew 0.13 mm day −1 and 0.008 g day −1 and those fed on yeast + rice flour grew 0.12 mm day −1 and 0.009 g day −1 . An experimental duration of 90 days was sufficient to detect significant changes to larval sea lamprey growth stemming from temperature variation. Overall, rearing of sea lamprey in captivity appears feasible at low density (31–32 g m −2 and 17–25 larvae m −2 ), but uncertainties remain regarding the most appropriate means of providing adequate feed for these fish in high-density conditions.

Aquaculture Research↗
USGS2012

Assessing consumption of bioactive micro-particles by filter-feeding Asian carp

Silver carp Hypophthalmichthys molitrix (SVC) and bighead carp H. nobilis (BHC) have impacted waters in the US since their escape. Current chemical controls for aquatic nuisance species are non-selective. Development of a bioactive micro-particle that exploits filter-feeding habits of SVC or BHC could result in a new control tool. It is not fully understood if SVC or BHC will consume bioactive micro-particles. Two discrete trials were performed to: 1) evaluate if SVC and BHC consume the candidate micro-particle formulation; 2) determine what size they consume; 3) establish methods to evaluate consumption of filter-feeders for future experiments. Both SVC and BHC were exposed to small (50-100 μm) and large (150-200 μm) micro-particles in two 24-h trials. Particles in water were counted electronically and manually (microscopy). Particles on gill rakers were counted manually and intestinal tracts inspected for the presence of micro-particles. In Trial 1, both manual and electronic count data confirmed reductions of both size particles; SVC appeared to remove more small particles than large; more BHC consumed particles; SVC had fewer overall particles in their gill rakers than BHC. In Trial 2, electronic counts confirmed reductions of both size particles; both SVC and BHC consumed particles, yet more SVC consumed micro-particles compared to BHC. Of the fish that ate micro-particles, SVC consumed more than BHC. It is recommended to use multiple metrics to assess consumption of candidate micro-particles by filter-feeders when attempting to distinguish differential particle consumption. This study has implications for developing micro-particles for species-specific delivery of bioactive controls to help fisheries, provides some methods for further experiments with bioactive micro-particles, and may also have applications in aquaculture.

Journal of Aquaculture Research & Development↗
USGS2020

The effects of swimming exercise and dissolved oxygen on growth performance, fin condition and survival of rainbow trout Oncorhynchus mykiss

Swimming exercise and dissolved oxygen (DO) are important parameters to consider when operating intensive salmonid aquaculture facilities. While previous research has focused on each of these two variables in rainbow trout Oncorhynchus mykiss , studies examining both variables in combination, and their potential interaction, are absent from the scientific literature. Both swimming exercise (usually measured in body lengths per second, or BL/s) and DO can be readily controlled in modern aquaculture systems; therefore, we sought to evaluate the effects of these variables, separately and combined, on several outcomes in rainbow trout including growth performance, fin health and survival. Rainbow trout fry (18 g) were stocked into 12 circular 0.5 m 3 tanks, provided with either high (1.5–2 BL/s) or low (approximately 0.5 BL/s) swimming exercise and high (100% saturation) or low (70% saturation) DO, and grown to approximately 1 kg. By the conclusion of the study, higher DO was independently associated with significantly ( p < .05) increased growth performance. Significant differences were not noted in other outcomes, namely feed conversion, condition factor and mortality, although caudal and right pectoral fin damage was associated with low oxygen and low swimming exercise treatments respectively. Cardiosomatic index was significantly higher among exercised fish. These results suggest that swimming exercise and DO at saturation during the culture of rainbow trout can be beneficial to producers through improved growth performance and cardiac health.

Aquaculture Research↗
USGS2021

International importance of Percids: Summary and looking forward

Research presented in the preceding chapters emphasizes recent advancements in the research, management, and aquaculture of Walleye, Sauger, and Yellow Perch in North America. These percid fishes, along with the European Perch and Pikeperch, are economically and ecologically important fishes in their native geographic range. Advances in techniques to evaluate current habitat and predict future habitat conditions provide managers with detailed baseline information and biophysical models useful for evaluating adaptive management practices. Current habitat use and movement assessments have improved substantially with technological advancements in acoustic tags and extensive receiver array networks, which, combined with genetic and genomic tools, are improving percid stock assessments and management. Advances in percid aquaculture techniques have improved growth, survival, and disease resistance, enhancing percid stocking efforts and the production of marketable fish. The exchange of information between researchers and managers will continue to advance techniques of percid management for commercial and recreational exploitation and improve aquaculture practices to provide a lucrative commercial aquaculture industry.

Book chapter↗