Abernathy Fish Technology Center

Longview, WA, United States

Abernathy Fish Technology Center

Longview, WA, United States
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Eya J.C.,West Virginia State University | Yossa R.,West Virginia State University | Ashame M.F.,West Virginia State University | Pomeroy C.F.,West Virginia State University | Gannam A.L.,Abernathy Fish Technology Center
Journal of Fish Biology | Year: 2014

A 2×3 factorial study was conducted to evaluate the effects of dietary lipid level on mitochondrial gene expression in mixed sex rainbow trout Oncorhynchus mykiss. Practical diets with a fixed crude protein content of 42%, formulated to contain 10% (42/10), 20% (42/20) and 30% (42/30) dietary lipid, were fed to triplicate groups of either low-feed efficient (F129; mean±s.d.=105·67±3·04g initial average mass) or high-feed efficient (F134; mean±s.d.=97·86±4·02g) families of fish, to apparent satiety, twice per day, for 108 days. At the end of the experiment, diets 42/20 and 42/30 led to similar fish condition factors, which were higher than that observed with diet 42/10 (P<0·05). F134 fish fed diet 42/10 showed the highest hepato-somatic index, while there was no significant difference among all the other treatments (P<0·05). When the group of F134 fish fed diet 42/10 was used as the calibrator for gene expression analysis, the five genes selected for their involvement in lipid metabolism (complex I-nd1, complex III-cytb, complex IV-cox1, complex IV-cox2 and complex V-atp6) were up-regulated in the muscle and down-regulated in both the liver and the intestine. There was a significant family×diet interaction regarding nd1, cox2 and atp6 in the liver; nd1, cytb, cox1, cox2 and atp6 in the intestine, and nd1, cytb, cox1, cox2 and atp6 in the muscle (P<0·05). The overall results of this study constitute basic information for the understanding of molecular mechanisms of lipid metabolism at the mitochondrial level in fishes. © 2014 The Fisheries Society of the British Isles.


Eya J.C.,West Virginia State University | Ukwuaba V.O.,West Virginia State University | Yossa R.,West Virginia State University | Gannam A.L.,Abernathy Fish Technology Center
International Journal of Molecular Sciences | Year: 2015

A 2 × 3 factorial study was conducted to evaluate the effects of dietary lipid level on the expression of mitochondrial and nuclear genes involved in electron transport chain in all-female rainbow trout Oncorhynchus mykiss. Three practical diets with a fixed crude protein content of 40%, formulated to contain 10% (40/10), 20% (40/20) and 30% (40/30) dietary lipid, were fed to apparent satiety to triplicate groups of either low-feed efficient (F120; 217.66 ± 2.24 g initial average mass) or high-feed efficient (F136; 205.47 ± 1.27 g) full-sib families of fish, twice per day, for 90 days. At the end of the experiment, the results showed that there is an interactive effect of the dietary lipid levels and the phenotypic feed efficiency (growth rate and feed efficiency) on the expression of the mitochondrial genes nd1 (NADH dehydrogenase subunit 1), cytb (Cytochrome b), cox1 (Cytochrome c oxidase subunits 1), cox2 (Cytochrome c oxidase subunits 2) and atp6 (ATP synthase subunit 6) and nuclear genes ucp2α (uncoupling proteins 2 alpha), ucp2β (uncoupling proteins 2 beta), pparα (peroxisome proliferator-activated receptor alpha), pparβ (peroxisome proliferatoractivated receptor beta) and ppargc1α (proliferator-activated receptor gamma coactivator 1 alpha) in fish liver, intestine and muscle, except on ppargc1α in the muscle which was affected by the diet and the family separately. Also, the results revealed that the expression of mitochondrial genes is associated with that of nuclear genes involved in electron transport chain in fish liver, intestine and muscle. Furthermore, this work showed that the expression of mitochondrial genes parallels with the expression of genes encoding uncoupling proteins (UCP) in the liver and the intestine of rainbow trout. This study for the first time presents the molecular basis of the effects of dietary lipid level on mitochondrial and nuclear genes involved in mitochondrial electron transport chain in fish. © 2015 by the authors; licensee MDPI, Basel, Switzerland.


Bohling J.,Montpellier University | Bohling J.,Abernathy Fish Technology Center | Haffray P.,French National Institute for Agricultural Research | Berrebi P.,Montpellier University
Aquaculture | Year: 2016

Animals in captivity are subject to similar evolutionary forces that act on natural populations, which can facilitate the generation of population genetic structure. Understanding the extent of genetic differentiation among captive populations provides insights into industry practices and the domestication process. We investigated the genetic structure of domestic brown trout (Salmo trutta) in France by surveying fish collected from 20 fish farms. Using microsatellite markers, we calculated basic measures of genetic diversity and differentiation among these various farms. We also evaluated population structure using tree-based approaches, model-based clustering methods, and ordination techniques. Differences in genetic diversity reflected founding histories and source stocks among the fish farms. Fish farms that raise trout originating from Mediterranean watersheds had lower levels of genetic diversity and much higher divergence than populations of Atlantic origin. Stocks believed to originate from the common Atlantic-based trout strain demonstrated low-levels of population structure. We observed fish of mixed ancestry in some fish farms and the presence of multiple genetic stocks within the same facility. Our findings reveal patterns of genetic structure that reflect differences in founding practices and movement of individuals and strains between fish farms. Such findings have consequences for fisheries managers stocking natural ecosystems with captive-reared fish, biologists attempting to understand the interactions between wild and domestic brown trout, and fish farmers involved in stocking or restoration activities. © 2016.


Banks M.A.,Oregon State University | Jacobson D.P.,Oregon State University | Meusnier I.,Center for Biology and Management of Populations | Greig C.A.,University of Swansea | And 6 more authors.
Animal Genetics | Year: 2014

The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution. © 2014 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.


Eya J.C.,West Virginia State University | Yossa R.,West Virginia State University | Ashame M.F.,West Virginia State University | Pomeroy C.F.,West Virginia State University | Gannam A.L.,Abernathy Fish Technology Center
Aquaculture | Year: 2013

A 2. ×. 3 factorial study was conducted to investigate the effects of dietary lipid levels on growth, feed utilization and mitochondrial enzyme activities in juvenile all-female rainbow trout (Oncorhynchus mykiss). Practical diets with a fixed crude protein content of 42%, formulated to contain 10% (42/10), 20% (42/20) and 30% (42/30) dietary lipid, were fed to apparent satiety to triplicate groups of either low-feed efficient (low-FE, 105.67. ±. 3.04. g initial average mass) or high-feed efficient (high-FE, 97.86. ±. 4.02. g) families of fish, twice per day, for 108. days. At the end of the experiment, the group of fish fed diets 42/20 and 42/30 showed higher growth and feed efficiency (FE), coupled with a lower daily feed consumption (FC), than fish fed 42/10 diet, although similar results were found with diets 42/10 and 42/30 for growth (P. <. 0.05). With similar FC, the high-FE family showed higher growth, FE, protein efficiency ratio (PER) and protein productive value (PPV) than the low-FE family (P. <. 0.05). Fish fed diets 42/20 and 42/30 had the highest PER and PPV (P. <. 0.05). The lipid efficiency ratio was highest in fish from the high-FE family fed diet 42/10 (P. <. 0.05). Fish fed diet 42/30 showed the highest visceral fat and viscerosomatic index (P. <. 0.05). In the liver, the respiratory chain enzymatic activity was significantly affected by both diet and family for complexes I and IV, and by diet for complexes II, III and V (P. <. 0.05). In the intestine, significant family. ×. diet interaction effects were observed for complexes III and IV (P. <. 0.05). There were both significant family and diet main effects on complexes I and II, whereas complex V was only affected by family (P. <. 0.05). In the muscle, significant (P. <. 0.05) diet. ×. family interaction effects were observed for complexes II and IV activities; complex III activity was significantly affected by the diet, whereas complex V activity was affected by both the diet and the family main effects; the activity of complex I was not affected by the treatments (P. >. 0.05). The overall results of this study established that feeding a 42% CP diet with a minimum of 20% dietary lipid leads to high growth, feed utilization on the one hand, and that these zootechnical parameters are coupled with high mitochondrial enzymatic function in the liver, the intestine and the muscle of rainbow trout. Also, as it was expected, the high-FE family showed higher response to treatments than the low-FE family. © 2013.


Lesica P.,University of Montana | Adams B.,Abernathy Fish Technology Center | Smith C.T.,Abernathy Fish Technology Center
Conservation Genetics | Year: 2016

Protecting genetic diversity throughout the range of a species is important for conservation, as doing so provides for long-term evolutionary potential and persistence under a changing environment. Conservation of diversity at the intraspecific level requires identification of all genetically distinct population segments within species; i.e., conservation units (CUs). Silene spaldingii occurs in grasslands of the Columbia Plateau region of western North America and is listed as threatened under the Federal Endangered Species Act. The recovery plan identified five physiographic regions across the range of the species to use as surrogates for genetic CUs. We collected leaf samples from an average of 26 plants from each of 19 of the largest populations across all five physiographic regions and used variable microsatellite and chloroplast DNA markers to determine how genetic variation is distributed across the range of the species and how well physiographic regions reflect population structure within this species. Results of several multivariate analyses clustered our samples into four genetic groups which did not correspond well with the physiographic regions. We observed little genetic differentiation among populations in the main range of the species which encompasses nearly all of four contiguous physiographic regions. However, three other distinct genetic groups were identified: two in the disjunct northeast corner and one at the southeast edge of the main range. Modification of the CUs to reflect the genetic groups rather than the physiographic regions would result in CUs which better reflect historical patterns of population structure. Moreover, use of the genetic units to inform translocation and genetic rescue efforts could improve our ability to mimic natural patterns of gene flow. Our results suggest that physiographic regions may not always be an accurate reflection of population structure for threatened or endangered species. © 2016 Springer Science+Business Media Dordrecht


Moran P.,Fisheries Science Center | Teel D.J.,Fisheries Science Center | Banks M.A.,Oregon State University | Beacham T.D.,Canadian Department of Fisheries and Oceans | And 10 more authors.
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2013

The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution and phenotypic plasticity have obscured range-wide patterns of life-history segregation with evolutionary lineage, yet the idea of the lineages themselves persists. We employed a large, internationally standardized, microsatellite data set to explore population structure at coast-wide scale and test for two divergent lineages, whether or not related to life history. We found at least 27 distinct lineages. However, relationships among groups were poorly resolved - essentially a star phylogeny. We found pervasive isolation by distance among groups, complicating cluster analysis. Only in the interior Columbia River (east of the Cascade Mountains) is there a deep genetic bifurcation that supports both the two-lineage hypothesis and the life-history segregation hypothesis. This broad-scale perspective helps reconcile different views of Chinook salmon phylogeography and life-history distribution.


PubMed | Abernathy Fish Technology Center and West Virginia State University
Type: Journal Article | Journal: International journal of molecular sciences | Year: 2015

A 2 3 factorial study was conducted to evaluate the effects of dietary lipid level on the expression of mitochondrial and nuclear genes involved in electron transport chain in all-female rainbow trout Oncorhynchus mykiss. Three practical diets with a fixed crude protein content of 40%, formulated to contain 10% (40/10), 20% (40/20) and 30% (40/30) dietary lipid, were fed to apparent satiety to triplicate groups of either low-feed efficient (F120; 217.66 2.24 g initial average mass) or high-feed efficient (F136; 205.47 1.27 g) full-sib families of fish, twice per day, for 90 days. At the end of the experiment, the results showed that there is an interactive effect of the dietary lipid levels and the phenotypic feed efficiency (growth rate and feed efficiency) on the expression of the mitochondrial genes nd1 (NADH dehydrogenase subunit 1), cytb (Cytochrome b), cox1 (Cytochrome c oxidase subunits 1), cox2 (Cytochrome c oxidase subunits 2) and atp6 (ATP synthase subunit 6) and nuclear genes ucp2 (uncoupling proteins 2 alpha), ucp2 (uncoupling proteins 2 beta), ppar (peroxisome proliferator-activated receptor alpha), ppar (peroxisome proliferatoractivated receptor beta) and ppargc1 (proliferator-activated receptor gamma coactivator 1 alpha) in fish liver, intestine and muscle, except on ppargc1 in the muscle which was affected by the diet and the family separately. Also, the results revealed that the expression of mitochondrial genes is associated with that of nuclear genes involved in electron transport chain in fish liver, intestine and muscle. Furthermore, this work showed that the expression of mitochondrial genes parallels with the expression of genes encoding uncoupling proteins (UCP) in the liver and the intestine of rainbow trout. This study for the first time presents the molecular basis of the effects of dietary lipid level on mitochondrial and nuclear genes involved in mitochondrial electron transport chain in fish.

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