Bonney Lake, WA, United States
Bonney Lake, WA, United States
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Vallejo R.L.,National Center for Cool and Cold Water Aquaculture | Leeds T.D.,National Center for Cool and Cold Water Aquaculture | Gao G.,National Center for Cool and Cold Water Aquaculture | Parsons J.E.,Troutlodge Inc | And 5 more authors.
Genetics Selection Evolution | Year: 2017

Background: Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation. Methods: We compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model. We also assessed the impact of sampling design on the accuracy of GEBV predictions. For these comparisons, we used BCWD survival phenotypes recorded on 7893 fish from 102 families, of which 1473 fish from 50 families had genotypes [57 K single nucleotide polymorphism (SNP) array]. Naïve siblings of the training fish (n = 930 testing fish) were genotyped to predict their GEBV and mated to produce 138 progeny testing families. In the following generation, 9968 progeny were phenotyped to empirically assess the accuracy of GEBV predictions made on their non-phenotyped parents. Results: The accuracy of GEBV from all tested GS models were substantially higher than the P-BLUP model EBV. The highest increase in accuracy relative to the P-BLUP model was achieved with BayesB (97.2 to 108.8%), followed by wssGBLUP at iteration 2 (94.4 to 97.1%) and 3 (88.9 to 91.2%) and ssGBLUP (83.3 to 85.3%). Reducing the training sample size to n = ~1000 had no negative impact on the accuracy (0.67 to 0.72), but with n = ~500 the accuracy dropped to 0.53 to 0.61 if the training and testing fish were full-sibs, and even substantially lower, to 0.22 to 0.25, when they were not full-sibs. Conclusions: Using progeny performance data, we showed that the accuracy of genomic predictions is substantially higher than estimates obtained from the traditional pedigree-based BLUP model for BCWD resistance. Overall, we found that using a much smaller training sample size compared to similar studies in livestock, GS can substantially improve the selection accuracy and genetic gains for this trait in a commercial rainbow trout breeding population. © 2017 The Author(s).


Vallejo R.L.,U.S. Department of Agriculture | Leeds T.D.,National Center for Cool and Cold Water Aquaculture | Gao G.,National Center for Cool and Cold Water Aquaculture | Parsons J.E.,Troutlodge Inc | And 5 more authors.
Genetics, selection, evolution : GSE | Year: 2017

BACKGROUND: Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation.METHODS: We compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model. We also assessed the impact of sampling design on the accuracy of GEBV predictions. For these comparisons, we used BCWD survival phenotypes recorded on 7893 fish from 102 families, of which 1473 fish from 50 families had genotypes [57 K single nucleotide polymorphism (SNP) array]. Naïve siblings of the training fish (n = 930 testing fish) were genotyped to predict their GEBV and mated to produce 138 progeny testing families. In the following generation, 9968 progeny were phenotyped to empirically assess the accuracy of GEBV predictions made on their non-phenotyped parents.RESULTS: The accuracy of GEBV from all tested GS models were substantially higher than the P-BLUP model EBV. The highest increase in accuracy relative to the P-BLUP model was achieved with BayesB (97.2 to 108.8%), followed by wssGBLUP at iteration 2 (94.4 to 97.1%) and 3 (88.9 to 91.2%) and ssGBLUP (83.3 to 85.3%). Reducing the training sample size to n = ~1000 had no negative impact on the accuracy (0.67 to 0.72), but with n = ~500 the accuracy dropped to 0.53 to 0.61 if the training and testing fish were full-sibs, and even substantially lower, to 0.22 to 0.25, when they were not full-sibs.CONCLUSIONS: Using progeny performance data, we showed that the accuracy of genomic predictions is substantially higher than estimates obtained from the traditional pedigree-based BLUP model for BCWD resistance. Overall, we found that using a much smaller training sample size compared to similar studies in livestock, GS can substantially improve the selection accuracy and genetic gains for this trait in a commercial rainbow trout breeding population.


Martin K.E.,Washington State University | Martin K.E.,Troutlodge Inc | Steele C.A.,Washington State University | Brunelli J.P.,Washington State University | Thorgaard G.H.,Washington State University
Transactions of the American Fisheries Society | Year: 2010

The genetic variation of many species in the Northern Hemisphere has been influenced by climatic changes during the Pleistocene Epoch. Phylogeographic studies can help determine intraspecific relationships and postglacial recolonization routes for many of these species, potentially leading to a more complete understanding of how flora and fauna respond to dramatic climate change. We analyzed the variation in the mitochondrial DNA sequences of Chinook salmon Oncorhynchus tshawytscha from California to the Kamchatka Peninsula, Russia, to gain insight into the role of Pleistocene glaciation in the genetic structuring of this species. The geographic distribution of haplotypes revealed high levels of genetic diversity in the Columbia River drainage. Nested clade analysis suggests northward expansion from this area during the late Pleistocene, a hypothesis that is further supported by evidence of demographic growth and population expansion in the northern portion of the species' range. Estimates of the divergence time between two phylogenetic clades are correlated with interglacial periods of the Pleistocene. The data suggest the absence of Chinook salmon from the current northern part of its distribution until the late Pleistocene, when northward expansion from a southern refugium occurred (during an interglacial period), followed by the recent genetic divergence of these northern populations. © American Fisheries Society 2010.


Sae-Lim P.,Wageningen University | Kause A.,Mtt Agrifood Research Finland | Mulder H.A.,Wageningen University | Martin K.E.,Troutlodge Inc | And 6 more authors.
Journal of Animal Science | Year: 2013

Rainbow trout is a globally important fish species for aquaculture. However, fish for most farms worldwide are produced by only a few breeding companies. Selection based solely on fish performance recorded at a nucleus may lead to lower-than-expected genetic gains in other production environments when genotype-by-environment (G × E) interaction exists. The aim was to quantify the magnitude of G × E interaction of growth traits (tagging weight; BWT, harvest weight; BWH, and growth rate; TGC) measured across 4 environments, located in 3 different continents, by estimating genetic correlations between environments. A total of 100 families, of at least 25 in size, were produced from the mating 58 sires and 100 dams. In total, 13,806 offspring were reared at the nucleus (selection environment) in Washington State (NUC) and in 3 other environments: a recirculating aquaculture system in Freshwater Institute (FI), West Virginia; a high-altitude farm in Peru (PE), and a cold-water farm in Germany (GER). To account for selection bias due to selective mortality, a multitrait multienvironment animal mixed model was applied to analyze the performance data in different environments as different traits. Genetic correlation (rg) of a trait measured in different environments and rg of different traits measured in different environments were estimated. The results show that heterogeneity of additive genetic variances was mainly found for BWH measured in FI and PE. Additive genetic coefficient of variation for BWH in NUC, FI, PE, and GER were 7.63, 8.36, 8.64, and 9.75, respectively. Genetic correlations between the same trait in different environments were low, indicating strong reranking (BWT: rg = 0.15 to 0.37, BWH: rg = 0.19 to 0.48, TGC: rg = 0.31 to 0.36) across environments. The rg between BWT in NUC and BWH in both FI (0.31) and GER (0.36) were positive, which was also found between BWT in NUC and TGC in both FI (0.10) and GER (0.20). However, rg were negative between BWT in NUC and both BWH (-0.06) and TGC (-0.20) in PE. Correction for selection bias resulted in higher additive genetic variances. In conclusion, strong G × E interaction was found for BWT, BWH, and TGC. Accounting for G × E interaction in the breeding program, either by using sib information from testing stations or environment- specific breeding programs, would increase genetic gains for environments that differ significantly from NUC. © 2013 American Society of Animal Science. All rights reserved.


Overturf K.,U.S. Department of Agriculture | Vallejo R.L.,U.S. Department of Agriculture | Palti Y.,U.S. Department of Agriculture | Barrows F.T.,U.S. Department of Agriculture | Parsons J.E.,Troutlodge Inc
Aquaculture International | Year: 2012

Microarray analysis was conducted using liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals fed a fishmeal or plant protein-based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 expressed sequence tags (ESTs). Eight of the differentially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes, we were able to map gene pathways and process interactions. From this information, we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential regulation of genes related to cell oxidative stress, proliferation, growth and survival. Furthermore, we inferred from the changes we observed in immune response gene expression that ingestion of this plant-based diet upregulated the expression of genes involved in immunoregulatory processes. © 2011 Springer Science+Business Media B.V.


Weber G.M.,U.S. Department of Agriculture | Martin K.,Troutlodge Inc | Kretzer J.,U.S. Department of Agriculture | Ma H.,U.S. Department of Agriculture | Dixon D.,Troutlodge Inc
Journal of Applied Aquaculture | Year: 2016

Incubation temperature is commonly used to manipulate hatch date in salmonids. Although rapid adjustments in temperature are required to meet target dates, there is little information available on the effects of such changes on embryo survival. We compared the effects of temperature treatments on survival at ~250 degree days (considered eyeing), calculated as the sum of mean daily water temperature in degrees Celsius, and at first feeding. Incubation at 5°C within the first day of fertilization reduced survival at eyeing compared to incubation at 10°C or 14°C. Survival at eyeing or first feeding did not differ between embryos rapidly switched between 5°C and 10°C at 100 degree days, and embryos acclimated to the change in temperature over a 4-h period. Switching embryos from 10°C to 2°C at 100 degree days reduced survival at eyeing and first feeding by about 14% and 18% respectively, although there were differences among studies. The more time spent incubating at suboptimal temperatures, 14°C, 5°C, or 2°C, versus at 10°C, the greater the impact on survival with more extreme temperatures such as 2°C compared with 5°C having a greater impact. These impacts can be minimized if the low temperatures are avoided for the first day of incubation and perhaps avoiding temperatures near or in excess of 2°C. © 2016, Taylor & Francis. All rights reserved.


Sae-Lim P.,Wageningen University | Sae-Lim P.,Mtt Agrifood Research Finland | Komen H.,Wageningen University | Kause A.,Wageningen University | And 4 more authors.
Journal of Animal Science | Year: 2012

Distributing animals from a single breeding program to a global market may not satisfy all producers, as they may differ in market objectives and farming environments. Analytic hierarchy process (AHP) is used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The aim of this study was to use an AHP-WGP based approach to derive desired genetic gains for rainbow trout breeding and to study whether breeding trait preferences vary depending on commercial products and farming environments. Two questionnaires were sent out. Questionnaire-A (Q-A) was distributed to 178 farmers from 5 continents and used to collect information on commercial products and farming environments. In this questionnaire, farmers were asked to rank the 6 most important traits for genetic improvement from a list of 13 traits. Questionnaire B (Q-B) was sent to all farmers who responded to Q-A (53 in total). For Q-B, preferences of the 6 traits were obtained using pairwise comparison. Preference intensity was given to quantify (in % of a trait mean; G%) the degree to which 1 trait is preferred over the other. Individual preferences, social preferences, and consensus preferences (Con-P) were estimated using AHP and WGP. Desired gains were constructed by multiplying Con-P by G%. The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Ranking of traits based on average Con-P values were Surv (0.271), FCR (0.246), TGC (0.246), LMat (0.090), FIL% (0.081), and CF (0.067). Corresponding desired genetic gains (in % of trait mean) were 1.63, 1.87, 1.67, 1.29, 0.06, and 0.33%, respectively. The results from Con-P values show that trait preferences may vary for different types of commercial production or farming environments. This study demonstrated that combination of AHP and WGP can be used to derive desired gains for a breeding program and to quantify differences due to variations market demand or production environment. © 2012 American Society of Animal Science. All rights reserved.


Sae-Lim P.,Wageningen University | Komen H.,Wageningen University | Kause A.,Mtt Agrifood Research Finland | Martin K.E.,Troutlodge Inc | And 3 more authors.
Aquaculture | Year: 2013

Enhancing selection using two-stage selection is normally implemented by pre-selection for tagging weight (BWT) and by final selection for ungutted harvest weight (BWH) and thermal growth coefficient from tagging to harvest (TGCTH). However, selection on harvest traits, i.e., gutted weight (GBWH), visceral percentage (VISW%), condition factor (CFH), and overall survival (SURV), can be enhanced by exploiting correlated traits. It can be hypothesized that the efficiency of two-stage selection on genetic response in BWH and TGCTH is dependent on their genetic (rg) and phenotypic (rp) correlations with BWT and therefore dependent on the time point of pre-selection. The aims of this study were, first, to estimate genetic parameters (heritability: h2, rp, and rg) for BWT (7months), BWS (weight at sorting, 9months), BWH (14months), TGCTH, GBWH, VISW%, CFH, and SURV. Second, these genetic parameters were used in two deterministic simulation studies; i) one- and two-stage selections to compare genetic responses in BWH and TGCTH, and ii) alternative selection indices using correlated traits to compare corresponding accuracy of selection (rIH) for slaughter traits, CFH, and SURV. Genetic parameters were estimated using an animal mixed model in ASReml on 2,041 fish records. The main results showed that, first, rg of BWT was 0.35 with BWH but -0.25 with TGCTH, whereas the rg of BWS was 0.72 with BWH but 0.39 with TGCTH. Pre-selection for BWS led to genetic response of 54.15g in BWH which was higher than the genetic response from pre-selection for BWT (51.90g). Similarly, pre-selection on BWS enhanced correlated genetic response in TGCTH to 0.30g(1/3)/°C*day. In contrast, pre-selection for BWT resulted in lower correlated genetic response in TGCTH of 0.20g(1/3)/°C*day. It can be concluded that genetic improvement of BWH and TGCTH can be enhanced by postponing pre-selection to a later age. However, an optimal time point for tagging and pre-selection should be found to minimize common environmental effects and rearing costs during communal rearing of full-sibs. Second, including GBWH in a selection index can reduce unfavourable selection responses in VISW%. The GBWH is highly genetically correlated with BWH and can be easily indirectly selected. TGCTH is a good predictor for selection for lower VISW%, and higher SURV, but not for higher CFH. To control genetic changes in the condition factor, it should be included to the selection index. © 2012 Elsevier B.V.


Grant
Agency: Department of Agriculture | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 386.63K | Year: 2014

Female rainbow trout show improved uniformity of growth, more desirable carcass traits and reduced expression of sexual maturation compared to mixed-sex stocks, thus improving efficiency and return for the trout farming industry. As a result, all-female stocks are much more desirable, and currently comprise the vast majority (over 90%) of the rainbow trout sold in the US. Current methods of producing all-female stocks involve the use of small amounts of hormones to effectively convert genetically female trout into functional males, which in turn are used to create all-female offspring. The use of hormones for this purpose is continually being evaluated by the FDA, however the ability to use the hormones long term is not certain. Thus, an alternative method for production of all-female stocks is needed to ensure future efficiency and stability of rainbow trout aquaculture.In our rainbow trout breeding populations we have identified rare individuals who are genetically female yet they produce functional male gonads despite having never receiving hormone treatments. They are thought to contain a genetic variant which, through selective breeding, we have harnessed and intend to utilize for production of all-female rainbow trout. Crossing these rare males with normal females produces 100% female offspring. This alternative method of producing all-female rainbow trout will be evaluated for large scale production, and identification of the genetic mechanisms involved will offer insight into sex differentiation in trout and other species. Should the new method prove viable for production of all-female rainbow trout without the use of hormones, it would ensure continued efficiency and stability of rainbow trout aquaculture.


Grant
Agency: Department of Agriculture | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 84.33K | Year: 2012

A majority of rainbow trout produced in the US are derived from all-female stocks due to improved harvest traits and efficiency over mixed sex stocks. The development of all-female stocks currently relies on the use of the testosterone derivative 17 & #945; & #8722;methyltestosterone, however the long term use of this method is not guaranteed as regulations governing the use of the substance are becoming more stringent. Troutlodge Inc. in cooperation with researchers at Washington State University, has isolated rare XX individuals that develop as functional males. The sex ratio of progeny produced by these rare individuals indicates an autosomal recessive mutation causing the maleness. We will test the feasibility and functionality of using these individuals as a new method of production of all female lines without the use of hormones. Fine mapping in an attempt to identify the specific sex-reversal locus would occur in Phase II of the grant.

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