scholarly journals Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon

2021 ◽  
Author(s):  
Kris A Christensen ◽  
Jérémy Le Luyer ◽  
Michelle T T Chan ◽  
Eric B Rondeau ◽  
Ben F Koop ◽  
...  
Keyword(s):  
Growth Rate ◽  
Liver Tissue ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Environment Interaction ◽  
Genotype By Environment ◽  
Gxe Interaction ◽  
Differentially Methylated Genes ◽  
Gxe Interactions ◽  
Term Analysis

Abstract Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.

Changes in the Average Size and Average Age of Pacific Salmon

1981 ◽  
Vol 38 (12) ◽  
pp. 1636-1656 ◽  
Author(s):  
W. E. Ricker
Keyword(s):  
Growth Rate ◽  
Chinook Salmon ◽  
Sockeye Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Gill Nets ◽  
Growing Seasons ◽  
Mean Size ◽  
Average Size

Of the five species of Pacific salmon in British Columbia, chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) are harvested during their growing seasons, while pink salmon (O. gorbuscha), chum salmon (O. keta), and sockeye salmon (O. nerka) are taken only after practically all of their growth is completed. The size of the fish caught, of all species, has decreased, but to different degrees and over different time periods, and for the most part this results from a size decrease in the population. These decreases do not exhibit significant correlations with available ocean temperature or salinity series, except that for sockeye lower temperature is associated with larger size. Chinook salmon have decreased greatly in both size and age since the 1920s, most importantly because nonmaturing individuals are taken by the troll fishery; hence individuals that mature at older ages are harvested more intensively, which decreases the percentage of older ones available both directly and cumulatively because the spawners include an excess of younger fish. Other species have decreased in size principally since 1950, when the change to payment by the pound rather than by the piece made it profitable for the gill-netters to harvest more of the larger fish. Cohos and pinks exhibit the greatest decreases, these being almost entirely a cumulative genetic effect caused by commercial trolls and gill nets removing fish of larger than average size. However, cohos reared in the Strait of Georgia have not decreased in size, possibly because sport trolling has different selection characteristics or because of the increase in the hatchery-reared component of the catch. The mean size of chum and sockeye salmon caught has changed much less than that of the other species. Chums have the additional peculiarity that gill nets tend to take smaller individuals than seines do and that their mean age has increased, at least between 1957 and 1972. That overall mean size has nevertheless decreased somewhat may be related to the fact that younger-maturing individuals grow much faster than older-maturing ones; hence excess removal of the smaller younger fish tends to depress growth rate. Among sockeye the decrease in size has apparently been retarded by an increase in growth rate related to the gradual cooling of the ocean since 1940. However, selection has had two important effects: an increase in the percentage of age-3 "jacks" in some stocks, these being little harvested, and an increase in the difference in size between sockeye having three and four ocean growing seasons, respectively.Key words: Pacific salmon, age changes, size changes, fishery, environment, selection, heritability

Pacific salmon (Oncorhynchus spp.) runs and consumer fitness: growth and energy storage in stream-dwelling salmonids increase with salmon spawner density

2012 ◽  
Vol 69 (1) ◽  
pp. 73-84 ◽  
Author(s):  
Daniel J. Rinella ◽  
Mark S. Wipfli ◽  
Craig A. Stricker ◽  
Ron A. Heintz ◽  
Matthew J. Rinella
Keyword(s):  
Growth Rate ◽  
Energy Density ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Nutritional Ecology ◽  
Dolly Varden ◽  
South Central ◽  
Dolly Varden Salvelinus Malma ◽  
N Enrichment

We examined how marine-derived nutrients (MDN), in the form of spawning Pacific salmon, influenced the nutritional status and δ15N of stream-dwelling fishes. We sampled juvenile coho salmon ( Oncorhynchus kisutch ) and Dolly Varden ( Salvelinus malma ) during spring and fall from 11 south-central Alaskan streams that ranged widely in spawning salmon biomass (0.1–4.7 kg·m–2). Growth rate (as indexed by RNA–DNA ratios), energy density, and δ15N enrichment in spring-sampled fishes increased with spawner biomass, indicating the persistence of spawner effects more than 6 months after salmon spawning. Point estimates suggest that spawner effects on nutrition were substantially greater for coho salmon than Dolly Varden (268% and 175% greater for growth and energy, respectively), indicating that both species benefitted physiologically, but that juvenile coho salmon accrued more benefits than Dolly Varden. Although the data were less conclusive for fall- than spring-sampled fish, they do suggest spawner effects were also generally positive during fall, soon after salmon spawned. In a follow-up analysis where growth rate and energy density were modeled as a function of δ15N enrichment, results suggested that both increased with MDN assimilation, especially in juvenile coho salmon. Our results support the importance of salmon runs to the nutritional ecology of stream-dwelling fishes.

scholarly journals Yield stability of rapeseed genotypes under drought stress conditions

2019 ◽  
Vol 79 (01) ◽  
Author(s):  
Mehdipour Sara ◽  
Rezaeizad Abbas ◽  
Azizinezhad Reza ◽  
Etminan Alireza
Keyword(s):  
Genotype X Environment ◽  
Genotype By Environment ◽  
Biplot Analysis ◽  
Gxe Interaction ◽  
Cropping Season ◽  
Moisture Regimes ◽  
Ammi Model ◽  
Gxe Interactions ◽  
Cropping Seasons ◽  
Poor Stability

Genotype by Environment (GxE) interactions of 29 rapeseed genotypes in normal irrigation and irrigation cut off from flowering and silique formation stages have been worked out from the data recorded during three cropping seasons. Combined variance analysis showed a significant variation for year (cropping season), moisture regimes, genotype, genotype x moisture regimes and genotype x year interactions. Results of AMMI model analysis showed that three first genotype x environment principal components (PC) were significant at 1% level of probability and fourth PC at 5% level. These four components explained 35.6, 24.4, 18.4 and 14.8 per cent of the GxE sum of squares, respectively. According to AMMI2 biplot analysis, genotypes such as L155, Neptune, Elvise, Jerry, GkGabriella, Sw102, GKH0224, Julius, GKH3705 and Sarigol were positioned in the center of the biplot so had the least GxE interaction and showed the most general compatibility. Based on simultaneous selection, winter type of genotypes namely, GKH2624, SW102, HW118, GKH3705, Wpn6 and L72 were identified as high yielding and stable whereas, spring genotypes namely, Zabol10, Dalgan, Jerome and Hyola4815 were identified as low yielding with poor stability.

scholarly journals Genotype by environment interaction for growth and survival rate in black tiger shrimp (Penaeus monodon) in generation 4

2019 ◽  
Vol 18 (5) ◽  
pp. 24-32
Author(s):  
Sang V. Nguyen
Keyword(s):  
Growth Rate ◽  
Survival Rate ◽  
Genetic Correlations ◽  
Growth Trait ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
The South ◽  
Selection Program ◽  
Genotype By Environment ◽  
Testing Environments

Genotype by environment interaction for growth rate in G1 of the same selection program has been published. However, there is no repeated figure in later generations for confirming and well-planning the design of selection program for further improvement. The experiment was conducted using selective population of generation 4 with 97 families tested in 3 environments. Growth (body weight) and survival rate at harvest weight were recorded and evaluated. There was no genotype by environment interaction for both traits with high genetic correlations of the same traits tested between ponds in the Central and in the South of Vietnam of 0.80 and 0.83, respectively. There was also no genotype by environment interaction for growth rate between ponds in the South of Vietnam and bio-security indoor tank with high genetic correlation of 0.91. These results indicated that the number of testing environments would be reduced to save the operation cost for a breeding program. Estimated genetic response was from moderate to high for growth trait corresponding to moderate to high heritabilities (0.20 - 0.45) and high for survival rate corresponding to high heritabilities (0.34 - 0.45).

scholarly journals A versatile, fast and unbiased method for estimation of gene-by-environment interaction effects on biobank-scale datasets

2021 ◽  
Author(s):  
Mohammad Khan ◽  
Matteo Di Scipio ◽  
Conor Judge ◽  
Nicolas Perrot ◽  
Michael Chong ◽  
...  
Keyword(s):  
Interaction Effects ◽  
Environment Interaction ◽  
Gxe Interaction ◽  
Genome Wide ◽  
Marginal Association ◽  
Unbiased Estimates ◽  
Gxe Interactions ◽  
The Uk ◽  
Variance Explained ◽  
Interaction Variance

AbstractCurrent methods to evaluate gene-by-environment (GxE) interactions on biobank-scale datasets are limited. MonsterLM enables multiple linear regression on genome-wide datasets, does not rely on parameters specification and provides unbiased estimates of variance explained by GxE interaction effects. We applied MonsterLM to the UK Biobank for eight blood biomarkers (N=325,991), identifying significant genome-wide interaction variance with waist-to-hip ratio for five biomarkers, with variance explained by interactions ranging from 0.11 to 0.58. 48% to 94% of GxE interaction variance can be attributed to variants without significant marginal association with the phenotype of interest. Conversely, for most traits, >40% of interaction variance was explained by less than 5% of genetic variants. We observed significant improvements in polygenic score prediction with incorporation of GxE interactions in four biomarkers. Our results imply an important contribution of GxE interaction effects, driven largely by a restricted set of variants distinct from loci with strong marginal effects.

scholarly journals Genotype by environment interaction and teak (Tectona grandis L.) selection in Costa Rica

2019 ◽  
Vol 68 (1) ◽  
pp. 116-121
Author(s):  
O. Murillo ◽  
M.D.V. de Resende ◽  
Y. Badilla ◽  
J.P. Gamboa
Keyword(s):  
Costa Rica ◽  
Genetic Correlation ◽  
Breeding Population ◽  
Environment Interaction ◽  
Pacific Region ◽  
Genotype By Environment ◽  
Progeny Trial ◽  
Northern Pacific ◽  
Gxe Interactions ◽  
Selection Of

Abstract A teak progeny trial was established with four replicates at different sites along the northern Pacific region of Costa Rica. The trials followed a randomized block design, with 28 open pollinated families and 36 seedlings per family per site. Data from 7 years-old trees was analyzed both for each test location separately and for all locations combined. High individual heritability was found for diameter, which translates to higher breeding potential. The all locations combined analysis showed high genetic variation, with individual heritabilities reaching up to 22 %. Genotype by Environment (GxE) interactions explained only 2.5 % of total phenotypic variation. The genetic correlation (rg) among all four sites was 0.69. Hence, it is concluded that GxE interactions are not problematic for breeding purposes since they are not complex in nature. This teak breeding population showed strong genetic stability and performed well in most environments in the study area. The Hojancha location showed high genetic correlation with all other sites; therefore, it should be chosen for future testing and selection of elite genotypes. Selection of the 20 best individuals, allowing for up to two individuals per family, would result in a 1.78 cm (11 %) gain in diameter. Furthermore, based on this selection the inbreeding coefficient (F) in the offspring would only reach 2.9 %, while the expected effective population size (Ne) would be16.97 individuals. This selection scheme could reduce rotation age by almost two years, since the diameter goal of 40 cm would be reached earlier than the usual 20 years cycle. The results suggest that the progeny trial can be maintained as a single breeding population, suitable for planting in any site along the Northern Pacific region of Costa Rica.

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