Population and family effects on gene transcriptional profiles of eight hybrid Chinook salmon (Oncorhynchus tshawytscha) populations: implications for conservation and aquaculture

Aquaculture has been the fastest growing food industry worldwide since 1985 and has contributed significantly to the Canadian economy. Thus, methods for increasing aquaculture production are currently being investigated, such as selective breeding programs. Here I developed transcriptional profiles of eight hybrid half-sibling populations of Chinook salmon (Oncorhynchus tshawytscha) and examined them for evidence of local adaptation and as a potential marker for marker-assisted selection method. I found evidence of local adaptation among the populations, further supporting this as a driving force behind the large variation witnessed in Chinook salmon life history variation. I used the transcriptional profiles developed for each population in the freshwater (juvenile) stage and tested for correlations with saltwater performance (growth rate and survival). I found significant correlations between saltwater performance factors and juvenile transcription, suggesting that saltwater performance in Chinook salmon can be predicted using freshwater transcription patterns. There were also significant correlations between freshwater and saltwater transcription, indicating possible mechanisms behind the correlation between freshwater and saltwater traits. Freshwater Chinook salmon transcriptional profiles are a promising novel marker for application in marker-assisted selection breeding programs in aquaculture. Overall, transcriptional profiling using selected known-function genes provide the ability to study both local adaptation and performance in Chinook salmon populations

R_Source_Code

This text file contains the R source code used for the analyses in the paper

PCR_Efficiencies

This file contains the PCR efficiencies of all candidate genes used in the study. The efficiencies were calculated using LinRegPCR

Raw_qPCR_Data

Raw qPCR data from a QuantStudio 12K Flex for all samples and candidate genes

Sample_Annotation

This file contains information for each sample in the study, including the individual sample's rearing tank, sire, population, weight, treatment group, etc

Processed_qPCR_Data

This file contains the information needed to normalize the Cq values from the raw data, as well as the final DCt values that were used in the manuscript

README

This document defines all abbreviations within the other data files

Variation in juvenile Chinook salmon (Oncorhynchus tshawytscha) transcription profiles among and within eight population crosses from British Columbia, Canada

Phenotypic differences among populations within a species have been reported for a variety of traits, ranging from life history to physiology to gene transcription. Population‐level phenotypic variation has been attributed to genetic differences resulting from genetic drift and/or local adaptation as well as environmental differences resulting from plasticity. We studied population‐ and family‐level variation in gene transcription for 22 fitness‐related genes, comprising immune, growth, metabolic, and stress processes in Chinook salmon (Oncorhynchus tshawytscha). We created hybrid Chinook salmon families from eight populations and treated them with an immune stimulus, a handling stress challenge, and held some as a no‐treatment control group. Population effects, sire effects, and narrow‐sense heritability (h2) were calculated for each candidate gene within each treatment group. We expected population to have a significant effect on gene transcription for many of our genes; however, we found a population effect for transcription at only one immune gene at rest. The limited number of significant population effects on gene transcription, combined with significant additive genetic variance within each population does not support the expectation of past strong selection pressures acting on heritable transcription profiles among populations. Instead, our results indicate that Chinook salmon likely adapt to their local environment through transcriptional plasticity rather than fixed differences. The expectation for fixed population‐level differences in gene transcription at fitness‐related genes, reflecting accepted models of local adaptation is high; however, comparisons among multiple populations using half‐sibling breeding designs are rare. Our work fills an important gap in our growing understanding of the process of among and within‐population divergence

Temporal σB stress-response profiles impact Bacillus subtilis fitness

ABSTRACTThe Gram-positive model organism Bacillus subtilis responds to environmental stressors by activating the alternative sigma factor σB. The sensing apparatus upstream of σB activation is thought to consist of cytoplasmic stressosomes—megadalton-sized protein complexes that include five paralogous proteins known as RsbRs. The RsbRs are presumed to be involved in stress sensing and the subsequent response. Perturbations to the RsbR complement in stressosomes by engineering cells that produce only one of the RsbR paralogs (“single-RsbR strains”) lead to altered σB response dynamics with respect to timing and magnitude. Here, we asked whether such changes to σB response dynamics impact the relative fitness of a strain. We competed strain pairs with different RsbR complements under ethanol and sodium chloride stress and found not only differences in relative fitness among wild-type and single-RsbR strains but also different relative fitness values in the two different stressors. We found that the presence of RsbRA, which dominates the wild-type σB response, enhances fitness in ethanol but is detrimental to fitness in NaCl. Meanwhile, RsbRD-only cells were among the most fit in NaCl. Strains producing hybrid RsbR fusion proteins displayed different fitness values that depended on the RsbR proteins from which they were derived. Our results here suggest that σB response dynamics can impact fitness, highlighting the physiological importance of the unusual stressosome-based general stress response system of B. subtilis.IMPORTANCEThe model bacterium Bacillus subtilis uses cytoplasmic multiprotein complexes, termed stressosomes, to activate the alternative sigma factor σB when facing environmental stresses. We have previously shown that genetically manipulating the complement of putative sensor proteins in stressosomes can alter the dynamics of the σB response in terms of its magnitude and timing. However, it is unknown whether these response dynamics impact the fitness of cells challenged by environmental stressors. Here, we examine the fitness of strains with different σB responses by competing strain pairs in exponential-phase co-cultures under environmental stress. We find that strains with different response dynamics show different competitive indices that differ by stressor. These results suggest that the dynamics of the σB response can affect the fitness of cells facing environmental stress, highlighting the relevance of different σB dynamics