Regulatory Processes That Control Haploid Expression of Salmon Sperm mRNAs

Objective  Various stages of mRNA processing are necessary for functionally important genes required during late-stage sperm differentiation. Protein–RNA complexes form that edit, stabilize, store, deliver, localize and regulate translation of sperm mRNAs. These regulatory processes are often directed by recognition sequence elements and the particular composition of the proteins associated with the mRNAs. Previous work has shown that the cAMP response element modulator (CREM), estrogen receptor-alpha (ERα) and forkhead box L2A (FOXL2A) proteins are present in late-stage salmon sperm. Here we investigate whether these and other regulatory proteins might control processing of mRNAs not expressed until the haploid stage of development. We also examine regulatory processes that prepare and present mRNAs that generate unique products essential for differentiating sperm (i.e. for flagellar assembly and function). Results  We provide evidence for potential sperm-specific recognition elements in 5′-untranslated regions (utrs) that may bind CREM, ERα, FOXL2A, Y-box and other proteins. We show that changes within the 5′-utrs and open reading frames of some sperm genes lead to distinct protein termini that may provide specific interfaces necessary for localization and function within the paternal gamete

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

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Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish

Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds

Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array

The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using a high-density SNP array. Linkage disequilibrium was estimated between a total of 93,502 SNPs found in 64 individuals (33 dams and 31 sires) from the breeding population. The markers encompass all 30 coho salmon chromosomes and comprise 1,684.62 Mb of the genome. The average density of markers per chromosome ranged from 48.31 to 66 per 1 Mb. The minor allele frequency averaged 0.26 (with a range from 0.22 to 0.27). The overall average linkage disequilibrium among SNPs pairs measured as r2 was 0.10. The Average r2 value decreased with increasing physical distance, with values ranging from 0.21 to 0.07 at a distance lower than 1 kb and up to 10 Mb, respectively. An r2 threshold of 0.2 was reached at distance of approximately 40 Kb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (>0.20 at distances lower than 1 Mb). Average r2 values were lower than 0.15 for all chromosomes at distances greater than 4 Mb. An effective population size of 43 was estimated for the population 10 generations ago, and 325, for 139 generations ago. Based on the effective number of chromosome segments, we suggest that at least 74,000 SNPs would be necessary for an association mapping study and genomic predictions. Therefore, the SNP panel used allowed us to capture high-resolution information in the farmed coho salmon population. Furthermore, based on the contemporary Ne, a new mate allocation strategy is suggested to increase the effective population size

Identification of Periostin as a Critical Marker of Progression/Reversal of Hypertensive Nephropathy

Progression of chronic kidney disease (CKD) is a major health issue due to persistent accumulation of extracellular matrix in the injured kidney. However, our current understanding of fibrosis is limited, therapeutic options are lacking, and progressive degradation of renal function prevails in CKD patients. Uncovering novel therapeutic targets is therefore necessary

Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states

Background: Triploid coho salmon are excellent models for studying gene dosage and the effects of increased cell volume on gene expression. Triploids have an additional haploid genome in each cell and have fewer but larger cells than diploid coho salmon to accommodate the increased genome size. Studying gene expression in triploid coho salmon provides insight into how gene expression may have been affected after the salmonid-specific genome duplication which occurred some 90 MYA. Triploid coho salmon are sterile and consequently can live longer and grow larger than diploid congeners in many semelparous species (spawning only once) because they never reach maturity and post-spawning mortality is averted. Triploid fishes are also of interest to the commercial sector (larger fish are more valuable) and to fisheries management since sterile fish can potentially minimize negative impacts of escaped fish in the wild. Results: The vast majority of genes in liver tissue had similar expression levels between diploid and triploid coho salmon, indicating that the same amount of mRNA transcripts were being produced per gene copy (positive gene dosage effects) within a larger volume cell. Several genes related to nutrition and compensatory growth were differentially expressed between diploid and triploid salmon, indicating that some loci are sensitive to cell size and/or DNA content per cell. To examine how robust expression between ploidies is under different conditions, a genetic/metabolic modifier in the form of different doses of a growth hormone transgene was used to assess gene expression under conditions that the genome has not naturally experienced or adapted to. While many (up to 1400) genes were differentially expressed between non-transgenic and transgenic fish, relatively few genes were differentially expressed between diploids and triploids with similar doses of the transgene. These observations indicate that the small effect of ploidy on gene expression is robust to large changes in physiological state. Conclusions: These findings are of interest from a gene regulatory perspective, but also valuable for understanding phenotypic effects in triploids, transgenics, and triploid transgenics that could affect their utility in culture conditions and their fitness and potential consequences of release into nature.Science, Faculty ofNon UBCZoology, Department ofReviewedFacult

Estimation of Conservation Unit and population contribution to Chinook salmon mixed-stock fisheries in British Columbia, Canada using direct DNA sequencing for single nucleotide polymorphisms

Determination of population structure and stock identification is a general problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For Chinook salmon (Oncorhynchus tshawytscha), a stock identification baseline comprised of some 125,198 individuals from 369 populations ranging from Russia to California was employed for genetic stock identification (GSI). GSI analysis based upon variation at up to 547 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 68 Conservation Units (CUs) in British Columbia, 23 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian Chinook salmon.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

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

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

Accurate estimation of conservation Unit contribution to coho salmon mixed-stock fisheries in British Columbia, Canada using direct DNA sequencing for single nucleotide polymorphisms

Determination of population structure and stock identification is a ubiquitous problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For coho salmon (Oncorhynchus kisutch), a stock identification baseline composed of some 57 982 individuals from 332 populations ranging from southeast Russia to California was employed for genetic stock identification (GSI). GSI analysis based upon variation at up to 480 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 37 conservation units (CU) in British Columbia, 13 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian coho salmon.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Parallel epigenetic modifications induced by hatchery rearing in a Pacific Salmon

A puzzling question in conservation biology is how to maintain overall fitness of individuals  bred in captive environment upon release into the wild, especially for rehabilitating declining or threatened species [1,2]. For salmonid species, a heritable change in fitness related traits and gene expression has been reported to occur in a single generation of captivity in hatchery environment [3–5]. Such rapid changes are congruent with models of  inadvertent domestication selection which may lead to maladaptation in the natural environment [4]. Arguably, the underlying mechanism by which captivity may induce  fitness difference between wild and captive congeners is still poorly understood. Short- term selection on complex phenotypic traits is expected to induce subtle changes in allele  frequency over multiple loci [7–9]. Yet, most studies investigating the molecular basis for  rapid change in fitness related traits occurring in hatchery have concentrated their effort on 34 finding evidence for selection at the genome level by identifying loci with large effect.  Numerous wild stocks of Pacific anadromous salmon and trout (genus Oncorhynchus  and Salmo) have experienced fluctuating abundance over the past century, with a series of  sharp declines [6–8]. With the objectives of preserving ecosystem integrity, enhancing. declining populations and sustaining fisheries, conservation hatcheries have been  flourishing. This is particularly true along the North American Pacific coast where billions of  salmonids, all species included, are released each year. Despite substantial improvement of  production management, the beneficial ecological role of hatcheries in enhancing and  restoring wild stocks is still debated, mainly because of the reduced fitness and  maladaptation of hatchery-fish when released in the wild [3,5,9]. Although previous studies  showed that domestication selection was involved in such fitness impairment, they also  observed that different environmental conditions (e.g. reduced fish density) significantly  modulated the physiological acclimation to hatchery environment [4].   Environmental stimuli are especially relevant during early embryonic development,  which also correspond to a sensitive methylation reprogramming window in vertebrates  [10,11]. It is therefore plausible that differences in rearing environment during early  development may result in epigenetic modifications that could in turn impact on fitness.  However, the only epigenetic study to date pertaining to captive rearing in salmonids and  performed using methylation-sensitive amplified fragments (MSAP) failed to identify  significant changes in methylation profile associated with hatchery rearing [12]   Here, we used a higher resolution approach to compare the genome-wide pattern of  methylation in hatchery-reared juvenile (smolt) Coho Salmon with that of their wild  counterparts in two geographically distant rivers in British Columbia, Canada. Using a  reduced representation bisulfite sequencing (RRBS) approach covering an average per  individual of about 70 million cytosines in CpG context, we identified 100 methylated  regions (DMRs) that differed in parallel between hatchery and natural origin salmon in both  rivers. The total variance of epigenetic variation among individuals explained by river or  origin and rearing environment in a RDA model was 16% (adj.R2=0.16), and both variables  equally explained about 8% of the variance after controlling for each other. The gene  ontology analysis revealed that regions with different methylation levels between hatchery  and natural origin salmon showed enrichment for ion homeostasis, synaptic and  neuromuscular regulation, immune and stress response, and control of locomotion  functions. We further identified 15,044 SNPs that allowed detection of significant  differences between either rivers or sexes. However, no effect of rearing environment was  observed, confirming that hatchery and natural origin fish of a given river belong to the  same panmictic population, as expected based on the hatchery programs applied in these  rivers (see Supplementary experimental procedures). Moreover, neither a standard  genome-scan approach nor a polygenic statistical framework allowed detection of selective  effects within a single generation between hatchery and natural origin salmon. Therefore,  this is the first study to demonstrate that parallel epigenetic modifications induced by  hatchery rearing during early development may represent a potential explanatory  mechanism for rapid change in fitness-related traits previously reported in salmonids