Different gene expression profiles between normal and thermally selected strains of rainbow trout, Oncorhynchus mykiss, as revealed by comprehensive transcriptome analysis

Tan, Engkong; Kinoshita, Shigeharu; Suzuki, Yutaka; Ineno, Toshinao; Tamaki, Koichi; Kera, Akio; Muto, Koji; Yada, Takashi; Kudoh, Shoji; Asakawa, Shuichi; Watabe, Shugo

doi:10.1016/j.gene.2015.10.028

Cited by 24 publications

(12 citation statements)

References 30 publications

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“…Indeed, the heat shock response (HSR) is a widely recognized response to various stressors in ectotherms and often occurs in a timely fashion and in large magnitude (Tomanek & Somero, ). We found that the most significantly induced genes in redband trout were heat shock proteins ( hsp30 and hsp70 ), a similar result as many other rainbow trout studies (Narum & Campbell, ; Narum, Campbell, et al., ; Tan et al., ). This result suggested a timely and rapid HSR under acute warming conditions (1°C per 6 min).…”

Section: Discussionsupporting

confidence: 89%

“…Additionally, quantitative trait loci (QTL) mapping has been conducted for upper thermal tolerance (Perry, Martyniuk, Ferguson, & Danzmann, ) to identify candidate genes (Quinn, McGowan, Cooper, Koop, & Davidson, ) despite being limited by low marker density across the genome. Furthermore, next‐generation sequencing technologies are advancing the detection of candidate genes throughout the transcriptome and genome (Narum & Campbell, ; Narum, Campbell, Meyer, Miller, & Hardy, ; Tan et al., ), along with the investigation of patterns of adaptive variation to local environments with population genomics (Bernatchez, ; Narum, Buerkle, Davey, Miller, & Hohenlohe, ; Stapley et al., ).…”

Section: Introductionmentioning

confidence: 99%

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Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

et al. 2018

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Heterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus mykiss gairdneri) in cardiorespiratory function, cellular response and genomic variation. In a common garden environment, fish from an extreme desert climate had significantly higher critical thermal maximum (p < .05) and broader optimum thermal window for aerobic scope (>3°C) than fish from cooler montane climate. In addition, the desert population had the highest maximum heart rate during warming (20% greater than montane populations), indicating improved capacity to deliver oxygen to internal tissues. In response to acute heat stress, distinct sets of cardiac genes were induced among ecotypes, which helps to explain the differences in cardiorespiratory function. Candidate genomic markers and genes underlying these physiological adaptations were also pinpointed, such as genes involved in stress response and metabolic activity (hsp40, ldh-b and camkk2). These markers were developed into a multivariate model that not only accurately predicted critical thermal maxima, but also evolutionary limit of thermal adaptation in these specific redband trout populations relative to the expected limit for the species. This study demonstrates mechanisms and limitations of an aquatic species to evolve under changing environments that can be incorporated into advanced models to predict ecological consequences of climate change for natural organisms.

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Section: Discussionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

et al. 2018

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“…Despite the enormous potential, the demand and use of genomic tools for breeding purposes seem to not be sufficiently established yet, even for major reared fish species such as rainbow trout [18,19]. Notwithstanding, the knowledge on the genetic background of domesticated rainbow trout hatchery strains greatly improved over the past years, above all also due to the opportunities of next-generation sequencing methods [20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout (Oncorhynchus mykiss) Breeding Strains by Using Next-Generation Sequencing

Ríos-Pérez

Brunner

Hadlich

et al. 2020

Genes

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Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (Oncorhynchus mykiss), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies.

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“…HSPs are molecular chaperones involved in temperature tolerance [7,9], e.g., by preventing protein aggregation, assisting damaged proteins, and acting as primary genes, to cope with heat stress in the cell [12]. HSPs are associated with heat stress in tilapia [4], rainbow trout [9,13], killifish [14], and catfish [15], and heat stress induces tissue damage through apoptosis and necrosis, which increases the rate of cell proliferation and metabolism for maintaining cell activities [5,12,14,16]. p53 relates to the p53 signaling pathway, which is activated by the external environment, especially heat stress conditions [17].…”

Section: Introductionmentioning

confidence: 99%

“…The thermal-tolerant rainbow trout showed higher expression levels of HSPs than the low thermal-tolerant group under heat stress in fin and gill tissues [9,20]. In addition, HSPs were also highly expressed in other tissues, such as the brain, liver, muscle, and heart, in the thermally selected strains of rainbow trout [13]. HSPs were also up-regulated to promote the degradation of damaged proteins in the ER pathway during heat stress [21].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Yamame (Oncorhynchus masou) in Normal Conditions after Heat Stress

Kraitavin

Yoshitake

Igarashi

et al. 2019

Biology

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Understanding the mechanism of high-temperature tolerance in cold-freshwater fish is crucial for predicting how certain species will cope with global warming. In this study, we investigated temperature tolerance in masu salmon (Oncorhynchus masou, known in Japan as ‘yamame’), an important aquaculture species. By selective breeding, we developed a group of yamame (F2) with high-temperature tolerance. This group was subjected to a high-temperature tolerance test and divided into two groups: High-temperature tolerant (HT) and non-high-temperature tolerant (NT). RNA was extracted from the gill and adipose fin tissues of each group, and the mRNA expression profiles were analyzed using RNA sequencing. A total of 2893 differentially expressed genes (DEGs) from the gill and 836 from the adipose fin were identified by comparing the HT and NT groups. Functional analyses were then performed to identify associated gene ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The HT group showed a high expression of heat shock protein 70 (HSP70) gene and enriched gene expression in the extracellular matrix (ECM), cell junction, and adhesion pathways in gill tissues compared to the NT group. The HT group also exhibited highly expressed genes in glycolysis and showed lower expression of the genes in the p53 signaling pathway in adipose fin tissues. Taken together, the difference of expression of some genes in the normal condition may be responsible for the difference in heat tolerance between the HT and NT yamame in the heat stress condition.

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Different gene expression profiles between normal and thermally selected strains of rainbow trout, Oncorhynchus mykiss, as revealed by comprehensive transcriptome analysis

Cited by 24 publications

References 30 publications

Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout (Oncorhynchus mykiss) Breeding Strains by Using Next-Generation Sequencing

Transcriptome Analysis of Yamame (Oncorhynchus masou) in Normal Conditions after Heat Stress

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