Application of genomic tools to study and potentially improve the upper thermal tolerance of farmed Atlantic salmon (Salmo salar).

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Eric H Ignatz, Melissa S Allen, Jennifer R Hall, Rebeccah M Sandrelli, Mark D Fast, Guy M L Perry, Matthew L Rise, A Kurt Gamperl
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引用次数: 0

Abstract

Background: The Atlantic salmon (Salmo salar) aquaculture industry must mitigate the impacts of rising ocean temperatures and the increased prevalence/severity of marine heat waves. Therefore, we investigated the genetic architecture and gene expression (transcriptomics) responsible for determining a salmon's upper thermal tolerance.

Results: A genome-wide association study (GWAS) was conducted using fin clips of salmon from a previous incremental thermal maximum (ITMax) challenge (n = 251) and the North American 50 K SNP chip. ITMax was a highly polygenic trait with low/moderate heritability (mean SNP-based h2 = 0.20 and pedigree-based h2 = 0.25). Using data from the same fish, a separate GWAS assessed thermal-unit growth coefficient (TGC). Five significant SNPs were detected on chromosomes three and five, and high heritability estimates were calculated for TGC measured as fish grew from 12 to 20 °C (mean SNP-based h2 = 0.62 and pedigree-based h2 = 0.64). RNA-seq analyses of liver samples (n = 5-6 family-1 temperature-1) collected from the four most and four least tolerant families at 10 and 20 °C were also used to provide insights into potential mechanisms modulating this species' thermal tolerance. Between the top and bottom families, 347 and 175 differentially expressed transcripts (FDR-adjusted p < 0.01; fold-change ≥|2.0|) were identified at 10 and 20 °C, respectively. GO term enrichment analysis revealed unique responses to elevated temperature between family rankings (e.g., 'blood coagulation', 'sterol metabolic process' and 'synaptic growth at neuromuscular junction'). qPCR analyses further confirmed differences pertaining to cholesterol metabolism (lpl), inflammation (epx, elf3, ccl20), apoptosis (htra1b, htra2, anxa5b), angiogenesis (angl4, pdgfa), nervous system processes (insyn2a, kcnj11l) and heat stress (serpinh1b-1, serpinh1b-2). Three differentially expressed transcripts (i.e., ppp1r9a, gal3st1a, f5) were located in close proximity (± 120 kbp) to near-significant SNPs from the GWAS. Interestingly, ppp1r9a and gal3st1a have putative neurological functions, while f5 regulates blood coagulation.

Conclusions: These analyses provide several putative biomarkers of upper thermal tolerance in salmon that could prove valuable in helping the industry develop more temperature-tolerant fish. Further, our study supports previous reports that ITMax has low/moderate heritability in this species, and suggests that TGC at elevated temperatures is highly heritable.

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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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