Dataset Information

Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon.

ABSTRACT: A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (Oncorhynchus tshawytscha; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.

SUBMITTER: Narum SR

PROVIDER: S-EPMC6083255 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon.

Narum Shawn R SR Di Genova Alex A Micheletti Steven J SJ Maass Alejandro A

Proceedings. Biological sciences 20180718 1883

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (<i>Oncorhynchus tshawytscha</i>; 2.36 Gb) that enabled association mapping of life-hi ...[more]

PMID: 30051839

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Project description:Disease-causing infectious agents are natural components of ecosystems and considered a major selective force driving the evolution of host species. However, knowledge of the presence and abundance of suites of infectious agents in wild populations has been constrained by our ability to easily screen for them. Using salmon as a model, we contrasted seasonal pathogenic infectious agents in life history variants of juvenile Chinook salmon from the Fraser River system (N = 655), British Columbia (BC), through the application of a novel high-throughput quantitative PCR monitoring platform. This included freshwater hatchery origin fish and samples taken at sea between ocean entry in spring and over-winter residence in coastal waters. These variants currently display opposite trends in productivity, with yearling stocks generally in decline and sub-yearling stocks doing comparatively well. We detected the presence of 32 agents, 21 of which were at >1% prevalence. Variants carried a different infectious agent profile in terms of (1) diversity, (2) origin or transmission environment of infectious agents, and (3) prevalence and abundance of individual agents. Differences in profiles tended to reflect differential timing and residence patterns through freshwater, estuarine and marine habitats. Over all seasons, individual salmon carried an average of 3.7 agents. Diversity changed significantly, increasing upon saltwater entrance, increasing through the fall and decreasing slightly in winter. Diversity varied between life history types with yearling individuals carrying 1.3-times more agents on average. Shifts in prevalence and load over time were examined to identify agents with the greatest potential for impact at the stock level; those displaying concurrent decrease in prevalence and load truncation with time. Of those six that had similar patterns in both variants, five reached higher prevalence in yearling fish while only one reached higher prevalence in sub-yearling fish; this pattern was present for an additional five agents in yearling fish only.

Dataset Information

Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon.

Publications

Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon.

Similar Datasets

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