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 (; 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 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.

Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment

“…Narum et al . () found consistent association of the two run phenotypes with this genomic region across three distinct phylogenetic lineages. The occurrence of these distinct types in many populations of O. mykiss and O. tshawytscha appears to be the result of pre–existing genetic variation at this gene locus, which has spread by migration and positive selection, thus questioning the previous paradigm that these traits had arisen by parallel evolution in each population (Prince et al ., ).…”

Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids

“…A number of laboratories are already conducting genomics analyses of Chinook salmon and/or steelhead, and many have tissue or DNA samples that could be analyzed with this question in mind. Some new information relevant to Questions 1 and 3 has already been compiled (Narum, Di Genova, Micheletti, & Maass, ; Thompson et al., ). Conversely, although Question 2 is obviously of considerable importance (correlation after all does not establish cause and effect), addressing it is logistically challenging for natural populations with life histories like Pacific salmon, so it probably will be a number of years before definitive answers can be obtained.…”

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

“…We explore the Pool‐seq‐only approach of Neethiraj et al () using the brown trout ( Salmo trutta ) which belongs to the family Salmonidae that is characterized by large genomes (c. 3 Gbp) with the added complexity of a whole‐genome duplication event that occurred roughly 90 million years ago (MYA) followed by subsequent, and ongoing, rediploidization (Berthelot et al, ; Lien et al, ; Nugent, Easton, Norman, Ferguson, & Danzmann, ). Currently, there are genome assemblies available for Atlantic salmon ( Salmo salar ; Davidsson et al, ; Lien et al, ), rainbow trout ( Oncorhynchus mykiss ; Berthelot et al, ), chinook salmon ( Oncorhynchus tshawytscha ; Christensen, Leong, et al, ; Narum, Genova, Micheletti, & Maass, ), Arctic charr ( Salvelinus alpinus; Christensen, Rondeau, et al, ), coho salmon ( Oncorhynchus kisutch ; GenBank assembly accession: ), and grayling ( Thymallus thymallus ; Sävilammi et al, ). The separation of brown trout and its closest relative the Atlantic salmon occurred c. 6–7 MYA (Pustovrh, Snoj, & Bajec, ), and nucleotide divergence between the two is below 2% (Leitwein et al, ).…”