scholarly journals Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

2021 ◽  
Author(s):  
Eric B Rondeau ◽  
Kris A. Christensen ◽  
Dionne Sakhrani ◽  
Carlo A Biagi ◽  
Mike Wetklo ◽  
...  
Keyword(s):  
British Columbia ◽  
Linkage Group ◽  
Genome Assembly ◽  
Chum Salmon ◽  
Pacific Salmon ◽  
Gene Annotation ◽  
Oncorhynchus Keta ◽  
Specific Level ◽  
Genome Wide ◽  
The Pacific

Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids,. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.

SEX DIFFERENTIATION IN THE PACIFIC SALMON ONCORHYNCHUS KETA (WALBAUM)

1953 ◽  
Vol 31 (2) ◽  
pp. 73-79 ◽  
Author(s):  
J. G. Robertson
Keyword(s):  
Germ Cells ◽  
Chum Salmon ◽  
Pacific Salmon ◽  
Sex Differentiation ◽  
Primordial Germ Cells ◽  
The Other ◽  
Oncorhynchus Keta ◽  
Progressive Development ◽  
The Pacific ◽  
Female Phase

The differentiation of the gonad is described in chum salmon embryos and alevins. Contrary to classical findings in teleosts, sex differentiation in the chum salmon proceeds in the male or female direction without an intermediate female phase. From an initially indifferent gonad there is a progressive development of one sex or the other. The organ forms as a fold from the splanchnic mesoderm and, at the time of first appearance, contains primordial germ cells. These enlarge to form the definitive germ cells which, after a series of divisions, form smaller oogonia or spermatogonia. Oogonia are followed by primary and secondary (growing) oocytes, the appearance of which is the criterion of sex distinction. Spermatogonia continue to multiply but do not undergo growth in the alevin. The ovary develops an open endovarial canal and is supported by a prominent mesovarium. The testis remains small and, in the alevin, develops no ducts. It is suspended by a mesorchium.

scholarly journals Marine growth patterns of southern British Columbia chum salmon explained by interactions between density-dependent competition and changing climate

2017 ◽  
Vol 74 (7) ◽  
pp. 1077-1087 ◽  
Author(s):  
Allan J. Debertin ◽  
James R. Irvine ◽  
Carrie A. Holt ◽  
Gladys Oka ◽  
Marc Trudel
Keyword(s):  
British Columbia ◽  
Chum Salmon ◽  
Pacific Salmon ◽  
Pink Salmon ◽  
Climate Variation ◽  
Growth Patterns ◽  
Oncorhynchus Gorbuscha ◽  
Oncorhynchus Keta ◽  
Density Dependent ◽  
Competition Effects

Thirty-nine years of scale growth measurements from Big Qualicum River chum salmon (Oncorhynchus keta) in southern British Columbia demonstrated that competition and climate variation affect marine growth and age-at-maturity. A longitudinal study design that accounted for correlation among individuals revealed growth at all ages was reduced when the biomass of North American chum, sockeye (Oncorhynchus nerka), and pink salmon (Oncorhynchus gorbuscha) was high. When North Pacific Gyre Oscillation (NPGO) was positive, indicating increased primary productivity, predicted growth increased. Climate variation influenced competition effects. For instance, density-dependent competition effects increased when NPGO became more positive and Pacific Decadal Oscillation became more negative (indicating cool conditions), causing the greatest range in predicted scale size. Chum salmon are likely to exhibit continued reduction in growth at age due to increased ocean temperatures driven by climate change and high aggregate salmon biomass that includes hatchery releases. If evidence of biomass and climate effects presented here are common among Pacific salmon populations, reduction of hatchery releases should be considered.

Biochemical Genetic Survey and Stock Identification of Chum Salmon (Oncorhynchus keta) in British Columbia

1987 ◽  
Vol 44 (10) ◽  
pp. 1702-1713 ◽  
Author(s):  
T. D. Beacham ◽  
A. P. Gould ◽  
R. E. Withler ◽  
C. B. Murray ◽  
L. W. Barner
Keyword(s):  
British Columbia ◽  
Chum Salmon ◽  
Electrophoretic Analysis ◽  
South Coast ◽  
Oncorhynchus Keta ◽  
Stock Identification ◽  
Fraser River ◽  
Genetic Method ◽  
Chum Salmon Oncorhynchus Keta ◽  
Queen Charlotte Islands

We examined genetic variability using electrophoretic analysis of 83 chum salmon (Oncorhynchus keta) stocks in British Columbia and used regional differences in genotypic frequencies of seven polymorphic loci to estimate stock compositions in a number of commercial and experimental test fisheries. Chum salmon from five regions could be discriminated: Queen Charlotte islands, north and central coast, west coast of Vancouver Island, the Fraser River and its tributaries, and the south coast (rivers draining into Johnstone Strait and the Strait of Georgia). Allelic frequencies from 33 stocks were generally stable over a period of 2 yr or more. South coast chum salmon was the dominant run migrating through upper Johnstone Strait in October 1982–85. The genetic method of stock identification provided managers with the relative proportions of Fraser River and other groups of chum salmon in a number of fisheries and allowed managers to regulate more effectively the exploitation rate of Fraser River chum salmon.

Population structure and stock identification of chum salmon (Oncorhynchus keta) from British Columbia determined with microsatellite DNA variation

2008 ◽  
Vol 86 (9) ◽  
pp. 1002-1014 ◽  
Author(s):  
Terry D. Beacham ◽  
Brian Spilsted ◽  
Khai D. Le ◽  
Michael Wetklo
Keyword(s):  
British Columbia ◽  
Population Structure ◽  
Chum Salmon ◽  
Oncorhynchus Keta ◽  
Stock Identification ◽  
Dna Variation ◽  
Coastal Fisheries ◽  
Chum Salmon Oncorhynchus Keta ◽  
Regional Estimates ◽  
Mixed Stock

Variation at 14 microsatellite loci was surveyed in 205 populations of chum salmon ( Oncorhynchus keta (Walbaum in Artedi, 1792)) from British Columbia to determine population structure and the possible application of microsatellites to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (FST) over all populations and loci was 0.016, with individual locus values ranging from 0.006 to 0.059. Sixteen regional stocks were defined in British Columbia for stock identification applications. Analysis of simulated fishery samples suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. The main stocks that constitute the October 2007 samples of migrating chum salmon through Johnstone Strait in southern British Columbia were Fraser River (45%–64%), southern British Columbia mainland (22%), and east coast Vancouver Island (13%–28%), within the range of those to be expected in samples from Johnstone Strait. Microsatellites have the ability to provide fine-scale resolution of stock composition in British Columbia coastal fisheries.

Genetic Relationships Among Chum Salmon Populations in Southeast Alaska and Northern British Columbia

1994 ◽  
Vol 51 (S1) ◽  
pp. 50-64 ◽  
Author(s):  
C. M. Kondzela ◽  
C. M. Guthrie ◽  
S. L. Hawkins ◽  
C. d. Russell ◽  
J. H. Helle ◽  
...  
Keyword(s):  
British Columbia ◽  
Chum Salmon ◽  
Genetic Relationships ◽  
The United States ◽  
Oncorhynchus Keta ◽  
Significant Heterogeneity ◽  
Southeast Alaska ◽  
Queen Charlotte Islands ◽  
Spawning Time ◽  
Mixed Stock

Allozymes from 46 loci were analyzed from chum salmon (Oncorhynchus keta) collected at 61 locations in southeast Alaska and northern British Columbia. Of the 42 variable loci, 21 had a common allele frequency <0.95. We observed significant heterogeneity within and among six regional groups: central southeast Alaska, Prince of Wales Island area, southern southeast Alaska – northern British Columbia, north-central British Columbia, and two groups in the Queen Charlotte Islands. Genetic variation among regions was significantly greater than within regions. The three island groups were distinct from each other and from the mainland populations. Allele frequencies were stable over time in 14 of 15 locations sampled for more than 1 yr. The geographic basis for heterogeneity among regions is confounded in part by spawning-time differences. The Prince of Wales and Queen Charlotte populations spawn in the fall; the mainland populations spawn mainly in the summer, although some overlap exists. Overall, most genetic diversity (97%) occurred within sampling locations; the remaining diversity was distributed almost equally within and among regions. Our genetic data may provide fishery managers a means to estimate stock composition in the mixed-stock fisheries near this boundary between the United States and Canada.

Rationalizing the Irrational: A Case Study in User Group Participation in Pacific Salmon Management

1987 ◽  
Vol 44 (10) ◽  
pp. 1796-1805 ◽  
Author(s):  
Ray Hilborn ◽  
Wilf Luedke
Keyword(s):  
Chum Salmon ◽  
Pacific Salmon ◽  
Political Activity ◽  
Oncorhynchus Keta ◽  
Recent Attempt ◽  
Decision Making Process ◽  
User Group ◽  
Salmon Fisheries ◽  
Insight Into

Acrimony between industry and government managers is commonplace in the management of many Pacific salmon fisheries. A case study of the chum salmon (Oncorhynchus keta) fisheries in southern British Columbia provides insight into the prevailing distrust between fishermen and managers. A recent attempt to bring planned management into what had often been an irrational and highly political activity is described. A management system called the "clockwork" provides all fishermen an opportunity for greater understanding of the management rationale and greater input into the decision-making process. The results of this attempt and implications for achieving management goals are discussed.

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