Gary H. Thorgaard

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.

8 Chromosome Set Manipulation and Sex Control in Fish

Publisher Summary This chapter describes the techniques used in chromosome set manipulation and reviews the results and prospects in the application of gynogenesis, androgenesis, and induced polyploidy to fish. Chromosome-set manipulation techniques of sperm chromosome inactivation (with radiation or chemicals) and suppression of cell divisions (with heat shock, cold shock, or pressure) can be readily applied to fish to produce gynogenetic and polyploid individuals. Gynogenetic individuals have all their chromosomes from the female parent and should all be females in species with XX females. Polyploids include triploids that are expected to be sterile, and tetraploids that have the potential of being fertile and producing sterile triploids when crossed to normal diploids. Partially inbred gynogenetic diploids and triploids may be produced by treatments causing retention of the second polar body of the egg. Completely homozygous gynogenetic diploids and tetraploids may be produced by treatments blocking the first mitotic division.

Status and opportunities for genomics research with rainbow trout

The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes.

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

Salmonid fishes exhibit extensive local adaptations owing to abundant environmental variation and precise natal homing. This extensive local adaptation makes conservation and restoration of salmonids a challenge. For example, defining unambiguous units of conservation is difficult, and restoration attempts often fail owing to inadequate adaptive matching of translocated populations. A better understanding of the genetic architecture of local adaptation in salmonids could provide valuable information to assist in conserving and restoring natural populations of these important species. Here, we use a combination of laboratory crosses and next‐generation sequencing to investigate the genetic architecture of the parallel adaptation of rapid development rate in two geographically and genetically distant populations of rainbow trout (Oncorhynchus mykiss). Strikingly, we find that not only is a parallel genetic mechanism used but that a conserved haplotype is responsible for this intriguing adaptation. The repeated use of adaptive genetic variation across distant geographical areas could be a general theme in salmonids and have important implications for conservation and restoration.

Ploidy manipulation and performance

Abstract The chromosome set manipulation techniques of induced polyploidy, gynogenesis and androgenesis are likely to have significant applications in aquaculture. Induced triploidy is valuable for production of sterile individuals and increasing hybrid survival, and may be useful for producing individuals with increased heterozygosity. Gynogenesis (all-maternal inheritance) has considerable potential for rapid generation of inbred lines and can be used to generate all-female populations and in gene-transfer studies. Androgenesis (all-paternal inheritance) might be used for rapid generation of inbred lines, in the recovery of genotypes from cryopreserved sperm and in studying the effects of mitochondrial genotype on performance.

Chromosomal Differences Among Rainbow Trout Populations

Most males showed a morphological difference between the X and Y chromosomes but a number of males with no apparent sex chromosome heteromorphism were observed. These fish were particularly common in some populations; these may represent areas in which the rearrangement resulting in a morphological difference between the X and Y has not become fixed in the population.

Polyploidy Induced by Heat Shock in Rainbow Trout

Abstract Polyploidy was induced in rainbow trout Salmo gairdneri when fertilized eggs were immersed in 36 C water for 1 minute. Triploids were produced if the eggs were treated 10 minutes after fertilization; tetraploids were produced by treatments 5 hours after fertilization. Sterile triploid trout and salmon potentially could grow and survive better than normal fish at sexual maturation. Heat-shock techniques also should be useful in the production of gynogenetic diploid trout and salmon for biological studies and breeding programs.

Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches

BackgroundRainbow trout are important fish for aquaculture and recreational fisheries and serves as a model species for research investigations associated with carcinogenesis, comparative immunology, toxicology and evolutionary biology. However, to date there is no genome reference sequence to facilitate the development of molecular technologies that utilize high-throughput characterizations of gene expression and genetic variation. Alternatively, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Although a large number (258,973) of EST sequences are publicly available, the nature of rainbow trout duplicated genome hinders assembly and complicates annotation.ResultsHigh-throughput deep sequencing of the Swanson rainbow trout doubled-haploid transcriptome using 454-pyrosequencing technology yielded ~1.3 million reads with an average length of 344 bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus (TC) sequences (average length of 662 bp) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing sequences resulted in 161,818 TCs (average length of 758 bp) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed high similarities to transcriptomes of other fish species with known genome sequences.ConclusionThe 454 library significantly increased the suite of ESTs available for rainbow trout, allowing improved assembly and annotation of the transcriptome. Furthermore, the 454 sequencing enables functional genome research in rainbow trout, providing a wealth of sequence data to serve as a reference transcriptome for future studies including identification of paralogous sequences and/or allelic variation, digital gene expression and proteomic research.

Genetic conservation of salmonid fishes

The problem is that, with the continuing degradation of water and habitat quality, selective harvesting, genetic enhancement programs, and the introduction of hatchery fish into wild populations, the genetic makeup of fish is changing radically. In 27 papers from a workshop held in Moscow, Idaho, an

The Genetic Basis of Smoltification-Related Traits in Oncorhynchus mykiss

The timing and propensity for migration between fresh- and seawater is a key theme in the diversity of life histories within the salmonid fishes. Across salmonid species, life-history strategies range from wholly freshwater-resident populations, to migratory and nonmigratory variation within populations, to populations and species that are primarily migratory. Despite the central theme of migration to the evolution of these fishes, the genetic architecture of migration-related processes is poorly understood. Using a genetic cross of clonal lines derived from migratory and nonmigratory life-history types of Onchorhynchus mykiss (steelhead and rainbow trout, respectively), we have dissected the genetic architecture of the complex physiological and morphological transformation that occurs immediately prior to seaward migration (termed smoltification). Quantitative trait loci (QTL) analyses were used to identify the number, effects, and genomic location of loci associated with smoltification-related traits, including growth and condition factor, body coloration, morphology, and osmoregulatory enzymes during the smoltification period. Genetic analyses revealed numerous QTL, but one locus in particular is associated with multiple traits in single and joint analyses. Dissecting the genetic architecture of this highly complex trait has profound implications for understanding the genetic and evolutionary basis of life-history diversity within and among migratory fishes.