-
[show abstract]
[hide abstract]
ABSTRACT: Although migration plays a critical role in the evolution and diversification of species, relatively little is known of the genetic architecture underlying this life history in any species. Rainbow and steelhead trout (Oncorhynchus mykiss) naturally segregate for both resident and migratory life-history types, respectively, as do other members of the salmonid family of fishes. Using an experimental cross derived from wild resident rainbow and wild migratory steelhead trout from Southeast Alaska and high throughput restriction-site associated DNA (RAD) tag sequencing, we perform a quantitative trait locus (QTL) analysis to identify the number, position, and relative contribution of genetic effects on a suite of 27 physiological and morphological traits associated with the migratory life history in this species. In total, 37 QTL are localized to 19 unique QTL positions, explaining 4-13.63% of the variation for 19 of the 27 migration-related traits measured. Two chromosomal positions, one on chromosome Omy12 and the other on Omy14 each harbor 7 QTL for migration-related traits, suggesting that these regions could harbor master genetic controls for the migratory life-history tactic in this species. Another QTL region on Omy5 has been implicated in several studies of adaptive life histories within this species and could represent another important locus underlying the migratory life history. We also evaluate whether loci identified in this out-crossed QTL study colocalize to genomic positions previously identified for associations with migration-related traits in a doubled haploid mapping family.
G3 (Bethesda, Md.). 09/2012; 2(9):1113-27.
-
[show abstract]
[hide abstract]
ABSTRACT: There are large differences between the sexes at the genetic level; these differences include heterogametic sex chromosomes and/or differences in expression of genes between the sexes. In rainbow trout (Oncorhynchus mykiss) qRT-PCR studies have found significant differences in expression of several candidate sex determining genes. However, these genes represent a very small fraction of the genome and research in other species suggests there are large portions of the transcriptome that are differentially expressed between the sexes. These differences are especially noticeable once gonad differentiation and maturation has occurred, but less is known at earlier stages of development. Here we use data from a microarray and qRT-PCR to identify genes differentially expressed between the sexes at three time points in pre-hatch embryos, prior to the known timing of sexual differentiation in this species.
The microarray study revealed 883 differentially expressed features between the sexes with roughly equal numbers of male and female upregulated features across time points. Most of the differentially expressed genes on the microarray were not related to sex function, suggesting large scale differences in gene expression between the sexes are present early in development. Candidate gene analysis revealed sox9, DMRT1, Nr5a1 and wt1 were upregulated in males at some time points and foxl2, ovol1, fst and cyp19a1a were upregulated in females at some time points.
This is the first study to identify sexual dimorphism in expression of the genome during embryogenesis in any fish and demonstrates that transcriptional differences are present before the completion of gonadogenesis.
BMC Genomics 08/2011; 12:404. · 4.07 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In rainbow trout (Oncorhynchus mykiss) and other fishes, embryonic development rate is an ecologically and evolutionarily important trait that is closely associated with survival and physiological performance later in life. To identify genes differentially regulated in fast and slow-developing embryos of rainbow trout, we examined gene expression across developmental time points in rainbow trout embryos possessing alleles linked to a major quantitative trait loci (QTL) for fast versus slow embryonic development rate. Whole genome expression microarray analyses were conducted using embryos from a fourth generation backcross family, whereby each backcross generation involved the introgression of the fast-developing alleles for a major development rate QTL into a slow-developing clonal line of rainbow trout. Embryos were collected at 15, 19, and 28 days post-fertilization; sex and QTL genotype were determined using molecular markers, and cDNA from 48 embryos were used for microarray analysis. A total of 183 features were identified with significant differences between embryonic development rate genotypes. Genes associated with cell cycle growth, muscle contraction and protein synthesis were expressed significantly higher in embryos with the fast-developing allele (Clearwater) than those with the slow-developing allele (Oregon State University), which may associate with fast growth and early body mass construction in embryo development. Across time points, individuals with the fast-developing QTL allele appeared to have earlier onset of these developmental processes when compared to individuals with the slow development alleles, even as early as 15 days post-fertilization. Differentially expressed candidate genes chosen for linkage mapping were localized primarily to regions outside of the major embryonic development rate QTL, with the exception of a single gene (very low-density lipoprotein receptor precursor).
Marine Biotechnology 03/2010; 13(2):215-31. · 3.43 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Distinct morphological variation is often associated with variation in life histories within and among populations of both plants and animals. In this study, we examined the heritability of morphology in three hatchery strains of brook trout (Salvelinus fontinalis), which were historically or are currently used for stocking and supplementation of both migratory and resident ecotypes in the upper Great Lakes region. In a common garden experiment, significant variation in body morphology was observed within and across populations sampled at three time periods. The most notable differences among strains were differences in dorso-ventral body depth and the shape of the caudal peduncle, with some differences in the anterior-posterior placement of the dorsal and ventral fins. Variation with and among 70 half-sib families indicates that heritabilities of morphology and body size were significant at most developmental time points both within and across strains. Heritabilities for morphological characters within strains ranged from 0 to 0.95 across time points. Significant within-strain heritabilities for length ranged from 0 to 0.93 across time points and for weight ranged from 0 to 0.88. Significant additive genetic variation exists within and across hatchery brook trout strains for morphology and size, indicating that these traits are capable of responding to natural or artificial selection.
PLoS ONE 01/2010; 5(9):e12950. · 4.09 Impact Factor
-
Krista M. Nichols
08/2009: pages 195 - 216; , ISBN: 9780813807379
-
[show abstract]
[hide abstract]
ABSTRACT: 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.
Genetics 07/2008; 179(3):1559-75. · 4.01 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Effects of maternal cytoplasmic environment (MCE) on development rate in rainbow trout were evaluated within a quantitative trait loci (QTL) analysis framework. Previous research had identified QTL for development rate in doubled haploid (DH) progeny produced from a cross between the Oregon State University (OSU) and the Swanson (SW) River rainbow trout clonal lines. In this study, progeny for QTL mapping were produced from a cross between the OSU and Clearwater (CW) River clonal lines. Doubled haploids were produced from the OSU x CW F1 by androgenesis using eggs from different females (or MCEs); with androgenesis, the maternal nuclear genome was destroyed by irradiation and diploidy was restored by blocking the first embryonic cleavage by heat shock. All embryos were incubated at the same temperature and development rate quantified as time to hatch. Using a linkage map constructed primarily with AFLP markers, QTL mapping was performed, including MCE covariates and QTL x MCE effects in models for testing. The major QTL for development rate in the OSU x SW cross overlaps with the major QTL found in this OSU x CW cross; effects at this locus were the same across MCEs. Both MCE and QTL x MCE effects contribute to variability in development rate, but QTL x MCE were minor and detected only at small-effect QTL.
Genetics 02/2007; 175(1):335-47. · 4.01 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The rainbow trout genetic linkage groups have been assigned to specific chromosomes in the OSU (2N=60) strain using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group. There was a rough correlation between chromosome size and size of the genetic linkage map in centimorgans for the genetic maps based on recombination from the female parent. Chromosome size and structure have a major impact on the female:male recombination ratio, which is much higher (up to 10:1 near the centromeres) on the larger metacentric chromosomes compared to smaller acrocentric chromosomes. Eighty percent of the BAC clones containing duplicate genes mapped to a single chromosomal location, suggesting that diploidization resulted in substantial divergence of intergenic regions. The BAC clones that hybridized to both duplicate loci were usually located in the distal portion of the chromosome. Duplicate genes were almost always found at a similar location on the chromosome arm of two different chromosome pairs, suggesting that most of the chromosome rearrangements following tetraploidization were centric fusions and did not involve homeologous chromosomes. The set of BACs compiled for this research will be especially useful in construction of genome maps and identification of QTL for important traits in other salmonid fishes.
Genetics 12/2006; 174(3):1661-70. · 4.01 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The DNA vaccine based on the glycoprotein gene of Infectious hematopoietic necrosis virus induces a non-specific anti-viral immune response and long-term specific immunity against IHNV. This study characterized gene expression responses associated with the early anti-viral response. Homozygous rainbow trout were injected intra-muscularly (I.M.) with vector DNA or the IHNV DNA vaccine. Gene expression in muscle tissue (I.M. site) was evaluated using a 16,008 feature salmon cDNA microarray. Eighty different genes were significantly modulated in the vector DNA group while 910 genes were modulated in the IHNV DNA vaccinate group relative to control group. Quantitative reverse-transcriptase PCR was used to examine expression of selected immune genes at the I.M. site and in other secondary tissues. In the localized response (I.M. site), the magnitudes of gene expression changes were much greater in the vaccinate group relative to the vector DNA group for the majority of genes analyzed. At secondary systemic sites (e.g. gill, kidney and spleen), type I IFN-related genes were up-regulated in only the IHNV DNA vaccinated group. The results presented here suggest that the IHNV DNA vaccine induces up-regulation of the type I IFN system across multiple tissues, which is the functional basis of early anti-viral immunity.
Molecular Immunology 06/2006; 43(13):2089-106. · 2.90 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Quantitative trait locus (QTL) mapping methodology for continuous normally distributed traits is the subject of much attention in the literature. Binary trait locus (BTL) mapping in experimental populations has received much less attention. A binary trait by definition has only two possible values, and the penetrance parameter is restricted to values between zero and one. Due to this restriction, the infinitesimal model appears to come into play even when only a few loci are involved, making selection of an appropriate genetic model in BTL mapping challenging. We present a probability model for an arbitrary number of BTL and demonstrate that, given adequate sample sizes, the power for detecting loci is high under a wide range of genetic models, including most epistatic models. A novel model selection strategy based upon the underlying genetic map is employed for choosing the genetic model. We propose selecting the "best" marker from each linkage group, regardless of significance. This reduces the model space so that an efficient search for epistatic loci can be conducted without invoking stepwise model selection. This procedure can identify unlinked epistatic BTL, demonstrated by our simulations and the reanalysis of Oncorhynchus mykiss experimental data.
Genetics 08/2005; 170(3):1281-97. · 4.01 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Meristic trait variation among species and populations has long been used as the basis for identification and classification
of fishes. Within Oncorhynchus mykiss, there is considerable variation in meristic characters such as numbers of vertebrae, lateral line scales, fin rays, gill
rakers, and pyloric caeca. In our laboratory the Oregon State University (OSU) rainbow trout and the Clearwater River (CW)
steelhead trout clonal lines, produced by androgenesis, exhibit significant differences in values for meristic traits, making
quantitative trait locus (QTL) analysis of these meristic characters possible. Our objective was to determine the number,
location, and effects of QTL associated with meristic characters in order to test two hypotheses: (1) that QTL for different
meristic traits co-localize to the same linkage group and (2) that meristic trait QTL co-localize to the same linkage group
as a previously identified development rate QTL. Doubled haploid individuals, produced by androgenesis from sperm from an
F1 hybrid between the OSU and CW lines, were used to evaluate the joint segregation of each meristic phenotype and Amplified
Fragment Length Polymorphic marker genotypes. Composite interval mapping revealed QTL for six of the seven traits analyzed.
One QTL each for scales above the lateral line and for gill rakers co-localized to the same position. Only one QTL for scales
above the lateral line co-localized to the same region as that for the development rate QTL, but a greater map resolution
is necessary to determine if these loci are truly the same. We failed to detect pleiotropy for most meristic trait QTL. Our
results suggest that different major loci are associated with variation in each meristic character and that the expression
of these loci may be influenced by maternal and external environmental factors.
Environmental Biology of Fishes 02/2004; 69(1):317-331. · 0.91 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Ceratomyxa shasta is enzootic to some rivers of the Pacific Northwest and California, and has caused extensive mortalities of salmonids, the only known host of the actinosporean stage of the pathogen. Mortalities from C. shasta are induced by severe inflammation and necrosis of the intestinal tract, and no therapeutants have been discovered for the treatment of ceratomyxosis. Inheritance studies by previous investigators suggested that C. shasta resistance is genetically controlled, but none have revealed the number and locations of gene regions associated with resistance. Here, we characterized differences in resistance among clonal lines, and used line crosses between clonal lines with resistance differences for a genetic analysis of C. shasta resistance in Oncorhynchus mykiss, following a short term in situ exposure to the pathogen. We found that Oregon State University (OSU) x Arlee (ARL) clonal hybrids were highly susceptible, while OSU x Clearwater (CW) hybrids were highly resistant to C. shasta. Doubled haploids, produced by androgenesis from an F1 hybrid between the OSU and CW lines, were evaluated for the co-segregation of molecular markers and resistance phenotype. Amplified fragment length polymorphic (AFLP) markers, used to construct a genetic linkage map in this cross, were tested for associations with resistance expressed as absolute survival (binary trait) and days to death (survival analysis). Segregation of the resistance phenotype suggested that the resistance was inherited as a single Mendelian locus, but the binary trait failed to map to a single genomic location. Markers identified in single-marker analyses were used in multiple-regression model selection, within both the linear regression and Cox proportional-hazards survival analysis frameworks, to determine the number and potential location of loci simultaneously contributing to variation in the survival phenotypes of doubled-haploid progeny. We found multiple genomic loci associated with C. shasta resistance through these models, confirming studies by previous investigators that suggested C. shasta resistance is polygenic.
Diseases of Aquatic Organisms 10/2003; 56(2):145-54. · 2.20 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Novel immune-type receptor ( NITR) genes that encode two extracellular immunoglobulin domains and cytoplasmic immunoreceptor tyrosine-based inhibition motifs (ITIMs) have been described previously in three lineages of bony fish. In the current study, four ITIM-containing NITR cDNAs are identified in the rainbow trout ( Oncorhynchus mykiss), and their expression patterns and genomic complexity are characterized. The ITIM-containing NITR2 gene maps 1.3 cM from an ITIM-containing C-type lectin receptor ( TCL-2) on linkage group XXI. A comprehensive, phylogenetic analysis of NITRs from rainbow trout and three other major lineages of bony fish defines conserved families of NITRs and suggests an ancient lineage of distinct groups of genes. Several probable scenarios that explain the origins of variant forms of NITRs are described.
Immunogenetics 01/2003; 54(9):662-70. · 2.93 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Backcrosses of clonal rainbow trout, Oncorhynchus mykiss, were used in an effort for fine-mapping of a quantitative trait locus (QTL) for rapid embryonic development rate (tth-1). A previously identified QTL was backcrossed for two successive generations from the Clearwater (fast developing) line into the Oregon State University (OSU) (slow developing) background. Microsatellites tightly linked to the QTL and each other were used to genotype individuals in both backcrosses. An association was found between the microsatellites and gamete production in the first backcross and precocious gamete production in the second backcross generation. These results suggest that a region near the QTL-linked microsatellites may influence early sexual maturity, as well as development rate. Two gynogenetic families were produced using individuals from the first backcross (BC1). These crosses were screened with the tth-1 linked microsatellites and time to hatch was quantified. The Clearwater genotype was associated with early time to hatch, while the OSU genotype was associated with late hatching. Genotypic variation at these microsatellite loci explained 28% and 26% of the variation in time to hatch. Heterozygote frequencies for the microsatellites in the two gynogenetic families were 0.0088 and 0.01, suggesting that the QTL is near the centromere. Fine-mapping was limited due to the low level of recombination observed on this linkage group in the gynogenetic families.
Aquaculture.
-
[show abstract]
[hide abstract]
ABSTRACT: Infectious hematopoietic necrosis (IHN) is a rhabdoviral disease of salmonid species. Single strand conformation polymorphism (SSCP) was used to identify association between DNA polymorphism of the major histocompatibility complex (MHC) class II beta-chain intron and IHN virus (IHNV) resistance in backcrosses of rainbow trout (Oncorhynchus mykiss) and cutthroat trout (O. clarki). Association was significant (P=0.024) in four half-sib families from one sire (number 2), but not among half-sibs from another sire (number 1). DNA sequencing analysis revealed that the polymorphism originating from sire 1 is the result of a single base substitution. Sire 2 polymorphism was caused by three different base substitutions. The source of the susceptible allele appears to be from cutthroat trout and not from the rainbow trout population used to produce the hybrids. The results suggest that MHC polymorphism can contribute to linkage and association studies of immunity to infectious diseases in rainbow trout.
Aquaculture.
