An application of Bayesian QTL mapping to early development in double haploid lines of rainbow trout including environmental effects

A Bayesian model and variable dimensional parameter estimation based on Markov chain Monte Carlo was applied to map quantitative trait loci (QTLs) in a doubled haploid mapping population of rainbow trout. To increase power, the analysis was performed using the multiple-QTL model, which simultaneously accounted for all the environmental and genetic main effects that influence the expression of early development life history traits. By doing so we obtained the posterior estimated effects for the environmental factors as well as the number, positions, and the effects for the QTLs. The analyses revealed QTLs for time at hatching, embryonic length and weight at swim-up stage. The posterior expectation of the number of QTLs in different linkage groups shows that at least four QTLs are needed to explain the observed differences in early development between the clonal lines. The Bayesian method effectively combined all the information available to accurately position these QTLs in the rainbow trout genome.

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QTL analysis of seed germination traits in tobacco (Nicotiana tabacum L.)

Journal of Applied Genetics ◽

10.1007/s13353-021-00623-6 ◽

2021 ◽

Author(s):

Monika Agacka-Mołdoch ◽

Mian Abdur Rehman Arif ◽

Ulrike Lohwasser ◽

Teresa Doroszewska ◽

Ramsey S. Lewis ◽

...

Keyword(s):

Nicotiana Tabacum ◽

Seed Germination ◽

Doubled Haploid ◽

Mapping Population ◽

Area Under The Curve ◽

Linkage Groups ◽

Polygenic Control ◽

Nicotiana Tabacum L ◽

Controlled Deterioration ◽

Germination Traits

AbstractGenetic mapping of seed germination traits has been performed with many plant species. In tobacco, however, investigations are rare. In the present study, a bi-parental mapping population consisting of 118 doubled haploid lines and derived from a cross between ‘Beinhart-1000’ and ‘Hicks’ was investigated. Four germination-related traits, total germination (TG), normal germination (NG), time to reach 50% of total germination (T50), and the area under the curve after 200 h of germination (AUC) were considered by examining seeds either untreated or after a moderate controlled deterioration (CD). Quantitative trait loci were found for all traits distributed on 11 out of the 24 linkage groups. It was demonstrated that, as in many other species, germination-related traits are very complex and under polygenic control.

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Assignment of Chinook Salmon (Oncorhynchus tshawytscha)Linkage Groups to Specific Chromosomes Reveals a Karyotype with Multiple Rearrangements of the Chromosome Arms of Rainbow Trout (Oncorhynchus mykiss)

G3 Genes|Genome|Genetics ◽

10.1534/g3.113.008078 ◽

2013 ◽

Vol 3 (12) ◽

pp. 2289-2295 ◽

Cited By ~ 15

Author(s):

Ruth B. Phillips ◽

Linda K. Park ◽

Kerry A. Naish

Keyword(s):

Rainbow Trout ◽

Oncorhynchus Mykiss ◽

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Linkage Groups ◽

Rainbow Trout Oncorhynchus Mykiss

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Behavioral Differences Among Rainbow Trout Clonal Lines

Behavior Genetics ◽

10.1023/b:bege.0000017879.68818.21 ◽

2004 ◽

Vol 34 (3) ◽

pp. 355-365 ◽

Cited By ~ 30

Author(s):

Megan D. Lucas ◽

Robert E. Drew ◽

Paul A. Wheeler ◽

Paul A. Verrell ◽

Gary H. Thorgaard

Keyword(s):

Rainbow Trout ◽

Behavioral Differences ◽

Clonal Lines

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A Detailed Linkage Map of Rainbow Trout Produced Using Doubled Haploids

Genetics ◽

10.1093/genetics/148.2.839 ◽

1998 ◽

Vol 148 (2) ◽

pp. 839-850

Author(s):

William P Young ◽

Paul A Wheeler ◽

Virginia H Coryell ◽

Paul Keim ◽

Gary H Thorgaard

Keyword(s):

Rainbow Trout ◽

Linkage Map ◽

Tandem Repeats ◽

Simple Sequence Repeat Locus ◽

Doubled Haploids ◽

Variable Number ◽

Linkage Groups ◽

Chromosomal Distribution ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Genomic Studies

Abstract We report the first detailed genetic linkage map of rainbow trout (Oncorhynchus mykiss). The segregation analysis was performed using 76 doubled haploid rainbow trout produced by androgenesis from a hybrid between the “OSU” and “Arlee” androgenetically derived homozygous lines. Four hundred and seventy-six markers segregated into 31 major linkage groups and 11 small groups (<5 markers/group). The minimum genome size is estimated to be 2627.5 cM in length. The sex-determining locus segregated to a distal position on one of the linkage groups. We analyzed the chromosomal distribution of three classes of markers: (1) amplified fragment length polymorphisms, (2) variable number of tandem repeats, and (3) markers obtained using probes homologous to the 5′ or 3′ end of salmonid-specific small interspersed nuclear elements. Many of the first class of markers were clustered in regions that appear to correspond to centromeres. The second class of markers were more telomeric in distribution, and the third class were intermediate. Tetrasomic inheritance, apparently related to the tetraploid ancestry of salmonid fishes, was detected at one simple sequence repeat locus and suggested by the presence of one extremely large linkage group that appeared to consist of two smaller groups linked at their tips. The double haploid rainbow trout lines and linkage map present a foundation for further genomic studies.

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Intraspecific phenotypic variation in life history traits ofDaphnia galeatapopulations in response to fish kairomones

PeerJ ◽

10.7717/peerj.5746 ◽

2018 ◽

Vol 6 ◽

pp. e5746 ◽

Cited By ~ 9

Author(s):

Verena Tams ◽

Jennifer Lüneburg ◽

Laura Seddar ◽

Jan-Phillip Detampel ◽

Mathilde Cordellier

Keyword(s):

Life History ◽

Environmental Change ◽

Phenotypic Variation ◽

Life History Traits ◽

Common Garden ◽

Population Level ◽

Geometric Morphometric ◽

Fish Kairomones ◽

Geometric Morphometric Analysis ◽

Clonal Lines

Phenotypic plasticity is the ability of a genotype to produce different phenotypes depending on the environment. It has an influence on the adaptive potential to environmental change and the capability to adapt locally. Adaptation to environmental change happens at the population level, thereby contributing to genotypic and phenotypic variation within a species. Predation is an important ecological factor structuring communities and maintaining species diversity. Prey developed different strategies to reduce their vulnerability to predators by changing their behaviour, their morphology or their life history. Predator-induced life history responses inDaphniahave been investigated for decades, but intra-and inter-population variability was rarely addressed explicitly. We addressed this issue by conducting a common garden experiment with 24 clonal lines of EuropeanDaphnia galeataoriginating from four populations, each represented by six clonal lines. We recorded life history traits in the absence and presence of fish kairomones. Additionally, we looked at the shape of experimental individuals by conducting a geometric morphometric analysis, thus assessing predator-induced morphometric changes. Our data revealed high intraspecific phenotypic variation within and between fourD. galeatapopulations, the potential to locally adapt to a vertebrate predator regime as well as an effect of the fish kairomones on morphology ofD. galeata.

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TEMPERATURE AND MYOGENIC FACTOR TRANSCRIPT LEVELS DURING EARLY DEVELOPMENT DETERMINES MUSCLE GROWTH POTENTIAL IN RAINBOW TROUT(ONCORHYNCHUS MYKISS) AND SEA BASS (DICENTRARCHUS LABRAX)

Journal of Experimental Biology ◽

10.1242/jeb.204.16.2763 ◽

2001 ◽

Vol 204 (16) ◽

pp. 2763-2771 ◽

Cited By ~ 3

Author(s):

D. WILKES ◽

S. Q. XIE ◽

N. C. STICKLAND ◽

H. ALAMI-DURANTE ◽

M. KENTOURI ◽

...

Keyword(s):

Rainbow Trout ◽

Muscle Fibre ◽

Early Development ◽

Sea Bass ◽

Growth Potential ◽

Mrna Levels ◽

European Sea Bass ◽

Transcript Levels ◽

Fibre Number ◽

Sea Bass Larvae

SUMMARY The influence of changes in environmental temperature on the mRNA levels of myogenic regulatory factors (MRFs), i.e. MyoD and myogenin, as well as myosin heavy chain (MyHC) were studied during early larval development in rainbow trout and sea bass. Phosphoimager analysis of northern blots indicated that there is an optimum temperature for the RNA transcript levels of MRF and MyHC RNA in trout and in sea bass larvae. In the trout strain studied, the highest concentration for MRF and MyHC transcripts was found at 8°C rather than 4°C or 20°C. In European sea bass, the highest concentrations of MRF and MyHC mRNA were observed at 15-20°C rather than 13°C. Raising sea bass larvae at 15°C was associated with higher MyHC gene expression as well as a trend towards an increase in total muscle fibre number and higher growth rates after transfer at ambient temperature. Results suggest that mRNA levels of MRF and MyHC can be used to optimise early development. An experiment in which the temperature was changed illustrates the consequence of precise temporal expression of MRF genes in specifying muscle fibre number at critical stages during early development.

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Polymorphism and differentiation of rainbow trout Y chromosomes

Genome ◽

10.1139/g04-059 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1105-1113 ◽

Cited By ~ 21

Author(s):

Alicia Felip ◽

Atushi Fujiwara ◽

William P Young ◽

Paul A Wheeler ◽

Marc Noakes ◽

...

Keyword(s):

Rainbow Trout ◽

Y Chromosome ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Morphological Differentiation ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Y Chromosomes ◽

Cytogenetic Analyses ◽

Clonal Lines ◽

Sex Locus

Most fish species show little morphological differentiation in the sex chromosomes. We have coupled molecular and cytogenetic analyses to characterize the male-determining region of the rainbow trout (Oncorhynchus mykiss) Y chromosome. Four genetically diverse male clonal lines of this species were used for genetic and physical mapping of regions in the vicinity of the sex locus. Five markers were genetically mapped to the Y chromosome in these male lines, indicating that the sex locus was located on the same linkage group in each of the lines. We also confirmed the presence of a Y chromosome morphological polymorphism among these lines, with the Y chromosomes from two of the lines having the more common heteromorphic Y chromosome and two of the lines having Y chromosomes morphologically similar to the X chromosome. The fluorescence in situ hybridization (FISH) pattern of two probes linked to sex suggested that the sex locus is physically located on the long arm of the Y chromosome. Fishes appear to be an excellent group of organisms for studying sex chromosome evolution and differentiation in vertebrates because they show considerable variability in the mechanisms and (or) patterns involved in sex determination.Key words: sex chromosomes, sex markers, cytogenetics, rainbow trout, fish.

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Intra- and inter-specific mitochondrial DNA sequence divergence in Salmo: rainbow, steelhead, and cutthroat trouts

Canadian Journal of Zoology ◽

10.1139/z85-307 ◽

1985 ◽

Vol 63 (9) ◽

pp. 2088-2094 ◽

Cited By ~ 29

Author(s):

Gary M. Wilson ◽

W. Kelley Thomas ◽

Andrew T. Beckenbach

Keyword(s):

Mitochondrial Dna ◽

Rainbow Trout ◽

Life Histories ◽

Sequence Divergence ◽

Cutthroat Trout ◽

Restriction Enzymes ◽

Restriction Endonuclease Analysis ◽

Salmo Gairdneri ◽

Intraspecific Divergence ◽

Clonal Lines

Two forms of Salmo gairdneh with different life histories (steelhead and rainbow trout) were compared using restriction endonuclease analysis of mitochondrial DNA. A total of 19 individuals from four populations were studied for each of the two forms, using 14 restriction enzymes. In addition, five cutthroat trout samples were included as an interspecific comparison. These enzymes revealed a total of 81 cut sites, representing a sample of more than 400 nucleotides per fish. Of these sites, 25 were phylogenetically informative, dividing the 43 fish into 10 clonal lines, 8 Salmo gairdneri and 2 Salmo clarki. Results indicated detectable divergence between all geographic populations of steelhead and rainbow trout except Pennask rainbow trout, Coquihalla steelhead, and Wampus Creek rainbow trout. Other steelhead populations analysed showed a closer phylogenetic relationship to each other than to rainbow trout populations analysed. Intraspecific divergence was in most cases 1% or less, with a 1.5% maximum. Interspecific divergence between S. gairdneri and S. clarki was between 2% and 3.5%.

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