4.6 Article

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Evolutionary Biology

Temporal and region-specific variations in genome-wide inbreeding effects on female size and reproduction traits of rainbow trout

Katy Paul et al.

Summary: Recent studies have found moderate to high levels of inbreeding in farmed rainbow trout lines, impacting traits such as spawning date and egg weight. Different genomic regions show variable effects of inbreeding on traits, highlighting the complexity of inbreeding depression and its genetic architecture. Region-specific metrics may help in accurately managing the trade-off between genetic merit and the negative effects of inbreeding.

EVOLUTIONARY APPLICATIONS (2022)

Article Biotechnology & Applied Microbiology

Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Carole Blay et al.

Summary: The study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has the potential to improve EPA and DHA proportions in aquaculture species.

BMC GENOMICS (2021)

Article Genetics & Heredity

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

Guangtu Gao et al.

Summary: This study utilizes the Canu pipeline to generate a de-novo assembly of the rainbow trout Arlee line, which is further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds. The assembly includes 32 chromosome sequences and a scaffold with the sex-determination gene (sdY), revealing some features of genetic diversity and genome structure in rainbow trout.

G3-GENES GENOMES GENETICS (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Genetics & Heredity

Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing

Sixin Liu et al.

Summary: This study identified and validated high-confidence SVs in rainbow trout using whole-genome re-sequencing, highlighting the significant contribution of transposable elements to SVs in this species. The findings demonstrated the robustness of the identified SVs and their potential phenotypic effects, providing a foundation for further studies in rainbow trout SVs.

FRONTIERS IN GENETICS (2021)

Article Genetics & Heredity

Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss

Carole Blay et al.

Summary: This study focused on estimating genetic parameters and detecting QTLs associated with growth, yield, and quality traits in rainbow trout. Heritability estimates for most traits were found to be moderate to strong, with polygenic traits identified. Genome-wide association studies identified genomic regions and candidate genes for further validation. MRI showed promise for measuring fat content and distribution, while digital image analysis was useful for quantifying color-related traits.

FRONTIERS IN GENETICS (2021)

Article Fisheries

Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries

Pierre Boudry et al.

Summary: Selective breeding has been successfully utilized in improving profitability and sustainability of aquatic species, and the implementation of genomic selection aims to further predict breeding value. While the potential of genomic selection is evident, customized species-specific applications are necessary to maximize its benefits for the aquaculture sector.

AQUACULTURE REPORTS (2021)

Article Genetics & Heredity

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

Guangtu Gao et al.

Summary: The study utilized the Canu pipeline to generate a de-novo assembly of the Arlee genome from high coverage PacBio long-reads sequence data, which was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to produce 32 major scaffolds. This is the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY).

G3-GENES GENOMES GENETICS (2021)

Article Biochemistry & Molecular Biology

The International Genome Sample Resource (IGSR) collection of open human genomic variation resources

Susan Fairley et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Fisheries

Isogenic lines in fish - a critical review

Roman Franek et al.

REVIEWS IN AQUACULTURE (2020)

Article Biotechnology & Applied Microbiology

Genetic architecture and genomic selection of female reproduction traits in rainbow trout

J. D'Ambrosio et al.

BMC GENOMICS (2020)

Article Biochemistry & Molecular Biology

Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium

Enrique Santiago et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Genetics & Heredity

A Major QTL for Resistance to Vibrio anguillarum in Rainbow Trout

Asma M. Karami et al.

FRONTIERS IN GENETICS (2020)

Article Ecology

Sex-dependent dominance maintains migration supergene in rainbow trout

Devon E. Pearse et al.

NATURE ECOLOGY & EVOLUTION (2019)

Article Agriculture, Dairy & Animal Science

1000 Bull Genomes Project to Map Simple and Complex Genetic Traits in Cattle: Applications and Outcomes

Ben J. Hayes et al.

Annual Review of Animal Biosciences (2018)

Article Agriculture, Dairy & Animal Science

Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon

J. Kijas et al.

ANIMAL GENETICS (2017)

Review Biology

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

Jessica Stapley et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Article Biochemistry & Molecular Biology

Genetic subdivision and candidate genes under selection in North American grey wolves

Rena M. Schweizer et al.

MOLECULAR ECOLOGY (2016)

Article Multidisciplinary Sciences

The Atlantic salmon genome provides insights into rediploidization

Sigbjorn Lien et al.

NATURE (2016)

Article Biology

Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

M. E. Goddard et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2016)

Article Multidisciplinary Sciences

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

Nicola J. Barson et al.

NATURE (2015)

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Article Biochemistry & Molecular Biology

The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout

Y. Palti et al.

MOLECULAR ECOLOGY RESOURCES (2015)

Article Multidisciplinary Sciences

Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

Silvia Teresa Rodriguez-Ramilo et al.

PLOS ONE (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Genetics & Heredity

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds

Salvatore Mastrangelo et al.

BMC GENETICS (2014)

Article Multidisciplinary Sciences

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

Camille Berthelot et al.

NATURE COMMUNICATIONS (2014)

Article Biotechnology & Applied Microbiology

Development of a high density 600K SNP genotyping array for chicken

Andreas Kranis et al.

BMC GENOMICS (2013)

Article Agriculture, Dairy & Animal Science

Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics

L. Silio et al.

JOURNAL OF ANIMAL BREEDING AND GENETICS (2013)

Article Agriculture, Dairy & Animal Science

High-density marker imputation accuracy in sixteen French cattle breeds

Chris Hoze et al.

GENETICS SELECTION EVOLUTION (2013)

Article Genetics & Heredity

Genetic Variants in REC8, RNF212, and PRDM9 Influence Male Recombination in Cattle

Cynthia Sandor et al.

PLOS GENETICS (2012)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors

Cecilia C. Sanchez et al.

BMC GENOMICS (2011)

Review Genetics & Heredity

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

John W. Davey et al.

NATURE REVIEWS GENETICS (2011)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

A map of human genome variation from population-scale sequencing

David Altshuler et al.

NATURE (2010)

Review Genetics & Heredity

Genotype imputation for genome-wide association studies

Jonathan Marchini et al.

NATURE REVIEWS GENETICS (2010)

Editorial Material Biochemistry & Molecular Biology

Centromeres Convert but Don't Cross

Paul B. Talbert et al.

PLOS BIOLOGY (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Genetics & Heredity

A high density linkage map of the bovine genome

Juan A. Arias et al.

BMC GENETICS (2009)

Article Biotechnology & Applied Microbiology

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

Cecilia Castano Sanchez et al.

BMC GENOMICS (2009)

Article Multidisciplinary Sciences

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

Nathan A. Baird et al.

PLOS ONE (2008)

Article Genetics & Heredity

PLINK: A tool set for whole-genome association and population-based linkage analyses

Shaun Purcell et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2007)

Article Fisheries

Wide range of susceptibility to rhabdoviruses in homozygous clones of rainbow trout

Edwige Quillet et al.

FISH & SHELLFISH IMMUNOLOGY (2007)

Article Biochemistry & Molecular Biology

Novel multilocus measure of linkage disequilibrium to estimate past effective population size

BJ Hayes et al.

GENOME RESEARCH (2003)

Review Biology

Chromosome evolution in the Salmonidae (Pisces):: an update

R Phillips et al.

BIOLOGICAL REVIEWS (2001)