Using next-generation sequencing to isolate mutant genes from forward genetic screens

Mapping-by-sequencing accelerates forward genetics in barley

(2014) Martin Mascher et al.   GENOME BIOLOGY

BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower

(2013) Maren Livaja et al.   BMC GENOMICS

Rapid identification of kidney cyst mutations by whole exome sequencing in zebrafish

(2013) S. Ryan et al.   DEVELOPMENT

Forward Genetics by Genome Sequencing Reveals That Rapid Cyanide Release Deters Insect Herbivory of Sorghum bicolor

(2013) K. Krothapalli et al.   GENETICS

RNA-seq-based mapping and candidate identification of mutations from forward genetic screens

(2013) A. C. Miller et al.   GENOME RESEARCH

MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq

(2013) J. T. Hill et al.   GENOME RESEARCH

Perspectives for identification of mutations in the zebrafish: Making use of next-generation sequencing technologies for forward genetic approaches

(2013) Katrin Henke et al.   METHODS

Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments

(2013) Ray Tobler et al.   MOLECULAR BIOLOGY AND EVOLUTION

The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK

(2013) Rajinder Singh et al.   NATURE

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

(2013) Karl J V Nordström et al.   NATURE BIOTECHNOLOGY

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined withde novoassembly of gap regions identifies the rice blast resistance genePii

(2013) Hiroki Takagi et al.   NEW PHYTOLOGIST

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

(2013) Hiroki Takagi et al.   PLANT JOURNAL

Mapping of Quantitative Trait Loci Underlying Cold Tolerance in Rice Seedlings via High-Throughput Sequencing of Pooled Extremes

(2013) Zemao Yang et al.   PLoS One

MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice

(2013) Rym Fekih et al.   PLoS One

Whole Genome Sequencing Identifies a Deletion in Protein Phosphatase 2A That Affects Its Stability and Localization in Chlamydomonas reinhardtii

(2013) Huawen Lin et al.   PLoS Genetics

The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

(2013) Erik Wijnker et al.   eLife

Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines

(2013) Robert S. Allen et al.   Frontiers in Plant Science

Network-enabled gene expression analysis

(2012) David Edwards et al.   BMC BIOINFORMATICS

Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing

(2012) Florencia del Viso et al.   BMC GENOMICS

Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria

(2012) Katarzyna KINGA Modrzynska et al.   BMC GENOMICS

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

(2012) Martin Trick et al.   BMC PLANT BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

(2012) Pablo A. Manavella et al.   CELL

Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing

(2012) N. Obholzer et al.   DEVELOPMENT

SNP-Ratio Mapping (SRM): Identifying Lethal Alleles and Mutations in Complex Genetic Backgrounds by Next-Generation Sequencing

(2012) H. Lindner et al.   GENETICS

Gene Discovery Using Mutagen-Induced Polymorphisms and Deep Sequencing: Application to Plant Disease Resistance

(2012) Y. Zhu et al.   GENETICS

CloudMap: A Cloud-Based Pipeline for Analysis of Mutant Genome Sequences

(2012) Gregory Minevich et al.   GENETICS

Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana

(2012) E. J. Belfield et al.   GENOME RESEARCH

Mutation mapping and identification by whole-genome sequencing

(2012) I. Leshchiner et al.   GENOME RESEARCH

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

(2012) V. Nolte et al.   GENOME RESEARCH

Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis

(2012) S. Swinnen et al.   GENOME RESEARCH

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Fast Isogenic Mapping-by-Sequencing of Ethyl Methanesulfonate-Induced Mutant Bulks

(2012) B. Hartwig et al.   PLANT PHYSIOLOGY

Fast Homozygosity Mapping and Identification of a Zebrafish ENU-Induced Mutation by Whole-Genome Sequencing

(2012) Marianne L. Voz et al.   PLoS One

Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

(2012) Sanzhen Liu et al.   PLoS One

Population bulk segregant mapping uncovers resistance mutations and the mode of action of a chitin synthesis inhibitor in arthropods

(2012) T. Van Leeuwen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex Chromosomal Exome Sequencing Accelerates Identification of ENU-Induced Mutations in the Mouse

(2012) Miao Sun et al.   G3-Genes Genomes Genetics

Whole-Genome Sequencing to Identify Mutants and Polymorphisms in Chlamydomonas reinhardtii

(2012) Susan K. Dutcher et al.   G3-Genes Genomes Genetics

Whole-Genome Sequencing of Sordaria macrospora Mutants Identifies Developmental Genes

(2012) Minou Nowrousian et al.   G3-Genes Genomes Genetics

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

(2012) T. D. Andrews et al.   Open Biology

Efficient mutation identification in zebrafish by microarray capturing and next generation sequencing

(2011) Franck Bontems et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach

(2011) Michal Mokry et al.   BMC GENOMICS

Identification of genes required for de novo DNA methylation in Arabidopsis

(2011) Maxim V.C. Greenberg et al.   Epigenetics

Bulk Segregant Analysis Followed by High-Throughput Sequencing Reveals the Neurospora Cell Cycle Gene, ndc-1 , To Be Allelic with the Gene for Ornithine Decarboxylase, spe-1

(2011) Kyle R. Pomraning et al.   EUKARYOTIC CELL

Rapid Identification of a Disease Allele in Mouse Through Whole Genome Sequencing and Bulk Segregation Analysis

(2011) C. N. Arnold et al.   GENETICS

Efficient Mapping and Cloning of Mutations in Zebrafish by Low-Coverage Whole-Genome Sequencing

(2011) M. E. Bowen et al.   GENETICS

Identification and Characterization of Genes Required for Compensatory Growth inDrosophila

(2011) Abigail R. Gerhold et al.   GENETICS

Rapid Mapping and Identification of Mutations inCaenorhabditis elegansby Restriction Site-Associated DNA Mapping and Genomic Interval Pull-Down Sequencing

(2011) Sean M. O’Rourke et al.   GENETICS

Revealing the genetic structure of a trait by sequencing a population under selection

(2011) L. Parts et al.   GENOME RESEARCH

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

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Identification of EMS-Induced Causal Mutations in a Non-Reference Arabidopsis thaliana Accession by Whole Genome Sequencing

(2011) N. Uchida et al.   PLANT AND CELL PHYSIOLOGY

Next-generation mapping of Arabidopsis genes

(2011) Ryan S. Austin et al.   PLANT JOURNAL

Mutation Detection with Next-Generation Resequencing through a Mediator Genome

(2011) Omri Wurtzel et al.   PLoS One

Phenotype Sequencing: Identifying the Genes That Cause a Phenotype Directly from Pooled Sequencing of Independent Mutants

(2011) Marc A. Harper et al.   PLoS One

Fast-forward genetics enabled by new sequencing technologies

(2011) Korbinian Schneeberger et al.   TRENDS IN PLANT SCIENCE

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa

(2011) Kevin McCluskey et al.   G3-Genes Genomes Genetics

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

(2011) Paul M. Magwene et al.   PLoS Computational Biology

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

(2011) Thomas L. Turner et al.   PLoS Genetics

Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis

(2011) Kevin Ashelford et al.   GENOME BIOLOGY

Mutation discovery in mice by whole exome sequencing

(2011) Heather Fairfield et al.   GENOME BIOLOGY

Calling SNPs without a reference sequence

(2010) Aakrosh Ratan et al.   BMC BIOINFORMATICS

Discovery of Mutations in Saccharomyces cerevisiae by Pooled Linkage Analysis and Whole-Genome Sequencing

(2010) S. R. Birkeland et al.   GENETICS

A Strategy for Direct Mapping and Identification of Mutations by Whole-Genome Sequencing

(2010) Steven Zuryn et al.   GENETICS

Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing

(2010) H. Wang et al.   GENOME RESEARCH

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

C. elegans Mutant Identification with a One-Step Whole-Genome-Sequencing and SNP Mapping Strategy

(2010) Maria Doitsidou et al.   PLoS One

Microtubule Actin Crosslinking Factor 1 Regulates the Balbiani Body and Animal-Vegetal Polarity of the Zebrafish Oocyte

(2010) Tripti Gupta et al.   PLoS Genetics

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

(2010) Jared W. Wenger et al.   PLoS Genetics

Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

(2010) Nara L. M. Sobreira et al.   PLoS Genetics

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

(2009) Ryan Lister et al.   CURRENT OPINION IN PLANT BIOLOGY

Identification of EMS-Induced Mutations in Drosophila melanogaster by Whole-Genome Sequencing

(2009) J. P. Blumenstiel et al.   GENETICS

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

(2009) S. Liu et al.   GENETICS

Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing

(2009) D. V. Irvine et al.   GENOME RESEARCH

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing

(2009) J. T. Cuperus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Systematic Approach to Mapping Recessive Disease Genes in Individuals from Outbred Populations

(2009) Friedhelm Hildebrandt et al.   PLoS Genetics

Rapid whole-genome mutational profiling using next-generation sequencing technologies

(2008) D. R. Smith et al.   GENOME RESEARCH

Caenorhabditis elegans mutant allele identification by whole-genome sequencing

(2008) Sumeet Sarin et al.   NATURE METHODS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies

(2008) Anjana Srivatsan et al.   PLoS Genetics

The art and design of genetic screens: maize

(2007) Héctor Candela et al.   NATURE REVIEWS GENETICS