Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing

Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato

(2015) Kenta Shirasawa et al.   PLANT BIOTECHNOLOGY JOURNAL

Optimization of crop productivity in tomato using induced mutations in the florigen pathway

(2014) Soon Ju Park et al.   NATURE GENETICS

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Tobacco rattle virus–based virus-induced gene silencing in Nicotiana benthamiana

(2014) Muthappa Senthil-Kumar et al.   Nature Protocols

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

(2014) Korbinian Schneeberger   NATURE REVIEWS GENETICS

microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development

(2014) Geraldo Felipe Ferreira e Silva et al.   PLANT JOURNAL

Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developingSolanum lycopersicum(tomato) fruit

(2014) Sophie Colombié et al.   PLANT JOURNAL

Identification of the carotenoid modifying genePALE YELLOW PETAL 1as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum)

(2014) Tohru Ariizumi et al.   PLANT JOURNAL

The tomato mutationnxd1reveals a gene necessary for neoxanthin biosynthesis and demonstrates that violaxanthin is a sufficient precursor for abscisic acid biosynthesis

(2014) Hadar Neuman et al.   PLANT JOURNAL

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

(2014) C. Sauvage et al.   PLANT PHYSIOLOGY

Hairy Root Transformation Using Agrobacterium rhizogenes as a Tool for Exploring Cell Type-Specific Gene Expression and Function Using Tomato as a Model

(2014) M. Ron et al.   PLANT PHYSIOLOGY

Efficient Gene Editing in Tomato in the First Generation Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated9 System

(2014) C. Brooks et al.   PLANT PHYSIOLOGY

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape

(2014) Y. Ichihashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

(2013) Mathilde Causse et al.   BMC GENOMICS

Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

(2013) H. Hirakawa et al.   DNA RESEARCH

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

Inhibition of CUTIN DEFICIENT 2 Causes Defects in Cuticle Function and Structure and Metabolite Changes in Tomato Fruit

(2013) Junji Kimbara et al.   PLANT AND CELL PHYSIOLOGY

Genome-Wide Analysis of Intraspecific DNA Polymorphism in ‘Micro-Tom’, a Model Cultivar of Tomato (Solanum lycopersicum)

(2013) Masaaki Kobayashi et al.   PLANT AND CELL PHYSIOLOGY

Investigating the role of vitamin C in tomato through TILLING identification of ascorbate-deficient tomato mutants

(2013) Pierre Baldet et al.   Plant Biotechnology

Micro-Tom mutants for functional analysis of target genes and discovery of new alleles in tomato

(2013) Daniel Just et al.   Plant Biotechnology

A Role for APETALA1/FRUITFULL Transcription Factors in Tomato Leaf Development

(2013) Y. Burko et al.   PLANT CELL

Analyses of Tomato Fruit Brightness Mutants Uncover Both Cutin-Deficient and Cutin-Abundant Mutants and a New Hypomorphic Allele of GDSL Lipase

(2013) J. Petit et al.   PLANT PHYSIOLOGY

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

(2013) Rym Fekih et al.   PLoS One

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

(2013) M. Itkin et al.   SCIENCE

Biochemical and histological characterization of tomato mutants

(2012) Carolina C. Monteiro et al.   ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS

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

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

The identification of cutin synthase: formation of the plant polyester cutin

(2012) Trevor H Yeats et al.   Nature Chemical Biology

Synchronization of the flowering transition by the tomato TERMINATING FLOWER gene

(2012) Cora A MacAlister et al.   NATURE GENETICS

The tomato SlSHINE3 transcription factor regulates fruit cuticle formation and epidermal patterning

(2012) Jian Xin Shi et al.   NEW PHYTOLOGIST

Failure of the Tomato Trans-Acting Short Interfering RNA Program to Regulate AUXIN RESPONSE FACTOR3 and ARF4 Underlies the Wiry Leaf Syndrome

(2012) T. Yifhar et al.   PLANT CELL

Pleiotropic Phenotypes of the sticky peel Mutant Provide New Insight into the Role of CUTIN DEFICIENT2 in Epidermal Cell Function in Tomato

(2012) S. S. Nadakuduti et al.   PLANT PHYSIOLOGY

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening

(2011) Antoine L. F. Gady et al.   MOLECULAR BREEDING

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Tomato TILLING Technology: Development of a Reverse Genetics Tool for the Efficient Isolation of Mutants from Micro-Tom Mutant Libraries

(2011) Yoshihiro Okabe et al.   PLANT AND CELL PHYSIOLOGY

TOMATOMA: A Novel Tomato Mutant Database Distributing Micro-Tom Mutant Collections

(2011) Takeshi Saito et al.   PLANT AND CELL PHYSIOLOGY

Shoot Branching and Leaf Dissection in Tomato Are Regulated by Homologous Gene Modules

(2011) B. L. Busch et al.   PLANT CELL

Role of tomato BRANCHED1-like genes in the control of shoot branching

(2011) Mar Martín-Trillo et al.   PLANT JOURNAL

Next-generation mapping of Arabidopsis genes

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

Convergence of developmental mutants into a single tomato model system: 'Micro-Tom' as an effective toolkit for plant development research

(2011) Rogério F Carvalho et al.   Plant Methods

Coupling Virus-Induced Gene Silencing to Exogenous Green Fluorescence Protein Expression Provides a Highly Efficient System for Functional Genomics in Arabidopsis and across All Stages of Tomato Fruit Development

(2011) L. Quadrana et al.   PLANT PHYSIOLOGY

SNP Discovery and Linkage Map Construction in Cultivated Tomato

(2010) K. Shirasawa et al.   DNA RESEARCH

The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato

(2010) Uri Krieger et al.   NATURE GENETICS

NEATTILL: A simplified procedure for nucleic acid extraction from arrayed tissue for TILLING and other high-throughput reverse genetic applications

(2010) Yellamaraju Sreelakshmi et al.   Plant Methods

An Induced Mutation in Tomato eIF4E Leads to Immunity to Two Potyviruses

(2010) Florence Piron et al.   PLoS One

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Cutin deficiency in the tomato fruit cuticle consistently affects resistance to microbial infection and biomechanical properties, but not transpirational water loss

(2009) Tal Isaacson et al.   PLANT JOURNAL

Flexible Tools for Gene Expression and Silencing in Tomato

(2009) A. I. Fernandez et al.   PLANT PHYSIOLOGY

A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation

(2009) D. Orzaez et al.   PLANT PHYSIOLOGY

Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development

(2009) F. Mounet et al.   PLANT PHYSIOLOGY

BatchPrimer3: A high throughput web application for PCR and sequencing primer design

(2008) Frank M You et al.   BMC BIOINFORMATICS

Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content

(2008) Navot Galpaz et al.   PLANT JOURNAL