Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study

Efficiency of genomic selection for tomato fruit quality

(2016) Janejira Duangjit et al.   MOLECULAR BREEDING

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

(2016) Gautier Sarah et al.   Molecular Ecology Resources

Genomic variation in tomato, from wild ancestors to contemporary breeding accessions

(2015) José Blanca et al.   BMC GENOMICS

Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection

(2014) Guillaume Bauchet et al.   BMC PLANT BIOLOGY

Chromosomal Evolution and Patterns of Introgression in Helianthus

(2014) J. G. Barb et al.   GENETICS

Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

(2014) C. Fraisse et al.   GENETICS

Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium

(2014) Renaud Rincent et al.   GENETICS

Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex

(2014) Joanne A. Labate et al.   GENOME

The genetic basis of fruit morphology in horticultural crops: lessons from tomato and melon

(2014) Antonio J. Monforte et al.   JOURNAL OF EXPERIMENTAL BOTANY

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding

(2014) Noe Fernandez-Pozo et al.   NUCLEIC ACIDS RESEARCH

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

Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans

(2014) Ai-Lin Chen et al.   PLoS One

A Genetic Atlas of Human Admixture History

(2014) G. Hellenthal et al.   SCIENCE

Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes

(2014) Shahal Abbo et al.   TRENDS IN PLANT SCIENCE

Genomic selection: genome-wide prediction in plant improvement

(2014) Zeratsion Abera Desta et al.   TRENDS IN PLANT SCIENCE

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

(2013) Joseph Lachance et al.   BIOESSAYS

SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato

(2013) Giandomenico Corrado et al.   BMC GENOMICS

Tomato breeding in the genomics era: insights from a SNP array

(2013) Marcela Víquez-Zamora et al.   BMC GENOMICS

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

(2013) Mathilde Causse et al.   BMC GENOMICS

Correcting Coalescent Analyses for Panel-Based SNP Ascertainment

(2013) J. R. McGill et al.   GENETICS

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Feeding the future

(2013) Susan McCouch et al.   NATURE

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A cytochrome P450 regulates a domestication trait in cultivated tomato

(2013) M. Chakrabarti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato

(2013) Chunzhi Zhang et al.   THEORETICAL AND APPLIED GENETICS

Does genomic selection have a future in plant breeding?

(2013) Elisabeth Jonas et al.   TRENDS IN BIOTECHNOLOGY

Resolution by recombination: breaking up Solanum pennellii introgressions

(2013) Saleh Alseekh et al.   TRENDS IN PLANT SCIENCE

Tomato Yield Heterosis Is Triggered by a Dosage Sensitivity of the Florigen Pathway That Fine-Tunes Shoot Architecture

(2013) Ke Jiang et al.   PLoS Genetics

The Genomic Signature of Crop-Wild Introgression in Maize

(2013) Matthew B. Hufford et al.   PLoS Genetics

The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases

(2013) Maarten G. Verlaan et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Improved Heritability Estimation from Genome-wide SNPs

(2012) Doug Speed et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Population Identification Using Genetic Data

(2012) Daniel John Lawson et al.   Annual Review of Genomics and Human Genetics

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

(2012) Joanne A Labate et al.   BMC PLANT BIOLOGY

Functional characterization of a tomato COBRA-like gene functioning in fruit development and ripening

(2012) Ying Cao et al.   BMC PLANT BIOLOGY

Next-generation education in crop genetics

(2012) Eyal Fridman et al.   CURRENT OPINION IN PLANT BIOLOGY

Inferring Population Histories Using Genome-Wide Allele Frequency Data

(2012) Mathieu Gautier et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Can genomics boost productivity of orphan crops?

(2012) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

A mixed-model approach for genome-wide association studies of correlated traits in structured populations

(2012) Arthur Korte et al.   NATURE GENETICS

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

(2012) Sung-Chur Sim et al.   PLoS One

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

(2012) Sung-Chur Sim et al.   PLoS One

Genome-Wide Association Mapping in Tomato ( Solanum lycopersicum ) Is Possible Using Genome Admixture of Solanum lycopersicum var. cerasiforme

(2012) Nicolas Ranc et al.   G3-Genes Genomes Genetics

Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis

(2012) John P. Hamilton et al.   Plant Genome

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

The risks of success in quality vegetable markets: Possible genetic erosion in Marmande tomatoes (Solanum lycopersicum L.) and consumer dissatisfaction

(2011) Joan Casals et al.   SCIENTIA HORTICULTURAE

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Robbie Waugh et al.   GENOME

Consumer Preferences for Fresh Tomato at the European Scale: A Common Segmentation on Taste and Firmness

(2010) Mathilde Causse et al.   JOURNAL OF FOOD SCIENCE

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

(2010) Keyan Zhao et al.   PLoS One

Population Structure and Cryptic Relatedness in Genetic Association Studies

(2010) William Astle et al.   STATISTICAL SCIENCE

Genetic and bioclimatic variation in Solanum pimpinellifolium

(2008) Elena Zuriaga et al.   GENETIC RESOURCES AND CROP EVOLUTION

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

GGT 2.0: Versatile Software for Visualization and Analysis of Genetic Data

(2008) Ralph van Berloo   JOURNAL OF HEREDITY

Plant breeders go back to nature

(2008) Dani Zamir   NATURE GENETICS

Status and Prospects of Association Mapping in Plants

(2008) Chengsong Zhu et al.   Plant Genome