Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping

Solanum pennelliibackcross inbred lines (BILs) link small genomic bins with tomato traits

(2016) Itai Ofner et al.   PLANT JOURNAL

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

(2016) Shifeng Cheng et al.   PLANT JOURNAL

Distinct Mechanisms of the ORANGE Protein in Controlling Carotenoid Flux

(2016) Noam Chayut et al.   PLANT PHYSIOLOGY

CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool

(2016) Oren Tzfadia et al.   Frontiers in Plant Science

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding

(2016) Javaid A. Bhat et al.   Frontiers in Genetics

Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties

(2015) Montserrat Saladié et al.   BMC GENOMICS

Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly

(2015) Jason M Argyris et al.   BMC GENOMICS

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit

(2015) Noam Chayut et al.   BMC PLANT BIOLOGY

Genetical genomics of Populus leaf shape variation

(2015) Derek R. Drost et al.   BMC PLANT BIOLOGY

Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits

(2015) Shiri Freilich et al.   BMC PLANT BIOLOGY

Anchoring the consensus ICuGI genetic map to the melon (Cucumis melo L.) genome

(2015) Aurora Diaz et al.   MOLECULAR BREEDING

A ‘golden’ SNP inCmOrgoverns the fruit flesh color of melon (Cucumis melo)

(2015) Galil Tzuri et al.   PLANT JOURNAL

Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression

(2015) Emily B. Josephs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants

(2015) Chibuikem I. N. Unamba et al.   Frontiers in Plant Science

Pentatricopeptide Repeat Proteins in Plants

(2014) Alice Barkan et al.   Annual Review of Plant Biology

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population

(2014) Zongliang Chen et al.   BMC GENOMICS

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

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

An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population

(2014) Jia Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genetical and Comparative Genomics ofBrassicaunder Altered Ca Supply IdentifiesArabidopsisCa-Transporter Orthologs

(2014) Neil S. Graham et al.   PLANT CELL

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

The PH gene determines fruit acidity and contributes to the evolution of sweet melons

(2014) Shahar Cohen et al.   Nature Communications

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

(2014) Rajeev K. Varshney et al.   PLOS BIOLOGY

Learning Gene Networks under SNP Perturbations Using eQTL Datasets

(2014) Lingxue Zhang et al.   PLoS Computational Biology

Genetic regulation and structural changes during tomato fruit development and ripening

(2014) Paolo Pesaresi et al.   Frontiers in Plant Science

Genetic and chemical characterization of an EMS induced mutation in Cucumis melo CRTISO gene

(2013) Navot Galpaz et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Gas chromatography-olfactometry and gas chromatography-tandem mass spectrometry analysis of fresh cantaloupe (Cucumis meloL. var.cantalupensisNaudin) aroma

(2013) Ying Wang et al.   FLAVOUR AND FRAGRANCE JOURNAL

Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest

(2013) Mei Xiao et al.   JOURNAL OF BIOTECHNOLOGY

The effects of genetic variation on gene expression dynamics during development

(2013) Mirko Francesconi et al.   NATURE

Catabolism ofl-methionine in the formation of sulfur and other volatiles in melon (Cucumis meloL.) fruit

(2013) Itay Gonda et al.   PLANT JOURNAL

Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing

(2013) X. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

(2013) Z.-Y. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

(2013) Jennifer Spindel et al.   THEORETICAL AND APPLIED GENETICS

Plastid-to-nucleus communication, signals controlling the running of the plant cell

(2012) Juan de Dios Barajas-López et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants

(2012) Francisco A Cubillos et al.   CURRENT OPINION IN PLANT BIOLOGY

Cloning, Expression and Purification of an Acetoacetyl CoA Thiolase from Sunflower Cotyledon

(2012) James H. Dyer et al.   International Journal of Biological Sciences

Effect of ripening and inter-cultivar differences on strawberry quality

(2012) T. Vandendriessche et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development

(2012) Huanan Jin et al.   PLANT JOURNAL

Sigma factor-mediated plastid retrograde signals control nuclear gene expression

(2012) Jesse D. Woodson et al.   PLANT JOURNAL

RNA-Seq vs Dual- and Single-Channel Microarray Data: Sensitivity Analysis for Differential Expression and Clustering

(2012) Alina Sîrbu et al.   PLoS One

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-expression and co-responses: within and beyond transcription

(2012) Takayuki Tohge et al.   Frontiers in Plant Science

A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

(2011) Aurora Diaz et al.   BMC PLANT BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Use of Non-Normalized, Non-Amplified cDNA for 454-Based RNA Sequencing of Fleshy Melon Fruit

(2011) Vitaly Portnoy et al.   Plant Genome

Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit

(2010) Itay Gonda et al.   JOURNAL OF EXPERIMENTAL BOTANY

Toward understanding genetic mechanisms of complex traits in rice

(2010) Wei Hao et al.   Journal of Genetics and Genomics

Draft genome sequence of the oilseed species Ricinus communis

(2010) Agnes P Chan et al.   NATURE BIOTECHNOLOGY

An Arabidopsis Pentatricopeptide Repeat Protein, SUPPRESSOR OF VARIEGATION7, Is Required for FtsH-Mediated Chloroplast Biogenesis

(2010) X. Liu et al.   PLANT PHYSIOLOGY

Natural Variation in Arabidopsis thaliana Revealed a Genetic Network Controlling Germination Under Salt Stress

(2010) Navot Galpaz et al.   PLoS One

A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes

(2010) R. Harel-Beja et al.   THEORETICAL AND APPLIED GENETICS

Identifying functional modules using expression profiles and confidence-scored protein interactions

(2009) Igor Ulitsky et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

Advances in Genetical Genomics of Plants

(2009) R. Joosen et al.   CURRENT GENOMICS

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Quantitative Genomics: Analyzing Intraspecific Variation Using Global Gene Expression Polymorphisms or eQTLs

(2008) Dan Kliebenstein   Annual Review of Plant Biology

Melon Fruits: Genetic Diversity, Physiology, and Biotechnology Features

(2008) Hector G. Nuñez-Palenius et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Determination and Isolation of a Thioesterase from Passion Fruit (Passiflora edulis Sims) That Hydrolyzes Volatile Thioesters

(2008) Edward J. Tapp et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

CLB19, a pentatricopeptide repeat protein required for editing ofrpoAandclpPchloroplast transcripts

(2008) Anne-Laure Chateigner-Boutin et al.   PLANT JOURNAL

The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds

(2008) Vitaly Portnoy et al.   PLANT MOLECULAR BIOLOGY

A Conserved Mutation in an Ethylene Biosynthesis Enzyme Leads to Andromonoecy in Melons

(2008) A. Boualem et al.   SCIENCE

Mapping of genetic loci that regulate quantity of beta-carotene in fruit of US Western Shipping melon (Cucumis melo L.)

(2008) H. E. Cuevas et al.   THEORETICAL AND APPLIED GENETICS

Identifying the molecular basis of QTLs: eQTLs add a new dimension

(2008) Bjarne G. Hansen et al.   TRENDS IN PLANT SCIENCE