Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome

Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)

(2017) Huahan Xie et al.   Frontiers in Plant Science

Transcriptional Responses to Pre-flowering Leaf Defoliation in Grapevine Berry from Different Growing Sites, Years, and Genotypes

(2017) Sara Zenoni et al.   Frontiers in Plant Science

Study of intra-varietal diversity in biotypes of Aglianico and Muscat of Alexandria (Vitis viniferaL.) cultivars

(2016) G. de Lorenzis et al.   AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH

Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat

(2016) Moritz Hess et al.   BMC GENOMICS

The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry

(2016) Daniela Lopes Paim Pinto et al.   Frontiers in Plant Science

Towards a scientific interpretation of the terroir concept: plasticity of the grape berry metabolome

(2015) Andrea Anesi et al.   BMC PLANT BIOLOGY

"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana

(2015) Eriko Sasaki et al.   PLoS Genetics

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

(2014) G Albert Wu et al.   NATURE BIOTECHNOLOGY

Genotype × environment interaction QTL mapping in plants: lessons from Arabidopsis

(2014) Mohamed El-Soda et al.   TRENDS IN PLANT SCIENCE

Genotype-by-Environment Interaction and Plasticity: Exploring Genomic Responses of Plants to the Abiotic Environment

(2013) David L. Des Marais et al.   Annual Review of Ecology Evolution and Systematics

The genomic determinants of genotype × environment interactions in gene expression

(2013) Vladislav Grishkevich et al.   TRENDS IN GENETICS

Open or Close the Gate – Stomata Action Under the Control of Phytohormones in Drought Stress Conditions

(2013) Agata Daszkowska-Golec et al.   Frontiers in Plant Science

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.

(2012) Philip R Young et al.   BMC GENOMICS

A genomic bias for genotype–environment interactions in C. elegans

(2012) Vladislav Grishkevich et al.   Molecular Systems Biology

The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program

(2012) M. Fasoli et al.   PLANT CELL

Genome-Wide Patterns of Arabidopsis Gene Expression in Nature

(2012) Christina L. Richards et al.   PLoS Genetics

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Ecophysiological, Genetic, and Molecular Causes of Variation in Grape Berry Weight and Composition: A Review

(2011) Zhan Wu Dai et al.   AMERICAN JOURNAL OF ENOLOGY AND VITICULTURE

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

A Map of Local Adaptation in Arabidopsis thaliana

(2011) A. Fournier-Level et al.   SCIENCE

Methods for Investigating Gene-Environment Interactions in Candidate Pathway and Genome-Wide Association Studies

(2010) Duncan Thomas   Annual Review of Public Health

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

(2010) A. McKenna et al.   GENOME RESEARCH

Optimization of a Method for the Extraction and Quantification of Carotenoids and Chlorophylls during Ripening in Grape Berries (Vitis viniferacv. Merlot)

(2010) Zindi Kamffer et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis)

(2010) Jason A. Holliday et al.   NEW PHYTOLOGIST

Plant phenotypic plasticity in a changing climate

(2010) A.B. Nicotra et al.   TRENDS IN PLANT SCIENCE

Managing grapevines to optimise fruit development in a challenging environment: a climate change primer for viticulturists

(2009) M. KELLER   AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Variation in gene expression ofAndropogon gerardiiin response to altered environmental conditions associated with climate change

(2009) Steven E. Travers et al.   JOURNAL OF ECOLOGY

Land and wine

(2009) Michael A. White et al.   Nature Geoscience