Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

Genomics of gene banks: A case study in rice

(2012) Susan R. McCouch et al.   AMERICAN JOURNAL OF BOTANY

Will genomic selection be a practical method for plant breeding?

(2012) Akihiro Nakaya et al.   ANNALS OF BOTANY

Drought-induced modifications of photosynthetic electron transport in intact leaves: Analysis and use of neural networks as a tool for a rapid non-invasive estimation

(2012) Vasilij Goltsev et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

GiA Roots: software for the high throughput analysis of plant root system architecture

(2012) Taras Galkovskyi et al.   BMC PLANT BIOLOGY

Genome-wide association studies for agronomical traits in a world wide spring barley collection

(2012) Raj K Pasam et al.   BMC PLANT BIOLOGY

A non-coding RNA locus mediates environment-conditioned male sterility in rice

(2012) Danmeng Zhu et al.   CELL RESEARCH

Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA

(2012) Hai Zhou et al.   CELL RESEARCH

Marker-Assisted Selection in Tomato Breeding

(2012) Majid R. Foolad et al.   CRITICAL REVIEWS IN PLANT SCIENCES

The determinants of leaf turgor loss point and prediction of drought tolerance of species and biomes: a global meta-analysis

(2012) Megan K. Bartlett et al.   ECOLOGY LETTERS

Identification and mapping of a QTL (qDTY1.1) with a consistent effect on grain yield under drought

(2012) Krishna Hari Ghimire et al.   FIELD CROPS RESEARCH

Field-based phenomics for plant genetics research

(2012) Jeffrey W. White et al.   FIELD CROPS RESEARCH

GlyPh: a low-cost platform for phenotyping plant growth and water use

(2012) Gustavo A. Pereyra-Irujo et al.   FUNCTIONAL PLANT BIOLOGY

Phenotyping plants: genes, phenes and machines

(2012) Roland Pieruschka et al.   FUNCTIONAL PLANT BIOLOGY

GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons

(2012) Kerstin A. Nagel et al.   FUNCTIONAL PLANT BIOLOGY

A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains

(2012) Alan B. Lenarcic et al.   GENETICS

Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

(2012) M. F. R. Resende et al.   GENETICS

Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

(2012) Yi Jia et al.   GENETICS

Genetic and Association Mapping Study of Wheat Agronomic Traits Under Contrasting Water Regimes

(2012) Dejan Dodig et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

(2012) P. Mabee et al.   JOURNAL OF APPLIED ICHTHYOLOGY

Multiparent intercross populations in analysis of quantitative traits

(2012) SUJAY RAKSHIT et al.   JOURNAL OF GENETICS

High-throughput Phenotyping and Genomic Selection: The Frontiers of Crop Breeding ConvergeF

(2012) Llorenç Cabrera-Bosquet et al.   Journal of Integrative Plant Biology

Phenotyping for Abiotic Stress Tolerance in MaizeF

(2012) Benhilda Masuka et al.   Journal of Integrative Plant Biology

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Harnessing the rhizosphere microbiome through plant breeding and agricultural management

(2012) Matthew G. Bakker et al.   PLANT AND SOIL

A multiparent advanced generation inter-cross population for genetic analysis in wheat

(2012) Bevan E. Huang et al.   PLANT BIOTECHNOLOGY JOURNAL

Quantifying succulence: a rapid, physiologically meaningful metric of plant water storage

(2012) R. MATTHEW OGBURN et al.   PLANT CELL AND ENVIRONMENT

SmartGrain: High-Throughput Phenotyping Software for Measuring Seed Shape through Image Analysis

(2012) T. Tanabata et al.   PLANT PHYSIOLOGY

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

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

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Indica rice chromosome segments for the improvement of Japonica inbreds and hybrids

(2012) Zhiquan Wang et al.   THEORETICAL AND APPLIED GENETICS

Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments

(2012) Dion Bennett et al.   THEORETICAL AND APPLIED GENETICS

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

(2012) Reyazul Rouf Mir et al.   THEORETICAL AND APPLIED GENETICS

Association mapping of plant resistance to insects

(2012) Karen J. Kloth et al.   TRENDS IN PLANT SCIENCE

Rapid determination of comparative drought tolerance traits: using an osmometer to predict turgor loss point

(2012) Megan K. Bartlett et al.   Methods in Ecology and Evolution

Marker-assisted selection for quantitative traits

(2012) Ivan Schuster   Crop Breeding and Applied Biotechnology

The Hordeum Toolbox: The Barley Coordinated Agricultural Project Genotype and Phenotype Resource

(2012) Victoria C. Blake et al.   Plant Genome

Phenotyping for drought tolerance of crops in the genomics era

(2012) Roberto Tuberosa   Frontiers in Physiology

Genomic Databases for Crop Improvement

(2012) Kaitao Lai et al.   Agronomy-Basel

Pea (Pisum sativum L.) in the Genomic Era

(2012) Petr Smýkal et al.   Agronomy-Basel

Mapping of QTL Associated with Drought Tolerance in a Semi-Automobile Rain Shelter in Maize (Zea mays L.)

(2011) Jing-jing ZHU et al.   Agricultural Sciences in China

High-throughput feature counting and measurement of roots

(2011) Asad Naeem et al.   BIOINFORMATICS

HTPheno: An image analysis pipeline for high-throughput plant phenotyping

(2011) Anja Hartmann et al.   BMC BIOINFORMATICS

qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds

(2011) Prashant Vikram et al.   BMC GENETICS

Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

(2011) BP Mallikarjuna Swamy et al.   BMC GENOMICS

PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

(2011) Juliette Fabre et al.   BMC PLANT BIOLOGY

Germplasm enhancement by developing advanced plant materials from diverse rice accessions

(2011) Shuichi Fukuoka et al.   BREEDING SCIENCE

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

From lab to field, new approaches to phenotyping root system architecture

(2011) Jinming Zhu et al.   CURRENT OPINION IN PLANT BIOLOGY

Rice near-isogenic-lines (NILs) contrasting for grain yield under lowland drought stress

(2011) R. Venuprasad et al.   FIELD CROPS RESEARCH

Enhancing drought tolerance in C4 crops

(2011) M. S. Lopes et al.   JOURNAL OF EXPERIMENTAL BOTANY

Independent variation in photosynthetic capacity and stomatal conductance leads to differences in intrinsic water use efficiency in 11 soybean genotypes before and during mild drought

(2011) Matthew E. Gilbert et al.   JOURNAL OF EXPERIMENTAL BOTANY

Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare

(2011) Hua Zhang et al.   Journal of Genetics and Genomics

High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform

(2011) Michael J. Thomson et al.   MOLECULAR BREEDING

A large-effect QTL for rice grain yield under upland drought stress on chromosome 1

(2011) R. Venuprasad et al.   MOLECULAR BREEDING

Environmental and genetic perturbations reveal different networks of metabolic regulation

(2011) A. J. Greenberg et al.   Molecular Systems Biology

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

(2011) J. T. Eppig et al.   NUCLEIC ACIDS RESEARCH

Barley: Emergence as a New Research Material of Crop Science

(2011) D. Saisho et al.   PLANT AND CELL PHYSIOLOGY

Mapping QTLs for yield components and chlorophyll a fluorescence parameters in wheat under three levels of water availability

(2011) Ilona Czyczyło-Mysza et al.   Plant Genetic Resources-Characterization and Utilization

Accurate inference of shoot biomass from high-throughput images of cereal plants

(2011) Mahmood R Golzarian et al.   Plant Methods

Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery

(2011) Rowan P Herridge et al.   Plant Methods

Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform

(2011) R. T. Clark et al.   PLANT PHYSIOLOGY

A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture

(2011) Guillaume Lobet et al.   PLANT PHYSIOLOGY

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

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

Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population

(2011) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of genome-wide selection efficiency in maize nested association mapping populations

(2011) Zhigang Guo et al.   THEORETICAL AND APPLIED GENETICS

Towards genomic selection in apple (Malus × domestica Borkh.) breeding programmes: Prospects, challenges and strategies

(2011) Satish Kumar et al.   Tree Genetics & Genomes

Producing more food with less water in a changing world: assessment of water productivity in 10 major river basins

(2011) Xueliang Cai et al.   WATER INTERNATIONAL

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

(2011) Keyan Zhao et al.   Nature Communications

Genomic Selection Accuracy using Multifamily Prediction Models in a Wheat Breeding Program

(2011) Elliot L. Heffner et al.   Plant Genome

Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.)

(2011) PJ. Maughan et al.   Plant Genome

Physiological drought tolerance and the structuring of tallgrass prairie assemblages

(2011) Sally S. Tucker et al.   Ecosphere

Agricultural Biodiversity Is Essential for a Sustainable Improvement in Food and Nutrition Security

(2011) Emile A. Frison et al.   Sustainability

Osmotic and ionic effects of various electrolytes on the growth of wheat

(2010) Pichu Rengasamy   AUSTRALIAN JOURNAL OF SOIL RESEARCH

Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)

(2010) Jianjun Xu et al.   BMC GENOMICS

Association genetics in crop improvement

(2010) J Antoni Rafalski   CURRENT OPINION IN PLANT BIOLOGY

Maize leaf temperature responses to drought: Thermal imaging and quantitative trait loci (QTL) mapping

(2010) Ya Liu et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Identification of microsatellite markers linked with yield components under drought stress at terminal growth stages in durum wheat

(2010) M. Golabadi et al.   EUPHYTICA

Increased productivity through integrated soil fertility management in cassava–legume intercropping systems in the highlands of Sud-Kivu, DR Congo

(2010) Pieter Pypers et al.   FIELD CROPS RESEARCH

The response of barley to salinity stress differs between hydroponic and soil systems

(2010) Ehsan Tavakkoli et al.   FUNCTIONAL PLANT BIOLOGY

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

(2010) Ben van Ommen et al.   Genes and Nutrition

A Hierarchical Bayesian Model for a Novel Sparse Partial Diallel Crossing Design

(2010) A. J. Greenberg et al.   GENETICS

Using genetic mapping and genomics approaches in understanding and improving drought tolerance in pearl millet

(2010) R. S. Yadav et al.   JOURNAL OF EXPERIMENTAL BOTANY

Characterization of root-yield-1.06, a major constitutive QTL for root and agronomic traits in maize across water regimes

(2010) Pierangelo Landi et al.   JOURNAL OF EXPERIMENTAL BOTANY

High-throughput shoot imaging to study drought responses

(2010) B. Berger et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.)

(2010) K. Neumann et al.   MOLECULAR BREEDING

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Phenomics: the next challenge

(2010) David Houle et al.   NATURE REVIEWS GENETICS

leafprocessor: a new leaf phenotyping tool using contour bending energy and shape cluster analysis

(2010) Andreas Backhaus et al.   NEW PHYTOLOGIST

Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat

(2010) Etienne Paux et al.   PLANT BIOTECHNOLOGY JOURNAL

Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles

(2010) C. A. Price et al.   PLANT PHYSIOLOGY

Development of a Novel Aluminum Tolerance Phenotyping Platform Used for Comparisons of Cereal Aluminum Tolerance and Investigations into Rice Aluminum Tolerance Mechanisms

(2010) A. N. Famoso et al.   PLANT PHYSIOLOGY

Map-based cloning of the rice cold tolerance gene Ctb1

(2010) Koji Saito et al.   PLANT SCIENCE

Chromosome Segment Substitution Lines: A Powerful Tool for the Introgression of Valuable Genes from Oryza Wild Species into Cultivated Rice (O. sativa)

(2010) M. Liakat Ali et al.   Rice

Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

(2010) Chih-Wei Tung et al.   Rice

Non-Coding Changes Cause Sex-Specific Wing Size Differences between Closely Related Species of Nasonia

(2010) David W. Loehlin et al.   PLoS Genetics

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

The HapMap and Genome-Wide Association Studies in Diagnosis and Therapy

(2009) Teri A. Manolio et al.   Annual Review of Medicine

Lamina2Shape—An image processing tool for an explicit description of lamina shape tested on winter wheat (Triticum aestivum L.)

(2009) Tino Dornbusch et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Orphan legume crops enter the genomics era!

(2009) Rajeev K Varshney et al.   CURRENT OPINION IN PLANT BIOLOGY

Effective use of water (EUW) and not water-use efficiency (WUE) is the target of crop yield improvement under drought stress

(2009) A. Blum   FIELD CROPS RESEARCH

Simultaneous phenotyping of leaf growth and chlorophyll fluorescence via GROWSCREEN FLUORO allows detection of stress tolerance inArabidopsis thalianaand other rosette plants

(2009) Marcus Jansen et al.   FUNCTIONAL PLANT BIOLOGY

High throughput phenotyping of root growth dynamics, lateral root formation, root architecture and root hair development enabled by PlaRoM

(2009) Nima Yazdanbakhsh et al.   FUNCTIONAL PLANT BIOLOGY

Factors Affecting Accuracy From Genomic Selection in Populations Derived From Multiple Inbred Lines: A Barley Case Study

(2009) S. Zhong et al.   GENETICS

Molecular marker assisted selection for improvement of the eating, cooking and sensory quality of rice (Oryza sativa L.)

(2009) Liang Jin et al.   JOURNAL OF CEREAL SCIENCE

Invited review: Genomic selection in dairy cattle: Progress and challenges

(2009) B.J. Hayes et al.   JOURNAL OF DAIRY SCIENCE

Constitutive water-conserving mechanisms are correlated with the terminal drought tolerance of pearl millet [Pennisetum glaucum (L.) R. Br.]

(2009) Jana Kholová et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide association study of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis

(2009) Hiroyoshi Iwata et al.   MOLECULAR BREEDING

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

DART: a software to analyse root system architecture and development from captured images

(2009) Jacques Le Bot et al.   PLANT AND SOIL

HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis

(2009) L. Wang et al.   PLANT PHYSIOLOGY

High-Throughput Quantification of Root Growth Using a Novel Image-Analysis Tool

(2009) A. French et al.   PLANT PHYSIOLOGY

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

The BUGS project: Evolution, critique and future directions

(2009) David Lunn et al.   STATISTICS IN MEDICINE

LAMINA: a tool for rapid quantification of leaf size and shape parameters

(2008) Max Bylesjö et al.   BMC PLANT BIOLOGY

Toward positional cloning ofFhb1, a major QTL for Fusarium head blight resistance in wheat

(2008) Sixin Liu et al.   CEREAL RESEARCH COMMUNICATIONS

From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants

(2008) Colin Cavanagh et al.   CURRENT OPINION IN PLANT BIOLOGY

Accuracy of Genomic Selection Using Different Methods to Define Haplotypes

(2008) M. P. L. Calus et al.   GENETICS

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS

Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics

(2008) Xinyou Yin et al.   NEW PHYTOLOGIST

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

(2008) Shulamit Avraham et al.   NUCLEIC ACIDS RESEARCH

EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture

(2008) Patrick Armengaud et al.   PLANT JOURNAL

Metabolomics-assisted breeding: a viable option for crop improvement?

(2008) Alisdair R. Fernie et al.   TRENDS IN GENETICS

Status and Prospects of Association Mapping in Plants

(2008) Chengsong Zhu et al.   Plant Genome

Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

(2007) B. C.Y Collard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES