Emerging Paradigms in Genomics-Based Crop Improvement

Development of genomics-based genotyping platforms and their applications in rice breeding

(2013) Haodong Chen et al.   CURRENT OPINION IN PLANT BIOLOGY

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

(2013) P.-R. Loh et al.   GENETICS

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis

(2013) U. Seren et al.   PLANT CELL

Phenoscope: an automated large-scale phenotyping platform offering high spatial homogeneity

(2013) Sébastien Tisné et al.   PLANT JOURNAL

RootNav: Navigating Images of Complex Root Architectures

(2013) M. P. Pound et al.   PLANT PHYSIOLOGY

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

(2013) C. R. Cavanagh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Joshua N. Cobb et al.   THEORETICAL AND APPLIED GENETICS

Will genomic selection be a practical method for plant breeding?

(2012) Akihiro Nakaya et al.   ANNALS OF BOTANY

SPICY: towards automated phenotyping of large pepper plants in the greenhouse

(2012) Gerie van der Heijden et al.   FUNCTIONAL PLANT BIOLOGY

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

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

Can genomics boost productivity of orphan crops?

(2012) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

(2012) Hui Li et al.   NATURE GENETICS

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

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

PhenoPhyte: a flexible affordable method to quantify 2D phenotypes from imagery

(2012) Jason M Green et al.   Plant Methods

Rosette Tracker: An Open Source Image Analysis Tool for Automatic Quantification of Genotype Effects

(2012) J. De Vylder et al.   PLANT PHYSIOLOGY

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.)

(2012) Satish Kumar et al.   PLoS One

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

Mapping QTL for agronomic traits in breeding populations

(2012) Tobias Würschum   THEORETICAL AND APPLIED GENETICS

Ten Years of the Collaborative Cross

(2012) David W. Threadgill et al.   G3-Genes Genomes Genetics

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

(2011) Anja Hartmann et al.   BMC BIOINFORMATICS

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

(2011) Juliette Fabre et al.   BMC PLANT BIOLOGY

Accuracy of Genomic Selection Prediction in Barley Breeding Programs: A Simulation Study Based On the Real Single Nucleotide Polymorphism Data of Barley Breeding Lines

(2011) Hiroyoshi Iwata et al.   CROP SCIENCE

Genomic Selection Accuracy for Grain Quality Traits in Biparental Wheat Populations

(2011) Elliot L. Heffner et al.   CROP SCIENCE

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

(2011) Kristen L Kump et al.   NATURE GENETICS

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Next-generation mapping of Arabidopsis genes

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

Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels

(2011) J. P. Cook et al.   PLANT PHYSIOLOGY

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

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

RooTrak: Automated Recovery of Three-Dimensional Plant Root Architecture in Soil from X-Ray Microcomputed Tomography Images Using Visual Tracking

(2011) S. Mairhofer et al.   PLANT PHYSIOLOGY

Joint QTL Linkage Mapping for Multiple-Cross Mating Design Sharing One Common Parent

(2011) Huihui Li 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

High-Resolution Genotyping of Wild Barley Introgression Lines and Fine-Mapping of the Threshability Locus thresh-1 Using the Illumina GoldenGate Assay

(2011) Inga Schmalenbach et al.   G3-Genes Genomes Genetics

High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype

(2011) Rosangela Sozzani et al.   GENOME BIOLOGY

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

Molecular breeding in developing countries: challenges and perspectives

(2010) J-M Ribaut et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2010) Susanna Atwell et al.   NATURE

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

(2010) Joy Bergelson et al.   NATURE REVIEWS GENETICS

Shovelomics: high throughput phenotyping of maize (Zea mays L.) root architecture in the field

(2010) Samuel Trachsel et al.   PLANT AND SOIL

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

(2010) W. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

(2010) J. Cockram et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular basis of trait correlations

(2010) Yongsheng Chen et al.   TRENDS IN PLANT SCIENCE

Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature

(2010) Benjamin Brachi et al.   PLoS Genetics

Complex-trait analysis in plants

(2010) Thomas Mitchell-Olds   GENOME BIOLOGY

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

(2009) Emma S Mace et al.   BMC PLANT BIOLOGY

Candidate Gene Association Mapping of Arabidopsis Flowering Time

(2009) I. M. Ehrenreich et al.   GENETICS

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Plasticity of Arabidopsis Root Gravitropism throughout a Multidimensional Condition Space Quantified by Automated Image Analysis

(2009) T. L. Durham Brooks et al.   PLANT PHYSIOLOGY

QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

(2009) Sureshkumar Balasubramanian et al.   PLoS One

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

(2009) Paula X. Kover et al.   PLoS Genetics

QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations

(2008) J. Yang et al.   BIOINFORMATICS

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

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

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS

Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement

(2008) S. P. Moose et al.   PLANT PHYSIOLOGY

Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations

(2008) C. K. Wong et al.   THEORETICAL AND APPLIED GENETICS

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics