Predictive breeding for maize: Making use of molecular phenotypes, machine learning, and physiological crop models

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

Efficient genetic value prediction using incomplete omics data

(2019) Matthias Westhues et al.   THEORETICAL AND APPLIED GENETICS

Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

(2019) Jacob D. Washburn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic prediction of maize yield across European environmental conditions

(2019) Emilie J. Millet et al.   NATURE GENETICS

­­­­Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays

(2019) Karl A. G. Kremling et al.   G3-Genes Genomes Genetics

Modelling the nitrogen dynamics of maize crops – Enhancing the APSIM maize model

(2018) S. Soufizadeh et al.   EUROPEAN JOURNAL OF AGRONOMY

Leveraging biological insight and environmental variation to improve phenotypic prediction: Integrating crop growth models (CGM) with whole genome prediction (WGP)

(2018) C.D. Messina et al.   EUROPEAN JOURNAL OF AGRONOMY

Beyond Genomic Prediction: Combining Different Types ofomicsData Can Improve Prediction of Hybrid Performance in Maize

(2018) Tobias A. Schrag et al.   GENETICS

Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits

(2018) Jiabo Wang et al.   HEREDITY

Field-based high-throughput phenotyping of plant height in sorghum using different sensing technologies

(2018) Xu Wang et al.   Plant Methods

Estimating parametric phenotypes that determine anthesis date in Zea mays: Challenges in combining ecophysiological models with genetics

(2018) Abhishes Lamsal et al.   PLoS One

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

(2018) William A. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic and environmental determinants and their interplay underlying phenotypic plasticity

(2018) Xin Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining High-Throughput Phenotyping and Genomic Information to Increase Prediction and Selection Accuracy in Wheat Breeding

(2018) Jared Crain et al.   Plant Genome

Genomic Selection Outperforms Marker Assisted Selection for Grain Yield and Physiological Traits in a Maize Doubled Haploid Population Across Water Treatments

(2018) Diego Cerrudo et al.   Frontiers in Plant Science

Beyond Genomic Prediction: Combining Different Types ofomicsData Can Improve Prediction of Hybrid Performance in Maize

(2018) Tobias A. Schrag et al.   GENETICS

Genomic Prediction of Breeding Values Using a Subset of SNPs Identified by Three Machine Learning Methods

(2018) Bo Li et al.   Frontiers in Genetics

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

Maize domestication and gene interaction

(2018) Michelle C. Stitzer et al.   NEW PHYTOLOGIST

A deep convolutional neural network approach for predicting phenotypes from genotypes

(2018) Wenlong Ma et al.   PLANTA

Leaf stable carbon isotope composition reflects transpiration efficiency in Zea mays

(2018) Robert J. Twohey et al.   PLANT JOURNAL

Breaking the curse of dimensionality to identify causal variants in Breeding 4

(2018) Guillaume P. Ramstein et al.   THEORETICAL AND APPLIED GENETICS

Development of a maize 55 K SNP array with improved genome coverage for molecular breeding

(2017) Cheng Xu et al.   MOLECULAR BREEDING

Genome-wide Association Studies in Maize: Praise and Stargaze

(2017) Yingjie Xiao et al.   Molecular Plant

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

(2017) Awais Rasheed et al.   Molecular Plant

Genomic innovation for crop improvement

(2017) Michael W. Bevan et al.   NATURE

A study of allelic diversity underlying flowering-time adaptation in maize landraces

(2017) J Alberto Romero Navarro et al.   NATURE GENETICS

Automated Identification of Northern Leaf Blight-Infected Maize Plants from Field Imagery Using Deep Learning

(2017) Chad DeChant et al.   PHYTOPATHOLOGY

Transcriptome-based prediction of hybrid performance with unbalanced data from a maize breeding programme

(2017) Carola Zenke-Philippi et al.   PLANT BREEDING

Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field

(2017) Francisco de Abreu e Lima et al.   PLANT JOURNAL

Omics-based hybrid prediction in maize

(2017) Matthias Westhues et al.   THEORETICAL AND APPLIED GENETICS

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Prediction of Multiple-Trait and Multiple-Environment Genomic Data Using Recommender Systems

(2017) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

(2017) Jinliang Yang et al.   PLoS Genetics

Effect of Trait Heritability, Training Population Size and Marker Density on Genomic Prediction Accuracy Estimation in 22 bi-parental Tropical Maize Populations

(2017) Ao Zhang et al.   Frontiers in Plant Science

Genomic Selection for Drought Tolerance Using Genome-Wide SNPs in Maize

(2017) Mittal Shikha et al.   Frontiers in Plant Science

Construction of the third-generation Zea mays haplotype map

(2017) Robert Bukowski et al.   GigaScience

Prediction of hybrid performance in maize with a ridge regression model employed to DNA markers and mRNA transcription profiles

(2016) Carola Zenke-Philippi et al.   BMC GENOMICS

Use of Crop Growth Models with Whole-Genome Prediction: Application to a Maize Multienvironment Trial

(2016) Mark Cooper et al.   CROP SCIENCE

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

(2016) Stefan M. Edwards et al.   GENETICS

Metabolomic prediction of yield in hybrid rice

(2016) Shizhong Xu et al.   PLANT JOURNAL

Open chromatin reveals the functional maize genome

(2016) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of the utility of gene expression and metabolic information for genomic prediction in maize

(2016) Zhigang Guo et al.   THEORETICAL AND APPLIED GENETICS

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

(2016) Stefan M. Edwards et al.   GENETICS

Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

(2016) Yeyin Shi et al.   PLoS One

Study on Essential Derivation in Maize: III. Selection and Evaluation of a Panel of Single Nucleotide Polymorphism Loci for Use in European and North American Germplasm

(2015) Yves Rousselle et al.   CROP SCIENCE

Industry-Scale Evaluation of Maize Hybrids Selected for Increased Yield in Drought-Stress Conditions of the US Corn Belt

(2015) Jim Gaffney et al.   CROP SCIENCE

Perspectives for Genomic Selection Applications and Research in Plants

(2015) Nicolas Heslot et al.   CROP SCIENCE

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Mechanisms for the relationships between water-use efficiency and carbon isotope composition and specific leaf area of maize (Zea mays L.) under water stress

(2015) Congzhi Zhang et al.   PLANT GROWTH REGULATION

Detection of QTL for metabolic and agronomic traits in wheat with adjustments for variation at genetic loci that affect plant phenology

(2015) Camilla B. Hill et al.   PLANT SCIENCE

Recombination in diverse maize is stable, predictable, and associated with genetic load

(2015) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms

(2015) Daniel Money et al.   G3-Genes Genomes Genetics

Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

(2015) Frank Technow et al.   PLoS One

Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants

(2015) Kelly Swarts et al.   Plant Genome

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

(2014) Sandra Unterseer et al.   BMC GENOMICS

Can current crop models be used in the phenotyping era for predicting the genetic variability of yield of plants subjected to drought or high temperature?

(2014) Boris Parent et al.   JOURNAL OF EXPERIMENTAL BOTANY

Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

(2014) Mark Cooper et al.   Crop & Pasture Science

Development and evaluation of a field-based high-throughput phenotyping platform

(2013) Pedro Andrade-Sanchez et al.   FUNCTIONAL PLANT BIOLOGY

Genomic prediction in CIMMYT maize and wheat breeding programs

(2013) J Crossa et al.   HEREDITY

Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle

(2013) Elizabeth M. Ross et al.   PLoS One

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A reaction norm model for genomic selection using high-dimensional genomic and environmental data

(2013) Diego Jarquín et al.   THEORETICAL AND APPLIED GENETICS

Gut–brain axis: how the microbiome influences anxiety and depression

(2013) Jane A. Foster et al.   TRENDS IN NEUROSCIENCES

The Pattern and Distribution of Deleterious Mutations in Maize

(2013) Sofiane Mezmouk et al.   G3-Genes Genomes Genetics

The Genomic Signature of Crop-Wild Introgression in Maize

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

Polyploids as a “model system” for the study of heterosis

(2013) Jacob D. Washburn et al.   Plant Reproduction

The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis

(2013) Marcos Malosetti et al.   Frontiers in Physiology

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality

(2012) N. Carreno-Quintero et al.   PLANT PHYSIOLOGY

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Genotype by Environment Interaction of Quantitative Traits: A Case Study in Barley

(2012) Fuping Zhao et al.   G3-Genes Genomes Genetics

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Genomic selection in plant breeding: from theory to practice

(2011) J.-L. Jannink et al.   Briefings in Functional Genomics

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

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

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

Gene–environment-wide association studies: emerging approaches

(2010) Duncan Thomas   NATURE REVIEWS GENETICS

Additive Genetic Variability and the Bayesian Alphabet

(2009) D. Gianola et al.   GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

How a century of ammonia synthesis changed the world

(2008) Jan Willem Erisman et al.   Nature Geoscience

Symbiotic gut microbes modulate human metabolic phenotypes

(2008) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA