Accelerating crop genetic gains with genomic selection

Development of Genomic Prediction in Sorghum

(2018) Colleen H. Hunt et al.   CROP SCIENCE

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

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

(2018) Xu Wang et al.   Plant Methods

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding

(2018) Fred van Eeuwijk et al.   PLANT SCIENCE

When less can be better: How can we make genomic selection more cost-effective and accurate in barley?

(2018) Amina Abed et al.   THEORETICAL AND APPLIED GENETICS

Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection

(2018) Gregor Gorjanc et al.   THEORETICAL AND APPLIED GENETICS

Translating High-Throughput Phenotyping into Genetic Gain

(2018) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

Effective Genomic Selection in a Narrow-Genepool Crop with Low-Density Markers: Asian Rapeseed as an Example

(2018) Christian R. Werner et al.   Plant Genome

Designer Roots for Future Crops

(2018) Kai P. Voss-Fels et al.   TRENDS IN PLANT SCIENCE

Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives

(2018) Asheesh Kumar Singh et al.   TRENDS IN PLANT SCIENCE

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

(2017) Punna Ramu et al.   NATURE GENETICS

Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery

(2017) John M Hickey et al.   NATURE GENETICS

Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application

(2017) Armin Scheben et al.   PLANT BIOTECHNOLOGY JOURNAL

Bayesian optimization for genomic selection: a method for discovering the best genotype among a large number of candidates

(2017) Ryokei Tanaka et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide regression models considering general and specific combining ability predict hybrid performance in oilseed rape with similar accuracy regardless of trait architecture

(2017) Christian R. Werner et al.   THEORETICAL AND APPLIED GENETICS

Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes

(2017) B. J. Hayes et al.   THEORETICAL AND APPLIED GENETICS

Efficiency of multi-trait, indirect, and trait-assisted genomic selection for improvement of biomass sorghum

(2017) Samuel B. Fernandes et al.   THEORETICAL AND APPLIED GENETICS

Prospective Targeted Recombination and Genetic Gains for Quantitative Traits in Maize

(2017) Rex Bernardo   Plant Genome

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

(2017) Jinliang Yang et al.   PLoS Genetics

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

(2017) Lunwen Qian et al.   Frontiers in Plant Science

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

(2017) Elliot L. Heffner et al.   Plant Genome

Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations

(2016) Gregor Gorjanc et al.   BMC GENOMICS

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

(2016) I. M. MacLeod et al.   BMC GENOMICS

Half a Century of Studying Genotype × Environment Interactions in Plant Breeding Experiments

(2016) Ani A. Elias et al.   CROP SCIENCE

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

(2016) Mark Cooper et al.   CROP SCIENCE

Models for Genome × Environment Interaction: Examples in Livestock

(2016) Ben J. Hayes et al.   CROP SCIENCE

Predicting Responses in Multiple Environments: Issues in Relation to Genotype × Environment Interactions

(2016) Marcos Malosetti et al.   CROP SCIENCE

Hybrid variation for root system efficiency in maize: potential links to drought adaptation

(2016) Erik J. van Oosterom et al.   FUNCTIONAL PLANT BIOLOGY

Accuracy of genomic predictions for feed efficiency traits of beef cattle using 50K and imputed HD genotypes1

(2016) D. Lu et al.   JOURNAL OF ANIMAL SCIENCE

Evolving gene banks: improving diverse populations of crop and exotic germplasm with optimal contribution selection

(2016) W.A. Cowling et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Role of Deleterious Substitutions in Crop Genomes

(2016) Thomas J. Y. Kono et al.   MOLECULAR BIOLOGY AND EVOLUTION

Influence of extreme weather disasters on global crop production

(2016) Corey Lesk et al.   NATURE

Rapid genotype imputation from sequence without reference panels

(2016) Robert W Davies et al.   NATURE GENETICS

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

(2016) Adriana García-Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model training across multiple breeding cycles significantly improves genomic prediction accuracy in rye (Secale cereale L.)

(2016) Hans-Jürgen Auinger et al.   THEORETICAL AND APPLIED GENETICS

Envirotyping for deciphering environmental impacts on crop plants

(2016) Yunbi Xu   THEORETICAL AND APPLIED GENETICS

Canopy Temperature and Vegetation Indices from High-Throughput Phenotyping Improve Accuracy of Pedigree and Genomic Selection for Grain Yield in Wheat

(2016) Jessica Rutkoski et al.   G3-Genes Genomes Genetics

Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass

(2016) Zibei Lin et al.   Plant Genome

A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine

(2016) Shanshan Yang et al.   Horticulture Research

Genomic Selection Improves Heat Tolerance in Dairy Cattle

(2016) J. B. Garner et al.   Scientific Reports

Limited-Transpiration Trait May Increase Maize Drought Tolerance in the US Corn Belt

(2015) Carlos D. Messina et al.   AGRONOMY JOURNAL

Adding Genetically Distant Individuals to Training Populations Reduces Genomic Prediction Accuracy in Barley

(2015) Aaron J. Lorenz 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

Resemblance between two relatives - animal and plant breeding

(2015) C.C. Schön et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction

(2015) R.F. Brøndum et al.   JOURNAL OF DAIRY SCIENCE

Soil water capture trends over 50 years of single-cross maize (Zea maysL.) breeding in the US corn-belt

(2015) Andres Reyes et al.   JOURNAL OF EXPERIMENTAL BOTANY

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

(2015) Philipp E. Bayer et al.   THEORETICAL AND APPLIED GENETICS

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

(2015) Jennifer Spindel et al.   PLoS Genetics

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

(2015) Frank Technow et al.   PLoS One

Impact of whole-genome amplification on the reliability of pre-transfer cattle embryo breeding value estimates

(2014) Habib A Shojaei Saadi et al.   BMC GENOMICS

Breeding drought-tolerant maize hybrids for the US corn-belt: discovery to product

(2014) Mark Cooper et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic selection: genome-wide prediction in plant improvement

(2014) Zeratsion Abera Desta et al.   TRENDS IN PLANT SCIENCE

Redesigning the exploitation of wheat genetic resources

(2014) C. Friedrich H. Longin et al.   TRENDS IN PLANT SCIENCE

Genomic selection in crops, trees and forages: a review

(2014) Z. Lin et al.   Crop & Pasture Science

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

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

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

Relatedness and Genotype × Environment Interaction Affect Prediction Accuracies in Genomic Selection: A Study in Cassava

(2013) Delphine Ly et al.   CROP SCIENCE

Post-GWAS: where next? More samples, more SNPs or more biology?

(2013) P Marjoram et al.   HEREDITY

Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield

(2013) M. Guo et al.   JOURNAL OF EXPERIMENTAL BOTANY

Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions

(2013) Nicolas Heslot et al.   THEORETICAL AND APPLIED GENETICS

Accelerating plant breeding

(2013) Gerald N. De La Fuente et al.   TRENDS IN PLANT SCIENCE

Field high-throughput phenotyping: the new crop breeding frontier

(2013) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

Precision phenotyping of biomass accumulation in triticale reveals temporal genetic patterns of regulation

(2013) Lucas Busemeyer et al.   Scientific Reports

The Pattern and Distribution of Deleterious Mutations in Maize

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

The U.S. drought of 2012 in perspective: A call to action

(2013) J.S. Boyer et al.   Global Food Security-Agriculture Policy Economics and Environment

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

(2012) Martin Trick et al.   BMC PLANT BIOLOGY

Potential and Optimization of Genomic Selection for Fusarium Head Blight Resistance in Six-Row Barley

(2012) A. J. Lorenz et al.   CROP SCIENCE

Efficiency of Managed-Stress Screening of Elite Maize Hybrids under Drought and Low Nitrogen for Yield under Rainfed Conditions in Southern Africa

(2012) Vanessa S. Weber et al.   CROP SCIENCE

Genome-wide selection in cassava

(2012) Eder Jorge de Oliveira et al.   EUPHYTICA

Prognosis for genetic improvement of yield potential and water-limited yield of major grain crops

(2012) Antonio J. Hall et al.   FIELD CROPS RESEARCH

A multisite managed environment facility for targeted trait and germplasm phenotyping

(2012) Greg J. Rebetzke et al.   FUNCTIONAL PLANT BIOLOGY

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

A Gene Regulatory Network Model for Floral Transition of the Shoot Apex in Maize and Its Dynamic Modeling

(2012) Zhanshan Dong et al.   PLoS One

Evaluation of Genomic Prediction Methods for Fusarium Head Blight Resistance in Wheat

(2012) Jessica Rutkoski et al.   Plant Genome

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

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

Environment characterization as an aid to wheat improvement: interpreting genotype–environment interactions by modelling water-deficit patterns in North-Eastern Australia

(2011) K. Chenu et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Accuracy of genomic selection in European maize elite breeding populations

(2011) Yusheng Zhao et al.   THEORETICAL AND APPLIED GENETICS

Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing

(2010) T. Meuwissen et al.   GENETICS

Yield–trait performance landscapes: from theory to application in breeding maize for drought tolerance

(2010) Carlos D. Messina et al.   JOURNAL OF EXPERIMENTAL BOTANY

Breeding Technologies to Increase Crop Production in a Changing World

(2010) M. Tester et al.   SCIENCE

Modeling QTL for complex traits: detection and context for plant breeding

(2009) Mark Cooper et al.   CURRENT OPINION IN PLANT BIOLOGY

Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A “Gene-to-Phenotype” Modeling Approach

(2009) Karine Chenu et al.   GENETICS

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

(2009) S. Zhong et al.   GENETICS

Increased accuracy of artificial selection by using the realized relationship matrix

(2009) B. J. HAYES et al.   Genetics Research

Mapping genes for complex traits in domestic animals and their use in breeding programmes

(2009) Michael E. Goddard et al.   NATURE REVIEWS GENETICS

Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach

(2008) Hans D. Daetwyler et al.   PLoS One

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits

(2008) William G. Hill et al.   PLoS Genetics