Works (20)

Updated: March 1st, 2024 16:27

2023 journal article

2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project

BMC GENOMIC DATA, 24(1).

co-author countries: Canada 🇨🇦 Germany 🇩🇪 France 🇫🇷 Panama 🇵🇦 United States of America 🇺🇸
author keywords: Maize; Genotype by environment; Phenotype; Variable environments; Grain yield
MeSH headings : Phenotype; Zea mays / genetics; Seasons; Genotype; Genome, Plant / genetics
Sources: Web Of Science, ORCID
Added: May 26, 2023

2023 article

2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative

Lima, D. C., Aviles, A. C., Alpers, R. T., Perkins, A., Schoemaker, D. L., Costa, M., … Leon, N. (2023, September 14). BMC RESEARCH NOTES, Vol. 16.

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
author keywords: Maize; Genotype by Environment; Grain Yield; Stability; Prediction
Sources: Web Of Science, ORCID
Added: October 23, 2023

2023 article

Genomes to Fields 2022 Maize genotype by Environment Prediction Competition

Lima, D. C., Washburn, J. D., Varela, J. I., Chen, Q., Gage, J. L., Romay, M. C., … Leon, N. (2023, July 17). BMC RESEARCH NOTES, Vol. 16.

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
author keywords: Grain yield; Maize; Root mean squared error
MeSH headings : Phenotype; Zea mays / genetics; Genotype; Genome, Plant / genetics; Edible Grain / genetics
Sources: Web Of Science, ORCID
Added: July 18, 2023

2023 journal article

Yield prediction through integration of genetic, environment, and management data through deep learning

G3-GENES GENOMES GENETICS, 13(4).

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
author keywords: phenotypic prediction; gene-by-environment interaction (GxE); GEM; convolutional neural network; deep learning
Sources: Web Of Science, ORCID
Added: February 12, 2024

2022 journal article

Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(14).

co-author countries: United States of America 🇺🇸
author keywords: uORF; proteome; rare alleles; maize; gene expression
MeSH headings : 5' Untranslated Regions; Open Reading Frames / genetics; Protein Biosynthesis / genetics; RNA, Messenger / genetics; RNA, Messenger / metabolism; Ribosomes / genetics; Ribosomes / metabolism; Zea mays / genetics; Zea mays / metabolism
Sources: Web Of Science, ORCID
Added: July 11, 2022

2022 article

Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning

(2022, July 30). [], Vol. 7.

Contributors: J. Gage n

Source: ORCID
Added: April 18, 2023

2021 journal article

Images carried before the fire: The power, promise, and responsibility of latent phenotyping in plants

The Plant Phenome Journal, 4(1).

By: M. Feldmann*, J. Gage*, S. Turner-Hissong & J. Ubbens*

co-author countries: Canada 🇨🇦 United States of America 🇺🇸

Contributors: J. Gage*

Source: ORCID
Added: April 18, 2023

2020 article

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

Franco, J. A. V., Gage, J. L., Bradbury, P. J., Johnson, L. C., Miller, Z. R., Buckler, E. S., & Romay, M. C. (2020, August 31). [], Vol. 8.

co-author countries: United States of America 🇺🇸

Contributors: J. Gage*

Source: ORCID
Added: April 18, 2023

2020 journal article

Maize genomes to fields (G2F): 2014–2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets

BMC Research Notes, 13(1).

By: B. McFarland*, N. AlKhalifah*, M. Bohn*, J. Bubert*, E. Buckler*, I. Ciampitti*, J. Edwards, D. Ertl* ...

co-author countries: Canada 🇨🇦 United States of America 🇺🇸

Contributors: J. Gage*

author keywords: Maize; Genome; Genotype; GBS; G x E; Hybrid; Inbred; Phenotype; Environment; Field metadata
MeSH headings : Datasets as Topic; Genome, Plant / genetics; Genotype; Phenotype; Plant Breeding; Zea mays / genetics
Source: ORCID
Added: December 8, 2020

2020 journal article

Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions

The Plant Cell, 32(7), 2083–2093.

co-author countries: United States of America 🇺🇸

Contributors: J. Gage*

MeSH headings : Chromosome Mapping; Crops, Agricultural; Plant Breeding; Quantitative Trait Loci; Zea mays / genetics
Source: ORCID
Added: April 18, 2023

2019 journal article

Genome-wide association analysis of stalk biomass and anatomical traits in maize.

BMC Plant Biology.

Joseph Gage

author keywords: Maize; Stover; Stalk; Plant height; Rind; Vascular bundle; Genome-wide association; Zmm22
MeSH headings : Biomass; Gene Expression Regulation, Plant / genetics; Genes, Plant / genetics; Genes, Plant / physiology; Genome-Wide Association Study; Plant Stems / anatomy & histology; Plant Stems / genetics; Plant Stems / growth & development; Polymorphism, Single Nucleotide / genetics; Quantitative Trait, Heritable; Zea mays / anatomy & histology; Zea mays / genetics; Zea mays / growth & development
Source: ORCID
Added: July 12, 2022

2019 journal article

In‐Field Whole‐Plant Maize Architecture Characterized by Subcanopy Rovers and Latent Space Phenotyping

The Plant Phenome Journal, 2(1), 1–11.

By: J. Gage*, E. Richards*, N. Lepak*, N. Kaczmar*, C. Soman, G. Chowdhary*, M. Gore*, E. Buckler*

co-author countries: United States of America 🇺🇸

Contributors: J. Gage*

Source: ORCID
Added: April 18, 2023

2019 dataset

LiDar Point Clouds of Hybrid Maize

CyVerse Data Commons.

Contributors: J. Gage

Source: ORCID
Added: July 12, 2022

2019 journal article

Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel

The Plant Genome.

Joseph Gage

MeSH headings : Genetic Variation; Genome, Plant; Genome-Wide Association Study; Inbreeding; Molecular Sequence Annotation; Plant Breeding; Polymorphism, Single Nucleotide; RNA, Plant; Reference Values; Sequence Analysis, RNA; Transcriptome; Zea mays / genetics
Source: ORCID
Added: July 12, 2022

2019 journal article

Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato.

Genetics.

Joseph Gage

author keywords: yield; epistasis; QTL; heterozygosity; sequencing; potato; outcrossed
MeSH headings : Diploidy; Epistasis, Genetic; Genes, Plant; Haplotypes; Heterozygote; Hybrid Vigor; Inbreeding; Polymorphism, Genetic; Quantitative Trait Loci; Solanum tuberosum / genetics
Source: ORCID
Added: July 12, 2022

2018 journal article

Comparing Genome-Wide Association Study Results from Different Measurements of an Underlying Phenotype.

G3 (Bethesda, Md.), 9.

By: J. Gage*, L. de & M. Clayton*

co-author countries: United States of America 🇺🇸
author keywords: AUC; GWAS; heritability; ROC
MeSH headings : Area Under Curve; Genome-Wide Association Study; Genotype; Inflorescence / anatomy & histology; Inflorescence / genetics; Phenotype; ROC Curve; Zea mays / anatomy & histology; Zea mays / genetics
Source: ORCID
Added: July 12, 2022

2018 journal article

Selection Signatures Underlying Dramatic Male Inflorescence Transformation During Modern Hybrid Maize Breeding.

Genetics, 9.

co-author countries: United States of America 🇺🇸
author keywords: maize; inflorescence; tassel; selection; GWAS
MeSH headings : Chromosome Mapping; Flowers / genetics; Genome-Wide Association Study; Genotype; Phenotype; Plant Breeding; Polymorphism, Single Nucleotide; Zea mays / genetics
Source: ORCID
Added: July 12, 2022

2017 journal article

TIPS: a system for automated image-based phenotyping of maize tassels

Plant Methods, 13(1), 21.

By: J. Gage*, N. Miller*, E. Spalding*, S. Kaeppler* & N. Leon*

co-author countries: United States of America 🇺🇸
author keywords: Zea mays L.; Tassel; Image analysis; Phenotyping; High-throughput; Inflorescence
Source: ORCID
Added: July 12, 2022

2017 journal article

The effect of artificial selection on phenotypic plasticity in maize

NATURE COMMUNICATIONS, 8(1).

By: J. Gage*, D. Jarquin*, C. Romay*, A. Lorenz*, E. Buckler*, S. Kaeppler*, N. Alkhalifah*, M. Bohn* ...

co-author countries: Canada 🇨🇦 India 🇮🇳 United States of America 🇺🇸

Contributors: J. Gage*, D. Jarquin*, C. Romay*, A. Lorenz*, E. Buckler*, S. Kaeppler*, N. Alkhalifah*, M. Bohn* ...

MeSH headings : Chimera; Gene Frequency; Genetic Variation; Genome, Plant; Phenotype; Plant Breeding; Polymorphism, Single Nucleotide; Selection, Genetic; Tropical Climate; Zea mays / genetics; Zea mays / physiology
Sources: ORCID, Web Of Science
Added: August 6, 2018

2013 journal article

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations.

TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 8.

By: J. Spindel*, M. Wright*, C. Chen*, J. Cobb*, J. Gage*, S. Harrington*, M. Lorieux*, N. Ahmadi*, S. McCouch*

co-author countries: France 🇫🇷 United States of America 🇺🇸
MeSH headings : Adaptation, Physiological / drug effects; Adaptation, Physiological / genetics; Aluminum / toxicity; Breeding; Chromosome Breakage; Chromosome Mapping / methods; Chromosome Segregation / genetics; Genetic Markers; Genotyping Techniques / methods; Oryza / genetics; Plant Leaves / anatomy & histology; Plant Leaves / drug effects; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci / genetics; Recombination, Genetic / genetics; Sequence Analysis, DNA / methods
Source: ORCID
Added: July 12, 2022

Employment

Updated: August 4th, 2022 13:06

2022 - present

North Carolina State University Raleigh, North Carolina, US
Crop and Soil Sciences

2020 - 2021

Cornell University Ithaca, New York, US
NSF Postdoctoral Fellow

2018 - 2019

USDA Agricultural Research Service Ithaca, NY, US
Research Geneticist

Education

Updated: March 18th, 2020 14:03

2013 - 2018

University of Wisconsin Madison Madison, WI, US
PhD, MS Plant Breeding and Plant Genetics, Biometry

Cornell University Ithaca, NY, US
B.S. Plant Sciences, Communication

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