Works (20)

Updated: April 3rd, 2024 20:48

2023 journal article

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

BMC GENOMIC DATA, 24(1).

author keywords: Maize; Genotype by environment; Phenotype; Variable environments; Grain yield
MeSH headings : Phenotype; Zea mays / genetics; Seasons; Genotype; Genome, Plant / genetics
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, NC State University Libraries, 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.

author keywords: Maize; Genotype by Environment; Grain Yield; Stability; Prediction
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
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.

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, NC State University Libraries, 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).

author keywords: phenotypic prediction; gene-by-environment interaction (GxE); GEM; convolutional neural network; deep learning
TL;DR: Deep learning provides a promising avenue for phenotypic prediction of complex traits in complex environments and a potential mechanism to better understand the influence of environmental and genetic factors. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, NC State University Libraries
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).

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
TL;DR: It is found that rare variants near the start codon of uORFs can repress or derepress mORF translation, causing allelic changes in protein abundance and providing evidence for the mechanisms by which natural sequence variation modulates gene expression, and ultimately, phenotype. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
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

TL;DR: Predicting maize yield using deep neural networks, comparing the efficacy of two model development methods, and examining the usefulness of incorporating interactions between disparate data types find a deep learning model with interactions has the best average performance. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
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*

Contributors: J. Gage*

TL;DR: The differences between, and challenges of, both traditional and latent phenotyping are discussed. (via Semantic Scholar)
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.

Contributors: J. Gage*

TL;DR: The pangenome was leveraged to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS, and provided an initial estimate of structural diversity of maize. (via Semantic Scholar)
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* ...

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
TL;DR: This report covers the public release of datasets for 2014–2017, which generated large-scale phenotypic, genotypes, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
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.

Contributors: J. Gage*

MeSH headings : Chromosome Mapping; Crops, Agricultural; Plant Breeding; Quantitative Trait Loci; Zea mays / genetics
TL;DR: A retrospective will summarize the design and intentions behind the NAM population; its application, the discoveries it has enabled, and its influence in other systems; and use the past decade of hindsight to consider whether and how it will remain useful in a new age of genomics. (via Semantic Scholar)
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
TL;DR: Substantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs and common regulatory elements underlie various stalk traits. (via Semantic Scholar)
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*

Contributors: J. Gage*

TL;DR: Subcanopy rovers enabled 3D characterization of thousands of hybrid maize plots and latent phenotypes from rovers are ready for application to plant biology and breeding. (via Semantic Scholar)
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
TL;DR: The draft de novo genome assembly of the ‘Oh43’‐type maize inbred ‘PHJ89’ is presented and genome‐wide association studies’ candidate gene predictions vary depending on the reference used. (via Semantic Scholar)
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
TL;DR: Genomic regions recalcitrant to inbreeding were associated with an increased density of genes, many of which demonstrated signatures of selection and floral tissue specificity, and indicated a widespread prevalence of dominance contributions in this population. (via Semantic Scholar)
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*

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
TL;DR: It is found that both increasing the number of causative loci and decreasing the heritability reduce a trait’s AUC, which provides a framework for deciding between competing phenotyping strategies when the ultimate goal is to generate and use phenotype-genotype associations from GWAS. (via Semantic Scholar)
Source: ORCID
Added: July 12, 2022

2018 journal article

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

Genetics, 9.

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
TL;DR: Evidence of selection at genomic regions associated with tassel morphology relative to genome-wide null distributions shows evidence of the tremendous effect selection has had on maize male inflorescence morphology. (via Semantic Scholar)
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*

author keywords: Zea mays L.; Tassel; Image analysis; Phenotyping; High-throughput; Inflorescence
TL;DR: The Tassel Image-based Phenotyping System (TIPS), which provides a platform for imaging tassels in the field immediately following removal from the plant, allows morphological features of maize tassels to be quantified automatically, with minimal disturbance, at a scale that supports population-level studies. (via Semantic Scholar)
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* ...

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
TL;DR: The authors find maize genomic regions selected for high productivity show reduced contribution to genotype by environment variation and provide evidence for regulatory control of phenotypic stability. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science; OpenAlex)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
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*

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
TL;DR: It is suggested that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research. (via Semantic Scholar)
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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