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Joseph Gage

Department of Crop and Soil Sciences

Assistant Professor

2316 Plant Sciences Building


Joe Gage’s research program is focused on linking crop genomic and phenomics to understand how to develop more resilient and productive crop varieties. Current projects include studying how sequence variation controls gene regulation; how gene regulation contributes to genotype-by-environment interactions; and novel methods for processing and interpreting high throughput phenotyping data.


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Date: 08/01/23 - 5/31/28
Amount: $760,000.00
Funding Agencies: National Institute of General Medical Sciences (NIGMS)

Organismal phenotypes in a given environment frequently differ from what might be expected based on genotypic or environmental data alone. These genotype-specific deviations, or gene-environment interactions (GxE), can constitute a large portion of phenotypic variation and are important for determining an individual???s wellbeing in its given environment. An individual adapted to a particular environment can respond appropriately to typical local stresses and nutrients, but may be maladapted in new or changing environments. GxE also makes it exceedingly difficult to predict organismal response to the environment: the magnitude and direction of GxE effects depend on the loci, alleles, traits, and environments involved. This complicates extrapolation of genomic prediction models into new populations or environments. Although it is well established that GxE is a major contributor to phenotypic variation, much less is known about the molecular mechanisms determining individuals??? differential response to environments. This is particularly true in complex, real world environments that are impossible to reproduce in laboratory experiments. Genomewide, allelic variation for gene expression cumulatively influences GxE of organism-level phenotypes, but the complex networks and patterns of gene regulation driving GxE are not well understood. Over the coming five years, this project will generate new datasets and analyze existing datasets to begin understanding and modeling the genomewide patterns of gene expression that cumulatively determine GxE in real world environments. In Aim 1, tissue samples from multi-environmental experiments will be used to evaluate the landscape of gene expression among genetically diverse individuals grown in a variety of environments. Specifically, we will investigate how changes to cis-regulatory sequences (e.g. transcription factor binding motifs) contribute to GxE for gene expression. Simultaneously, we will identify genes that show GxE for expression levels and model how they contribute to GxE for organism-level phenotypes. In Aim 2, we will use existing datasets independent yet complementary to those generated in Aim 1 to test whether GxE in organism-level phenotypes can be predicted directly from sequence variation. Together the multi-scale projects in this study range from the sequence level to the entire organism. By studying GxE at multiple scales and with a variety of different data types, this study will strengthen our understanding of how allelic sequence variation changes gene regulatory networks and drives local adaptation. These findings are important for understanding how organisms adapt to new environments and for better predicting organismal response to the environment.

Date: 08/01/20 - 7/31/25
Amount: $283,649.00
Funding Agencies: USDA - Agriculture Research Service (ARS)

The overall goal of the project is to increase the genetic diversity of maize in farmer's fields through the development of agronomically superior semi-exotic germplasm. Yield and disease evaluations must be conducted in order to identify this superior germplasm, and this funding will help support these evaluations.

Date: 09/15/19 - 9/14/24
Amount: $479,739.00
Funding Agencies: USDA - Agriculture Research Service (ARS)

The objectives of this cooperative research agreement are to evaluate, identify and develop sources of resistance to diseases in winter wheat.

Date: 07/01/23 - 6/30/24
Amount: $30,160.00
Funding Agencies: USDA - Agriculture Research Service (ARS)

North Carolina State University (Cooperator) and the Agricultural Research Service (ARS or Agency) desire to enter into this Agreement for the purpose of supporting research to be carried out at ARS and Cooperator facilities. ARS desires the Cooperator to provide goods and services necessary to carry out research of mutual interest within the Raleigh, NC location. Specifically, the Agency Location is engaged in research addressing Genetics of Disease Resistance and Food Quality Traits in Corn. U

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