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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #437816

Research Project: Phenotypic Characterization of a Tomato Epi-RIL Population

Location: Plant, Soil and Nutrition Research

Project Number: 8062-21000-047-024-A
Project Type: Cooperative Agreement

Start Date: Feb 24, 2020
End Date: Feb 15, 2022

Thousands of tomato QTLs have been described with no information about what proportion is epigenetic. Genetic variation in cultivated tomato is limited, despite substantial phenotypic diversity suggesting a significant epigenetic component. It will benefit our understanding of the fundamental processes regulating gene expression and the metabolome and inform future breeding strategies in tomato and other crops to better understand the influence of epigenetic variation in crop biology and variation. To do so we will exploit a population of tomato lines engineered to have substantial epigenetic variation, specifically in the context of DNA cytosine methylation, to assess the degree and stability of epigenetic variation. We will grow and phenotype these lines for fruit development and ripening, general growth habit, size form and stature in both greenhouse and field trials to assess phenotypes and their stability. These activities will serve as a prelude to fine analysis of putative EPI-alleles.

We will study an epigenetically modified recombinant inbred line (epiRIL) population with a random distribution of epialleles, derived from a cross between a wild-type tomato line and one where a gene involved in maintaining DNA methylation {either DNA METHYTRANSFERASE-1 (MET1) or DNA DEMETHYTRANSFERASE-1 (DDM-1)} is compromised. The population will be grown in field and greenhouse settings to examine the nature and stability of epigenetic variants and their potential for utilization in crop improvement.