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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 #435077

Research Project: Transgenerational Adaptation of Plants to Acidic pH and Toxic Metals in Soil

Location: Plant, Soil and Nutrition Research

Project Number: 8062-21000-049-001-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Aug 1, 2018
End Date: Mar 31, 2023

Previous work on tomato (Solanum lycopersicum 'Micro Tom') has shown that progeny in successive generations produced larger plants with bigger roots under Al stress, compared to the non-primed plants. The goals of this proposal are to develop the research capacities for investigating and utilizing the transgenerational plasticity observed in these tomato plants and to build a research leadership team who will deliver the science and technology in sustainable agriculture. The project has three specific objectives: 1. Identification of the molecular triggers of the stress-induced transgenerational epigenetic reprogramming and its association with gene expression patterns by the simultaneous profiling of DNA methylomes [whole-genome bisulfite sequencing (WGBS) and identification of differentially methylated regions (DMRs)], Transcriptomes [using RNA-seq and the identification of differential expression genes (DEGs)] and Proteomes [relative protein quantification by multidimensional mass spectrometry (MS) using the tandem mass tag technology], followed by integrated analysis of these multi-omics data. 2. Development of a technique (virus-induced gene silencing) to validate the roles of epigenetic genes in the phenotypic plasticity for adaptation to acid, Al toxic soils. 3. Development and implementation of a Tomato Cyber Lab for data management, sharing and analysis, for a more effective utilization of instrumentation and expertise resources across multiple research institutions. The project will produce new ways in improving plant productivity under acid, toxic Al stress.

To achieve the objectives of this proposal, a number of different state of the art approaches will be applied synergistically to discover the molecular mechanisms that underlie the epigenetic modulation of phenotype with respect to increased tolerance to Al3+ observed when tomato plants are grown under sub lethal, Al3+ challenged conditions for successive generations. These approaches include quantitative multiplexed proteomics using amine specific, isobaric, isotope coded labels; Whole Genome Bisulfite Sequencing (WGBS), and Virus Induced Gene Silencing (VIGS). The ARS will largely be responsible for the proteomics aspects of the project plan whereas Cooperators will provide access to the biological materials and be responsible for both the WGBS and VIGS analysis. All parties will participate in various aspects of the data handling and analysis and will cooperate in the development of an online resource for facile data sharing and analysis. The ARS will provide training to and mentor of students and faculty from the cooperating universities with respect to the acquisition and analysis of quantitative proteomic data.