2014
The Impact of Tissue Culture on the Soybean Epigenome (1420-532-5645)
Contributor/Checkoff:
Category:
Sustainable Production
Keywords:
(none assigned)
Parent Project:
This is the first year of this project.
Lead Principal Investigator:
Blake Meyers, University of Delaware
Co-Principal Investigators:
Project Code:
1420-532-5645
Contributing Organization (Checkoff):
Institution Funded:
Brief Project Summary:

Unique Keywords:
#breeding & genetics, #soybean bioengineering, #soybean biotechnology
Information And Results
Project Deliverables

The deliverables include the libraries described above, which will be released to the public via Genbank and our existing public websites. In addition, we anticipate that this work will produce at least one significant publication describing the results.

Final Project Results

This project was initiated preceding the incorporation and standardization of KPIs. The progress of objectives are as follows:

Achieving objectives:
• As of the project end, most of the expected data was generated. The researchers had proposed to conduct bisulfite sequencing, small RNA, and mRNA analysis on materials which have undergone regeneration from tissue culture. These materials were to include two independent regenerated lines, at both the T0 (first transformed, or in this case, regenerated) line, and four generations later in the T4 generation. Plants from the same seed stock that did not undergo regeneration were to be analyzed as controls. They were able to complete data generation from 10 libraries.
• Replicated library sets were sequenced and the final total coverage of the libraries was ~30X (or 15X per strand of DNA, ideal for the identification of differentially methylated regions (DMRs).

Not Achieving the objectives:
• While this project has ended, not all the final steps are completed. Data analysis is still underway. This will involve (1) the identification of DMRs from the BS-seq data, the comparison of the DMRs with the small RNA data, using the small RNAs as validation of the DMRs (since they usually correlate very well), and the identification of any differentially expressed genes in the mRNA data that may result from the DMRs triggered by the tissue culture.
• The researchers anticipate that the DMRs will be characterized by the end of 2014, and the integration of small RNA and mRNA will follow as will publications of the results.

The United Soybean Research Retention policy will display final reports with the project once completed but working files will be purged after three years. And financial information after seven years. All pertinent information is in the final report or if you want more information, please contact the project lead at your state soybean organization or principal investigator listed on the project.