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United States Department of Agriculture

Agricultural Research Service

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Location: Plant, Soil and Nutrition Research

2010 Annual Report

1a. Objectives (from AD-416)
The objective of this SCA is to increase our understanding of plant genomes through sequence generation and characterization.

1b. Approach (from AD-416)
Plant genomes are large and complex genomes, making them a challenge to sequence and characterize their genomes’. With recent changes in sequencing technology it is now possible to generate sequence at fraction of the cost. But the sequence that is generated has different qualities that will require changes in the way we process and interpret this sequence. Experimental and computational approaches will be reviewed and develop to make use of the new short read technologies. This will include library development, integration of different sequencing methodologies, and development of computational pipelines to process, store and interpret the data sets.

3. Progress Report
In FY 2010, collaboration focused on the development of standards and analysis tools to make use of short-read sequencing, specifically the use of Illumina technology for analyzing and characterizing genome sequence. Although one of the collaboration groups has interest in plant related research, a major focus is using short-sequence sequencing as a method to identify sequence associated variation and its relationship to cognitive disorders. For this work, the group uses this technology to produce genome sequence for re-sequencing as well as de-novo assembly and expression, sequence and methylation-state variation in complete genomes, as well as optimizing for targeted regions. As part of this collaboration, members have attended bi-weekly group meetings that discuss production and analysis of sequence allowing technology transfer between the groups for library production as well as downstream sequence analysis. Preliminary successes and failure associated with multiplexing of samples to reduce cost as well as scale, have been discussed. Collaborators have worked with personnel in each other’s group to optimize genome DNA preparation genomic DNA libraries. The collaboration has directly support the production cost for sequencing efforts for genome assembly, genotyping, expression profiling of small RNAs and cDNAs. This work specifically contributed to the resources on the MaizeHapMap project, the USDA Grape Genetic Trait index (Vitis rotundifolia), and preliminary assembly of Solanum pimpinellifolium, the wild progenitor of the domesticated Heinz variety of tomato (Solanum lycopersicum). This work was done in collaboration with Drs. Ed Buckler USDA ARS, GanYang Zhang USDA ARS, and Zach Lippman CSHL. In addition to sequencing analysis, the SCA has also provided resources that target specific objective 1.2, “Identification of regulatory sequences.” This collaborative work supported both computation and experimental analysis. In the last resources were dedicated to identifying microRNAs that are expressed in roots, prioritize promoter screening. In addition the current TF library is being transferred to a new vector with increased sensitivity for the HIS promoter. The work also supported screening of small RNA and cDNA libraries from tissues isolated for specific tissues or response to biotic and abiotic stress in sorghum and maize. Research conducted under this agreement was monitored through in persons meetings between the ADODR and the Cooperator.

4. Accomplishments

Last Modified: 08/15/2017
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