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United States Department of Agriculture

Agricultural Research Service

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Location: Plant, Soil and Nutrition Research

2012 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 2012, collaboration focused on the development of resources to support genome assemblies and gene networks. Although one of the collaboration groups has interest in plant-related research, a major focus is using next-generation sequencing technology 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, and optimization for targeted regions. As part of this collaboration, members have attended 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 failures associated with PacBio technologies have been discussed. Collaborators have worked with personnel in each other’s groups to optimize assembly approaches for these genomes. This work was in collaboration of the NSF-funded wheat gene-space project. In addition, this collaboration has supported the sequencing and analysis of small RNA libraries, cDNA-based libraries (RNA sequence), and genomic libraries from several plant species. In the last year, focus has been on rice, maize, wheat, and sorghum. This data has supported the baseline annotations and regulator sequence objectives of the in-house project. Experimental approaches for methylation and transcription profiling was an area of focus. For the maize inflorescence development objective, analysis workflows were updated and preliminary analyses of co-expressed genes have identified candidates based on guilt-by-association for genes involved in inflorensence determinacy in maize. We refined the computational pipeline for analysis of shotgun bisulfite sequencing data to determine context-specific shifts in methylation on a genome-wide scale across different tissues and developmental stages in maize as well as the sequencing resources to support genetic and molecular characterization of miRNA-focused networks. In the last year, additional miRNA and highly connected transcription factor promoters have been screened. Analysis of this network identified a set of Zinc finger homeodomain transcription factors that are highly connected in the network. In addition, genetic mutant resources have been extended to support in vivo characterization and perturbation of the network. Seventy-five per cent of the mutants screened show a molecular phenotype in the root, while only a small percentage show a morphological phenotype. This is likely associated with the functional redundancy of genes.

4. Accomplishments

Last Modified: 2/23/2016
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