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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Research Project #430989

Research Project: Genomics of Agricultural Species, and Their Pests and Pathogens

Location: Genomics and Bioinformatics Research

Project Number: 6066-21310-005-23-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jun 15, 2016
End Date: Jun 14, 2019

Objective:
The Institute for Genomics, Biocomputing & Biotechnology (IGBB) at Mississippi State University (MS State) and the ARS’s Genomics & Bioinformatics Research Unit (GBRU) will continue their collaborative, synergistic research on the biomolecular interactions underlying the adaptive and agronomic features of agricultural species. Goals of the current project include (but are not limited to) [a] development of reference quality genome sequences for three wild tetraploid cotton species (Gossypium mustelinum, G. tomentosum, and G. darwinii); [b] proteome analysis of G. mustelinum as a means to better annotate its genome via proteogenomic mapping; [c] genome sequencing of several cotton pests and pathogens (e.g., tobacco thrip - Frankiella fusca; boll weevil - Anthonomus grandis); [d] differential gene expression and proteome analyses of pests/pathogens and host plants during infestation/infection; [e] genome-wide association studies (GWAS) of soybean and its pathogens Macrophomina phaseolina and Cercospora sojina, the causative agents of charcoal-rot and frog-eye leaf spot, respectively; and [f] completion of a reference quality genome for Amaranthus palmeri, an important weed pest in the southern U.S. All of the research will utilize the IGBB’s expertise in computational biology and bioinformatics. Data and results will be leveraged to better understand cotton and other agricultural species and their relationships with pests and pathogens. The research, which will be conducted in collaboration with several ARS groups and academic scientists, will provide genomic information that can be integrated into breeding programs and used in plant improvement. Moreover, it will illuminate pest/pathogen biochemical pathways that can be targeted to minimize pest/pathogen damage.

Approach:
Next Generation Sequencing (NGS) technologies will be used to generate DNA and transcriptome sequence data. Proteomics data will be generated using the Institute for Genomics, Biocomputing & Biotechnology”s (IGBB) linear Trap Quadropole (LTQ) Orbitrap Velos mass spectrometer. The IGBB will utilize its supercomputing capacity and expertise to conduct genome assembly, SNP (Single Nucleotide Polymorphism) calling, comparative genomics research, and GWAS (Genome-Wide Association Studies) experiments. RT-qPCR (RNA detection and quantification method) will be used to validate RNASeq (determination of gene expression via sequencing of RNA) based differential gene expression results.