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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #427202

Research Project: Sequence-Based Genotyping, Bioinformatics, and Data Curation to Enhance Sorghum Germplasm Evaluation and Hybrid Development

Location: Crop Germplasm Research

Project Number: 3091-21000-043-01-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2014
End Date: Jul 31, 2019

Objective:
This project aims to utilize recent advances in high-throughput genotyping, bioinformatics, and RNAseq technology to acquire knowledge of sorghum genes and germplasm, and utilize this information to enhance the rate of genetic gain for complex traits such as grain yield and cytoplasmic-male sterility. Over the years, the cooperator has established the bioinformatic infrastructure and data curation to support sequence-based evaluation of sorghum gene sequence, gene expression, and sorghum germplasm. The cooperator will analyze sequence of sorghum DNA and RNA (RNAseq) in support of the ARS effort to convert tropical sorghum via the Sorghum Conversion Program and the effort to elucidate the genetic basis of cytoplasmic-male sterility. In this agreement, the cooperator will undertake a multi-faceted bioinformatics analysis of sorghum germplasm and genes, and will curate the terabytes of sequence information generated by the ARS parent project.

Approach:
Conduct bioinformatic analyses of genotype-by-sequencing data from 1000 F3 genotypes each year arising from the MMR Genetics LLC-ARS Sorghum Conversion Program. Transfer the results of the bioinformatic analyses to the ARS parent project within 1 month of receiving the raw sequencing data. Direct Ph.D candidate in the execution of gene expression (RNAseq) studies of sorghum panicles collected from hybrid sorghum and parental inbreds, and conduct bioinformatic analyses to identify those genes whose expression is critical to pollen fertility restoration and cytoplasmic-male sterility. Curate and secure all data collected from this work for a period of five years and provide ready access of the data to the ARS parent project during the duration of the agreement. Upon termination of the agreement, transfer all data to the ARS parent project if requested.