Location: Crop Germplasm Research
Project Number: 3091-21000-043-003-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2019
End Date: Jul 31, 2022
Objective:
This collaborative project aims to utilize recent advances in genome sequencing, bioinformatics, RNAseq technology, and UPLC-based grain composition analyses to acquire knowledge of sorghum germplasm and utilize this information to enhance the rate of genetic gain for complex traits including the black-grained sorghum. Over the years, Texas A&M University (TAMU) scientists have established the bioinformatic infrastructure and data curation to support NexGen sequence-based evaluation of sorghum gene sequence, gene expression, and sorghum germplasm. TAMU scientists will analyze sequence of sorghum DNA and RNA (RNAseq) in support of ARS' effort to elucidate the genetic and environmental basis of high-antioxidant black-pericarp sorghum. The RNAseq and genome re-sequencing data, along with UPLC grain composition analyses, will be generated by a TAMU Ph.D candidate whose doctoral degree program is co-chaired by the ARS and TAMU. In this agreement, TAMU scientists and the Ph.D candidate will undertake a multi-faceted bioinformatics analysis of the sorghum pericarp genome, flavonoid composition, and pericarp gene expression, and will curate the terabytes of sequence information generated by the ARS parent project.
Approach:
Conduct bioinformatic analyses of RNAseq and genome resequencing data from elite inbreds and a recombinant inbred line population arising from the Texas A&M University sorghum research Program. Transfer the results of the bioinformatic analyses to the ARS within 1 month of receiving and curating the raw sequencing data each year. Direct Ph.D candidate in the execution of gene expression (RNAseq) studies of sorghum pericarp tissues collected from recombinant inbreds and elite black sorghums, and conduct bioinformatic analyses to identify those genes whose environmentally-controlled expression is critical to the flavonoid composition of black pericarp. Curate and secure all data collected from this work and provide ready access to the data to the ARS parent project during the duration of the agreement. Upon the termination of the agreement, transfer all data to the ARS parent program if requested.
