Project abstract for group garvin

Genome and Transcriptome Analysis of Cereal Grasses

Modern crop improvement increasingly relies on large DNA and RNA sequencing datasets obtained by inexpensive high-throughput sequencing methods. The Garvin lab is employing such datasets for improvement of both wheat and oat. Wheat research is targeting the enhancement of disease resistance through discovery and deployment of novel genes associated with nonhost resistance to the disease stem rust from the model grass Brachypodium distachyon. This project involves a novel method for rapid mapping of genes implicated in natural variation for stem rust resistance in Brachypodium, which relies on mapping DNA-based short reads to the reference Brachypodium genome sequence to identify islands of high SNP frequency in which the genes reside. Secondly, wild rice is an important niche grain for Minnesota agriculture. There are very few in genome resources for this crop. Thus, this group is developing transcript assemblies of wild rice as a new genome resource for marker development and identification of genes implicated in fungal disease resistance. Lastly, the researchers are developing a transcript assembly for oat, the sixth most important cereal grain crop in the world. There is a dearth of genome resources for oat. Thus they are using RNA-Seq to develop a gene expression atlas of developing oat seeds as well as quantifying the expression of genes in metabolic pathways responsible for synthesis of health-promoting compounds. The size of the datasets for these projects necessitates the computing power of MSI resources for this research.
A bibliography for papers acknowledging MSI resources is attached.