Genome and Transcriptome Sequencing of Intermediate Wheatgrass (Thinopyrum intermedium) Provides Resources for the Development of a New Perennial Grain Crop.

Perennial crop species are central to the overall sustainable intensification of cropping systems for food, feed, and fiber.  Dual-use crops that can serve as a biofuel feedstock and source of edible grain add additional economic potential to the cropping systems that are needed to meet projected demand for both food and fuel.  Intermediate wheatgrass (Thinopyrum intermedium, L.) is a strong perennial species, with prolific biomass production and relatively large seeds and high grain yield.  A distant relative of common wheat, the grain is of high quality and value, and the biomass production is similar to switchgrass.  The availability of genomic resources opens vast possibilities for accelerated improvement of crop species like intermediate wheatgrass.  However, there’s been limited molecular breeding and genomic efforts in intermediate wheatgrass, largely due to its allohexaploid genome (2n=6x=42) and estimated genome size of 13 Gb. To facilitate sequencing of an outcrossing species with a genome of this magnitude, we have a haploid line in hand derived from a twin seedling, confirmed by chromosome counting and flow cytometry.  Whole genome sequencing of the haploid line has been initiated, starting with 30X coverage shotgun sequencing using 250 bp paired-end reads on the Illumina HiSeq 2500 platform.  A comprehensive reference transcriptome assembly has also been generated from the haploid line that will be used for gene prediction and annotation of the draft genome assemblies.  Finally, several tissue specific RNAseq datasets have been generated, and a vernalization time series RNAseq experiment has been conducted. These resources will provide vital information for ongoing breeding and molecular studies to improve intermediate wheatgrass as a perennial grain species.