Developing a Genomic Toolbox for the Improvement of Intermediate Wheatgrass As a Perennial Grain Crop

Perennial crop species are central to the overall sustainable intensification of cropping systems for food, feed, fiber, and fuel. Dual-use crops that can serve as a biofuel feedstock in addition to a source of edible grain add additional economic return to the cropping systems that are needed to meet projected demand for both food and fuel. The rapid development of new perennial crop species to enhance the sustainable intensification of agriculture is now possible using genomics-assisted breeding. Intermediate wheatgrass (Thinopyrum intermedium) is a promising perennial crop that can provide ecosystem services to protect soil and water health, grain for food production, and biomass for energy. We have generated a draft genome sequence from a haploid line in collaboration with NRGene using the DeNovoMAGIC 2.0 assembly pipeline. This assembly represents over 92% of the predicted genome size and consists of 237,622 scaffolds with a scaffold N50 of 2.7 Mb. Two F1 populations consisting of 182 individuals have been resequenced at low depth to anchor and order the assembly using POPSEQ. A comprehensive reference transcriptome has also been generated from the haploid line that will be used for gene prediction and annotation of the draft genome. This assembly has enabled an omics approach for investigating the molecular mechanisms underlying free threshing seed in intermediate wheatgrass, a key target trait. Collectively, these genomic resources are providing vital information for ongoing breeding and molecular studies to improve intermediate wheatgrass as a perennial grain crop.