Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

Soybean [Glycine max (L.) Merr.] breeding in the United States currently relies on a narrow genetic base. For decades, but more intensely in recent years, efforts have been made to incorporate exotic soybean germplasm into the breeding pool. Although wild soybean (G. soja Seib. and Zucc.) is genetically much more diverse than soybean, much less effort has been devoted to utilizing wild soybean in soybean breeding. The objectives of this research were to identify high‐yielding lines derived from crosses between five wild soybean accessions and soybean cultivars and determine if there are differences in the genetic contributions of each wild soybean parent. Each wild soybean was crossed to Williams 82, and the F1 plants were backcrossed to Williams 82 to create the backcross generation (BC1) lines. The BC2 parent lines were developed through family selection and backcrossed to Williams 82, IA2052, IA3023, or LN97–15076. Family selection beginning in the F2 generation was used to develop lines from plant introduction (PI) 507807 and PI 549046. The lines from PI 479767 and PI 483461 were selected by early generation testing through yield testing F2 lines in the F3 and F4 generations. The lines derived from PI 65549 were developed from a single seed descent (SSD) population. Field evaluation of the derived lines identified lines that are not significantly different from their recurrent parents. Using single nucleotide polymorphism (SNP) markers, we found unique contributions being made by the G. soja parents. Despite intense selection pressure to recover good agronomic types, an average of 13% of SNP alleles in the derived lines came from the G. soja parents.

Background: Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites.Results: We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1-26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors.Conclusions: We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.