A footprint of past climate change on the diversity and population structure of Miscanthus sinensis

Abstract

Background and Aims: Miscanthus is a perennial C4 grass that is a leading potential feedstock for the emerging bioenergy industry in North America, Europe, and China. However, only a single sterile genotype of M. ×giganteus (Mxg), a nothospecies derived from diploid M. sinensis (Msi) and tetraploid M. sacchariflorus (Msa), is currently available to farmers for biomass production. To facilitate breeding of Miscanthus, we characterized genetic diversity and population structure of Msi in its native range of East Asia. Methods: We studied 767 accessions, including 617 Msi from most of its native range in China, Japan, and South Korea, 77 ornamental cultivars, and 43 naturalized individuals from the U.S. Accessions were evaluated with 21,207 restriction site associated DNA sequencing single nucleotide polymorphism (SNP) markers, 424 GoldenGate SNPs, and ten plastid microsatellite markers. Key Results: Six genetic clusters of Msi from geographically distinct regions in Asia were identified. Genetic data indicated that 1) Southeast China was the origin of Msi populations found in temperate eastern Asia, which was consistent with this area having likely been a refugium during the last glacial maximum (LGM), 2) Msi migrated directly from Southeast China to Japan before migrating to the same latitudes in China and Korea, which was consistent with the known sequence of warming post-LGM, 3) ornamental Msi cultivars were derived from the Southern Japan population, and U.S. naturalized populations were derived from a subset of the ornamental cultivars, and 4) many ornamental cultivars previously described as Msi have hybrid ancestry from Msa and Msi, whereas U.S. naturalized populations of Msi do not. Conclusions: Population structure of Msi was driven by patterns of warming since the LGM, and secondarily by geographic barriers. This study will facilitate germplasm conservation, association analyses, and identification of potential heterotic groups for the improvement of Miscanthus as a bioenergy crop.