A genome-wide association study of wild Miscanthus in the Russian Far East

Miscanthus is a genus of C4 perennial East Asian grasses that is emerging as a leading bioenergy crop. Clark et al. collected germplasm of M. sacchariflorus and M. sinensis in the Russian Far East, at the northern extent of the range of these two species.

Collection locations, temperature data and population structure of Miscanthus in eastern Russia.
Collection locations, temperature data and population structure of Miscanthus in eastern Russia. (A) Miscanthus sacchariflorus collection sites are indicated with pies, with colours representing assignment (Q values) to four genetic clusters determined by Structure, using 29 260 RAD-seq SNPs across 160 individuals. Q values were highly similar among individuals within each site. Miscanthus sinensis individuals are indicated by squares, and colours indicate assignment to previously identified populations in East Asia (Clark et al., 2014) by discriminant analysis of principal components using 24 132 RAD-seq SNPs. The inset shows frequency of stands of M. sacchariflorus observed at least 100 m apart along four stretches of highway. (B) USDA plant hardiness zones, based on data from 1982–2011 from NAPPFAST (2012). (C) Mean temperatures during January based on data from 1950–2000 available at WorldClim (Hijmans et al., 2005).

Geographic distributions suggest greater winter hardiness in M. sacchariflorus than in M. sinensis. Accessions were genotyped using restriction site associated DNA sequencing (RAD-seq) and a preliminary genome-wide association (GWA) analysis was performed to identify biomass traits in M. sacchariflorus. The data highlights the value of phenotypic data obtained in situ during germplasm collection and will have implications for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. The authors propose a strategy to facilitate the rapid utilisation of new germplasm collections by implementing low-cost SNP genotyping to conduct GWA analysis of phenotypic data obtained at collection sites, with the aim of providing plant breeders with actionable information on desirable traits and alleles found in accessions.

Further reading

Lindsay V. Clark, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Douglas A. Johnson, Jens Bonderup Kjeldsen, Karen Koefoed Petersen, Uffe Jørgensen, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Hua Zhao, Xiaoli Jin, Junhua Peng, Toshihiko Yamada, Erik J. Sacks, 2016, 'Ecological characteristics andin situgenetic associations for yield-component traits of wild Miscanthus from eastern Russia', Annals of Botany, vol. 118, no. 5, pp. 941-955 http://dx.doi.org/10.1093/aob/mcw137