Genetic Mapping for Winter‐Hardiness in a Miscanthus sacchariflorus × M. sinensis (Hardy × Non‐Hardy) F 2 Population

ABSTRACT Winter survival remains a primary limitation to the deployment of Miscanthus biomass cultivars in temperate climates. To investigate the genetic architecture underlying this trait, we studied an F 2 population ( n = 247) derived from a cross between the winter‐hardy M. sacchariflorus ‘Robustus’ and the non‐hardy M. sinensis ssp. condensatus ‘Cosmo Revert’. Phenotypic data on overwintering ability, hardiness score, and summer vigor were collected following the establishment year winter (2015–2016) and after an especially cold winter in 2018–2019, during which the soil temperature at 10 cm reached −4.2°C. Composite interval mapping (CIM) with a high‐density SNP linkage map identified 14 quantitative trait loci (QTL), and genome‐wide association studies (GWAS) incorporating both additive and dominant models detected an additional 23 loci, resulting in a total of 37 QTLs. Six QTL regions on five chromosomes were detected repeatedly across traits and/or analyses. In all cases, alleles inherited from the hardy M. sacchariflorus parent were associated with increased winter‐hardiness, whereas alleles from the non‐hardy M. sinensis parent were associated with decreased hardiness. We identified fourteen candidate genes within 10 kb of QTL peaks and that were orthologs of genes previously implicated in cold stress tolerance, including glycosyl and oxidoreductases, rare‐cold‐inducible (RCI) genes, peroxidase proteins, LRR sensors, cytochrome P450s, and stress‐responsive transcription factors. Largely non‐overlapping QTL sets for first‐year versus mature‐plant winter‐hardiness suggested distinct physiological mechanisms underlying differing strategies of overwintering. The consistently favorable effects of the hardy‐parent’s alleles, together with high heritability, suggest that marker‐assisted selection can accelerate the development of winter‐hardy Miscanthus .