QTL Detection for Flowering-Time Related Traits in Miscanthus sinensis Using a Staggered-Start Design

The perennial crop miscanthus is being exploited for energy and industrial end-uses. Our objective was to map quantitative trait loci (QTLs) for several flowering-time related traits in Miscanthus sinensis to enhance its breeding. A diploid population of 159 genotypes was extensively phenotyped for flowering-time related traits in 2018 and 2019, using a staggered-start design to distinguish the plant age effect from the climatic condition effect. This revealed that the climatic condition effect was more significant than the age effect. The best linear unbiased predictors of genotype (G), genotype × age interaction (G × A), and genotype × climatic condition interaction (G × C) effects were then estimated using two linear mixed models for each trait. For the anther appearance (AA) and the interval between heading and flowering (IHF), 25 QTLs were associated with genotype effects and 34 with interaction effects, accounting for 2.7 to 30.7% of the phenotypic variation. Regarding the QTLs detected for AA, the allelic effects varied with climatic condition. Interestingly, the QTL effects were smaller for G × A than for G × C. By decomposing the year effect into age and climatic condition effects, the staggered-start design improved QTL detection, which helped decipher the genetic determinism that corresponds to the interaction effects of genotype with age and climatic condition. Finally, a protein sequence alignment with known flowering-time related genes in maize and sorghum revealed the presence of two homologous genes potentially associated with flowering-time in miscanthus within the support interval positions of seven QTL clusters. This study enriched the genetic information on M. sinensis flowering-time and can provide a reference for subsequent genetic breeding.