Miscanthus interspecific hybrids have been proved to have better adaptability in marginal lands than their parents. Miscanthus sacchariflorus and Miscanthus lutarioriparius were used as the parents to develop hybrids. We performed the transcriptome for 110 F1 hybrids of Miscanthus sacchariflorus × Miscanthus lutarioriparius and their parents that had been established on the Loess Plateau mine area, to estimate the population’s genetic expression variation, and illuminate the adaptive mechanism of the F1 population. The result speculated that the F1 population has mainly inherited the stress response metabolic pathway of its female parent (M. sacchariflorus), which may be responsible for its higher environmental adaptability and biomass yield compared with male parents. Based on PopART, we assembled a leaf reference transcriptome for M. sacchariflorus (LRTMS) and obtained 8116 high-quality transcripts. When we analyze the differential expression of genes between F1 population and parent, 39 and 56 differentially expressed genes were screened out in the female parent and male parent, respectively. The enrichment analysis showed that pathways of carbohydrate metabolism, lipid metabolism, biosynthesis of secondary metabolites and circadian rhythm-plant played a key role in resisting the harsh environment. The carbohydrate metabolism and lipid metabolism were also significantly enriched, and the synthesis of these substances facilitated the yield. The results provided an insight into breeding Miscanthus hybrids more suited to the harsh environment of the Loess Plateau.

Miscanthus is a perennial bioenergy crop suited to marginal and degraded land, yet relatively little is known about the genetic basis of biomass-related variation in interspecific hybrids across years. We evaluated 100 F₁ genotypes from Miscanthus sacchariflorus × M. lutarioriparius for two growing seasons at a reclaimed mine site and analyzed 16 agronomic, biomass-related, and physiological traits using an existing linkage map of 461 SNP marker positions across 19 linkage groups. No single-trait peak exceeded its trait-specific 5% permutation threshold. The clearest repeated suggestive signal occurred in the proximal region of LG9: marker2342 (11.571 cM) showed the strongest across-year signals for plant height and tiller length, while the adjacent marker2343 (10.561 cM) gave the strongest across-year signal for tiller number. Four correlated architecture traits were also summarized by principal component analysis. PC1 explained 73.2–76.6% of their variation, and in 2019 marker0580 on LG3 (12.516 cM) exceeded the genome-wide threshold (LOD 3.67 vs. 3.47). This association remained significant after removal of the single rare genotype-class observation but was not reproduced in 2018; formal marker × year interaction tests confirmed temporal heterogeneity for all four component traits. Biomass and physiological signals were weaker and less repeatable. Thus, the study identifies a repeated but moderate LG9 pattern and a stronger, temporally variable LG3 signal expressed at this reclaimed site; it does not establish loci specifically conferring adaptation to reclaimed mine land. These regions provide priorities for validation using larger populations, denser marker coverage, additional years, and contrasting environments before their value for marker-assisted breeding can be assessed.