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Background Miscanthus × giganteus is widely recognized as a promising lignocellulosic biomass crop due to its advantages of high biomass production, low environmental impacts, and the potential to be cultivated on marginal land. However, the high costs of bioethanol production still limit the current commercialization of lignocellulosic bioethanol. The lignin in the cell wall and its by-products released in the pretreatment step is the main component inhibiting the enzymatic reactions in the saccharification and fermentation processes. Hence, genetic modification of the genes involved in lignin biosynthesis could be a feasible strategy to overcome this barrier by manipulating the lignin content and composition of M. × giganteus. For this purpose, the essential knowledge of these genes and understanding the underlying regulatory mechanisms in M. × giganteus is required. Results In this study, MgPAL1, MgPAL5, Mg4CL1, Mg4CL3, MgHCT1, MgHCT2, MgC3′H1, MgCCoAOMT1, MgCCoAOMT3, MgCCR1, MgCCR2, MgF5H, MgCOMT, and MgCAD were identified as the major monolignol biosynthetic genes in M. × giganteus based on genetic and transcriptional evidence. Among them, 12 genes were cloned and sequenced. By combining transcription factor binding site prediction and expression correlation analysis, MYB46, MYB61, MYB63, WRKY24, WRKY35, WRKY12, ERF021, ERF058, and ERF017 were inferred to regulate the expression of these genes directly. On the basis of these results, an integrated model was summarized to depict the monolignol biosynthesis pathway and the underlying regulatory mechanism in M. × giganteus. Conclusions This study provides a list of potential gene targets for genetic improvement of lignocellulosic biomass quality of M. × giganteus, and reveals the genetic, transcriptional, and regulatory landscape of the monolignol biosynthesis pathway in M. × giganteus.

The regeneration from embryogenic callus of higher plants in tissue culture is regulated by explants types and developmental stage and also regulated by some genes. In Miscanthus lutarioriparius, five candidate genes were selected to decide the differential expression between embryogenic and non-embryogenic calli, including MlARF-GEP (guanine nucleotide-exchange protein of ADP ribosylation factor), MlKHCP (kinesin heavy chain like protein), MlSERK1 (somatic embryogenesis receptor-like kinases 1), MlSERK2 (somatic embryogenesis reportor-like kinases 2), and MlTypA (tyrosine phosphorylation protein A) with Genbank accession numbers KU640196–KU640200. Multiple sequence alignment analysis showed that five genes were highly conserved among members of their gene families respectively. Phylogenetic relationship analysis showed that five genes were closest with homologous genes of Zea mays and Sorghum. The qRT-PCR results showed significant differences of five genes expression pattern between two different callus types, the relative expression in embryogenic callus was detected to exceed in non-embryogenic callus. Furthermore, simple sequence repeats (SSR) marker statistics results via Chi-square showed a significant correlation between MlSERK1 genotype and induction of embryogenic callus in M. lutarioriparius. This study may lay the foundation of the molecular mechanism on the embryogenic callus induction of M. lutarioriparius and perhaps provide some gist for further study on genetic manipulation.