Research on genetic diversity and genomes of Miscanthus for optimizing their biotechnological potential

Plants of the genus Miscanthus are a promising perennial energy crop, combining high biomass productivity, resistance to abiotic stress, and low agricultural technology requirements. This review summarizes recent advances in genomic and transcriptomic studies of the molecular genetic mechanisms underlying the economically valuable traits of Miscanthus. Data on whole-genome assemblies of key species – M. sinensis (Msi), M. sacchariflorus (Msa), M. floridulus (Mfl), and M. lutarioriparius (Mlu) – are presented using various technologies (Illumina, PacBio, Oxford Nanopore, Hi-C). Genomic studies have revealed the complex evolution of the genus, including paleoallopolyploidy, chromosomal fusions, and duplications, which accounts for the high genetic diversity of these species. Their genome assemblies at the complete chromosome level have become the basis for comparative genomics, establishing taxonomic relationships (including the recognition of Mlu as a subspecies of Msa and Mfl as a subtype of Msi), and studying synteny with related crops such as sorghum. The information on the Miscanthus genome allows for the complete and accurate identification of a set of genes targeting breeding for the most important biotechnological traits. At the same time, the commercial hybrid M. × giganteus (M × g) is characterized by extremely low levels of genetic polymorphism, making it vulnerable to pathogens and climate fluctuations. The integration of genetic polymorphism data, phylogeography, and functional annotation of genomes opens up opportunities for the development of new, productive, and environmentally friendly Miscanthus varieties through interspecific crossings, ploidy modification, and genetic engineering. These advances contribute to the optimization of the biotechnological potential of Miscanthus for the production of biofuels and other biomaterials and the restoration of degraded lands.

1. Andrić S., Knežević G., Maletić S., Rončević S., Isakovski M.K., Zeremski T., Beljin J. An experimental assessment of Miscanthus × giganteus for landfill leachate treatment: a case study of the grebača landfill in obrenovac. Processes. 2025;13(3):768. doi 10.3390/pr13030768

2. Brosse N., Dufour A., Meng X.Z., Sun Q.N., Ragauskas A. Miscanthus: a fast-growing crop for biofuels and chemicals production. Biofuels Bioprod Biorefin. 2012;6(5):580-598. doi 10.1002/bbb.1353

3. Cappelletto P., Mongardini F., Barberi B., Sannibale M., Brizzi M., Pignatelli V. Papermaking pulps from the fibrous fraction of Miscanthus × giganteus. Ind Crop Prod. 2000;11(2-3):205-210. doi 10.1016/S0926-6690(99)00051-5

4. Chen Y.X., Yu Q. Surface modification of miscanthus fiber with hydrophobic silica aerogel for high performance bio-lightweight concrete. Constr Build Mater. 2024;411:134478. doi 10.1016/j.conbuildmat.2023.134478

5. Chen Z., He Y., Iqbal Y., Shi Y., Huang H., Yi Z. Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq. BMC Genomics. 2022;23(1):43. doi 10.1186/s12864-021-08277-8

6. Cichorz S., Gośka M., Litwiniec A. Miscanthus: genetic diversity and genotype identification using ISSR and RAPD markers. Mol Biotechnol. 2014;56(10):911-924. doi 10.1007/s12033-014-9770-0

7. Clark L.V., Stewart J.R., Nishiwaki A., Toma Y., Kjeldsen J.B., Jørgensen U., Zhao H., Peng J., Yoo J.H., Heo K., Yu C.Y., Yamada T., Sacks E.J. Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression. J Exp Bot. 2015;66(14):4213-4225. doi 10.1093/jxb/eru511

8. Clark L.V., Jin X., Petersen K.K., Anzoua K.G., Bagmet L., Chebukin P., Deuter M., … Yamada T., Yoo J.H., Yu C.Y., Long S.P., Sacks E.J. Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea. Ann Bot. 2019;124(4):731-748. doi 10.1093/aob/mcy161

9. Clifton-Brown J., Hastings A., Mos M., McCalmont J.P., Ashman C., Awtycarroll D., Flavell R. Progress in upscaling Miscanthus biomass production for the European bio-economy with seed-based hybrids. Glob Change Biol Bioenergy. 2017;9(1):6-17. doi 10.1111/gcbb.12357

10. Debode J., De Tender C., Cremelie P., Lee A.S., Kyndt T., Muylle H., De Swaef T., Vandecasteele B. Trichoderma-inoculated miscanthus straw can replace peat in strawberry cultivation, with beneficial effects on disease control. Front Plant Sci. 2018;9:213. doi 10.3389/fpls.2018.00213

11. De Vega J., Donnison I., Dyer S., Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus [version 1; peer review: 2 approved]. F1000Res. 2021;10:29. doi 10.12688/f1000research.44714.1

12. Dorogina O.V., Kuban I.N., Zueva G.A., Zhmud E.V., Vasilyeva O.Yu. Morphological variability and genetic structure of Miscanthus sinensis (Poaceae) cultivated in the forest-steppe of Western Siberia. Vavilov J Genet Breed. 2025;29(2):210-218. doi 10.18699/vjgb-25-24

13. Grzegórska A., Czaplicka N., Antonkiewicz J., Rybarczyk P., Baran A., Dobrzyński K., Zabrocki D., Rogala A. Remediation of soils on municipal rendering plant territories using Miscanthus × giganteus. Environ Sci Pollut Res Int. 2023;30(9):22305-22318. doi 10.1007/s11356-022-23724-z

14. Hodkinson T.R., Klaas M., Jones M.B., Prickett R., Barth S. Miscanthus: a case study for the utilization of natural genetic variation. Plant Genet Resour. 2015;13(3):219-237. doi 10.1017/S147926211400094X

15. Jury C., Thomas H.L., Carrère H. Life cycle assessment of two alkaline pretreatments of sorghum and miscanthus and of their batch co-digestion with cow manure. BioEnerg Res. 2022;15:810-833. doi 10.1007/s12155-021-10369-y

16. Li S.‐S., Zhou H.‐F., Chen W.‐L., Yan J., Cai Z., Wei R.‐X., Chen C.‐H., Han B., Li J.‐Q., Sang T., Ge S. Population genetics and evolutionary history of Miscanthus species in China. J Syst Evol. 2019;57(5):530-542. doi 10.1111/jse.12497

17. Li W., Ciais P., Makowski D., Peng S. A global yield dataset for major lignocellulosic bioenergy crops based on field measurements. Sci Data. 2018;5:180169. doi 10.1038/sdata.2018.169

18. Liu H., Wu S., Li A., Ruan J. SMARTdenovo: a de novo assembler using long noisy reads. GigaByte. 2021;2021:gigabyte15. doi 10.46471/gigabyte.15

19. Ma X.-F., Jensen E., Alexandrov N., Troukhan M., Zhang L., Thomas-Jones S., Farrar K., Clifton-Brown J., Donnison I., Swaller T., Flavell R. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis. PLoS One. 2012;7(3):e33821. doi 10.1371/journal.pone.0033821

20. Mamirova A., Pidlisnyuk V., Amirbekov A., Ševců A., Nurzhanova A. Phytoremediation potential of Miscanthus sinensis And. in organochlorine pesticides contaminated soil amended by Tween 20 and Activated carbon. Environ Sci Pollut Res Int. 2021;28(13):16092-16106. doi 10.1007/s11356-020-11609-y

21. Miao J., Feng Q., Li Y., Zhao Q., Zhou C., Lu H., Fan D., … Huang T., Li L., Huang X., Sang T., Han B. Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome. Nat Commun. 2021;12(1):2458. doi 10.1038/s41467-021-22738-4

22. Mironova G.F., Budaeva V.V., Skiba E.A., Gismatulina Y.A., Kashcheyeva E.I., Sakovich G.V. Recent advances in Miscanthus macromolecule conversion: a brief overview. Int J Mol Sci. 2023;24(16):13001. doi 10.3390/ijms241613001

23. Mitros T., Session A.M., James B.T., Wu G.A., Belaffif M.B., Clark L.V., Shu S., … Hudson M.E., Sacks E.J., Moose S.P., Swaminathan K., Rokhsar D.S. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun. 2020;11(1):5442. doi 10.1038/s41467-020-18923-6

24. Nagel K., Hoilett N.O., Mottaleb M.A., Meziani M.J., Wistrom J., Bellamy M. Physicochemical characteristics of biochars derived from corn, hardwood, miscanthus, and horse manure biomasses. Commun Soil Sci Plant Anal. 2019;50(8):987-1002. doi 10.1080/00103624.2019.1594881

25. Nie G., Zhang X.Q., Huang L.K., Xu W.Z., Wang J.P., Zhang Y.W., Ma X., Yan Y.H., Yan H.D. Genetic variability and population structure of the potential bioenergy crop Miscanthus sinensis (Poaceae) in southwest china based on SRAP markers. Molecules. 2014;19(8): 12881-12897. doi 10.3390/molecules190812881

26. Nsanganwimana F., Al Souki K.S., Waterlot C., Douay F., Pelfrêne A., Ridošková A., Louvel B., Pourrut B. Potentials of Miscanthus × giganteus for phytostabilization of trace element-contaminated soils: ex situ experiment. Ecotoxicol Environ Saf. 2021;214:112125. doi 10.1016/j.ecoenv.2021.112125

27. Rayburn A.L., Crawford J., Rayburn C.M., Juvik J.A. Genome size of three Miscanthus species. Plant Mol Biol Rep. 2009;27:184-188. doi 10.1007/s11105-008-0070-3

28. Sanford G.R., Oates L.G., Jasrotia P., Thelen K.D., Robertson G.P., Jackson R.D. Comparative productivity of alternative cellulosic bioenergy cropping systems in the North Central USA. Agric Ecosyst Environ. 2016;216:344-355. doi 10.1016/j.agee.2015.10.018

29. Sang T., Zhu W. China’s bioenergy potential. Glob Change Biol Bioenergy. 2011;3(2):79-90. doi 10.1111/j.1757-1707.2010.01064.x

30. Schäfer J., Sattler M., Iqbal Y., Lewandowski I., Bunzel M. Characterization of Miscanthus cell wall polymers. Glob Change Biol Bioenergy. 2019;11(1):191-205. doi 10.1111/gcbb.12538

31. Shavyrkina N.A., Budaeva V.V., Skiba E.A., Gismatulina Y.A., Sakovich G.V. Review of current prospects for using miscanthus-based polymers. Polymers. 2023;15(14):3097. doi 10.3390/polym15143097

32. Simão F.A., Waterhouse R.M., Ioannidis P., Kriventseva E.V., Zdobnov E.M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19): 3210-3212. doi 10.1093/bioinformatics/btv351

33. Simpson J.T., Wong K., Jackman S.D., Schein J.E., Jones S.J.M., Birol İ. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009;19(6):1117-1123. doi 10.1101/gr.089532.108

34. Stanke M., Steinkamp R., Waack S., Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004;32:W309-W312. doi 10.1093/nar/gkh379

35. Sun Q., Lin Q., Yi Z.L., Yang Z.R., Zhou F.S. A taxonomic revision of Miscanthus s.l. (Poaceae) from China. Bot J Linn Soc. 2010;164(2): 178-220. doi 10.1111/j.1095-8339.2010.01082.x

36. Swaminathan K., Chae W.B., Mitros T., Varala K., Xie L., Barling A., Glowacka K., Hall M., Jezowski S., Ming R., Hudson M., Juvik J.A., Rokhsar D.S., Moose S.P. A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. BMC Genomics. 2012;13:142. doi 10.1186/1471-2164-13-142

37. Técher D., Martinez-Chois C., Laval-Gilly P., Henry S., Bennasroune A., D’Innocenzo M., Falla J. Assessment of Miscanthus × giganteus for rhizoremediation of long term PAH contaminated soils. Appl Soil Ecol. 2012;62:42-49. doi 10.1016/j.apsoil.2012.07.009

38. Trieu A., Belaffif M.B., Hirannaiah P., Manjunatha S., Wood R., Bathula Y., Billingsley R.L., Arpan A., Sacks E.J., Clemente T.E., Moose S.P., Reichert N.A., Swaminathan K. Transformation and gene editing in the bioenergy grass Miscanthus. Biotechnol Biofuels Bioprod. 2022;15:148. doi 10.1186/s13068-022-02241-8

39. Van Weyenberg S., Ulens T., de Reu K., Zwertvaegher I., Demeyer P., Pluym L. Feasibility of Miscanthus as alternative bedding for dairy cows. Vet Med. 2016;60(3):121-132. doi 10.17221/8059-VETMED

40. Wang C., Kong Y., Hu R., Zhou G. Miscanthus: a fast-growing crop for environmental remediation and biofuel production. Glob Change Biol Bioenergy. 2021;13(1):58-69. doi 10.1111/gcbb.12761

41. Yan H., Zhang X., Fu C., Huang L., Yin G., Nie G., Liu W., Chen T., Lee S., Ma X., Peng Y., Yan Y., Ling Y., Liu W. Chloroplast DNA variation and genetic structure of Miscanthus sinensis in southwest China. Biochem Syst Ecol. 2015;58:132-138. doi 10.1016/j.bse.2014.11.007

42. Yang Y., Saand M.A., Huang L., Abdelaal W.B., Zhang J., Wu Y., Li J., Sirohi M.H., Wang F. Applications of multi-omics technologies for crop improvement. Front Plant Sci. 2021;12:563953. doi 10.3389/fpls.2021.563953

43. Zhang G., Ge C., Xu P., Wang S., Cheng S., Han Y., Wang Y., … Ming R., Dong S., Ma J., Zhang X., Chen C. The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae. Nat Plants. 2021;7(5):608-618. doi 10.1038/s41477-021-00908-y

44. Zhao H., Wang B., He J., Yang J., Pan L., Sun D., Peng J. Genetic diversity and population structure of Miscanthus sinensis germplasm in China. PLoS One. 2013;8(10):e75672. doi 10.1371/journal.pone.0075672