Multi-omics analysis reveals key genomic insights into salt tolerance mechanisms in Miscanthus sacchariflorus and M. lutarioriparius

Soil salinization threatens global agriculture, yet marginal lands like saline soil offer potential for cultivating biomass energy crops. Miscanthus sacchariflorus and M. lutarioriparius are promising lignocellulosic biomass crops for such lands due to their high productivity and adaptability. Their cultivation avoids competition with food crops and improves soil quality. However, research on their salt tolerance mechanisms is limited due to complex genomes. This study combined genome-wide association studies (GWAS), selective sweep analysis, comparative transcriptomics, and weighted gene co-expression network analysis (WGCNA) to elucidate the genetic basis of salt tolerance in these species. Physiological and biochemical analyses of highly salt-tolerant accession M135 and highly salt-sensitive accession M198 revealed adaptive mechanisms, including upregulating the proline synthesis gene (Delta-1-pyrroline-5-carboxylate synthetase, P5CS ) to promote proline accumulation for osmotic balance, enhancing POD and SOD activities and related gene expression for antioxidant capacity, and increasing K⁺ uptake for ion homeostasis. Whole genome resequencing of 220 accessions identified 6294,909 SNPs. GWAS identified 58 significant SNP-associated genes linked to 14 salt tolerance traits. Selective sweep analysis of 15 salt-tolerant and 15 salt-sensitive accessions identified five candidate genes under selection. Comparative transcriptomics of M135 and M198 under 0 and 150 mM NaCl identified 3071 DEGs, including 169 transcription factors. WGCNA highlighted three gene modules associated with eight physiological and biochemical indices, involving 8079 genes. Two key candidate genes, Ml02G026570 (SCPL51) and Ml05G037700 (PDIL2–2), were identified through multi-omics analysis. This study provides potential target genes for genetic improvement of salt tolerance in M. sacchariflorus and M. lutarioriparius , supporting marginal land development and ecological improvement.