Key factors of Miscanthus lutarioriparius L. Liu ex Renvoize & S. L. Chen local adaptation based on population transcriptomes

Based on population transcriptomic data of 10 representative populations of Miscanthus lutarioriparius, we studied the key factors impacting local adaptations of the species. We used single nucleotide polymorphisms (SNPs) to phase haplotypes and analyze differentially expressed genes among environments and inferred haplotypes. These genes were then classified into four categories: those significantly affected by the environment (E), significantly affected by haplotypes (G), significantly affected by environmental and haplotype interactions (G & E), and not significantly affected. Based on further analysis, the G & E and E gene sets played importance roles in the local population. The gene expression of G & E was more sensitive to other factors, while the E gene set of was relatively stable. The former was significantly enriched in ribosomal pathway-related functional genes, and the latter was significantly enriched in protein folding-related functional genes. These functional genes were involved in responses to external pressure. Therefore, we inferred that the differential expression of these genes was mainly affected by the environment and the interaction between genotypes and the environment.