Genomic Dissection of Local Adaptation in Elymus sibiricus: Integrating SLAF Sequencing, Genetic Diversity, Genotype-Environment Association, and Common Garden Experiments

Background Unraveling the genetic basis underlying local adaptation represents a pivotal area of research within ecological and evolutionary biology. In the present study, we explored the genomic mechanisms that underpin the local adaptation of Elymus sibiricus , an indigenous grass species predominantly distributed in the temperate alpine regions of the Eurasian continent. Results Population structure analyses categorize 318 accessions of E. sibiricus into three distinct groups: XJ (Xinjiang), NC (North of China), and the QTP (Qinghai-Xizang Plateau). Furthermore, through selection sweep analysis, we have pinpointed specific genes that show evidence of selection across these three groups, with these genes implicated in pathways related to local climate adaptation. A total of six gene exchange events among the 13 subgroups were detected, and the dynamics of population history revealed marked fluctuations in the effective population size of each subgroup in the recent past. Notably, we observed significant genetic differentiation (as measured by Fst) among the subgroups, suggesting that local climate acts as a primary driver of population structure in different groups of E. sibiricus . Consequently, we performed genetic–environment association (GEA) analysis and successfully identified a substantial number of candidate genes that correlate with temperature and rainfall, predominantly involved in pathways such as Phenylpropanoid biosynthesis. In addition, we conducted a three-year common garden experiment in Hongyuan county, Sichuan, assessing six morphological indicators, including adaptive traits such as biomass, followed by genome-wide association (GWAS) analysis. Conclusion The genes selected across populations, as well as those associated with local climate and adaptive phenotypes through association analysis, provide insights into the mechanism underlying the broad climate adaptability of E. sibiricus .