Abstract: Functional gene expression is a basic life process that connects the coding information of a gene to protein products. The level of gene expression is considered as a quantitative trait between genotype and phenotype and plays an important role in response to climatic and environmental changes. First, we systematically summarize regulatory elements of gene expression in plant species and empirical evidence, including the effects of transcription factors and small RNAs on gene expression regulation. Second, this review discusses the eQTL mapping for regulatory elements of gene expression through gene expression-based genome-wide association study (GWAS) and the limitations of this method. This review analyzes the intraspecific variation in gene expression in theory under the processes of mutation, drift and selection and the testing methods. This review also analyzes the interspecific evolution of gene expression under the mutation and drift processes or under the phylogeny-based drift-selection processes and the testing methods. Finally, this review discusses the regulation of gene expression by the plant mating system. Selfing reduces the effective population size, mutation rate, recombination rate and competition from exogenous pollen, and changes the efficacy of natural selection in the gametophytic and sporophytic phases. Selfing regulates intraspecific gene expression variation and interspecific gene expression evolution. This review comprehensively comments on theoretical and practical research progress and existing questions, which aids in our deep understanding of plant gene expression regulation and evolution mechanisms.

Key words: gene expression, regulatory element, natural selection, quantitative trait, mating system