Adaptive changes encompass physiological, morphological, or behavioral modifications occurring in organisms in response to specific environmental conditions. These modifications may become established within a population through natural selection. While adaptive changes can influence individuals or populations over short timeframes, evolution involves the inheritance and accumulation of these changes over extended periods under environmental pressures through natural selection. At present, addressing climate change, emerging infectious diseases, and food security are the main challenges faced by scientists. A comprehensive and profound understanding of the mechanisms of adaptive evolution is of great significance for solving these problems. The genetic basis of these adaptations can be examined through classical genetics, which includes stochastic gene mutations and chromosomal instability, as well as epigenetics, which involves DNA methylation and histone modifications. These mechanisms not only govern the rate and magnitude of adaptive changes but also affect the transmission of adaptive traits to subsequent generations. In the study of adaptive changes under controlled conditions, short-term controlled experiments are commonly utilized in microbial and animal research to investigate long-term evolutionary trends. However, the application of this approach in plant research remains limited. This review systematically compiles the findings on adaptive changes and their genetic foundations in organisms within controlled environments. It aims to provide valuable insights into fundamental evolutionary processes, offering novel theoretical frameworks and research methodologies for future experimental designs, particularly in the field of plant studies.

Perilla frutescens(L.) Britt. (P. frutescens) is an important medicinal and aromatic plant, whose leaf color and chemotype strongly influence its medicinal quality and economic value. All the previously discovered perillene (PL)-type P. frutescens are double-sided green, and whether the PL-type trait is tightly linked with the green-leaf trait in genetics remains to be clarified. This study aimed to address this question and attempt to create purple-leaf PL-type germplasm through perillaldehyde (PA) × PL hybridization. Three parallel experiments were conducted using purple-leaf PA-type P. frutescens as male parents and green-leaf PL-type P. frutescens as female parents. Chemotypes were identified by gas chromatography (GC). Association analyses between leaf color and chemotype were performed in segregating F₂ populations. Genes involved in leaf color formation and PL biosynthesis were mapped onto the published Hoko-3 reference genome to provide genomic evidence for the genetic relationship between the two traits. All F₁ individuals were uniformly PA-type. The three F₂ populations exhibited distinct leaf color–chemotype association patterns: Z01 (n = 118) showed a strong association (Fisher’s exact p = 9.13 × 10⁻¹⁰; φ = 0.564), Z02 (n = 117) showed no detectable association (p = 0.9; φ = 0.012), and Z03 (n = 88) showed a moderate association (p = 0.00669; φ = 0.289). Importantly, purple-leaf PL-type recombinants were obtained in F₂ populations and stably maintained through subsequent generations (F₃–F₅), demonstrating that the PL-type trait is not tightly linked with the green-leaf trait in P. frutescens. Genomic mapping genes related to leaf color and PL biosynthesis are distributed across multiple chromosomes and usually present as multiple loci, which is consistent with the pattern of incomplete linkage. The PL-type trait is recessive and not genetically tightly linked to the green-leaf traits in P. frutescens. The successful creation of a purple-leaf PL-type germplasm breaks the historical phenotypic constraint and provides a novel material for further dissection of the molecular mechanisms regulating secondary metabolism and organ coloration in P. frutescens.