Naturally transgenic plants are plants that have undergone Agrobacterium-mediated transformation under natural conditions without human involvement. Among Arachis hypogaea L., A. duranensis Krapov. & W.C. Greg, A. ipaensis Krapov. & W.C. Greg, A. monticola Krapov. & Rigoni, and A. stenosperma Krapov. & W.C. Greg are known to contain sequences derived from the T-DNA of “Agrobacterium”. In the present study, using molecular genetics and bioinformatic methods, we characterized natural transgenes in 18 new species from six sections of the genus Arachis. We found that small fragments of genes for enzymes of the agropine synthesis pathway were preserved only in some of the studied samples and were lost in the majority of the species during evolution. At the same time, genes, similar to cucumopine synthases (cus-like), remained intact in almost all of the investigated species. In cultivated peanuts, they are expressed in a tissue-specific manner. We demonstrated the intraspecific variability of the structure and expression of the cus-like gene in cultivated peanuts. The described diversity of gene sequences horizontally transferred from Agrobacterium to plants helps to shed light on the phylogeny of species of the genus Arachis and track possible hybridization events. Data on the ability of certain species to hybridize are useful for planning breeding schemes aimed at transferring valuable traits from wild species into cultivated peanuts.

Domestication of rice (Oryza sativa L.), one of the five earliest cereal crops, gave rise to a characteristic “domestication syndrome” marked by loss of natural seed dispersal, enlargement and colour change of the caryopsis, shortening of seed dormancy, and transition to an annual life cycle. Archaeological, physiological-genetic and molecular evidence is synthesised here to summarise the mechanisms underlying these key agronomic traits. Reduced seed shattering is linked to mutations andallelic diversification at loci SH4, qSH1, SH5, SHAT1, CPL1, OsSh1/ObSH3, ObSH11, NPC1, OSH15, GRF4 and OsLG1/SPR3, which govern formation and degradation of the spikelet abscission layer. Grain size is determined by QTL GW2, GS3, GS5 and TGW6, modulating cell division and endosperm development and thus shaping thousand-grain weight and yield. Pericarp pigmentation is controlled by Rc and Rd together with the Kala1–Kala3–Kala4 cassette; structural rearrangements in theKala4 promoter trigger ectopic expression of a bHLH factor and anthocyanin accumulation, whereas a 14-bp deletion in Rc converted most cultivars to the white-grained type and was later functionally restored via CRISPR/Cas9. Collectively, these findings provide a genetic foundation for targeted improvement of yield, harvestability and nutritional quality in modern rice breeding.