The sources of genome variability as domestication drivers (review)

Plant and animal domestication is the key event in the history of mankind, its mechanisms have attracted the attention of many researchers, especially in recent decades due to the well-known decline in biodiversity, including in agricultural species. According to the definition proposed by Melinda Zeder (M.A. Zeder, 2015), domestication is the stable mutualistic relationship in a number of generations in which the domesticator influences the reproduction of the domesticates, optimizing their lifestyle for the supply of the needing resource to human, and thanks to which the domesticates gain advantages over other individuals of the species. Such relationships are accompanied by interspecific coevolution, they are present not only in humans and domestic species of plants and animals, but also in representatives of wild species, for example, insects, fungi. As a universal feature of domestic species in comparison with closely related wild ones, a high phenotypic diversity is considered, which was noticed by Charles Darwin (Ch. Darwin, 1951). Pairwise genomic comparisons of such species as domestic dog and wolf, wild and domestic cat, domesticated and wild rabbit reveal a relatively increased density of a number of mobile genetic elements in domesticated animals compared to wild ones. In recent years, mobile genetic elements, or transposons (TEs), have been considered as the main factors of genomic transformations, gene, genomic duplications, genomic and gene reconstructions, as well as horizontal exchanges of genetic information (K.R. Oliver, W.K. Greene, 2009). The number of comparative genomic studies of TEs in domesticated species is small, and the role of such elements in domestication, as a rule, is not discussed. However, it can be expected that universal mechanisms of genome variability underlie all evolutionary events, including in response to the new niche-construction during domestication. The presented review systematizes such mechanisms. TEs providing deep genomic transformations, active and passive forms of their interactions with the host genome are considered (K.R. Oliver et al., 2009). Examples of the emergence of new genes based on TEs, such as the synticin gene, are described (C. Herrera-Úbeda et al., 2021), the synaptic plasticity regulator gene arc (Activity Regulated Cytoskeleton Associated Protein) (C. Herrera-Úbeda et al., 2021), the bex gene family encoding, in particular, the neuron growth factor receptor (E. Navas-Pérez et al., 2020; R.P. Cabeen et al., 2022). Conflict and cooperative interactions with the host genome during retrotransposon movements and different mechanisms of their effects on gene expression profiles are discussed. The participation of TEs in the formation and variability of networks of genomic regulatory elements, in particular microRNAs, is considered. Examples of the involvement of microRNAs in the control and formation of economically valuable traits in domesticated plants and animals are presented. The accumulated data suggest that the leading source of large phenotypic variability of domesticated species is the relatively high saturation of their genomes with mobile genetic elements and, as a consequence, an increase in the variability of genomic regulatory networks in the formation of a new niche during domestication by humans.