Impacts of Somatic Genome Variation on Genetic Theories and Breeding Concepts, and the Distinction between Mendelian Genetic Variation, Somagenetic Variation, and Epigenetic Variation

The 'genome' of a cell is the cell's genome network, including both nuclear and cytoplasmic genomes. 'Somatic genome' is the genome of somatic cells, somatic nuclei, and asexually propagated cells, including, for example, body cells and the vegetative cell of pollen. 'Somatic genome variation' (SGV) is the variation at the sequence and/or ploidy levels of somatic genomes, whereas 'somagenetic variation' includes both SGV and some non-Mendelian genetic variations, such as length changes in repetitive sequences and telomeres, of the germline genome. The most basic genetic theories in conventional breeding are Mendelian inheritance laws, the Weismann barrier theory, and Johannsen's concepts of gene, genotype, phenotype, homozygous lines (or pure lines), and heterozygous lines. These classical genetic theories and concepts concern solely the nuclear genome in reproductive cells, ignore cytoplasmic inheritance, reject any contribution to progeny from somatic cells, and exclude developmental and environmental changes in genetic materials. Molecular and genomic research has found that (1) both the nucleus and the cytoplasm have genomes, (2) the genome network in somatic cells has environmental and developmental variations, (3) plant reproductive cells are differentiated from somatic cells, (4) stress signals from somatic cells can cause epigenetic and somagenetic variations in the reproductive cells, and (5) some genes are generated somatically. Somagenetic variation in somatic cells is SGV and is the genetic basis for various somatic breeding technologies. Thus the theories and concepts in genetics and breeding should be updated in order to assist with data interpretation in genetic analysis and to make breeding and clonal propagation more science-based. This chapter classifies genome-related variations into Mendelian genetic variation, somagenetic variation, and epigenetic variation ('epi' means not the genome itself); revisits the above-mentioned classical genetic theories; and updates the definitions of gene, genotype, phenotype, homozygous line, and heterozygous line.