A genome may be defined as the set of chromosomes (or genes) within a gamete of a species. As previously stated, DNA is the hereditary material of organisms. Most of the DNA (hence most of the genes) in plants occurs in the nucleus in linear structures called chromosomes. The nuclear genes are subject to Mendelian inheritance (are transmitted according to the laws
of Mendel through the processes of nuclear division).
In addition to the nucleus, DNA occurs in some plastids (organelles that are capable of dividing,
growing, and differentiating into different forms). These plastids are chloroplasts. DNA also occurs in the mitochondria. The DNA in these organelles is not subject to Mendelian inheritance but follows what is called cytoplasmic (or extrachromosomal or extranuclear) inheritance. The distribution of DNA into gametes following nuclear division is unpredictable and not equitable.
Molecular techniques may be used to separate nuclear DNA from non-nulcear DNA during DNA extraction from a tissue, for independent analysis. Some extranuclear genes are of special importance to plant breeding. Some male sterility genes are located in the mitochondria. As will be described later, cytoplasmic male sterility (CMS) is used in the breeding of corn and many other species. It is used to eliminate the need for emasculation (a time-consuming and tedious operation to prepare plants for crossing by removing the anthers). Also, because genes occur in the cytoplasm but pollen grains (plant male sex units) lack cytoplasm, it is important in
a hybrid program which of the two parents is used as female (provides both nuclear genes and cytoplasmic genes) and which as male (provides only nuclear genes).
Genes carried in the maternal cytoplasm may influence the hybrid phenotype, an effect called the maternal effect. When uncertain about the presence of any special beneficial genes in the cytoplasm, some breeders conduct reciprocal crossing in which the parents take turns in being used as the female parent.