subgenome

A subgenome is one of the distinct genomic contributions within a polyploid organism, typically arising in allopolyploids that result from hybridization between two or more species. Each donor genome contributes a set of chromosomes that are retained in the nucleus, and the term is often used when the parental lineages can be identified. In autopolyploids, where multiple copies originate from the same species, the term subgenome is less commonly applied.

In polyploid genomes, subgenomes may show differential retention of genes (fractionation) and structural rearrangements. Over time, one subgenome can become more transcriptionally active than others, a phenomenon known as subgenome dominance. This dominance can reflect differences in gene content, regulatory elements, transposable element density, or epigenetic marks. Researchers study homeologous gene pairs (homeologs) across subgenomes to understand divergence, expression patterns, and functional specialization. The interplay among subgenomes influences trait expression, epigenetics, and genome stability.

Prominent examples include bread wheat (Triticum aestivum), a hexaploid with A, B, and D subgenomes derived from three ancestral species; cotton (Gossypium hirsutum) with A and D subgenomes; and canola (Brassica napus) with A and C subgenomes. In these systems, comparative genomics and chromosome sequencing help trace subgenome origins, assess fractionation, and identify subgenome-specific marker genes.

Studying subgenomes informs crop breeding and evolutionary biology, but presents challenges in genome assembly and annotation due to high similarity among homeologs and extensive rearrangements. Researchers use synteny mapping, gene fractionation profiles, and sequence divergence to delineate subgenomes and understand their contributions to phenotype.