subgenomes

Subgenomes are the distinct parental genomes that together comprise the genome of a polyploid organism. In allopolyploids, which form by hybridization between species followed by chromosome doubling, the resulting genome is partitioned into subgenomes that reflect the contributions of each ancestral lineage. Subgenomes are often labeled with letters (A, B, C, D) to trace their origin, and their identity is established by comparative genomics with the diploid relatives.

Following polyploidization, genomes undergo fractionation, a process of gene loss and rearrangement that tends to be biased toward certain subgenomes. This can lead to subgenome dominance, where one subgenome contributes more to gene expression, retains more genes, and governs regulatory networks, while other subgenomes are relatively silenced or reorganized. Mechanisms underlying dominance include changes in cis-regulatory sequences, differences in trans-acting factors, and epigenetic modifications such as DNA methylation.

Subgenome dynamics influence phenotype, adaptation, and fertility. They affect how chromosomes pair during meiosis and how homoeologous exchanges occur, with consequences for breeding and trait stability. Domestication often interacts with subgenome behavior, guiding which alleles become prevalent.

Examples include bread wheat (Triticum aestivum), a hexaploid with subgenomes A, B, and D; cotton (Gossypium hirsutum), an allotetraploid with subgenomes A and D; and Brassica napus, an allotetraploid with subgenomes A and C. Studying subgenomes involves comparative genomics, analyses of homeolog expression, and mapping of structural variation to understand how combined genomes function as a cohesive unit. Homeologs are the duplicated gene copies derived from different subgenomes within these polyploids.