Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective

Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.

Automated summary

Allopolyploids are formed by hybridization between different evolutionary lineages with genome doubling. Homoeologous chromosomes can undergo recombination immediately after allopolyploid formation and continue over successive generations. Homoeologous exchanges have both negative and positive effects, leading to unbalanced gametes, reduced fertility, novel phenotypic diversity, and the formation of neo-allopolyploids. The causes and consequences of homoeologous exchanges vary across lineages, generations, and genomes. Recent technological advances provide insights into the mechanistic basis of homoeologous exchanges in allopolyploid angiosperms, which have implications for understanding allopolyploid evolution and developing important traits in polyploid crops.