Recombination suppression in plant adaptation and speciation

Abstract

Recombination suppression is increasingly recognized as an important facilitator of genomic divergence and speciation, especially under ongoing gene flow. In plants, however, the broader evolutionary consequences and the mechanisms by which recombination suppression arises and spreads are still incompletely understood, reflecting the inherent complexity of plant genomes shaped by polyploidy, structural variation, and epigenetic regulation. Advances in long-read sequencing and haplotype-resolved assemblies now enable fine-scale mapping of recombination landscapes across diverse plant systems. Here, we synthesize current knowledge on how recombination suppression contributes to the linkage of adaptive alleles, restricts gene flow, promotes genomic divergence, and facilitates the evolution of sex chromosomes. We further examine the diverse genomic contexts in which recombination suppression originates, including structural variants, selfish genetic elements such as transposable elements, epigenetic modifications, and centromeres. By integrating insights across genomic, ecological and evolutionary scales, we provide a conceptual framework for understanding the multifaceted roles of recombination suppression in plant adaptation and speciation, and highlight key open questions for future research.