Three activities hallmark meiotic cell division: homologous chromosome pairing, synapsis, and recombination. Recombination and synapsis are well-studied but homologous pairing still holds many black boxes. In the past several years, many studies in plants have yielded insights into the mechanisms of chromosome pairing interactions. Research in several plant species showed the importance of telomere clustering on the nuclear envelope (telomere bouquet formation) in facilitating alignment of homologous chromosomes. Homologous pairing was also shown to be tied to the early stages of recombination by mutant analyses in Arabidopsis and maize. In contrast, little is known about the mechanisms that guide homolog interaction after their rough alignment by the bouquet and before the close-range recombination-dependent homology search. The relatively large and complex genomes of plants may require additional mechanisms, not needed in small genome eukaryotes, to distinguish between local homology of duplicated genes or transposable elements and global chromosomal homology. Plants provide an excellent large genome model for the study of homologous pairing and dissection of this process.

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