Plant chromosome homology: hypotheses relating rendezvous, recognition and reciprocal exchange

Many higher eukaryotes have dispersed repetitive DNA and multiple instances of segmental duplications. As well, many plants and lower animals are polyploids. Thus restricting reciprocal genetic exchange to truly homologous chromosomes is likely a multi-step process. We propose the following sequence of events. First the ability to form a synaptonemal complex (SC) prematurely (i.e. before homology checking/recognition) is precluded by the organization of chromosomes during premeiotic S phase. Next rough alignment is accomplished regionally by having key allelic transcription units brought to the same transcription center. Once rough alignment is accomplished, close alignment can occur in conjunction with homology checking/recognition. Successful homology checking produces changes that now permit SC formation within the region of the check. Some organisms (with challenges to true homology such as dispersed repetitive DNA and segmental duplications) may require that, for a region to be competent to form an SC, successful homology checks must occur at both ends of the region. Successful early SC formation may provide an environment in which recombination intermediates can be earmarked for resolution into crossovers. Later in prophase I SC formation can occur nonhomologously, if two unsynapsed chromosomal axes meet.