High-Resolution Landscape of Meiotic Recombination Hotspots in Maize

Meiotic recombination is the most important source of genetic variations in higher eukaryotes.  Recombination is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early prophase of meiosis.  The DSBs are subsequently repaired, resulting in crossovers (CO) and non-crossovers (NCO).  In most eukaryotes, recombination events are not distributed evenly along chromosomes.  Instead, regions with high recombination rates (recombination hotspots) are interspersed with regions of low recombination rates (coldspots).  How specific chromosomal sites become recombination hotspots or coldspots is poorly understood.  We generated a genome-wide map of DSB hotspots in the maize B73 inbred line to elucidate factors determining the location of recombination events.  We found that recombination in maize is initiated in all chromosome regions, including those known to be devoid of COs, such as centromeres and the pericentromeric regions.  The vast majority of DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons.  In contrast, only one-quarter of DSB hotspots are located in genic regions.  Hotspots in repetitive and genic regions exhibit several distinct features, including the fact that only genic region hotspots contribute to the formation of COs.  Our data also show that DSB hotspots in of maize exhibits characteristics not reported previously in mouse or yeast.  Understanding recombination patterns will shed light on the mechanisms affecting dynamics of the maize genome and help devise methods for more efficient breeding.