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The 140-kb interval of the maize genome contains at least four genes and ^A2). Partial sequence analysis of two haplotypes has revealed many single nucleotide polymorphisms and InDel polymorphisms, including several large structural polymorphisms. The physical positions of 101 meiotic recombination breakpoints are not distributed uniformly across the interval and are instead concentrated within three recombination hot spots. Two of these recombination hot spots are genie (aI and yzl) and one is apparently non-genic. The xl gene is not a recombination hot spot. Thus, these results suggest that not all hot spots are genes and indicate that not all genes are hot spots. Two of the 101 recombination events arose by means of either noncrossover events involving conversion tract lengths of at least 17 kb or double-crossover events. Only one recombination breakpoint mapped to the ==80-kb distal portion of the al-sh2 interval that contains large amounts of repetitive DNA including retrotransposons; in this region the ratio of genetic to physical distance is less than 0.5% of the genome's average. These results establish that the retrotransposon fraction of the maize genome is relatively inert recombinationally. Introduction Homologous meiotic recombination recombines physically linked genetic material via reciprocal crossovers (COs) and unilateral NCOs. According to the canonical double' Reprinted with permission offMd.S, 2002, 99(9), 6157-6162. strand break (DSB) repair model (1,2) a meiotic recombination event of either type is initiated by a DSB and depending on how the recombination intermediate, a double Holliday junction (DHJ), is resolved, a CO or NCO results. Recently, a modified DSB repair model has been proposed in which an early commitment is made to enter either the CO or NCO pathway (3). Bacterial, fungal, plant and mammalian genomes all exhibit recombination "hot spots" and "cold spots", where recombination rates per kb are much higher or lower than the genome average (4-6). Even though the sizes of the genomes of diverse eukaryotic organisms are quite different, the lengths of their genetic maps are fairly constant. Based on this observation, and the assumption (now being confirmed by genome sequencing projects) that these genomes contain similar numbers of genes, it was hypothesized that recombination occurs primarily in genes (7). Several observations are consistent with this hypothesis: (/) all recombination hot spots identified to date in the approximate 2,500-Mb and 5,289-cM (centimorgan) (Georgia Davis, personal communication) maize genome are genes (6), even though the bulk of this genome consists of repetitive DNA such as retrotransposons (8); (#) gene-rich chromosomal regions of wheat (9-11) and barley (12) are more recombinationally active than gene-poor regions; and (z/z) in Arabidopsis (13) and tomato (14, 15) recombination is suppressed in chromosomal regions near the gene-poor centromeres (16, 17). Two alternative hypotheses have been proposed to explain the correlation between recombination rates and gene density (6). One is that genes per ae are recombinationally hyperactive such that chromosomal regions with high gene densities are recombinationally hyperactive. The alternative hypothesis is that genes per ae do not exhibit recombinational

Characterization of meiotic recombination in maize using the a1-sh2 interval as a model system