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

Meiotic recombination across the ~130--140 kb a1-sh2 interval was characterized, aiming to answer the question Why does recombination occurs non-randomly in the maize genome? The a1-sh2 interval contains at least four genes (a1, yz1, x1 and sh2). Initially, the breakpoints associated with 101 recombinants isolated from a stock that carries maize A1 Sh2 and a1::rdt sh2 haplotypes were physically mapped relative to sequence polymorphisms. These breakpoints are concentrated in three recombination hot spots that are located in the proximal 10% of the a1-sh2 interval. Two hot spots are genic ( a1 and yz1) and one is apparently non-genic. The x1 gene is not a recombination hot spot. These results established that not all hot spots are genes and not all genes are hot spots. The retrotransposon fraction of the a1-sh2 interval is relatively inert recombinationally.;To test the roles cis-genetic modifiers play in regulating meiotic recombination, recombination events between the a1 and sh2 loci were isolated from three near-isogenic stocks that carry structurally distinct teosinte A1 Sh2 haplotypes (from Z. mays spp. mexicana Chalco, Z. mays spp. parviglumis and Z. luxurians ) and a common maize a1::rdt sh2 haplotype. Genetic distances across the a1-sh2 interval varied three fold. In each teosinte haplotype, over 85% of recombination events resolved in the proximal 10% of the a1-sh2 interval. Even so, significant differences were observed in the distributions of recombination breakpoints across subintervals among haplotypes. Each of the three previously detected recombination hot spots was detected in at least one of the three teosinte haplotypes and two of these hot spots were not detected in at least one teosinte haplotype. Moreover, novel hot spots were detected in two teosinte haplotypes. Due to the near-isogenic nature of the three stocks, the observed variation in the distribution of recombination events is the consequence of cis-modifications. Although generally negatively correlated with rates of recombination/Mb, frequencies of sequence polymorphisms do not fully account for the nonrandom distribution of recombination breakpoints. This study indicates that estimates of linkage disequilibrium must be interpreted with caution when considering whether a gene has been under selection