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Originally published as Genetics Published Articles Ahead of Print on June 3, 2005.
Genetics, Vol. 170, 1929-1944, August 2005, Copyright © 2005
doi:10.1534/genetics.104.034454
Cis-effects on Meiotic Recombination Across Distinct a1-sh2 Intervals in a Common Zea Genetic Background
Hong Yao*,
,1 and
Patrick S. Schnable*,,
,
,2
* Interdepartmental Genetics Program, Development and Cell Biology
Department of Genetics, Development and Cell Biology
Department of Agronomy, Iowa State University, Ames, Iowa 50011-3650
Center for Plant Genomics, Iowa State University, Ames, Iowa 50011-3650
2 Corresponding author: Department of Agronomy, 2035B Roy J. Carver Co-Laboratory, Iowa State University, Ames, IA 50011-3650.
E-mail: schnable{at}iastate.edu
Genetic distances across the a1-sh2 interval varied threefold in 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. In each haplotype >85% of recombination events resolved in the proximal 10% of the 
130-kb a1-sh2 interval. Even so, significant differences in the distributions of recombination breakpoints were observed 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 per megabase, levels of sequence polymorphisms do not fully account for the nonrandom distribution of recombination breakpoints. This study also suggests that estimates of linkage disequilibrium must be interpreted with caution when considering whether a gene has been under selection.
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