Determination of Rates and Patterns of Recombination at the Maize Red Color (r1) Locus

• Main Author: Dietrich, William R.
• Format: Others
• Published: VCU Scholars Compass 1998
• Subjects: Biology
• Online Access: http://scholarscompass.vcu.edu/etd/4530; http://scholarscompass.vcu.edu/cgi/viewcontent.cgi?article=5591&context=etd

Homologous recombination has been studied in many plant and animal systems. In maize, most recombination occurs intragenically. The current study assessed the frequency and location of meiotic recombination at the maize red color (r1) gene. Three independent mutant (colorless seed) alleles derived from the colored seed allele, R-sc:124, were made heterozygous with the colored plant allele, r-r:n142. Each mutant resulted from the insertion of a Dissociation (Ds) transposable element into the 3' end of R-sc:124. In the presence of Activator (Ac), each Ds insertion allele (r-sc:mutables) produced spotted seeds and germinal reversion to fully colored seeds due to the vi excision of Ds. In the absence of Ac, each insertion allele stable and produces colorless or very faintly pigmented seeds. The r-sc:mutable/r-r:n142 heterozygotes were pollinated with R-g:8pale, an r1 allele that produces pale brown seeds, in the absence of Ac, to recover revertant progeny likely resulting from recombination rather than Ds excision. Revertant progeny were self pollinated to verify paternity. Molecular analysis using polymerase chain reaction, Southern blot and DNA sequence analyses showed that 92 out of 94 of the revertant alleles arose via a crossover event between the r-sc:mutable and r-r:n142 chromosomes. The remaining two revertant alleles likely arose via gene conversion, double cross over or cryptic Ac activity. The ratio of genetic to physical distance (1/ρ) calculated for the 3' end of r1 is approximately 0.07 cM/kb, which is comparable to 1/ρ values calculated for a1, b1, bz1 and wx1 loci. Given the average value for 1/ρ throughout the genome is 0.00021 cM/kb, this analysis supports the hypothesis that recombination in maize primarily occurs intragenically and that r1 serves as a recombination hotspot in the maize genome. Molecular analysis also revealed that the majority of exchanges occurred at the 3' end of r1 as has been previously observed. The pattern of recombination observed at r1 is different from those observed at other maize loci. The recovery of substantially more cross over events (92/94) relative to non-crossover events (2/94) or the nature of the recombination event is consistent with previous observations at a1, b1, and bz1. The frequency of potential gene conversion is estimated at 3.97 x 1 o-s and the gene conversion tract length is maximally 2.5 kb. The possibility of the influence of insertional mutations, amount and structure of DNA sequence homology, cis- and trans- factors and preference for cross over versus non-crossover events could explain the observed pattern at r1.