Genetics. Published Articles Ahead of Print: July 2, 2006, Copyright © 2006
doi:10.1534/genetics.105.053942


A more recent version of this article appeared on October 1, 2006.

REGULAR RESEARCH PAPERS

Gene conversion between direct non-coding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.)

Feng Zhang 1 and Thomas Peterson 1*

1 Iowa State University

* To whom correspondence should be addressed. E-mail: thomasp{at}iastate.edu.

Submitted on November 25, 2005
Revised on January 12, 2006
Accepted on 19 June 2006


Abstract

While evolution of coding sequences has been intensively studied, diversification of non-coding regulatory regions remains poorly understood. In this study, we investigated the molecular evolution of an enhancer region located 5 kb upstream of the transcription start site of the maize pericarp color1 (p1) gene. The p1 gene encodes an R2R3 Myb-like transcription factor that regulates flavonoid biosynthetic pathway in maize floral organs. Distinct p1 alleles exhibit organ-specific expression patterns on kernel pericarp and cob glumes. A cob glume-specific regulatory region has been identified in the distal enhancer. Further characterization of 6 single-copy p1 alleles, including P1-rr (red pericarp/red cob) and P1-rw (red pericarp and white cob), reveals 3 distinct enhancer types. Sequence variations in the enhancer are correlated with the p1 gene expression patterns in cob glume. Structural comparisons and phylogenetic analyses suggest that evolution of the enhancer region is likely driven by gene conversion between long direct non-coding repeats (~ 6 kb in length). Given that tandem and segmental duplication are common in both animal and plant genomes, our studies suggest that recombination between non-coding duplicated sequences could play an important role in creating genetic and phenotypic variations.

Key Words: Gene conversion, Non-coding regulatory sequences, enhancer, maize, p1 gene