Organ-specific regulation and molecular evolution of the maize pericarp color1 gene
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The maize pericarp color1 (p1) gene encodes an R2R3 Myb-like transcription factor that regulates the flavonoid biosynthetic pathway in floral organs, most notably kernel pericarp and cob. Alleles of the p1 gene condition distinct tissue-specific pigmentation patterns. To elucidate the molecular basis of these allele-specific expression patterns, we characterized two novel P1-rw alleles, P1-rw1077 and P1-rw751::Ac. Structural analysis of P1-rw1077 indicated that this allele was generated by recombination between p1 and the tightly linked paralogous gene, p2. In the resulting gene, the p1 coding sequence was replaced by the p2 coding sequence, while the flanking p1 regulatory sequences remained largely preserved. The red pericarp color specified by P1-rw1077 suggests that the p1- and p2-encoded proteins are functionally equivalent as regulatory factors in the flavonoid biosynthesis pathway. Sequence analysis shows that the P1-rw1077 allele lacks a 386 bp sequence in an enhancer region 5 kb upstream of the transcription start site. An independently-derived P1-rw allele contains an Ac insertion into the same sequence, indicating that this site likely contains cob glume-specific regulatory elements.;The p1 alleles exhibit a high degree of genetic and phenotypic diversities. To understand the driving force(s) for generation of those diversities, 6 single copy p1 alleles were characterized and compared. Structural and sequence analyses revealed 3 distinctive enhancer types. The structure of the distal enhancer region correlates with the expression of each allele in cob glumes. Further investigation suggests that homologous recombination between the 5' and 3' non-coding direct repeats promotes diversification of the distal enhancer. As a result, novel distal enhancer types were generated during the p1 evolution, giving rise to a novel phenotypic variation. Moreover, based on the structures in the non-coding regions, we proposed a stepwise model to account for evolutionary pathways of the distinct p1 alleles. In this model, recombination between duplicated non-coding repeats is the major driving force in diversifying the p1 alleles, and creating novel cis-regulatory regions. Because tandem and segmental duplication are common in both animal and plant genomes, homologous recombination between non-coding duplicated sequences could have been an important means to generate genetic and phenotypic variations.