Gene conversion within regulatory sequences generates maize r alleles with altered gene expression.

Area of Science:

• Plant genetics
• Molecular biology
• Gene regulation

Background:

• The maize R locus encodes a transcription factor controlling anthocyanin pigment development.
• Alleles R-sc and R-p exhibit distinct tissue specificity and flanking sequences, highlighting gene regulatory diversity.
• Transposable element Ds6 inserts into R-sc mutants (sc:m) to study gene regulation.

Purpose of the Study:

• Investigate gene regulatory mechanisms of the maize R locus.
• Analyze the origin of colored seed derivatives (Sc+) from sc:m mutants.
• Characterize novel R-allele phenotypes arising from recombination and gene conversion.

Main Methods:

• Analysis of meiotic recombination in maize heterozygotes (P and sc:m).
• Phenotypic characterization of colored seed derivatives (Sc+).
• DNA sequencing to identify genetic changes in Sc+ derivatives.

Main Results:

• sc:m alleles with Ds6 insertions produced Sc+ derivatives via crossover and noncrossover pathways.
• Noncrossover Sc+ derivatives included Scp(+) (progenitor-like) and Scp(e) (novel phenotypes).
• Novel Scp(e) phenotypes exhibited strong Sc+ expression and resembled natural r alleles.

Conclusions:

• Gene conversion between the R-sc promoter and a homologous region near R-p explains Sc+ derivative formation.
• Recombinational intermediates involving sc:m and P can lead to Ds6 element deletion.
• This study elucidates complex gene regulatory mechanisms and generates novel R-allele variants in maize.