A capture-based assay for detection and characterization of transposon polymorphisms in maize

Area of Science:

• Genetics
• Molecular Biology
• Plant Science

Background:

• Transposable elements (TEs) contribute to genetic and phenotypic diversity by altering gene expression.
• Genome-wide detection of TE polymorphisms across large populations is challenging.
• Understanding TE functional roles requires efficient genotyping methods.

Purpose of the Study:

• To develop and validate a targeted sequencing approach for high-throughput genotyping of transposon polymorphisms.
• To investigate the association between transposon polymorphisms and gene expression variation in maize.
• To assess the functional impact of specific transposon insertions on gene regulation.

Main Methods:

• Development of a targeted sequencing assay to genotype 965 transposon presence/absence polymorphisms.
• Application of the assay to a diverse panel of 16 maize (Zea mays L.) inbred lines.
• Integration of transposon polymorphism data with gene expression data and validation using PCR and luciferase assays.

Main Results:

• The targeted sequencing assay reliably genotyped transposon polymorphisms, with high consistency (98.6%) compared to PCR-based methods.
• Approximately 70% of targeted regions were effectively assayed across genotypes.
• ~18% of assayed transposon polymorphisms showed association with variable gene expression levels in maize.
• Functional validation confirmed the regulatory impact of specific transposon polymorphisms on gene expression.

Conclusions:

• Targeted sequencing is an effective, high-throughput method for exploring transposon function and impact on gene expression.
• This approach facilitates the study of TE-mediated genetic diversity and its contribution to phenotypic variation.
• The findings provide a valuable resource for maize genetics and breeding programs seeking to leverage TE diversity.