mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development

Area of Science:

• Genetics and Genomics
• Bioinformatics
• Molecular Biology

Background:

• Insertion-Deletion (InDel) markers are crucial for genetics, genomics, and marker-assisted breeding due to their genetic information content and cost-effectiveness.
• Next-generation sequencing (NGS) has accelerated sequence data generation and genome-wide variation identification.
• Existing NGS tools for InDel mining require a reference genome, limiting their use in unsequenced organisms, and often produce short InDels unsuitable for gel-based genotyping.

Purpose of the Study:

• To develop an enhanced platform for identifying longer InDels.
• To enable InDel marker discovery in the absence of a reference genome.
• To provide a tool compatible with gel-based genotyping platforms.

Main Methods:

• Developed mInDel (multiple InDel), a next-generation variant calling tool for InDel marker discovery.
• Employs de novo assembly of raw sequence reads into contigs.
• Identifies InDel polymorphisms via sliding window alignment on assembled contigs.

Main Results:

• mInDel successfully identifies InDel polymorphisms without a reference genome.
• The software offers an option to combine multiple InDels for improved gel-based genotyping.
• Demonstrated usability and validated marker accuracy using maize NGS data.

Conclusions:

• mInDel is a novel and practical tool for rapid, genome-wide InDel marker discovery.
• Its reference-genome-independent nature and flexibility with genotyping platforms broaden its applicability in genetics research and plant breeding.
• The mInDel pipeline is publicly available for use.