Versatile web tool for the automatic identification of intronic regions of genes in complex genomes for generating ILP markers (Triticum aestivum L. example)

DOI: https://doi.org/10.7124/FEEO.v39.1845
Keywords: genetic markers, ILP markers, Triticum aestivum, CDS, exon-intron gene structure

Abstract

Aim. Develop a user-friendly and versatile web tool for the automatic identification of intronic regions of genes along with adjacent short exon fragments (50 bp) in genomic data for their subsequent use in generating ILP (Intron Length Polymorphism) markers. The tool works directly with GFF3 and FASTA files and is designed to simplify the analysis of complex genomes, particularly those of wheat. Results. A serverless cloud system was developed, capable of rapidly processing large volumes of data. For example, analyzing a single wheat chromosome took only 118 seconds. Thanks to optimized search algorithms, the system efficiently identifies target genetic regions even in large genomes. Testing on the 2B chromosome of Triticum aestivum revealed 15,664 intron loci across 4,005 genes, achieving a high density of 3.91 markers per gene. Conclusions. The developed system significantly accelerates the identification of genetic markers (ILP markers) and allows generation of large marker libraries even for complex genomes. Moreover, the results are immediately suitable for subsequent primer design, which saves time and simplifies researchers’ work.

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