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bioRxiv · 10.64898/2025.12.21.694342

QTLIT: A user-friendly Shiny app for Quantitative Trait Loci (QTL) analysis

Mondal, T. K.·Roy, A.·Angadi, U. B.·Mazumder, A.
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Abstract

Identification of Quantitative Trait Loci from DNA sequence data is a multistep process, which is difficult for the plant breeders. To make the QTL identification breeders friendly, we developed QTLIT, a tool comprised of popular R packages and open sources software under a single umbrella for QTL analysis that enables intuitive exploration, multidimensional analyses, and visualization of results generated from any kind of DNA sequence data that deals with Single Nucleotide Polymorphism (SNP) variation. This tool requires raw or processed FASTQ files and proceed it for SNP identification to further perform QTL analysis on genomic regions of interest along with phenotyping data of various pedigree-based mapping populations. QTLIT generates a full range of plots such as VCF quality, linkage map, LOD score etc. It has broad range of applications and options for different parameters which the user can adjust as per their requirements. Moreover, it has two separate interfaces where one can utilize this tool to generate alignment files and/or variant calling for other downstream analysis. QTLIT is a fast and intuitive QTL analysis tool suitable for a wide range of users due to its architecture and its user-friendly graphical interface. QTLIT source code is available at https://github.com/TKM-Lab/QTLIT and the user interface version is available on http://14.139.229.202:8080/QTLIT.

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Mondal, T. K., Roy, A., Angadi, U. B., Mazumder, A.. 2025-12-23. QTLIT: A user-friendly Shiny app for Quantitative Trait Loci (QTL) analysis. https://doi.org/10.64898/2025.12.21.694342

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