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HaploVar: An R package for defining local haplotype variants for trait association and trait prediction analyses
Tessa R MacNish1,2, Hawlader A Al-Mamun1,2,3, Thomas Bergmann1,2
1School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia.
Bioinformatics (Oxford, England)
|December 6, 2025
Summary
HaploVar is a new tool that identifies local haplotypes to improve both genome-wide association studies (GWAS) and genomic selection (GS) in marker-assisted breeding (MAB). This tool enhances breeding pipelines by leveraging DNA regions inherited together for more accurate trait identification.
Area of Science:
- Genetics
- Bioinformatics
- Plant and Animal Breeding
Background:
- Marker-assisted breeding (MAB) utilizes molecular markers to identify desirable traits in breeding programs.
- Genome-wide association studies (GWAS) and genomic selection (GS) are key MAB methods.
- Local haplotypes, DNA regions inherited together, can enhance the accuracy of GWAS and GS.
Purpose of the Study:
- To introduce HaploVar, a novel local haplotyping tool.
- To improve the accuracy and power of both GWAS and GS pipelines.
- To provide a tool compatible with existing major GWAS and GS software.
Main Methods:
- Development of HaploVar, a local haplotyping tool.
- Formatting HaploVar output for compatibility with major GWAS and GS tools.
- Utilizing local haplotypes to enhance prediction accuracy in GS and GWAS.
Main Results:
- HaploVar identifies local haplotypes crucial for MAB.
- The tool is designed to improve both GWAS and GS pipelines.
- HaploVar's output is compatible with all major GWAS and GS tools.
Conclusions:
- HaploVar offers a new approach to local haplotyping for MAB.
- The tool can be applied to any haplotype-based MAB study.
- HaploVar enhances the utility of local haplotypes for both GWAS and GS.
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