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geneHapR: an R package for gene haplotypic statistics and visualization.

Renliang Zhang1, Guanqing Jia2, Xianmin Diao3

  • 1Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

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|May 15, 2023
PubMed
Summary

A new R package, geneHapR, simplifies identifying and visualizing gene haplotypes. This tool aids in understanding gene function and selecting beneficial alleles for crop improvement.

Keywords:
Haplotype identificationLD-blockNetworkRVisualizationgeneHapR

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Breeding

Background:

  • Next-generation sequencing and genomic variation data enable superior allele identification for marker-assisted selection.
  • Clarifying functional gene haplotypes is crucial for modern genetic studies.

Purpose of the Study:

  • To introduce 'geneHapR', an R package for haplotype identification, statistical analysis, and visualization of candidate genes.
  • To provide a tool for integrating genotype, genomic annotation, and phenotypic data.

Main Methods:

  • The 'geneHapR' package integrates diverse datasets for comprehensive analysis.
  • Utilizes variant visualization, network construction, and phenotypic comparison to analyze haplotypes.
  • Includes functions for Linkage Disequilibrium block analysis and haplotype geo-distribution visualization.

Main Results:

  • 'geneHapR' facilitates the identification and statistical analysis of candidate gene haplotypes.
  • Enables visualization of genotype variations, evolutionary relationships, and phenotypic effects of haplotypes.
  • Supports Linkage Disequilibrium analysis and geographical mapping of haplotype distributions.

Conclusions:

  • 'geneHapR' offers an accessible tool for haplotype identification and visualization in candidate genes.
  • Provides valuable insights for gene functional dissection.
  • Aids in the pyramiding of beneficial alleles for future breeding programs.