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RecView: an interactive R application for locating recombination positions using pedigree data.

Hongkai Zhang1, Bengt Hansson2

  • 1Department of Biology, Lund University, Lund, 22362, Sweden. hongkai.zhang@biol.lu.se.

BMC Genomics
|November 25, 2023
PubMed
Summary

RecView, an R package, precisely locates recombination positions in genomes using pedigree data. This tool aids in understanding selection and drift by mapping genetic recombination events along chromosomes.

Keywords:
CrossoverNext generation sequencingNon-crossoverR ShinyRecombinationSNP

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Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Recombination shuffles alleles, enabling independent gene evolution and enhancing selection efficiency.
  • Quantifying recombination is crucial for understanding selection and drift impacts on genes and chromosomes.

Purpose of the Study:

  • To present RecView, an R application and package for pinpointing recombination positions.
  • To facilitate the analysis of recombination using whole-genome genotype data from pedigrees.

Main Methods:

  • RecView analyzes grandparent-of-origin for informative alleles across offspring chromosomes.
  • It infers recombination sites using algorithms based on allele origin proportion changes or continuity.
  • The tool processes multiple offspring and chromosomes, reporting positions in base pairs with precision estimates.

Main Results:

  • RecView successfully identified specific recombination positions in the great reed warbler genome.
  • The application demonstrated high precision in locating recombination events using genotype data.

Conclusions:

  • RecView is an effective and user-friendly tool for precise recombination mapping.
  • The RecView package is publicly available on GitHub for broader research application.