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Related Experiment Video

Updated: Jun 20, 2025

Induction and Evaluation of Inbreeding Crosses Using the Ant, Vollenhovia Emeryi
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FnR: R package for computing inbreeding and numerator relationship coefficients.

Mohammad Ali Nilforooshan1

  • 1Livestock Improvement Corporation, Private Bag 3016, Hamilton, 3240, New Zealand. mohammad.nilforooshan@lic.co.nz.

BMC Ecology and Evolution
|July 18, 2024
PubMed
Summary
This summary is machine-generated.

The R package FnR efficiently calculates animal relationship coefficients, crucial for conservation and breeding programs. This free, open-source software optimizes mating plans by minimizing inbreeding and maximizing effective population size in large datasets.

Keywords:
BreedingGenetic diversityInbreedingNumerator relationship matrixPedigreeR package

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Area of Science:

  • Animal genetics and genomics
  • Quantitative genetics
  • Conservation biology

Background:

  • Inbreeding and relationship coefficients are vital for effective animal breeding and conservation strategies.
  • Monitoring inbreeding rates and optimizing mating plans are critical for both small conserved and large commercial populations.
  • Efficient, free, and open-source software can significantly aid researchers and students in these endeavors.

Purpose of the Study:

  • To introduce an efficient R package (FnR) for calculating numerator relationship coefficients.
  • To address computational challenges in determining relationships, particularly when progeny data is limited.
  • To provide a tool that minimizes inbreeding and maximizes effective population size in animal populations.

Main Methods:

  • The study utilized an R package that calculates relationship coefficients by introducing dummy progenies for individuals lacking direct offspring in the pedigree.
  • Benchmarking involved calculating relationship coefficients for large datasets (up to 800 animals within a pedigree of over 2.7 million).
  • Runtime and memory usage were assessed under different scenarios, including pre-calculated inbreeding coefficients and diagonal elements of D.

Main Results:

  • The FnR package demonstrated high efficiency, calculating 200,000 relationship coefficients within minutes on standard hardware.
  • Performance was significantly improved by providing pre-calculated inbreeding coefficients (reducing runtime by over 65%) and diagonal elements of D (further reduction).
  • The software exhibited low memory usage, performing analyses on a machine with only 1 GB of RAM.

Conclusions:

  • The R package FnR is a time and memory-efficient, free, and open-source tool beneficial for large-scale conservation and breeding programs.
  • Saving the latest inbreeding coefficient estimates is recommended for resuming calculations with new animals.
  • Calculating 'd' coefficients from scratch was rapid, suggesting minimal benefit in storing them for future use.