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GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach
R Baumung1, J Farkas, D Boichard
1Division of Livestock Sciences, University of Natural Resources and Applied Life Sciences, Vienna, Austria.
Summary
GRain software aids in testing inbreeding depression hypotheses using gene dropping methods. It calculates classical and novel ancestral inbreeding coefficients, enabling detailed genetic analyses.
Area of Science:
- Population Genetics
- Quantitative Genetics
- Bioinformatics
Background:
- Inbreeding depression impacts populations, necessitating methods to study its genetic basis.
- Understanding the genetic contributions of ancestors is crucial for conservation and breeding programs.
Purpose of the Study:
- To introduce GRain, a novel software tool for analyzing inbreeding depression.
- To facilitate hypothesis testing regarding the purging and heterogeneity of inbreeding depression.
- To provide advanced genetic coefficient calculations for complex pedigrees.
Main Methods:
- Utilizes a stochastic approach based on the gene dropping method.
- Calculates classical inbreeding coefficients.
- Introduces and calculates novel ancestral inbreeding coefficients and an Ancestral History Coefficient (AHC).
Main Results:
- GRain computes various inbreeding coefficients, including classical, ancestral, and AHC.
- The software enables the calculation of partial coefficients for heterogeneity and purging analysis.
- AHC quantifies allele instances in Identity By Descent (IBD) status during pedigree segregation.
Conclusions:
- GRain offers a comprehensive tool for inbreeding depression research.
- The software facilitates detailed genetic analyses of complex pedigrees and ancestral contributions.
- GRain supports advanced hypothesis testing in population and conservation genetics.
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