Evolution of Methods for the Quantitative Assessment of Inbreeding in Livestock

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Genomics

Background:

• Inbreeding assessment is crucial for livestock genetic risk evaluation and breeding program management.
• Methods have evolved from probabilistic pedigree-based models to direct genome structure analysis.
• Understanding autozygosity is key to managing genetic diversity and progress.

Purpose of the Study:

• To systematize the evolution of inbreeding assessment approaches.
• To compare different methods including pedigree-based, runs of homozygosity (ROH), and homozygous-by-descent (HBD) models.
• To highlight the distinct aspects of autozygosity captured by various coefficients.

Main Methods:

• Review of classical inbreeding coefficient (F) based on identity by descent (IBD).
• Analysis of marker-based, segment-based runs of homozygosity (ROH) methods.
• Examination of probabilistic homozygous-by-descent (HBD) models and their comparison.

Main Results:

• Pedigree-based (F_ped), genomic relationship matrix (F_GRM), ROH-based (F_ROH), and HBD-based (F_HBD) coefficients capture distinct autozygosity features and are not interchangeable.
• Transition from integral to stratified autozygosity analyses allows differentiation between ancient and recent inbreeding.
• Methodological limitations and sensitivity to parameters like marker density and population structure are discussed.

Conclusions:

• A comprehensive assessment of inbreeding using multiple methods is necessary.
• Standardization of analytical protocols is required for effective application in modern livestock breeding.
• Differentiating ancient and recent inbreeding provides deeper insights for genetic management.