Czech J. Anim. Sci., 2024, 69(7):269-279 | DOI: 10.17221/91/2024-CJAS

Commonly used genomic estimators of individual inbreeding in livestockReview

Adrián Halvoník, Nina Moravčíková, Monika Chalupková, Radovan Kasarda

Institute of Nutrition and Genomics, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Nitra, Slovakia

Abstract: Management of inbreeding is one of the crucial parts of breeding programs in livestock populations. Traditionally, the inbreeding coefficient is calculated using pedigree data; however, it can also be estimated from genomic data. Nowadays, various approaches to estimating genomic-based inbreeding coefficients are increasingly integrated into research and breeding practices. These genomic estimators can supplement or replace pedigree-based coefficients. Each genomic-based inbreeding coefficient has its own properties and different ranges of values, and some of them need specific settings for calculation. Moreover, depending on the methodological approach, genomic estimators are sensitive to the population structure, genotyping technology applied, and the quality control of obtained genomic data. It is important to consider all these factors when calculating and especially when interpreting the final genomic inbreeding values. For these reasons, using genomic-based inbreeding coefficients can be more challenging than using pedigree-based ones. In this review, we comprehensively evaluate the most commonly used genomic estimators of individual inbreeding in livestock, providing an in-depth analysis of their advantages and limitations while offering insights into the methodological considerations and best practices for their accurate calculation and interpretation.

Keywords: genomic relationship matrix; inbreeding coefficient; PLINK; runs of homozygosity; single nucleotide polymorphism (SNP)

Received: June 6, 2024; Accepted: July 18, 2024; Published: August 1, 2024  Show citation