Quantitative genetics model as the unifying model for defining genomic relationship and inbreeding coefficient

Area of Science:

• Quantitative genetics
• Genomics
• Animal breeding

Background:

• Traditional quantitative genetics models are foundational for understanding genetic relationships.
• Genomic relationships offer a more precise alternative to pedigree-based estimations.
• Accurate measures of genomic relatedness and inbreeding are crucial for selective breeding programs.

Purpose of the Study:

• To derive and compare multiple definitions of genomic additive and dominance relationships.
• To investigate the impact of different standardization assumptions on these relationships.
• To introduce and validate a new genomic inbreeding coefficient for predicting offspring inbreeding levels.

Main Methods:

• Utilized the traditional quantitative genetics model to derive six definitions of genomic relationships.
• Assessed theoretical differences based on SNP effect and variance assumptions.
• Employed genomic best linear unbiased prediction (GBLUP) and genomic restricted maximum likelihood (GREML) for heritability estimation.
• Developed and evaluated a new genomic inbreeding coefficient against pedigree-based methods.

Main Results:

• Genomic relationships generally aligned with pedigree data but exhibited unique genomic specificity and significant variations.
• Six definitions yielded consistent results for additive heritability (GREML) and additive effects prediction (GBLUP).
• Differences in dominance heritability estimates emerged between definitions based on equal SNP effects versus equal SNP variance.
• The proposed genomic inbreeding coefficient showed the highest correlation with pedigree inbreeding coefficients.

Conclusions:

• Multiple definitions of genomic relationships can be derived, offering insights into genomic specificity and potential for minimizing relatedness.
• Genomic relationships provide valuable, albeit variable, information beyond traditional pedigree data.
• The novel genomic inbreeding coefficient offers a robust and accurate method for predicting offspring inbreeding levels in livestock populations.