Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation

Area of Science:

• Animal Breeding and Genetics
• Quantitative Genetics
• Genomic Evaluation

Background:

• Single-step methods integrate genomic data into genetic evaluations.
• Compatibility issues exist between marker-based and pedigree-based relationship matrices.
• Existing adjustments overlook the use of observed phenotypes and genotypes.

Purpose of the Study:

• To propose a novel method for single-step genetic evaluation.
• To address the compatibility issue by adjusting the pedigree relationship matrix.
• To extend single-step evaluations using a joint likelihood of phenotypes and genotypes.

Main Methods:

• Adjusting the pedigree-based relationship matrix to be compatible with the marker-based matrix.
• Utilizing a joint likelihood function incorporating both observed phenotypes and marker genotypes.
• Employing a parameter (γ) for base population relatedness and inbreeding, and a scaling parameter for the marker matrix.

Main Results:

• The adjustment parameters depend on both observed phenotypes and genotypes.
• A strong association was found between the adjustment parameters.
• The proposed method performed at least as well as existing adjustment methods.

Conclusions:

• Adjusting the pedigree-based relationship matrix offers a new approach for compatibility.
• Using the full joint likelihood improves single-step genetic evaluations.
• The method effectively handles the compatibility challenge in genomic evaluations.