Short communication: Methods to compute genomic inbreeding for ungenotyped individuals

Area of Science:

• Animal Breeding and Genetics
• Quantitative Genetics
• Bioinformatics

Background:

• Genomic inbreeding measures offer higher accuracy than pedigree-based methods.
• Genomic inbreeding cannot be directly computed for ungenotyped animals.
• The H matrix in single-step methods projects genomic relationships to all animals.

Purpose of the Study:

• To develop exact computational methods for estimating genomic inbreeding in ungenotyped animals.
• To address the limitation of calculating the diagonal elements of the H matrix.
• To enable regular estimation of genomic inbreeding for all individuals in a population.

Main Methods:

• Proposed three exact computational methods to compute the diagonal of the H matrix.
• Method 1: Utilizes an existing algorithm for Hx products for each ungenotyped individual.
• Method 2 & 3: Involve quadratic forms with pedigree and genomic relationships, with Method 3 optimizing for genotyped animals.

Main Results:

• Developed and tested three novel methods for computing genomic inbreeding in ungenotyped animals.
• Achieved satisfactory computing times, with the third method being the most efficient.
• Demonstrated feasibility in datasets ranging from small to large populations.

Conclusions:

• The proposed methods enable the estimation of genomic inbreeding coefficients for ungenotyped animals.
• These computational advancements facilitate more accurate genetic evaluations and breeding strategies.
• Regular genomic inbreeding estimation is now feasible for large animal populations.