Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Bioinformatics

Background:

• Multiple-trait derivative-free REML programs are vital for genetic improvement in livestock and companion animals.
• Traditional software relied on pedigree data, limiting accuracy with advances in genomic information.
• Genomic marker data offers a more precise way to estimate genetic relationships.

Purpose of the Study:

• To enhance existing REML software with genomic relationship matrix capabilities.
• To provide flexibility in incorporating both pedigree and marker data.
• To improve the prediction of breeding values and estimation of genetic variance components.

Main Methods:

• Developed a new program module for the multiple-trait derivative-free REML software.
• Enabled the use of arbitrary relationship matrices derived from genetic markers.
• Integrated standard pedigree files with marker-based relationship matrices.

Main Results:

• The updated software allows seamless integration of pedigree and genomic marker data.
• Demonstrated flexibility in relationship matrix calculations.
• Successfully applied the enhanced software in a canine hip dysplasia QTL association study.

Conclusions:

• The enhanced REML software provides a powerful, flexible tool for genetic analysis.
• Incorporating genomic data significantly improves the accuracy of breeding value prediction.
• This advancement is crucial for accelerating genetic gain in various species.