Evaluation of parentage testing using single nucleotide polymorphism markers for draft horses in Japan

Area of Science:

• Animal Genetics
• Molecular Biology
• Genomic Science

Background:

• Parentage testing is crucial for animal breeding and genetic management.
• Single nucleotide polymorphism (SNP) markers offer a powerful tool for genetic analysis.
• Evaluating SNP utility in specific horse breeds is essential for accurate genetic verification.

Purpose of the Study:

• To assess the effectiveness of the International Society for Animal Genetics (P-ISAG) 147 SNP panel for parentage testing in Japanese Breton (BR) and Percheron (PR) horses.
• To compare the performance of the P-ISAG panel with a larger set of 561 SNPs for parentage discovery.

Main Methods:

• Genomic DNA extraction from 98 horses (47 BR, 51 PR) in Japan.
• Sequencing using next-generation sequencing and analysis of the P-ISAG 147 SNP panel and 414 additional autosomal SNPs.
• Calculation of combined probabilities of exclusion (PEs) and evaluation of parent-offspring pairs.

Main Results:

• The P-ISAG panel demonstrated high accuracy for parentage verification in both breeds, with PEs exceeding 0.9999.
• No exclusions or doubtful cases were found in 35 validated parent-offspring pairs using the P-ISAG panel.
• Parentage discovery cases showed a 0.18% false acceptance rate, indicating a need for additional markers.

Conclusions:

• The P-ISAG 147 SNP panel is highly effective for parentage verification in Japanese Breton and Percheron horses.
• For parentage discovery in horses with unknown relationships, a larger SNP set (561 SNPs) combining the P-ISAG panel and additional autosomal markers is recommended for improved accuracy.