Screening of Y-chromosomal STR loci and development of a multiplex PCR system for paternal lineage identification in horses.

Authors: Li Yuanyuan, Fu Chunzheng, Yun Xirong, Zhang Hetong, Yang Tao, Feng Mo, Wang Xinyu, Qian Shiyu, Xing Wenhui, Yang Ran, Wu Jiahui, Liu Yu, Zhao Chunjiang

Journal: Equine veterinary journal

DOI: 10.1002/evj.70153 PubMed: 41806849Log in to save

Summary

# Editorial Summary The paternal identification landscape in equine breeding has lacked practical tools suited to the scale of modern stud operations, prompting this research team to evaluate Y-chromosomal short tandem repeats (Y-STRs) as a viable alternative to conventional autosomal markers. Rather than relying on labour-intensive, multi-reaction genotyping protocols, the authors screened candidate Y-STR loci and developed a consolidated multiplex PCR system capable of delivering paternal lineage results within a single reaction. Y-STRs offer distinct technical advantages—notably strict patrilineal inheritance and resistance to recombination—making them theoretically superior to autosomal approaches for confirming sire identity and tracing male ancestry in stud books. The resulting multiplex panel should substantially reduce both the per-sample cost and hands-on time previously demanded by existing methods, whilst establishing standardised loci that facilitate consistent reporting across laboratories and breed societies. For practitioners managing pedigree verification, parentage disputes, or breed integrity programmes, this development represents a significant step towards accessible, reliable genetic authentication in routine equine practice.

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Practical Takeaways

•Breeders and breed registries can use validated Y-STR multiplex PCR systems for reliable and cost-effective paternal verification without multiple separate reactions
•This molecular tool provides a standardized, efficient alternative to traditional pedigree documentation methods for confirming sire identity
•Implementation reduces labor and materials costs while improving accuracy of paternal lineage records in breeding programs

Key Findings

•Y-chromosomal STRs offer advantages over autosomal STRs for paternal lineage analysis due to strict paternal inheritance and lack of recombination
•Development of a multiplex PCR system enables cost-effective and efficient genotyping for paternal identification in horses
•Validated Y-STR loci and standardized genotyping systems were previously lacking, limiting practical application in equine breed management

Conditions Studied

pedigree verificationpaternal lineage identificationbreed management

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