Evidence map›Paper›PMID 41806849›Full record

ArticleEquine veterinary journal2026

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

Yuanyuan Li, Chunzheng Fu, Xirong Yun, Hetong Zhang, Tao Yang, Mo Feng, Xinyu Wang, Shiyu Qian, Wenhui Xing, Ran Yang and 3 more

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Article in Equine veterinary journal, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

13 authors.

Yuanyuan LiCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Chunzheng FuInstitute of Sericulture, Chengde Medical University, Chengde, China.
Xirong YunCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Hetong ZhangCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Tao YangCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Mo FengCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Xinyu WangCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Shiyu QianCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Wenhui XingCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Ran YangCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Jiahui WuCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Yu LiuCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Chunjiang ZhaoCollege of Animal Science and Technology, China Agricultural University, Beijing, China.ORCID https://orcid.org/0000-0002-2016-8738

Funding

Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry Z171100002217072National Germplasm Center of Domestic Animal ResourcesNational Natural Science Foundation of China 32302731Program for Changjiang Scholars and Innovative Research Team in University IRT1191Project on the Third National Survey of the Livestock and Poultry Genetic Resources 19221073
6 · The paper itself

Abstract

backgroundWith growing demand for pedigree verification and breed management in horses (Equus caballus), reliable paternal lineage tools are essential. Y-chromosomal STRs (Y-STRs) have advantages over autosomal STRs due to paternal inheritance and lack of recombination. However, few validated loci and no standardised efficient genotyping systems limit their use. Current methods often require multiple reactions, increasing cost and labour. Thus, identifying informative Y-STR loci and developing a multiplex PCR system for cost-effective paternal lineage analysis is urgently needed.

objectivesTo identify informative horse Y-STR loci and develop a multiplex PCR system for paternal lineage tracing, breed conservation, pedigree verification, and forensic settings. STUDY

designExperimental study.

methodsY-STR loci were screened from the horse reference genome based on repeat motif, number, and location. Primers were designed and tested on stallions and mares to confirm Y-specificity. Loci with stable, male-specific amplification were combined with known markers into a multiplex PCR system. Sensitivity, repeatability, reproducibility, and performance were evaluated, and locus polymorphism was assessed in Debao ponies, Mongolian horses, Thoroughbreds, and Arabian horses.

resultsTwenty candidate loci were screened, and 15 of them showed clear, reproducible male-specific amplification. Three novel polymorphic loci were identified and combined with 5 known markers into 2-plex and 6-plex panels. Most loci were polymorphic in Debao ponies (PIC: 0.000-0.575) and Mongolian horses (PIC: 0.000-0.375), while less polymorphism was detected in Thoroughbreds (PIC: 0.000-0.099) and Arabian horses (PIC: 0.000-0.099). The optimised multiplex PCR system demonstrated high sensitivity, repeatability, and compatibility. MAIN LIMITATIONS: Reproducibility and stability across labs and platforms require further validation.

conclusionsFifteen new Y-STR loci were identified, and 3 of them were polymorphic. Novel optimised multiplex PCR systems were developed for the identification of horse paternal lines, providing reliable tools for equine genetic study, breeding, and forensic applications.

Indexed as

Microsatellite RepeatsMultiplex Polymerase Chain ReactionY ChromosomeAnimalsFemaleHorsesMalePedigreeReproducibility of Resultshorsemultiplex PCRpaternal lineage identificationSTR

Identifiers

PMID41806849
PMCPMC13447914

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