Xinjiang, a region in China renowned for its rich equine genetic resources, harbors a diverse array of native horse breeds. These breeds are highly adapted to their environments and possess valuable traits, yet their conservation faces challenges due to the introduction of external breeds and evolving agricultural practices. A significant hurdle in effective conservation has been the lack of comprehensive understanding regarding the population structure of these native breeds. This study addresses this gap by presenting the first in-depth Single Nucleotide Polymorphism (SNP) analysis of seven Xinjiang native horse breeds. Utilizing 10X whole-genome sequencing, this research provides critical insights into their genetic diversity, population structure, and evolutionary relationships.
1. Introduction to Xinjiang’s Equine Heritage
The domestic horse (Equus ferus caballus) has played a pivotal role in human civilization for millennia, with domestication occurring approximately 5,500 years ago. Over time, horses spread across Eurasia, adapting to diverse environments and giving rise to numerous breeds. China boasts a rich tapestry of horse breeds, and the Xinjiang Uygur Autonomous Region (XUAR) stands out as a major horse-producing area. Historically, horses in Xinjiang have been primarily valued for meat production, with many breeds maintained through traditional, free-grazing methods. However, increasing demand for equestrian activities and tourism has led to crossbreeding with breeds like Thoroughbreds and Arabians to enhance performance traits. While this can improve productivity in cultivated breeds, it poses a significant threat to the genetic purity of native Xinjiang breeds, some of which risk extinction due to small population sizes and unmanaged breeding practices. Previous research on Xinjiang horses has largely focused on microsatellite markers, leaving a gap in comprehensive genome-wide analyses. This study aims to fill that void by providing the first extensive genomic analysis of seven Xinjiang native horse breeds, offering crucial data for their conservation and management.
2. Materials and Methods: Unraveling Genetic Secrets
To understand the genetic landscape of Xinjiang’s native horses, this study collected peripheral blood samples from 70 horses across seven distinct breeds: Kazakh horse from the Altay region (KA), Kazakh horse from the Yili region (KY), Yanqi (YQ), Balikun (BLK), Kyrgyz (KE), Tashkurgan (TX), and Kunlun (KL). DNA was extracted, and whole-genome resequencing was performed on the Illumina HiSeqX Ten platform. Sequencing data from an additional 32 horses from various domestic and wild breeds were downloaded from the NCBI database for comparative analysis.
2.1 SNP Detection and Quality Control
After sequencing, raw data underwent rigorous quality control. High-quality reads were mapped to the domestic horse reference genome (EquCab3.0). SNPs were identified using SAMtools and GATK. To ensure data integrity, loci with low detection rates, minor allele frequencies, or high missing genotype rates were filtered out. Linkage disequilibrium (LD) was also assessed to further refine the dataset, ensuring the reliability of subsequent analyses.
2.2 Genetic Diversity and Population Structure Analysis
Genetic diversity was quantified using measures such as observed heterozygosity (Obs Het), expected heterozygosity (Exp Het), and the inbreeding coefficient (Fis). Population differentiation was assessed using the fixation index (Fst). Principal Component Analysis (PCA) was employed to visualize genetic relationships, and phylogenetic trees were constructed using the neighbor-joining method to illustrate evolutionary lineages. Population structure was further analyzed using the fastSTRUCTURE package.
3. Results: A Glimpse into Xinjiang’s Horse Genetics
The comprehensive SNP analysis yielded significant findings regarding the genetic makeup of Xinjiang’s native horse breeds.
3.1 Genetic Diversity Insights
The study revealed that Xinjiang native horse breeds possess relatively low genetic diversity compared to breeds like the Mongolian and Tibetan horses. While heterozygosity values were similar across the Xinjiang breeds, the observed heterozygosity was generally lower than expected, suggesting some degree of inbreeding or genetic drift. The Yanqi (YQ) population exhibited the highest inbreeding coefficient (Fis), while the Kyrgyz (KE) and Kunlun (KL) populations showed the lowest, likely influenced by stallion distribution. The Polymorphic Information Content (PIC/Pi) indicated that the Kunlun (KL) population displayed higher levels of genetic polymorphism.
In terms of genetic differentiation (Fst), Xinjiang native horse breeds showed minimal divergence among themselves (Fst values below 0.01). However, they were genetically distinct from European, Central Asian, and Western Asian breeds, with Arabian and Akhal-Teke horses showing the highest differentiation. Notably, Przewalski’s horses, though diverged for a long time, exhibited lower Fst values with domestic breeds than expected, possibly due to shared ancestral polymorphisms.
Linkage disequilibrium (LD) decay rates were lower in Xinjiang native horse breeds compared to other domestic and foreign breeds, suggesting higher genetic diversity. Thoroughbreds, subjected to intensive selective breeding, showed the lowest genetic diversity.
3.2 Unraveling Genetic Structure
Principal Component Analysis (PCA) indicated a clear separation between Chinese native horse breeds and foreign breeds, with Xinjiang breeds clustering together with considerable overlap. This suggests a shared genetic heritage and potentially historical gene flow among these breeds. The PCA also highlighted significant genetic differentiation between Central and Western Asian breeds, reinforcing the Fst results.
Phylogenetic analysis revealed that Xinjiang native horse breeds form a distinct group, largely separate from other Chinese and foreign breeds. Within Xinjiang, a distinction emerged between northern and southern breeds, aligning with geographic separation. The Tashkurgan (TX) and Kunlun (KL) horses appeared to form a unique clade, suggesting they might represent distinct, potentially undiscovered breeds.
Population structure analysis, particularly at K=6, further distinguished the Xinjiang native horse breeds. The complexity observed at higher K values suggests that genetic variation is influenced not only by drift and mutation but also by prolonged gene flow.
4. Discussion: Implications for Conservation and Breeding
This study provides the first comprehensive genomic analysis of Xinjiang native horse breeds, offering valuable insights into their genetic distinctiveness and diversity. The observed low levels of inbreeding in most Xinjiang breeds are consistent with traditional open grazing practices, indicating resilience to inbreeding. Conversely, breeds like the Thoroughbred exhibited very low genetic diversity due to intensive artificial selection.
The genetic distinctiveness of Xinjiang horse breeds from other populations can be attributed to long-term independent evolution, historical bottlenecks, adaptation to unique environments, and targeted selection for specific traits. Their close relationship with Tibetan and Mongolian horses suggests historical gene flow. Crossbreeding practices, while potentially improving performance, pose a significant risk to the genetic purity of these native breeds, emphasizing the need for careful management.
The potential identification of Tashkurgan and Kunlun horses as distinct cryptic breeds warrants further investigation. Understanding the genetic makeup of these breeds is crucial for developing effective conservation strategies, including delineating protected areas and implementing breeding programs to prevent inbreeding and hybridization.
5. Conclusion: Safeguarding Xinjiang’s Equine Genetic Legacy
This research has illuminated the genetic diversity and population structure of Xinjiang’s native horse breeds. The findings underscore their unique genetic background, the evidence of gene exchange among them, and the differentiation between northern and southern groups. The potential existence of new cryptic breeds highlights the ongoing need for detailed genetic characterization. The data generated provides a foundational resource for informing future policies on horse breeding, conservation, and the sustainable utilization of Xinjiang’s invaluable equine genetic resources. These insights are critical for safeguarding this rich heritage for generations to come.
Data Availability Statement
The genomic data generated in this study is publicly available in the NCBI SRA repository under accession number PRJNA1185891.
Ethics Statement
All animal procedures were approved by the Institutional Animal Care and Use Committee at Tarim University. The study adhered to local legislation and institutional guidelines. Written informed consent was obtained from all animal owners prior to sample collection.
Author Contributions
[As listed in the original article, providing contributions for each author.]Funding
This research was supported by grants from the National Natural Science Foundation of China, the Graduate Research Innovation Project of Tarim University, the Open project of Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, and the Agricultural germplasm resources survey, collection, protection and identification service project of the Ministry of Agriculture and Rural Affairs.
Acknowledgments
The authors express gratitude to various agricultural bureaus and officials across Xinjiang for their support. Computational resources were provided by the bioinformatics computing platform at Tarim University. Constructive comments were received from Prof. Indira Beishova, Prof. Malika Shamekova, and Prof. Abdugani Abdurasulov.
Conflict of Interest
The authors declare no commercial or financial relationships that could be construed as a conflict of interest.
Supplementary Material
Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fgene.2025.1439312/full#supplementary-material
