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Animal genetics2024; doi: 10.1111/age.13424

Study on the origin of the Baise horse based on whole-genome resequencing.

Abstract: The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse.
© 2024 Stichting International Foundation for Animal Genetics.
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Publication Date: 2024-04-07 PubMed ID: 38584302DOI: 10.1111/age.13424Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research focuses on tracing the origin and ancestral composition of the Baise horse, a native breed from southwestern China. Whole-genome resequencing data of multiple horse breeds revealed that foreign horse breeds didn’t significantly contribute to the Baise horse’s formation, and its closest genetic relations were with two other southwestern horse populations, the Debao pony and the Jinjiang horse.

Methods

  • The study used whole-genome resequencing data from 236 horses belonging to several breeds, including seven indigenous Chinese horses, five foreign horse breeds, and four Przewalski’s horses. Whole-genome resequencing sheds light on a wide range of genetic variations and is a powerful tool for tracing origin and evolution.
  • The investigators then analyzed the genetic relationships between the Baise horse and the various other horse breeds to trace the breed’s origin and ancestral makeup.

Findings

  • The researchers found that foreign horse breeds didn’t significantly influence the Baise horse’s genesis. This negates any theoretical contribution from bodies outside of China in the formation of this breed.
  • The genetic affinity of the Baise horse is closest to the Debao pony and Jinjiang horse, both of which are from the same southwestern region of China. This correlation hints at a significant role of geography, aligning with biological patterns where genetically similar species often share a spatial relationship.
  • The study also noted a gene flow from the Chakouyi horse into the Baise horse, indicating a genetic contribution from the former in the formation of the latter.

Conclusion

  • The study confirmed that the genesis of the Baise horse didn’t involve any participation from foreign breeds, implying that it is a native breed of China with no substantial crossbreeding with foreign species.
  • Geographical proximity emerged as a critical factor in determining the genetic relationship in the case of the Baise horse. This means that the closer a breed was to the Baise horse in terms of geographical distribution, the more genetically similar it likely was.
  • The researchers also suggested that trade activities along ancient routes might have facilitated the gene flow among indigenous horse breeds, leading to the formation of the Baise horse.

Cite This Article

APA
Lin X, Feng M, Li Y, Liu Y, Wang M, Li Y, Yang T, Zhao C. (2024). Study on the origin of the Baise horse based on whole-genome resequencing. Anim Genet. https://doi.org/10.1111/age.13424

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English

Researcher Affiliations

Lin, Xiaoran
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Beijing General Station of Animal Husbandry, Beijing, China.
Feng, Mo
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Li, Ying
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Liu, Yu
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Wang, Min
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Li, Yuanyuan
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Yang, Tao
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Zhao, Chunjiang
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • National Engineering Laboratory for Animal Breeding, Beijing, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China.
  • Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China.

Grant Funding

  • U23A20224 / The China Regional Innovation and Development Joint Fund Project sponsored by the National Natural Science Foundation
  • 19221073 / The Project on the Third National Survey of the Livestock and Poultry Genetic Resources sponsored by the Ministry of Agriculture and Rural Affairs
  • 125C0505 / The Project on the Survey of the Livestock and Poultry Genetic Resources in the Qinghai-Tibet Plateau sponsored by the Ministry of Agriculture and Rural Affairs
  • Z171100002217072 / The project of the Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry sponsored by the People's Government of Beijing Municipality
  • IRT1191 / The Program for Changjiang Scholars and Innovative Research Team in University sponsored by the Ministry of Education
  • The Germplasm Bank for Domesticated Animals sponsored by Ministry of Agriculture and Rural Affairs

References

This article includes 33 references
  1. Alexander DH, Novembre J, Lange K. Fast model‐based estimation of ancestry in unrelated individuals. Genome Research 19, 1655–1664.
  2. Bhati M, Kadri NK, Crysnanto D, Pausch H. Assessing genomic diversity and signatures of selection in original Braunvieh cattle using whole‐genome sequencing data. BMC Genomics 21(27), 1–14.
  3. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.
  4. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second‐generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4(7), 1–16.
  5. Chang H, Han G, Mao Y, Bai D. Animal genetic resources in China, Horses Donkeys Camels. Beijing, China: China Agriculture Press.
  6. Cunningham F, Allen JE, Allen J, Alvarez‐Jarreta J, Amode MR, Armean IM. Ensembl 2022. Nucleic Acids Research 50, D988–D995.
  7. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA. The variant call format and VCFtools. Bioinformatics 27, 2156–2158.
  8. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008.
  9. Felsenstein J. PHYLIP. https://evolution.genetics.washington.edu/phylip.html.
  10. Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B. Genomic insights into the conservation of wild and domestic animal diversity: a review. Gene 886, 147719.
  11. Han L, Abney M. Identity by descent estimation with dense genome‐wide genotype data. Genetic Epidemiology 35, 557–567.
  12. Hou WT. A brief analysis of the origin and development of the pony in China (in Chinese). Agricultural Archaeology 1, 340–344.
  13. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254–267.
  14. Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49, W293–W296.
  15. Li H, Durbin R. Fast and accurate short read alignment with burrows‐wheeler transform. Bioinformatics 25, 1754–1760.
  16. Li H, Durbin R. Fast and accurate long‐read alignment with burrows‐wheeler transform. Bioinformatics 26, 589–595.
  17. Li Y, Liu Y, Wang M, Lin X, Li Y, Yang T. Whole‐genome sequence analysis reveals the origin of the Chakouyi horse. Genes (Basel) 13(2411), 1–13.
  18. Li YL, Liu JX. StructureSelector: a web‐based software to select and visualize the optimal number of clusters using multiple methods. Molecular Ecology Resources 18, 176–177.
  19. Liang YB, Xu DX, Su JL. Cultivar investigation of the Baise horse (in Chinese). China Herbivores 30, 76–78.
  20. Liu S, Fu C, Yang Y, Zhang Y, Ma H, Xiong Z. Current genetic conservation of Chinese indigenous horses revealed with Y‐chromosomal and mitochondrial DNA polymorphisms. G3 (Bethesda) 11, jkab008.
  21. Ma H, Wang S, Zeng G, Guo J, Guo M, Dong X. The origin of a coastal indigenous horse breed in China revealed by genome‐wide SNP data. Genes (Basel) 10(241), 1–27.
  22. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A. The genome analysis toolkit: a MapReduce framework for analyzing next‐generation DNA sequencing data. Genome Research 20, 1297–1303.
  23. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome‐wide allele frequency data. PLoS Genetics 8, e1002967.
  24. Purcell S, Neale B, Todd‐Brown K, Thomas L, Ferreira MA, Bender D. PLINK: a tool set for whole‐genome association and population‐based linkage analyses. American Journal of Human Genetics 81, 559–575.
  25. Shi S. Ethnic flows from upper reaches of the Yellow River to Tibetan‐Yi corridor at the Neolithic culture (in Chinese). Journal of Southwest Minzu University (Humanities and Social Sciences Edition) 10, 1–7.
  26. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy‐Moonshine A. From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics 43, 11.0.1–11.0.33.
  27. Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer‐Verlag.
  28. Xia X, Zhang S, Zhang H, Zhang Z, Chen N, Li Z. Assessing genomic diversity and signatures of selection in Jiaxian red cattle using whole‐genome sequencing data. BMC Genomics 22, 43.
  29. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome‐wide complex trait analysis. American Journal of Human Genetics 88, 76–82.
  30. Yang Y, Zhu Q, Liu S, Zhao C, Wu C. The origin of Chinese domestic horses revealed with novel mtDNA variants. Animal Science Journal 88, 19–26.
  31. Zhang C, Dong SS, Xu JY, He WM, Yang TL. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786–1788.
  32. Zhang S, Yao Z, Li X, Zhang Z, Liu X, Yang P. Assessing genomic diversity and signatures of selection in Pinan cattle using whole‐genome sequencing data. BMC Genomics 23(460), 1–10.
  33. Zhang Z. The nationalities on horseback in ancient Yunnan province and their related issues (in Chinese). Journal of Yunnan Minzu University (Philosophy and Social Sciences Edition) 2, 13‐20+77.

Citations

This article has been cited 1 times.
  1. Han J, Shao H, Sun M, Gao F, Hu Q, Yang G, Jafari H, Li N, Dang R. Genomic insights into the genetic diversity and genetic basis of body height in endangered Chinese Ningqiang ponies. BMC Genomics 2025 Mar 24;26(1):292.
    doi: 10.1186/s12864-025-11484-2pubmed: 40128652google scholar: lookup
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