CKM intron: an appropriate marker for the determination of the genetic relationships among horse populations and breeds

Abstract

To date, the origins, domestication, and genetic structure of Chinese Mongolian horses (CMH) are poorly understood. Furthermore, there have been sparse reports on the genetic differences between CMH and Thoroughbred. In order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed an extensive survey of creatine kinase (muscle isoenzyme; CKM) variations among six populations of indigenous CMH, cultivated Sanhe horses, and imported Thoroughbred. Twenty-three single-nucleotide polymorphisms were found among the 343 horse sequences. From these, 40 haplotypes were inferred. Haplotype diversity (H) values differed from 0.6424 to 0.7881 and nucleotide diversity (π) values ranged from 0.00150 to 0.00211. The differences between Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations with respect to CKM intron sequences suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and CMH are very closely related and the introgression (interbreeding) between them is serious. Our results suggest that Sanhe and Wushen require prompt and powerful protection. Overall, CKM intron was an appropriate marker for the determination of genetic relationships among horse populations and breeds.

Keywords:

• Horse breeds
• genetic structure
• sequences polymorphism
• CKM gene
• breeding
• China

Acknowledgments

The authors would like to kindly thank to Ying Xiao and Genshun Liu (Chifeng Boen Pharmaceutical Management Co., Ltd, Chifeng), Ruixia Zhao (Chifeng Agricultural and Husbandry Research Institute, Chifeng) for assistance in sample collection.

Authors’ contributions

Huaidong Wang, YS, and MD designed the study. Huidong Wang and JC performed the experiments. JL, SL and BL facilitated the sampling process. JC analyzed the data and drafted the manuscript. All authors have read and approved the final manuscript.

Additional information

Funding

This work was supported by the project of Accurate Certification on the breeds’ qualities of livestock and poultry from Ministry of Agriculture and Rural Affairs [Grant No. 202123]; Natural Science Foundation of Shandong province [ZR2022QC091]; Special project on the systematic evaluation and screening of donkey breeds’ qualities of Yellow River reaches from Vocational College of Dongying; Natural Science Foundation of Inner Mongolia Autonomous Region, grant number 2020MS03074; and Higher Education Science Research Project of Inner Mongolia Autonomous Region, grant number NJZY23037.