1
|
Chen J, Wang H, Li J, Liu S, Li B, Sun Y, Wang H, Manglai D. CKM intron: an appropriate marker for the determination of the genetic relationships among horse populations and breeds. Anim Biotechnol 2023; 34:3962-3970. [PMID: 37593944 DOI: 10.1080/10495398.2023.2247445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
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.
Collapse
Affiliation(s)
- Jianxing Chen
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Huidong Wang
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Jing Li
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Shuqin Liu
- Gene Bank for Equine Genetic Resources of Shandong Province, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Benke Li
- Binzhou Refferral Center for Agricultural Technologies, Binzhou, China
| | - Yujiang Sun
- Gene Bank for Equine Genetic Resources of Shandong Province, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Vocational College of Dongying, Dongying, China
| | - Huaidong Wang
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
| | - Dugarjaviin Manglai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| |
Collapse
|
2
|
Orazymbetova Z, Ualiyeva D, Dossybayev K, Torekhanov A, Sydykov D, Mussayeva A, Baktybayev G. Genetic Diversity of Kazakhstani Equus caballus (Linnaeus, 1758) Horse Breeds Inferred from Microsatellite Markers. Vet Sci 2023; 10:598. [PMID: 37888550 PMCID: PMC10611244 DOI: 10.3390/vetsci10100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Understanding the genetic diversity and structure of domesticated horse (Equus caballus) populations is critical for long-term herd management and breeding programs. This study examines 435 horses from Kazakhstan, covering seven groups in three geographic areas using 11 STR markers. Identified are 136 alleles, with the mean number of alleles per locus ranging from 9 to 19. VHL20 is the most variable locus across groups, while loci HTG4, AHT4, AHT5, HTG7, and HMS3 are variable in most populations. The locus AHT5 in the Emba population shows the highest frequency of rare alleles, while the lowest frequency, 0.005, is observed in the Kulandy population. All loci were highly informative for the Kazakhstani populations of E. caballus, with PIC values higher than 0.5. Pairwise variations in Wright's FST distances show that the examined varieties have little genetic differentiation (0.05%), indicating a high degree of admixture and a continuing lineage sorting process. Phylogenetic and population structure analyses reveal three major clusters of Kazakh horses, representing (I) the Uralsk population of the Kushum breed and the monophyly of two groups: (II) the Kozhamberdy population of the Mugalzhar breed, and (III) the Mugalzhar-Kushum breed populations. Kazakhstani horse populations, while being regionally isolated, were recently in contact with each other.
Collapse
Affiliation(s)
- Zarina Orazymbetova
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Daniya Ualiyeva
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
- Institute of Zoology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Kairat Dossybayev
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Aibyn Torekhanov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| | - Dauren Sydykov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| | - Aizhan Mussayeva
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Gabiden Baktybayev
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| |
Collapse
|
3
|
Kefena E, Rosenbom S, Beja-Pereira A, Kurtu MY, Han JL, Dessie T. Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers. Trop Anim Health Prod 2021; 53:334. [PMID: 34018049 DOI: 10.1007/s11250-021-02776-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
We investigated the genetic diversity and population genetic structure of six morphologically distinct Ethiopian donkey populations using 12 equine microsatellite markers. The donkey populations were Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI). Blood samples were collected from 180 genetically unrelated donkeys (30 individuals per population). Population genetic diversity estimates showed that total number and mean number of observed alleles, average observed and expected heterozygosity were 94, 5.208 ± 0.0229, 0.555 ± 0.023 and 0.588 ± 0.022, respectively. Highly significant deficiency in heterozygote was detected within the overall samples (FIS = 0.055 ± 0.021; P < 0.001). Though highly significant (P < 0.001), heterozygote deficiency within populations relative to total population was moderate (FST = 0.046 ± 0.016), suggesting a higher diversity within the populations (95.4%) than between populations. Various genetic distance estimation methods produced a similar topology of un-rooted dendrograms that grouped the overall Ethiopian donkeys into lowland (Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe) genetic lineages. Likewise, Bayesian clustering analysis produced a similar pattern of clustering that was highly concordant with traditional donkey classification systems in Ethiopia.
Collapse
Affiliation(s)
- E Kefena
- Department of Animal Genetics and Breeding, Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia.
| | - S Rosenbom
- Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal
| | - A Beja-Pereira
- Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal.,Department of Geosciences, Environment and Spatial Planning (DGAOT), Faculty of Sciences, University of Porto, Rua Campo Alegre 687, 4169-007, Porto, Portugal
| | - M Yusuf Kurtu
- Department of Animal and Range Sciences, Haramaya University, P.O. Box 38, Dire Dawa, Ethiopia
| | - J L Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.,Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - T Dessie
- Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| |
Collapse
|