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Huang B, Khan MZ, Chai W, Ullah Q, Wang C. Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys. Animals (Basel) 2023; 13:2725. [PMID: 37684989 PMCID: PMC10486882 DOI: 10.3390/ani13172725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Donkeys (Equus asinus) play a pivotal role as essential livestock in arid and semi-arid regions, serving various purposes such as transportation, agriculture, and milk production. Despite their significance, donkey breeding has often been overlooked in comparison to other livestock species, resulting in limited genetic improvement programs. Preserving donkey genetic resources within each country necessitates the establishment of breed conservation programs, focusing on managing genetic diversity among populations. In recent years, significant strides have been made in sequencing and analyzing complete mitochondrial DNA (mtDNA) molecules in donkeys. Notably, numerous studies have honed in on the mitochondrial D-loop region, renowned for its remarkable variability and higher substitution rate within the mtDNA genome, rendering it an effective genetic marker for assessing genetic diversity in donkeys. Furthermore, genetic markers at the RNA/DNA level have emerged as indispensable tools for enhancing production and reproduction traits in donkeys. Traditional animal breeding approaches based solely on phenotypic traits, such as milk yields, weight, and height, are influenced by both genetic and environmental factors. To overcome these challenges, genetic markers, such as polymorphisms, InDel, or entire gene sequences associated with desirable traits in animals, have achieved widespread usage in animal breeding practices. These markers have proven increasingly valuable for facilitating the selection of productive and reproductive traits in donkeys. This comprehensive review examines the cutting-edge research on mitochondrial DNA as a tool for assessing donkey biodiversity. Additionally, it highlights the role of genetic markers at the DNA/RNA level, enabling the informed selection of optimal production and reproductive traits in donkeys, thereby driving advancements in donkey genetic conservation and breeding programs.
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Affiliation(s)
- Bingjian Huang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252000, China
- College of Life Sciences, Liaocheng University, Liaocheng 252059, China
| | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252000, China
- Faculty of Veterinary and Animal Sciences, University of Agriculture, Dera Ismail Khan 29220, Pakistan
| | - Wenqiong Chai
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252000, China
| | - Qudrat Ullah
- Faculty of Veterinary and Animal Sciences, University of Agriculture, Dera Ismail Khan 29220, Pakistan
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252000, China
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Ahlawat S, Sharma U, Arora R, Sharma R, Chhabra P, Veer Singh K, Vijh RK. Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys. Gene 2023:147627. [PMID: 37429369 DOI: 10.1016/j.gene.2023.147627] [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: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | | | - R K Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal
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Xia J, Chang L, Xu D, Jia Y, Ding Y, Cao C, Geng Z, Jin S. Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family. Animals (Basel) 2023; 13:ani13030531. [PMID: 36766420 PMCID: PMC9913526 DOI: 10.3390/ani13030531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The Huaibei grey donkey (HGD) is an endangered species and a vital native breed in Anhui Province, China. However, its complete mitogenome, phylogeny, and maternal origin remain unclear. The objectives of this study were to detect the genetic diversity of the HGD and investigate its phylogenetic relationship with other breeds to inform conservation management. The complete mitogenome of the HGD was sequenced through next-generation sequencing, and the most variable region in the mitochondrial DNA displacement-loop (D-loop) was amplified via a polymerase chain reaction (PCR). Next, we used the median-joining network (MJN) to calculate the genetic relationships among populations and the neighbor-jointing method to build a phylogenetic tree and speculate as to its origin. The results showed that the mitogenome contains 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. Analyzing the D-loop region of the HGDs, we identified 23 polymorphic sites and 11 haplotypes. The haplotype and nucleotide diversity were 0.87000 (Hd) and 0.02115 (Pi), respectively. The MJN analysis indicated that the HGD potentially has two maternal lineages, and phylogenetic analysis indicated that the Somali lineage could be the most probable domestication center for this breed. Therefore, our mitogenome analysis highlights the high genetic diversity of the HGD, which may have originated from the Somali wild ass, as opposed to the Asian wild ass. This study will provide a useful resource for HGD conservation and breeding.
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Affiliation(s)
- Jingjing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Liang Chang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dashuang Xu
- Anhui Livestock and Poultry Genetic Resources Protection Center, Hefei 231283, China
| | - Yuqing Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yuanfei Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Correspondence: ; Tel.:+86-551-6578-6328; Fax:+86-551-6578-6326
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Alves JS, de Araujo Oliveira CA, Escodro PB, Pinto LFB, Costa RB, de Camargo GMF. Genetic origin of donkeys in Brazil. Trop Anim Health Prod 2022; 54:291. [PMID: 36094617 DOI: 10.1007/s11250-022-03280-x] [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] [Received: 03/24/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The genetic groups of native donkeys in Brazil are characterized by adaptation to the local environment. However, the donkey population in the country is declining, mainly because of agricultural mechanization and transportation that has led to the abandonment and the consequent indiscriminate slaughter of these animals. There are three local genetic groups of distinct geographic and temporal formation. However, analyses of their origin, phylogenetic relationship, and population structure are scarce. Within this context, molecular markers such as the mitochondrial control region (D-loop) are useful for these analyses. MATERIAL AND METHODS This study aimed to evaluate the variation and origin of maternal lineages of groups of naturalized donkeys in Brazil (Brazilian, Nordestino, and Pêga). RESULTS AND DISCUSSION We detected five mitochondrial haplotypes with 19 polymorphic sites, two of them exclusively found in the Nordestino donkey; this group is in fact more distant from the others. Phylogenetic analysis indicates maternal contributions of two clades (Nubian and Somali) to the formation of the genetic groups of donkeys, a fact that explains the high diversity, structure, and distances of the groups, reported here for the first time. CONCLUSION : This analysis contributes production and conservation of native donkey breeds. It also gives clues about the formation of the Iberian breeds from which Brazilian donkeys originated.
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Affiliation(s)
- Jackeline Santos Alves
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Chiara Albano de Araujo Oliveira
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Pierre Barnabé Escodro
- Centro de Engenharias e Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Luis Fernando Batista Pinto
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Raphael Bermal Costa
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Gregório Miguel Ferreira de Camargo
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil.
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Li B, Feng C, Zhu S, Zhang J, Irwin DM, Zhang X, Wang Z, Zhang S. Identification of Candidate Circular RNAs Underlying Intramuscular Fat Content in the Donkey. Front Genet 2020; 11:587559. [PMID: 33424924 PMCID: PMC7793956 DOI: 10.3389/fgene.2020.587559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022] Open
Abstract
Intramuscular fat (IMF) content is a crucial indicator of meat quality. Circular RNAs (circRNAs) are a large class of endogenous RNAs that are involved in many physiological processes. However, the expression and function of circRNA in IMF in the donkey remains unresolved. Here we performed an expression profiling of circRNAs in the donkey longissimus dorsi muscle and identified 12,727 candidate circRNAs. Among these, 70% were derived from the exons of protein genes. Furthermore, a total of 127 differentially expressed (DE) circRNAs were identified in high (H) and low (L) IMF content groups, including 63 upregulated and 64 downregulated circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the host genes of the DE circRNAs showed that the host genes were enriched in lipid metabolism related GO terms (e.g., fatty acid beta-oxidation using acyl-CoA dehydrogenase and MLL3/4 complex), and signaling pathways (e.g., TGF-beta and lysine degradation signaling pathway). Further analyses indicated that 127 DE circRNAs were predicted to potentially interact with miRNAs, leading to the construction of circRNA-miRNA regulatory network. Multiple circRNAs can potentially function as sponges of miRNAs that regulate the differentiation of adipocytes. Our results provide valuable expression profile information for circRNA in the donkey and new insight into the regulatory mechanisms of circRNAs in the regulation of IMF content.
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Affiliation(s)
- Bojiang Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chunyu Feng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shiyu Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xiaoying Zhang
- Liaoning Province Engineering Center of Modern Agricultural Production Base, Shenyang, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region. Animals (Basel) 2020; 10:ani10111970. [PMID: 33120938 PMCID: PMC7692571 DOI: 10.3390/ani10111970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary This paper represents the first fundamental report of mtDNA diversity in Turkish indigenous donkey breeds and presents findings for the origin and genetic characterization of donkey populations dispersed in seven geographical regions in Turkey, and thus reveals insights into their genetic history. The median-joining network and phylogenetic tree exhibit two different maternal lineages of the 16 Turkish indigenous donkey populations. Abstract In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.
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Santos Alves J, da Silva Anjos M, Silva Bastos M, Sarmento Martins de Oliveira L, Pereira Pinto Oliveira I, Batista Pinto LF, Albano de Araújo de Oliveira C, Bermal Costa R, Miguel Ferreira de Camargo G. Variability analyses of the maternal lineage of horses and donkeys. Gene 2020; 769:145231. [PMID: 33065240 DOI: 10.1016/j.gene.2020.145231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 11/17/2022]
Abstract
Equid breeds originating from the Iberian Peninsula and North Africa are believed to have genetically contributed to the formation of breeds and ecotypes from Brazil. The country has numerous breeds and ecotypes of horses and donkeys but there are no extensive studies on maternal genetic diversity and their origins. This study reports the results of the first genetic analysis of all horse and donkey breeds/ecotypes from Brazil based on sequences of the mitochondrial DNA control region (D-loop) whose main objective was to characterize the genetic variation in these animals. These analyses will contribute to the understanding of the current population structure and diversity of breeds/ecotypes of horses and donkeys raised in the Brazil. We analyzed 310 D-loop sequences representing 41 breeds/ecotypes of Equus caballus and Equus asinus, including 14 native horse breeds/ecotypes, 3 native donkey breeds/ecotypes and 24 cosmopolite horse breeds. The results revealed that the breeds are well structured genetically and that they comprise different groups. A total of 80 and 14 haplotypes were identified for horses and donkeys, respectively. Most of the horse mtDNA haplotypes were shared by many breeds, whereas donkey mtDNA haplotypes seemed to be more group-especif. Some groups presented a low intrabreed distance and/or a low haplotype/nucleotide diversity such as Lavradeiro, Crioulo, Piquira and Percheron horses and Brazilian donkey. Thus, specific actions must be designed for each population. The different levels of genetic diversity provided important information for conservation resource management of adapted groups as well as for mating orientation of breed associations. Some autochthonous ecotypes require attention because of their low genetic variability.
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Affiliation(s)
- Jackeline Santos Alves
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brazil
| | - Marcia da Silva Anjos
- Programa de Pós-Graduação em Biodiversidade e Evolução da UFBA, Salvador, BA, Brazil
| | - Marisa Silva Bastos
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brazil
| | | | | | | | | | - Raphael Bermal Costa
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brazil
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Stanisic L, Aleksić JM, Dimitrijevic V, Kovačević B, Stevanovic J, Stanimirovic Z. Banat donkey, a neglected donkey breed from the central Balkans (Serbia). PeerJ 2020; 8:e8598. [PMID: 32175186 PMCID: PMC7059758 DOI: 10.7717/peerj.8598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/19/2020] [Indexed: 11/20/2022] Open
Abstract
The dominant donkey breed in the Balkans is the mid-sized Balkan donkey with a grey to chocolate coat color. Local breeders from Serbia, however, still maintain a few larger individuals of a lighter coat color, named Banat donkey, and speculate that they are descendants of a Spanish donkey heard that had been transferred to the Banat region by the Hapsburg Queen Maria Theresa in the XVIII century for a specific purpose, to work in local vineyards. We have previously found a unique nuclear gene-pool and a prevalence of mitochondrial Clade 2 haplotypes in several such animals. In this study, we: (i) perform a comparative analysis of 18 morphological traits of the Banat donkey (seven individuals), Balkan donkey (53 individuals from two sub-populations of this breed) and the potential hybrids (eight individuals), and demonstrate the morphological distinctiveness of the Banat donkey, highlighting the diagnostic traits for distinguishing the breed: hip height, croup width, body length and chest depth; (ii) re-analyse published nuclear microsatellite data for these groups, and reveal that, although severely depopulated, the genetically distinct Banat donkey is not severely affected by the loss of genetic diversity and inbreeding; (iii) demonstrate that previously published Banat donkey mitochondrial haplotypes, analyzed genealogically together with those reported in ancient and modern individuals from Spain, Italy, Turkey, Cyprus and Africa, are shared with three Spanish breeds and individuals belonging to Amiata and some other Italian breeds. A unique morphological feature present in Banat and Somali wild donkeys, but also in Amiata donkeys, black stripes on legs, suggests that the origin of Clade 2 donkeys may be much more complex than previously thought. Actions to preserve the Banat donkey, a valuable but critically endangered genetic resource (<100 individuals), are urgent.
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Affiliation(s)
- Ljubodrag Stanisic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena M. Aleksić
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
| | - Vladimir Dimitrijevic
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Branislav Kovačević
- Institute of Lowland Forestry and Environment (ILFE), University of Novi Sad, Novi Sad, Serbia
| | - Jevrosima Stevanovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Zoran Stanimirovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
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Ma XY, Ning T, Adeola AC, Li J, Esmailizadeh A, Lichoti JK, Agwanda BR, Isakova J, Aldashev AA, Wu SF, Liu HQ, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Adedokun RAM, Olaogun SC, Sanke OJ, Mangbon GF, Chen X, Yang WK, Wang Z, Peng MS, Ommeh SC, Li Y, Zhang YP. Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences. Zool Res 2020; 41:51-60. [PMID: 31709786 PMCID: PMC6956721 DOI: 10.24272/j.issn.2095-8137.2020.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication. However, domestication histories of these two lineages remain enigmatic. We therefore compared several population characteristics between these two lineages based on global sampling, which included 171 sequences obtained in this study (including Middle Asian, East Asian, and African samples) plus 536 published sequences (including European, Asian, and African samples). The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop (D-loop) sequences, respectively. The Clade I lineage experienced an increase in population size more than 8 000 years ago and shows a complex haplotype network. In contrast, the population size of the Clade II lineage has remained relatively constant, with a simpler haplotype network. Although the distribution of the two lineages was almost equal across the Eurasian mainland, they still presented discernible but complex geographic bias in most parts of Africa, which are known as their domestication sites. Donkeys from sub-Saharan Africa tended to descend from the Clade I lineage, whereas the Clade II lineage was dominant along the East and North coasts of Africa. Furthermore, the migration routes inferred from diversity decay suggested different expansion across China between the two lineages. Altogether, these differences indicated non-simultaneous domestication of the two lineages, which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa, respectively.
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Affiliation(s)
- Xi-Yao Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Tiao Ning
- Agriculture College, Kunming University, Kunming, Yunnan 650214, China.,Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, Kunming University, Kunming, Yunnan 650214, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jie Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman PB 76169-133, Iran
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock and Fisheries, Nairobi 00100, Kenya
| | - Bernard R Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 00100, Kenya
| | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Almaz A Aldashev
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | | | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
| | - Zhe Wang
- Department of Physiology, Hebei Medical University, Shijiazhuang, Hebei 050017, China.,Hebei Key Laboratory of Animal Science, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Sheila C Ommeh
- Animal Biotechnology Group, Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya. E-mail:
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China.,State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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