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Cai C, Xie L, Xing J, Lu T, Qi X, Li L, Chen X, Akhtar MF, Jin Y, Liu G. Effects of concentrate feeding sequence on VFA production, and cecal microbiota of Dezhou donkeys by metagenomic technology. Front Vet Sci 2024; 11:1401980. [PMID: 38895717 PMCID: PMC11183499 DOI: 10.3389/fvets.2024.1401980] [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: 03/16/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
Microorganisms residing in the cecum of donkeys are crucial for physiological processes, nutrient metabolism, and immune function. Feeding methods can affect the dynamic balance of animal gut microbiota, thereby affecting indicators such as volatile fatty acids. This study explores suitable feeding methods to promote actual production by changing the feeding order of concentrate. Fifteen Dezhou donkeys with similar age and weight profiles were randomly divided into three groups with the concentrate feeding sequence: fiber-to-concentrate (FC), concentrate-to-fiber (CF), and total mixed ration (TMR). The experiment spanned a duration of 82 days. The analyses conducted were primarily aimed at determining the effects of feeding on gut microbes, primarily using metagenomic sequencing techniques. The experimental findings revealed that the levels of valeric acid were notably higher in the CF and TMR groups compared to the FC group (p < 0.05). These results suggest that the feeding sequence exerts a certain impact on the microbial composition within the cecum of Dezhou donkeys. At the phylum level, the predominant microbiota consisted of Firmicutes and Bacteroidetes, with the CF group displaying a higher relative abundance of Firmicutes compared to both the FC and TMR groups. At the genus level, Prevotella, Bacteroides, and Fibrobacter were the dominant bacterial genera identified in cecum. The functional gene annotation analysis indicated a significantly lower abundance of lacZ (K01190), Por/nifJ (K03737), and ppdK (K01006) genes in CF group relative to the FC and TMR groups (p < 0.05), highlighting their roles in galactose metabolism and glycolysis, respectively. Moreover, the CF group exhibited a higher concentration of antibiotic resistance genes (tetO and tet44) in the gut microbiota compared to the TMR and FC groups (p < 0.05), underscoring the presence of numerous antibiotic resistance genes within the phyla Bacteroidetes, Firmicutes, and Proteobacteria. In conclusion, different precision feed sequences significantly impact the levels of volatile fatty acids in Dezhou fattening donkeys, modify the composition and functional genes of the cecal microbiota, and elucidate the microbial mechanisms influenced by the feeding sequence on the growth and metabolism. These insights are anticipated to provide a foundation for the rational design of precision feed sequences in practical agricultural settings.
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Affiliation(s)
- Changyun Cai
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Lan Xie
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Jingya Xing
- College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Ting Lu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Xingzhen Qi
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Lanjie Li
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
- Office of International Programs, Liaocheng University, Liaocheng, China
| | - Xue Chen
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Muhammad Faheem Akhtar
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Yaqian Jin
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Guiqin Liu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of BlackDonkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
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Chen J, Zhang S, Liu S, Dong J, Cao Y, Sun Y. Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds. Anim Biotechnol 2023; 34:1828-1839. [PMID: 35382683 DOI: 10.1080/10495398.2022.2053145] [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: 11/01/2022]
Abstract
This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.
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Affiliation(s)
- Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, China
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Jianbao Dong
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Yanhang Cao
- Modern Animal Husbandry Development Service Center of Dongying, Dongying, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Vocational College of Dongying, Dongying, China
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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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4
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Wang L, Sheng G, Preick M, Hu S, Deng T, Taron UH, Barlow A, Hu J, Xiao B, Sun G, Song S, Hou X, Lai X, Hofreiter M, Yuan J. Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys. Front Genet 2021; 12:759831. [PMID: 34721545 PMCID: PMC8554150 DOI: 10.3389/fgene.2021.759831] [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: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Both molecular data and archaeological evidence strongly support an African origin for the domestic donkey. Recent genetic studies further suggest that there were two distinct maternal lineages involved in its initial domestication. However, the exact introduction time and the dispersal process of domestic donkeys into ancient China are still unresolved. To address these questions, we retrieved three near-complete mitochondrial genomes from donkey specimens excavated from Gaoling County, Shaanxi Province, and Linxia Basin, Gansu Province, China, dated at 2,349-2,301, 469-311, and 2,160-2,004 cal. BP, respectively. Maximum-likelihood and Bayesian phylogenetic analyses reveal that the two older samples fall into the two different main lineages (i.e., clade Ⅰ and clade Ⅱ) of the domestic donkey, suggesting that the two donkey maternal lineages had been introduced into Midwestern China at least at the opening of Silk Road (approximately the first century BC). Bayesian analysis shows that the split of the two donkey maternal lineages is dated at 0.323 Ma (95% CI: 0.583–0.191 Ma) using root-tip dating calibrations based on near-complete mitogenomes, supporting the hypothesis that modern domestic donkeys go back to at least two independent domestication events. Moreover, Bayesian skyline plot analyses indicate an apparent female population increase between 5,000 and 2,500 years ago for clade I followed by a stable population size to the present day. In contrast, clade II keeps a relatively stable population size over the past 5,000 years. Overall, our study provides new insights into the early domestication history of Chinese domestic donkeys.
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Affiliation(s)
- Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, China
| | - Guilian Sheng
- School of Environmental Studies, China University of Geosciences, Wuhan, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Michaela Preick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Songmei Hu
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Tao Deng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, Beijing, China
| | - Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Jiaming Hu
- School of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Bo Xiao
- School of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Guojiang Sun
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, China
| | - Shiwen Song
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xindong Hou
- School of Environmental Studies, China University of Geosciences, Wuhan, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Junxia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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5
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Shen J, Yu J, Dai X, Li M, Wang G, Chen N, Chen H, Lei C, Dang R. Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys. J Genet Genomics 2021; 48:737-745. [PMID: 34373218 DOI: 10.1016/j.jgg.2021.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 12/28/2022]
Abstract
Donkey (Equus asinus) is an important livestock animal in China because of its draft and medicinal value. After a long period of natural and artificial selection, the variety and phenotype of donkeys have become abundant. We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds. According to population structure, most Chinese domestic donkeys showed a dominant ancestral type. However, the Chinese donkeys still represented a significant geographical distribution trend. In the selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small donkey groups, we identified selective signals, including NCAPG and LCORL, which are related to rapid growth and large body size. Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.
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Affiliation(s)
- Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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6
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Xia X, Yu J, Zhao X, Yao Y, Zeng L, Ahmed Z, Shen S, Dang R, Lei C. Genetic diversity and maternal origin of Northeast African and South American donkey populations. Anim Genet 2019; 50:266-270. [PMID: 30854699 DOI: 10.1111/age.12774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2019] [Indexed: 11/29/2022]
Abstract
To investigate the mtDNA variation and origin of maternal lineages in South American donkeys and to reassess the domestication of donkeys in northeast Africa, we analyzed sequences (489 bp of the D-loop) from 323 domestic donkeys sampled from Peru, Brazil, Ethiopia and Egypt. Altogether, the 323 sequences displayed 53 different haplotypes (45 in Ethiopia, 14 in Egypt, eight in Peru and six in Brazil). Among the four populations, Egyptian donkeys possessed the highest haplotype diversity (0.910 ± 0.032), followed by Brazilian donkeys (0.879 ± 0.060). The Clade I haplotypes dominated in Peruvian donkeys (65%), whereas Clade II haplotypes dominated in Brazilian donkeys (67%). Estimates of FST values showed a high genetic differentiation between Peruvian and Brazilian donkey populations (FST = 0.4066), which could be explained by the complex introduction history of South American donkeys. Phylogeographic analysis indicates that northeast Africa could be the most probable domestication center for Clade I donkeys. Analysis of molecular variance confirmed a weak genetic structure in domestic donkey populations among four continents (Europe, Asia, Africa and South America).
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Affiliation(s)
- X Xia
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - J Yu
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No.78, E-jiao Street, Done-E Country, Shandong Province, 252201, China
| | - X Zhao
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Y Yao
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - L Zeng
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Z Ahmed
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Shen
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No.78, E-jiao Street, Done-E Country, Shandong Province, 252201, China
| | - R Dang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - C Lei
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Han H, Chen N, Jordana J, Li C, Sun T, Xia X, Zhao X, Ji C, Shen S, Yu J, Ainhoa F, Chen H, Lei C, Dang R. Genetic diversity and paternal origin of domestic donkeys. Anim Genet 2017; 48:708-711. [PMID: 28929497 DOI: 10.1111/age.12607] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2017] [Indexed: 11/30/2022]
Abstract
Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male-specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome-specific microsatellites (Y-STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y-STRs-EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4-were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y-chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China.
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Affiliation(s)
- H Han
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - N Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - J Jordana
- Facultat de Veterinària, Department Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Bellaterra, 08193, Spain
| | - C Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - T Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Xia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - C Ji
- Donge Ejiao Company Limited by Shares, Donge, Shandong, 252299, China
| | - S Shen
- Donge Ejiao Company Limited by Shares, Donge, Shandong, 252299, China
| | - J Yu
- Donge Ejiao Company Limited by Shares, Donge, Shandong, 252299, China
| | - F Ainhoa
- Facultat de Veterinària, Department Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Bellaterra, 08193, Spain
| | - H Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - C Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - R Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Stanisic LJ, Aleksic JM, Dimitrijevic V, Simeunovic P, Glavinic U, Stevanovic J, Stanimirovic Z. New insights into the origin and the genetic status of the Balkan donkey from Serbia. Anim Genet 2017; 48:580-590. [PMID: 28815638 DOI: 10.1111/age.12589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2017] [Indexed: 11/30/2022]
Abstract
The Balkan donkey (Equus asinus L.) is commonly regarded as a large-sized, unselected, unstructured and traditionally managed donkey breed. We assessed the current genetic status of the three largest E. asinus populations in the central Balkans (Serbia) by analysing the variability of nuclear microsatellites and the mitochondrial (mtDNA) control region of 77 and 49 individuals respectively. We further analysed our mtDNA dataset along with 209 published mtDNA sequences of ancient and modern individuals from 19 European and African populations to provide new insights into the origin and the history of the Balkan donkey. Serbian donkey populations are highly genetically diverse at both the nuclear and mtDNA levels despite severe population decline. Traditional Balkan donkeys in Serbia are rather heterogeneous; we found two groups of individuals with similar phenotypic features, somewhat distinct nuclear backgrounds and different proportions of mtDNA haplotypes belonging to matrilineal Clades 1 and 2. Another group, characterized by larger body size, different coat colour, distinct nuclear gene pool and predominantly Clade 2 haplotypes, was delineated as the Banat donkey breed. The maternal landscape of the large Balkan donkey population is highly heterogeneous and more complex than previously thought. Given the two independent domestication events in donkeys, multiple waves of introductions into the Balkans from Greece are hypothesized. Clade 2 donkeys probably appeared in Greece prior to those belonging to Clade 1, whereas expansion and diversification of Clade 1 donkeys within the Balkans predated that of Clade 2 donkeys.
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Affiliation(s)
- L J Stanisic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - J M Aleksic
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, PO Box 23, 11010, Belgrade, Serbia
| | - V Dimitrijevic
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - P Simeunovic
- Department of Farm Animal Diseases, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - U Glavinic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - J Stevanovic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - Z Stanimirovic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
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9
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Han L, Zhu S, Ning C, Cai D, Wang K, Chen Q, Hu S, Yang J, Shao J, Zhu H, Zhou H. Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys. BMC Evol Biol 2014; 14:246. [PMID: 25433485 PMCID: PMC4263014 DOI: 10.1186/s12862-014-0246-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/17/2014] [Indexed: 11/16/2022] Open
Abstract
Background The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced. Results Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. Conclusions This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.
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Affiliation(s)
- Lu Han
- Key-Lab for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, 130012, PR China. .,Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China. .,Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Songbiao Zhu
- Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China.
| | - Chao Ning
- Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China.
| | - Dawei Cai
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Kai Wang
- Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China.
| | - Quanjia Chen
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Songmei Hu
- Archaeological Research Institute of Shaanxi Province, Xi' an, 710054, PR China.
| | - Junkai Yang
- Institute for Archaeology and Relic Conservation of Xi' an, Xi' an, 710068, PR China.
| | - Jing Shao
- Archaeological Research Institute of Shaanxi Province, Xi' an, 710054, PR China.
| | - Hong Zhu
- Key-Lab for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, 130012, PR China. .,Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Hui Zhou
- Key-Lab for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, 130012, PR China. .,Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China. .,Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
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