Domestication of the donkey: timing, processes, and indicators

Transcriptomic analysis of different intramuscular fat contents on the flavor of the longissimus dorsi tissues from Guangling donkey

BACKGROUND

In this study, researchers aimed to explore the impact of intramuscular fat (IMF) concentration on the flavor of donkey meat, specifically in the longissimus dorsi muscle of Guangling donkeys. The internal volatile organic compounds that cause the flavor differences between donkey muscles are not clear at present. Transcriptomic technologies were utilized to analyze gene expression and its relationship to donkey meat flavor.

METHOD

Thirty Guangling donkeys had their IMF content evaluated in the longissimus dorsi muscle. Based on IMF content, 16 donkeys of similar ages were divided into two groups: low-fat (L) and high-fat (H). Headspace solid-phase microextraction Gas chromatography-mass spectrometry (HS-SPME-GC-MS) and headspace solid phase microextraction mass spectrometry were used to identify potential flavor components that differed between the two groups.

RESULTS

Five key volatile substances were identified, and WGCNA and KEGG analysis was conducted to analyze the genes associated with these substances. The results showed that pathways like PPAR signaling, nucleotide excision repair, glucagon signaling, arachidonic acid metabolism, and glycolysis/glycogenesis were involved in lipid deposition. Additionally, a gene-gene interaction network map was constructed, highlighting the importance of hub genes such as EEF2, DDX49, GAP43, SNAP25, NDUFS8, MRPS11, RNASEH2A, POLR2E, POLR2C and ALB in regulating key flavor substances.

CONCLUSION

This study provided valuable insights into the regulation of genes and protein expression related to flavor substances in donkey meat. It also deepened understanding of the influence of IMF on flavor and laid a foundation for future molecular breeding improvements in Guangling donkeys.

Mule embryos share identical morphological features to horse embryos

This study aimed to compare the morphometry of horse and mule embryos. The study's hypothesis was that the micronuclei and nuclear fragmentation indexes are higher in mule embryos than in horse embryos. Twenty-two mares were randomly assigned in a crossover design to receive semen from a horse and a donkey; thirteen horse and thirteen mule embryos were obtained. Embryos were recovered eight days post-ovulation and classified according to the stage of development and quality with a score from 1 (excellent) to 4 (degenerate). Embryos were stained with Hoechst33342, and images were acquired with a fluorescence microscope. Nuclei were categorized as compact, mitotic, or fragmented; the fragmented and mitotic indexes were calculated based on their proportion over the total amount of nuclei counted. Embryo size and nuclear morphometry were assessed through ImageJ. Data analyses were carried out with GraphPad using ANOVA and T-test; significance was set at P < 0.05. The number of positive flushes in cycles bred with donkey or stallion semen did not differ when compared per cycle or per ovulation (13 vs. 12) (P > 0.05). One set of twins was recovered from a mare bred to the stallion that had a double ovulation; a mule and horse embryos were both recovered from eight mares. There was no difference in size between mule and horse embryos (915.5 ± 288 μm vs. 575.8 ± 69.6 μm) (P > 0.05) size of the study. The mule embryos scored between grade 1 (n = 9) and grade 2 (n = 4); similarly, the horse embryos scored between grade 1 (n = 6) and grade 2 (n = 7). The evaluation of the nuclear morphometry revealed that horse and mule embryos have a similar number of compact nuclei per sector (148.7 ± 6.8 nuclei/sector in mule embryos vs. 156.5 ± 8.5 nuclei/sector in horse embryos) (P > 0.05); however, the number of mitotic nuclei tended to be higher in mule embryos (5.2 ± 0.82) than in horse embryos (3.3 ± 0.3) (P = 0.08). The fragmented nuclei index was similar between mule (0.25 ± 0.1%) and horse (0.22 ± 0.1%) embryos (P = 0.4); the mitotic nuclei index was higher in mule embryos (3.2 ± 0.4%) than in horse embryos (2.2 ± 0.2%) (P = 0.02). In conclusion, embryo morphology of mares bred to a donkey and a horse shares similar nuclear ultrastructure features, except that mule embryos have a higher mitotic index.

Mitochondrial DNA diversity and maternal origins of Pakistani donkey

Abstract Domestic donkey plays a key role as a draft animal in rural economy of Pakistan where its population is increasing every year. The complete mtDNA control region of forty randomly sampled donkeys was PCR- amplified and sequenced bi-directionally using specific primers. Distinct mtDNA haplotypes obtained in the current study (KY446001−KY446011) were subjected to haplotype (h) and nucleotide diversity (π) measures using DnaS as well as to phylogenetic, Network, and AMOVA analyses. There were a total 27 polymorphic sites present within 11 unique mtDNA haplotypes from the studied 40 animals from different regions. Neighbor-joining network and median-joining network both illustrated the splitting of all these haplotypes into two well-defined Nubian and Somali lineages, confirming African maternal origin of Pakistani domestic donkey. Diversity parameters h (0.967± 0.037) and π (0.02917± 0.00307) were found to reveal high levels of genetic diversity in Pakistani donkeys. AMOVA demonstrated only 1% of genetic differences between two mtDNA maternal lineages, pointing to lack of population substructure in Pakistani donkeys as is the case with worldwide domestic donkey population. Pakistani donkeys have African maternal origin and high levels of mtDNA diversity. High genetic diversity may be due to non-selective breeding and heteroplasmy. We herein provide the first report on mtDNA diversity of control region in Pakistani domestic donkey.

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

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.

Serological Examinations of Significant Viral Infections in Domestic Donkeys at the Special Nature Reserve "Zasavica", Serbia

The paper presents the findings of specific antibodies in the blood sera of donkeys against the following viruses: equine infectious anemia virus (EIAV), African horse sickness virus (AHSV), equine herpesvirus type 1 (EHV-1), equine influenza virus subtype H3N8 (EIV) and equine arteritis virus (EAV). The analyses were conducted during the year 2022. From a total of 199 donkeys bred in "Zasavica", blood was sampled from 53 animals (2 male donkeys and 51 female donkeys), aged 3 to 10 years. Specific antibodies against EIAV were not detected in any of the tested animals using the agar-gel immunodiffusion (AGID) assay. No specific antibodies against AHSV, tested by enzyme-linked immunosorbent assay (ELISA), or antibodies against EAV, tested by the virus neutralization test (VNT) and ELISA were detected in any of these animals. A positive serological result for EHV-1 was determined by the VNT in all animals, with antibody titer values ranging from 1:2 to 1:128, while a very low antibody titer value for EIV (subtype H3N8) of 1:16 was determined in 18 donkeys using the hemagglutination inhibition test (HI test).

Means of Livelihood, Clean Environment to Women Empowerment: The Multi-Faceted Role of Donkeys

Despite the substantial contribution donkeys make to the livelihood of the world's poorest populations, the existence of donkeys has received little notice worldwide. This article reviews the value of donkeys in a variety of sectors, including agriculture, construction industry, and mining, as well as their role in empowering women and achieving sustainable development goals. However, donkeys and mules are not given enough credit or attention in terms of developing strategies regarding their role in reducing poverty. There is a dearth of information and statistics on their impact across industries, the factors contributing to the donkey population dropping, the socioeconomic status of the dependent communities, and related animal and human welfare issues.

Complex (multispecies) livestock keeping: Highland agricultural strategy in the northern Horn of Africa during the Pre-Aksumite (1600 BCE–400 BCE) and Aksumite (400 BCE–CE 800) periods

The earliest settlements and states in the Horn of Africa were founded in mid to high-elevation areas by farmers and herders who were pioneers in agriculture and herding. Even today, places between mid- and high-elevation remain densely populated. The ancient Pre-Aksumites and Aksumites (1600 cal BCE–800 cal CE) of the north Ethiopian and Eritrean highlands established one of the most powerful states in the Horn of Africa in these high elevation areas through control of long-distance trade and intensive and extensive agriculture. However, despite the fact that agriculture was a significant source of wealth and subsistence for these ancient polities, there has been little research into the agricultural strategies of Pre-Aksumite and Aksumite societies. Using archaeological and faunal data collected from the site of Mezber dating from 1600 cal BCE to 400 cal CE, as well as prevsiously published data, this article provides zooarchaeological evidence for the earliest farming practices in the Horn of Africa. The research demonstrates a resilient highland agricultural strategy based on multispecies animal and plant resources, similar to most tropical agricultural systems today. A second important strategy of Pre-Aksumite farmers was the incorporation of both indigenous and exogenous plants and animals into their subsistance strategies. The Mezber site also offers one of the most thoroughly collected data to support multispecies farming practice in the north Ethiopian and Eritrean highlands.

Origin, Evolution, and Research Development of Donkeys

Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population.

The genomic history and global expansion of domestic donkeys

Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

A prevalence and molecular characterization of novel pathogenic strains of Macrococcus caseolyticus isolated from external wounds of donkeys in Khartoum State -Sudan

A pathogenic strain of Macrococcus caseolyticus (M. caseolyticus) was isolated from wounds infection during an investigation on donkeys in Khartoum State. (122) samples were collected from external wounds (head, abdomen, back and leg) during different seasons. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified 31 virulent genes of disease and defense, including methicillin-resistant genes, TatR family and ANT(4')-Ib. Plasmid rep22 was identified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel M. caseolyticus strain (DaniaSudan). The MLST-tree-V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain DaniaSudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. Mice modeling showed bacteremia and many clinical signs (swelling, allergy, wounds, and hair loss). Enlargement, hyperemia, adhesions and abscesses were observed in many organs.Constructive conclusionThe prevalence of the strain was 4.73%, with significant differences between collection seasons and locations of wounds. A highly significant association between doses (105 CFU/ml, 102 CFU/ml, Intra-peritoneum and sub-cutaneous) and swelling, developing of allergy and loss of hair (p = 0.001, p = 0.000 and p = 0.005) respectively were seen.This result represents the first report of pathogenic strains of M. caseolyticus worldwide.

Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids

The diversity of livestock coat color results from human positive selection and is an indispensable part of breed registration. As an important biodiversity resource, Asiatic wild ass has many special characteristics, including the most visualized feature, its yellowish-brown coat color, and excellent adaptation. To explore the genetic mechanisms of phenotypic characteristics in Asiatic wild ass and its hybrids, we resequenced the whole genome of one Mongolian Kulan (a subspecies of Asiatic wild ass) and 29 Kulan hybrids (Mongolian Kulan ♂×Xinjiang♀), and the ancestor composition indicated the true lineage of the hybrids. XP-EHH (Cross Population Extended Haplotype Homozygosity), θπ-ratio (Nucleotide Diversity Ratio), CLR (Composite Likelihood Ratio) and θπ (Nucleotide Diversity) methods were used to detect the candidate regions of positive selection in Asiatic wild ass and its hybrids. Several immune genes (DEFA1, DEFA5, DEFA7, GIMAP4, GIMAP1, IGLC1, IGLL5, GZMB and HLA) were observed by the CLR and θπ methods. XP-EHH and θπ-ratio revealed that these genes are potentially responsible for coat color (KITLG) and meat quality traits (PDE1B and MYLK2). Furthermore, the heatmap was able to show the clear difference in the haplotype of the KITLG gene between the Kulan hybrids and Asiatic wild ass group and the Guanzhong black donkey group, which is a powerful demonstration of the key role of KITLG in donkey color. Therefore, our study may provide new insights into the genetic basis of coat color, meat quality traits and immunity of Asiatic wild ass and its hybrids.

Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.

Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next-generation sequencing

Donkeys are widely distributed labour animals in the world. During the process of the domestication and artificial selection of domestic donkeys, body sizes show significant differences among different breeds of donkeys. Based on the genome resequencing data of 103 Chinese indigenous donkeys from 11 breeds (Biyang, Dezhou, Guangling, Hetian, Jiami, Kulun, Qingyang, Turfan, Tibetan, Xinjiang, and Yunnan), seven Spanish donkeys from two breeds (Zamorano~Leonés and Andalusian), and three wild donkeys, we investigated the population structures of Chinese domestic donkeys with different body sizes. We used F_ST and XP-EHH analyses to explore the selected regions related to body sizes. The results showed that Chinese indigenous donkeys have a closer relationship with African wild donkeys than with Asian wild donkeys. LCORL/NCAPG, FAM184B, TBX3, and IHH were identified as genes with strong signals in analysis of selection signature (F_ST and XP-EHH) in large and small donkeys. The seven identified variants can be served as candidate loci affecting the body size of Chinese donkeys. Five of seven loci were located in intron 9 of FAM184B and were in a haplotype block, and one of the identified variants (Chr03:112664848) located in the CDS region of the LCORL gene was found to cause stop-loss. These candidate genes and variants shed new light on the molecular basis of donkey body size and will facilitate the breeding activities of donkeys.

Comparing the Profiles of Raw and Cooked Donkey Meat by Metabonomics and Lipidomics Assessment

Heat cooking of meat gives it a specific taste and flavor which are favored by many consumers. While the characteristic taste components of chicken, duck, pig, and seafood have been studied, there is a lack of information about the molecular components that give donkey meat its unique taste. Here, the characterization profiles of raw donkey meat (RDM) and cooked donkey meat (CDM) meat by metabonomics and lipidomics. The results showed that a total of 186 metabolites belonging to 8 subclasses were identified in CDM and RDM, including carbohydrates (27.42%), amino acids (17.20%), lipids (13.44%), and nucleotides (9.14%). In total, 37 differential metabolites were identified between CDM and RDM. Among these, maltotriose, L-glutamate, and L-proline might predominantly contribute to the unique umami and sweet taste of donkey meat. Comprehensive biomarker screening detected 9 potential metabolite markers for the discrimination among RDM and CDM, including L-glutamate, gamma-aminobutyric acid, and butane-1, 2, 3, 4-tetrol. Moreover, a total of 992 and 1,022 lipids belonging to 12 subclasses were identified in RDM and CDM, respectively, mainly including triglycerides (TGs) and glycerophospholipids (GPs). Of these lipids, 116 were significantly different between CDM and RDM. The abundances of 61 TGs rich in saturated and monounsaturated fatty acids were retained in CDM, whereas the abundances of 37 GPs rich in polyunsaturated fatty acids were reduced, suggesting that TGs and GPs might be the predominant lipids for binding and generating aroma compounds, respectively. A total of 13 lipids were determined as potential markers for the discrimination among RDM and CDM, including PC(O-16:2/2:0), LPE(22:5/0:0), and PC(P-16:0/2:0). In conclusion, this study provided useful information about the metabolic and lipid profiles of donkey meat which may explain its unique taste and flavor, which could serve as a basis for the development and quality control of donkey meat and its products.

The pharmacokinetics and pharmacodynamics of midazolam after intravenous administration to donkeys (Equus africanus asinus)

The pharmacokinetics and pharmacodynamics of midazolam were studied in eight 1-to-3-year-old healthy gelded donkeys. Blood samples were obtained. Heart rate, respiratory rate, rectal temperature, sedation/excitement, ataxia, and response to tactile and auditory stimuli were recorded at baseline until 48 hours after intravenous (IV) midazolam (0.1 mg/kg) administration. Plasma midazolam and 1-hydroxymidazolam were measured using reversed-phase high-performance liquid chromatography. Pharmacokinetic variables were calculated using non-compartmental analysis. Physiologic data were analyzed using a mixed-effects model followed by Dunnett's test and behavioral data were analyzed using a Friedman test then a Dunn's test; P < 0.05 was considered significant. Midazolam was detectable for up to 60 minutes post-treatment in 7 donkeys. The median total body clearance, volume of distribution at steady state, elimination half-life, and area under concentration-time profile were 1210 mL/kg/h, 359 mL/kg, 0.27 hours, and 82.7 h × ng/mL, respectively. 1-hydroxymidazolam was detected (29 to 105 ng/mL) between 5 to 15 minutes post-treatment in 4 donkeys. Compared to baseline, rectal temperature and ataxia increased from 90 to 720 minutes (P ≤ 0.038) and 3 to 15 minutes (P ≤ 0.024) post-treatment, respectively. No other parameters showed statistically significant differences. Healthy donkeys cleared midazolam rapidly from plasma after IV administration. Transient ataxia and recumbency without sedation were observed.

Comparative Transcriptomics Uncover the Uniqueness of Oocyte Development in the Donkey

The donkey is an important domestic animal, however the number of donkeys world-wide is currently declining. It is therefore important to protect their genetic resources and to elaborate the regulatory mechanisms of donkey reproduction, particularly, oocyte development. Here, we adopted comparative transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) to uncover the uniqueness of donkey oocyte development compared to cattle, sheep, pigs, and mice, during the period from germinal vesicle (GV) to metaphase II (MII). Significantly, we selected 36 hub genes related to donkey oocyte development, including wee1-like protein kinase 2 (WEE2). Gene Ontology (GO) analysis suggested that these genes are involved in the negative regulation of cell development. Interestingly, we found that donkey specific differentially expressed genes (DEGs) were involved in RNA metabolism and apoptosis. Moreover, the results of WGCNA showed species-specific gene expression patterns. We conclude that, compared to other species, donkey oocytes express a large number of genes related to RNA metabolism to maintain normal oocyte development during the period from GV to MII.

The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia

Before the introduction of domestic horses in Mesopotamia in the late third millennium BCE, contemporary cuneiform tablets and seals document intentional breeding of highly valued equids called kungas for use in diplomacy, ceremony, and warfare. Their precise zoological classification, however, has never been conclusively determined. Morphometric analysis of equids uncovered in rich Early Bronze Age burials at Umm el-Marra, Syria, placed them beyond the ranges reported for other known equid species. We sequenced the genomes of one of these ~4500-year-old equids, together with an ~11,000-year-old Syrian wild ass (hemippe) from Göbekli Tepe and two of the last surviving hemippes. We conclude that kungas were F1 hybrids between female domestic donkeys and male hemippes, thus documenting the earliest evidence of hybrid animal breeding.

Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys

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.

Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study

BACKGROUND

It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field.

RESULTS

Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls.

CONCLUSIONS

The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

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.

Detection and Molecular Characterization of Two Gammaherpesviruses from Pantesco Breed Donkeys during an Outbreak of Mild Respiratory Disease

Equid and asinine gammaherpesviruses (GHVs; genus Percavirus) are members of the Herpesviridae family. Though GHVs have been reported in horse populations, less studies are available on gammaherpesviral infections in donkeys. This study reports the co-infection with two GHVs in Pantesco breed donkeys, an endangered Italian donkey breed. Samples (n = 124) were collected on a breeding farm in Southern Italy from 40 donkeys, some of which were healthy or presented erosive tongue lesions and/or mild respiratory signs. Samples were analysed by using a set of nested PCRs targeting the DNA polymerase, glycoprotein B, and DNA-packaging protein genes, and sequence and phylogenetic analyses were performed. Twenty-nine donkeys (72.5%) tested positive, and the presence of Equid gammaherpesvirus 7 and asinine herpesvirus 5 was evidenced. In 11 animals, we found evidence for co-infection with viruses from the two species. Virions with herpesvirus-like morphology were observed by electron microscopic examination, and viruses were successfully isolated in RK-13-KY cell monolayers. The histological evaluation of tongue lesions revealed moderate lympho-granulocytic infiltrates and rare eosinophilic inclusions. The detection of GHVs in this endangered asinine breed suggests the need long-life monitoring within conservation programs and reinforces the need for further investigations of GHV’s pathogenetic role in asinine species.

Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds

The mitochondrial DNA (mtDNA) D-loop of endangered and critically endangered breeds has been studied to identify maternal lineages, characterize genetic inheritance, reconstruct phylogenetic relations among breeds, and develop biodiversity conservation and breeding programs. The aim of the study was to determine the variability remaining and the phylogenetic relationship of Martina Franca (MF, with total population of 160 females and 36 males), Ragusano (RG, 344 females and 30 males), Pantesco (PT, 47 females and 15 males), and Catalonian (CT) donkeys by collecting genetic data from maternal lineages. Genetic material was collected from saliva, and a 350 bp fragment of D-loop mtDNA was amplified and sequenced. Sequences were aligned and evaluated using standard bioinformatics software. A total of 56 haplotypes including 33 polymorphic sites were found in 77 samples (27 MF, 22 RG, 8 PT, 19 CT, 1 crossbred). The breed nucleotide diversity value (π) for all the breeds was 0.128 (MF: 0.162, RG: 0.132, PT: 0.025, CT: 0.038). Principal components analysis grouped most of the haplogroups into two different clusters, I (including all haplotypes from PT and CT, together with haplotypes from MF and RG) and II (including haplotypes from MF and RG only). In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs.

From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management

Simple Summary

Horses were domesticated later than any other major livestock species. Their role in shaping ancient civilizations cannot be overestimated. As a primary means of transportation, an essential asset in warfare, and later one of the key elements of circus entertainment, horses quickly became luxurious goods. Vast amounts of money were invested in the horse industry resulted resulting in the rapid development of horse breeding and husbandry. This review examines paleogenetic, archeological, and classical studies on managing horses in antiquity. Many ancient approaches and practices in horse management are still relevant today and some of them, now abandoned, are worth re-examination.

Abstract

The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.

Donkey Industry in China: Current Aspects, Suggestions and Future Challenges

Donkey domestication has been essential to human culture and development and has played an important role in economic and social life in human history. China is one of the largest donkey breeders worldwide; donkey farming for meat, milk and hide production is becoming an important industry in rural China as it provides income to the rural livelihoods of many people. Currently, the donkey industry in China is small and relatively young, but it is growing fast. The industry is not adequately exploited economically, which means that it requires the diminution of its role in the traditional activities of rural households and a reorientation towards a more profitable industry. Given the growing importance of the donkey industry in rural China, this paper aims to outline the current situations of the donkey industry in China in terms of animal stock, breeds and distribution, donkey products, suggestions and future challenges to the development of the donkey industry.

Assessment of genetic diversity using microsatellite markers to compare donkeys (Equus asinus) with horses (Equus caballus)

Objective

The study aimed to evaluate the diversity of donkey populations by comparing with the diversity of Thoroughbred and Jeju Halla horses; identified breeding backgrounds can contribute to management and conservation of donkeys in South Korea.

Methods

A total of 100 horse (50 Thoroughbreds and 50 Jeju Halla horses) and 79 donkeys samples were genotyped with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20), to identify genetic diversity and relationships among horses and donkeys.

Results

The observed number of alleles per locus ranged from 1 (ASB17, HMS1) to 14 (AHT5), with a mean value of 4.87, 8.00, and 5.87 in Thoroughbreds, Jeju Halla horses, and donkeys, respectively. Of the 15 markers, AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, and LEX3 loci had relatively high polymorphism information content (PIC) values (PIC>0.5) in these three populations. Mean levels of genetic variation were H_E = 0.6721 and H_O = 0.6600 in Thoroughbreds, H_E = 0.7898 and H_O = 0.7100 in Jeju Halla horses, and H_E = 0.5635 and H_O = 0.4861 in donkeys. Of the 15 loci in donkeys, three loci had negative inbreeding coefficients (FIS), with a moderate mean FIS (0.138). The FIS estimate for the HTG4 marker was highest (0.531) and HMS6 marker was lowest (−0.001). The total probability of exclusion value of 15 microsatellite loci was 0.9996 in donkeys.

Conclusion

Genetic cluster analysis showed that the genetic relationship among 79 donkeys was generally consistent with pedigree records. Among the three breeds, donkeys and Thoroughbred horses formed clearly different groups, but the group of Jeju Halla horses overlapped with that of Thoroughbred horses, suggesting that the loci would be suitable for donkey parentage testing. Therefore, the results of this study are a valid tool for genetic study and conservation of donkeys.

Rethinking the evidence for early horse domestication at Botai

Despite its transformative impact on human history, the early domestication of the horse (Equus caballus) remains exceedingly difficult to trace in the archaeological record. In recent years, a scientific consensus emerged linking the Botai culture of northern Kazakhstan with the first domestication of horses, based on compelling but largely indirect archaeological evidence. A cornerstone of the archaeological case for domestication at Botai is damage to the dentition commonly linked with the use of bridle mouthpieces, or "bit wear." Recent archaeogenetic analyses reveal, however, that horse remains from Botai are not modern domesticates but instead the Przewalski's horse, E. przewalskii-warranting reevaluation of evidence for domestication. Here, we compare osteological traits hypothesized to have been caused by horse transport at Botai with wild Pleistocene equids in North America. Our results suggest that damage observed in Botai horse teeth is likely generated by natural disturbances in dental development and wear, rather than through contact with bridle equipment. In light of a careful reconsideration of the mid-Holocene archaeological record of northern Eurasia, we suggest that archaeological materials from Botai are most effectively explained through the regularized mass harvesting of wild Przewalski's' horses-meaning that the origins of horse domestication may lie elsewhere.

A hepatitis B virus causes chronic infections in equids worldwide

Preclinical testing of novel therapeutics for chronic hepatitis B (CHB) requires suitable animal models. Equids host homologs of hepatitis C virus (HCV). Because coinfections of hepatitis B virus (HBV) and HCV occur in humans, we screened 2,917 specimens from equids from five continents for HBV. We discovered a distinct HBV species (Equid HBV, EqHBV) in 3.2% of donkeys and zebras by PCR and antibodies against EqHBV in 5.4% of donkeys and zebras. Molecular, histopathological, and biochemical analyses revealed that infection patterns of EqHBV resembled those of HBV in humans, including hepatotropism, moderate liver damage, evolutionary stasis, and potential horizontal virus transmission. Naturally infected donkeys showed chronic infections resembling CHB with high viral loads of up to 2.6 × 10⁹ mean copies per milliliter serum for >6 mo and weak antibody responses. Antibodies against Equid HCV were codetected in 26.5% of donkeys seropositive for EqHBV, corroborating susceptibility to both hepatitis viruses. Deltavirus pseudotypes carrying EqHBV surface proteins were unable to infect human cells via the HBV receptor NTCP (Na⁺/taurocholate cotransporting polypeptide), suggesting alternative viral entry mechanisms. Both HBV and EqHBV deltavirus pseudotypes infected primary horse hepatocytes in vitro, supporting a broad host range for EqHBV among equids and suggesting that horses might be suitable for EqHBV and HBV infections in vivo. Evolutionary analyses suggested that EqHBV originated in Africa several thousand years ago, commensurate with the domestication of donkeys. In sum, EqHBV naturally infects diverse equids and mimics HBV infection patterns. Equids provide a unique opportunity for preclinical testing of novel therapeutics for CHB and to investigate HBV/HCV interplay upon coinfection.

Donkey genomes provide new insights into domestication and selection for coat color

Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.

A new donkey reference genome and comparisons with wild asses yields insights into the evolutionary history of donkey domestication and identifies a genetic variant that results in the non-Dun coat colours of domestic donkeys.

Donkey Fascioliasis Within a One Health Control Action: Transmission Capacity, Field Epidemiology, and Reservoir Role in a Human Hyperendemic Area

A One Health initiative has been implemented for fascioliasis control in a human hyperendemic area for the first time. The area selected for this multidisciplinary approach is the Northern Bolivian Altiplano, where the highest prevalences and intensities in humans have been reported. Within the strategic intervention axis of control activities concerning animal reservoirs, complete experimental studies, and field surveys have been performed to assess the fascioliasis transmission capacity and epidemiological role of the donkey for the first time. Laboratory studies with altiplanic donkey-infecting Fasciola hepatica and altiplanic Galba truncatula snail vector isolates demonstrate that the donkey assures the viability of the whole fasciolid life cycle. Several aspects indicate, however, that F. hepatica does not reach, in the donkey, the level of adaptation it shows in sheep and cattle in this high altitude hyperendemic area. This is illustrated by a few-day delay in egg embryonation, longer prepatent period despite similar miracidial infectivity and shorter patent period in the intramolluscan development, lower cercarial production per snail, different cercarial chronobiology, shorter snail survival after shedding end, shorter longevity of shedding snails, and lower metacercarial infectivity in Wistar rats. Thus, the role of the donkey in the disease transmission should be considered secondary. Field survey results proved that liver fluke prevalence and intensity in donkeys are similar to those of the main reservoirs sheep and cattle in this area. Fasciolid egg shedding by a donkey individual contributes to the environment contamination at a rate similar to sheep and cattle. In this endemic area, the pronounced lower number of donkeys when compared to sheep and cattle indicates that the epidemiological reservoir role of the donkey is also secondary. However, the donkey plays an important epidemiological role in the disease spread because of its use by Aymara inhabitants for good transport, movements, and travel from one locality/zone to another, a repercussion to be considered in the present geographical spread of fascioliasis in the Altiplano due to climate change. Donkey transport of parasite and vector, including movements inside the zone under control and potential introduction from outside that zone, poses a problem for the One Health initiative.

Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

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 (H_D) and nucleotide diversity (π_D), 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.

Welfare Assessment and Identification of the Associated Risk Factors Compromising the Welfare of Working Donkeys (Equus asinus) in Egyptian Brick Kilns

Simple Summary

Working donkeys suffer from many welfare challenges associated with, for example, physical health, poor living conditions, and unfair treatment. The aim of this study is to assess the welfare of working donkeys in the El-Saf brick kilns, identifying the health risk factors, establishing welfare regulations, enacting legislation, and implementing welfare strategies aimed at improving the quality of life of donkeys and owners within communities. The study found that working donkeys in Egypt suffer from many types of wounds associated with parts of the harness, such as the saddle, breeching, and neck collar, and with excessive force/beating, the shaft of the cart, and improper tethering. They often live in unhealthy housing situations, and a high percentage suffer from aggressive behavior. The study found an association between these health risks, behavioral parameters, and body condition in Egyptian working donkeys. Body condition was affected by multiple factors, including the number of hours worked/day, the number of donkeys/kilns, the distance from loading to unloading bricks in an oven, and the amount of concentrated food/donkey.

Abstract

Donkeys are a cornerstone in human existence, having played an important role throughout history in different economic activities, such as working in brick kilns in Egypt. This study was conducted from January 2017 to the end of April 2017 in the El-Saf brick kilns, which are located to the south of the Giza Governorate and 57 Km away from Cairo. Physical clinical health and behavior data were collected from 179 donkeys spanning over a random sample of 20 brick kilns selected from the El-Saf brick kilns. Behavioral, physical health, harness, and environmental parameters were assessed and recorded. The study found that 80 ± 3% (n = 179) of kiln donkeys have some type of wound, and the most serious wound is a beating wound (49 ± 3.7%), which is caused by drivers hitting the donkeys. The drivers are mostly children, who have insufficient knowledge, skills, and attitudes to effectively communicate with their donkeys and no motivation to enhance the welfare of these equids. Other wounds are related to the harness, such as the breeching (10 ± 2.2%), saddle (43 ± 3.7%), neck collar (40 ± 3.6%), and shaft of the cart (12 ± 2.4%). A poor body condition was seen in 56 ± 3.7% of kiln donkeys. A correlation in terms of the prevalence of wounds was found between the body condition (p-value < 0.01) and/or cleanliness of the harness. There was a negative association between the body condition and wound prevalence in brick kilns (Pearson coefficient of correlation −0.71). The physical enviromental factors that affect the body condition of working donkeys are the working hours of donkeys/day, the number of donkeys in a kiln, the distance from loading to the oven, and the concentrated food/donkey (p-value < 0.01). These three variables can explain 78.85% of the variability in body conditions based on a 1–5 scale. In addition to health parameters, behavior parameters, such as the donkeys’ general attitude, reaction to observers, and chin contact are associated with the body condition (p-value < 0.01). As a consequence, it is important for the owners of working donkeys to pay attention to their body condition in order to avoid compromising their body condition and welfare.

Morphometric measurements of the feet of working donkeys Equus asinus in Egypt

Working equids rely on sound, balanced hooves, but data describing the typical morphology of the legs and feet of working donkeys are currently lacking. To address this gap in knowledge, the front and hind feet of twenty healthy working donkeys were measured and compared. Hoof width, weight-bearing lengths, heel width, dorsal hoof wall length and lateral and medial heel length of the hoof wall were determined, as well as toe angle, heel angle, hoof pastern axis, coronary band angle and a measure of ‘ground surface size’. Viewed from the ground surface of the foot, front feet were more rounded and significantly larger than hind feet. Measures of medial-lateral balance and toe-heel angle ratio were within the recommended healthy guidelines for horses. Hoof pastern axis was broken forward for the studied animals, which supports previous research suggesting that a broken forward hoof pastern axis is normal for donkeys, although further study would be required to confirm whether this conformation is natural. Significant correlations were found between estimated body mass and hoof width in both the front and hind feet. These measurements provide valuable insight into the relationship between hoof and body characteristics, which may aid the development of guidelines for the trimming and management of working donkey hooves. Further study is, however, advised to confirm natural hoof conformation.

Cross-anatomical, radiographic and computed tomographic study of the stifle joint of donkeys (Equus africanus asinus)

The present investigation was conducted to provide a full anatomical description of the stifle joint of donkeys using 3D computed tomography imaging technique, in addition to the classic anatomical methods, such as radiography and cross-anatomical sectioning. The radiography and CT imaging of stifle joint were interpreted in comparison with cross-sectional anatomical sections. Volume-rendering reconstruction techniques (3D-CT) were used to describe the anatomical structure of stifle joint. The used twelve adult healthy donkeys were free from any musculoskeletal disorders. Four donkeys were used for the gross anatomical observations, four for CT and radiography and two live animals for determination the site of injections. The results of this study revealed that the complex stifle joint was formed from three joints: femorotibial, femoropatellar and proximal tibiofibular. The articular surfaces were described for each joint, and the synovial layer of the articular capsule formed three main joint sacs: femoropatellar, medial femorotibial and lateral femorotibial sacs. The ligaments of stifle joint were recorded, and meniscal ligaments included cranial and caudal ligaments of medial and lateral menisci and meniscofemoral ligament of lateral meniscus. The cruciate ligaments were also described and they included the cranial and caudal cruciate ligaments, while the patellar ligament included the medial, middle and lateral patellar ligaments. The arterial supply and the site of injection of the stifle joint were described. In conclusion, the 3D reconstruction CT provided well-defined baseline reference image for the stifle joint of donkeys for anatomist, radiologist, surgeons and researchers.

Banat donkey, a neglected donkey breed from the central Balkans (Serbia)

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.

Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

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.

Donkey Nutrition and Malnutrition

The domestic donkey is a unique equid species with specific nutritional requirements. This article examines the importance of feeding strategies that mimic the donkey's natural environment using poor nutritional quality fibers and access to browsing materials. The relationship between nutrition and health is examined and practical approaches to the healthy and sick donkey are discussed.

Genetic diversity and maternal origin of Northeast African and South American donkey populations

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 F_ST values showed a high genetic differentiation between Peruvian and Brazilian donkey populations (F_ST  = 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).

Simple sequence repeat (SSR) genotypic data reveal high genetic diversity in Rajasthan donkey of India

Spiti is the only breed of donkey in the list of 160 breeds registered so far for the indigenous germplasm. It points towards the fact that Indian donkey diversity is largely unexplored, in spite of its role in support system of poorest of the poor countrymen. Rajasthan state harbours more than eighty thousand donkey. Genetic diversity underpins population resilience and persistence so a need was felt for the systematic and scientific evaluation of existing diversity in this population. The diversity status of Rajasthan donkey population was investigated by using 20 microsatellite markers. Two of the loci, HMS5 and ASB17, depicted less than 4 alleles and were thus excluded from further analyses. Rajasthan donkey was found to host considerable diversity. This conclusion is evidenced by the number of alleles observed across loci (average 8.16±0.89), and by mean observed heterozygosity (0.688±0.06). Signatures of inbreeding could not be detected by the FIS indices in the Rajasthan donkey population. The population did not suffer any bottleneck in the recent past. The study provides the first scientific assessment of the genetic diversity status of Rajasthan donkey population. This information on the genetic analysis can be used in conjunction with the information on physical and phenotypic characteristics and management practices for registration of this population as a breed.

Earliest evidence for equid bit wear in the ancient Near East: The "ass" from Early Bronze Age Tell eṣ-Ṣâfi/Gath, Israel

Analysis of a sacrificed and interred domestic donkey from an Early Bronze Age (EB) IIIB (c. 2800-2600 BCE) domestic residential neighborhood at Tell eṣ-Ṣâfi/Gath, Israel, indicate the presence of bit wear on the Lower Premolar 2 (LPM2). This is the earliest evidence for the use of a bit among early domestic equids, and in particular donkeys, in the Near East. The mesial enamel surfaces on both the right and left LPM2 of the particular donkey in question are slightly worn in a fashion that suggests that a dental bit (metal, bone, wood, etc.) was used to control the animal. Given the secure chronological context of the burial (beneath the floor of an EB IIIB house), it is suggested that this animal provides the earliest evidence for the use of a bit on an early domestic equid from the Near East.

Improved de novo genomic assembly for the domestic donkey

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

New insights into the origin and the genetic status of the Balkan donkey from Serbia

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.