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 lipid molecules and volatile organic compounds (VOCs) in milk are heavily influenced by diet. However, little is known about how roughage affects the lipid and VOC contents of donkey milk. Accordingly, in the present study, donkeys were fed corn straw (G1 group), wheat hulls (G2 group), or wheat straw (G3 group), and the lipid and VOC profiles of their milk were determined using LC–MS and GC–MS. Of the 1842 lipids identified in donkey milk, 153 were found to be differential, including glycerolipids, glycerophospholipids, and sphingolipids. The G1 group showed a greater variety and content of triacyclglycerol species than the G2 and G3 groups. Of 45 VOCs, 31 were identified as differential, including nitrogen compounds, esters, and alcohols. These VOCs were significantly increased in the G2 and G3 groups, with the greatest difference being between the G1 and G2 groups. Thus, our study demonstrates that dietary roughage changes the lipid and VOC profiles of donkey milk.

Lipids play important biological roles, such as providing essential fatty acids and signaling. The wide variety and structural diversity of lipids, and the limited technical means to study them, have seriously hampered the resolution of the mechanisms of action of lipids. With advances in mass spectrometry (MS) and bioinformatic technologies, large amounts of lipids have been detected and analyzed quickly using MS-based lipidomic techniques. Milk lipids, as complex structural metabolites, play a crucial role in human health. In this review, the lipidomic techniques and their applications to dairy products, including compositional analysis, quality identification, authenticity identification, and origin identification, are discussed, with the aim of providing technical support for the development of dairy products.

An increase in the number of vertebrae can significantly affect the meat production performance of livestock, thus increasing carcass weight, which is of great importance for livestock production. The homeobox gene C8 (HOXC8) has been identified as an essential candidate gene for regulating vertebral development. However, it has not been researched on the Dezhou donkey. This study aimed to verify the Dezhou donkey HOXC8 gene’s polymorphisms and assess their effects on multiple vertebral numbers and carcass weight. In this study, the entire HOXC8 gene of the Dezhou donkey was sequenced, SNPs at the whole gene level were identified, and typing was accomplished utilizing a targeted sequencing genotype detection technique (GBTS). Then, a general linear model was used to perform an association study of HOXC8 gene polymorphism loci, multiple vertebral numbers, and carcass weight for screening candidate markers that can be used for molecular breeding of Dezhou donkeys. These findings revealed that HOXC8 included 12 SNPs, all unique mutant loci. The HOXC8 g.15179224C>T was significantly negatively associated with carcass weight (CW) and lumbar vertebrae length (LL) (p < 0.05). The g.15179674G>A locus was shown to be significantly positively associated with the number of lumbar vertebrae (LN) (p < 0.05). The phylogenetic tree constructed for the Dezhou donkey HOXC8 gene and seven other species revealed that the HOXC8 gene was highly conserved during animal evolution but differed markedly among distantly related animals. The results suggest that HOXC8 is a vital gene affecting multiple vertebral numbers and carcass weight in Dezhou donkeys, and the two loci g.15179224C>T and g.15179674G>A may be potential genetic markers for screening and breeding of new strains of high-quality and high-yielding Dezhou donkeys.

Circular RNAs (circRNAs) are a class of noncoding RNAs with a covalently closed loop. Studies have demonstrated that circRNA can function as microRNA (miRNA) sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in donkeys remain unknown. We performed RNA-seq to detect circRNA expression profiles of adult donkey testes. Length distribution and other characteristics were shown a total of 1971 circRNAs were differentially expressed and 12,648 and 6261 circRNAs were detected from the testis and caput epididymis, respectively. Among these circRNAs, 1472 circRNAs were downregulated and 499 circRNAs were upregulated in the testis. Moreover, KEGG pathway analyses and Gene Ontology were performed for host genes of circRNAs. A total of 39 upregulated circRNA host genes were annotated in spermatogenesis terms, including PIWIL2, CATSPERD, CATSPERB, SPATA6, and SYCP1. Other host genes were annotated in the focal adhesion, Rap1 signaling pathway. Downregulated expressed circRNA host genes participated in the TGF-β signaling pathway, GnRH signaling pathway, estrogen signaling pathway, and calcium signaling pathway. Our discoveries provide a solid foundation for identifying and characterizing critical circRNAs involved in testis development or spermatogenesis.

As the initiation point of digestion, the oral microbiome is important in maintaining oral and systemic health. However, the composition of oral microbial communities and the influence of weaning on the oral microbiota of donkey foals remains poorly characterized. The present study used buccal swab samples to determine the changes in oral microbial communities occurring at the time of weaning. A total of 20 oral swab samples were collected from two groups: preweaning donkey foals (PreW group, n = 10) and postweaning donkey foals (PostW group, n = 10). The donkey oral microbiome was analyzed by 16S rRNA gene sequencing using Illumina MiSeq. This study is the first report of the donkey oral microbiome in association with weaning. Compared to the preweaning donkeys, the oral bacteria diversity in the postweaning donkeys was increased, with a higher Simpson index. Changes in the composition of the oral microbiota between the PreW and PostW groups were observed in the present study. At the phylum level, the relative abundance of Firmicutes and Myxococcota was significantly greater in the PostW than in the PreW group. At the genus level, the Gemella, unclassified_o__Lactobacillales, and Lactobacillus were increased in the postweaning donkeys. The donkeys’ oral microbial functions were predicted using PICRUSt, and the functions related to carbohydrate metabolic pathways were significantly enriched in the oral microbiome in the PostW donkeys. In summary, the current study provides a deeper insight into the oral microbiota changes during the weaning period, and the influence of weaning together with the documented changes in diversity and composition will help us to obtain a better understanding of their long-term health impact within the oral cavities of donkey foals. However, a major limitation of the present study was that the samples were obtained from different animals in the PreW and PostW groups, which may have resulted in variability among the different individuals. Further investigation is needed to monitor the shift in oral microbes in the same individuals during the weaning period.