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To date, the origins, domestication, and genetic structure of Chinese Mongolian horses (CMH) are poorly understood. Furthermore, there have been sparse reports on the genetic differences between CMH and Thoroughbred. In order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed an extensive survey of creatine kinase (muscle isoenzyme; CKM) variations among six populations of indigenous CMH, cultivated Sanhe horses, and imported Thoroughbred. Twenty-three single-nucleotide polymorphisms were found among the 343 horse sequences. From these, 40 haplotypes were inferred. Haplotype diversity ( H ) values differed from 0.6424 to 0.7881 and nucleotide diversity ( π ) values ranged from 0.00150 to 0.00211. The differences between Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations with respect to CKM intron sequences suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and CMH are very closely related and the introgression (interbreeding) between them is serious. Our results suggest that Sanhe and Wushen require prompt and powerful protection. Overall, CKM intron was an appropriate marker for the determination of genetic relationships among horse populations and breeds.

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity., (© 2023. The Author(s).)

Background: Horse testis development and spermatogenesis are complex physiological processes., Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis., Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to "spermatogenesis," male gamete generation," "spermatid development" and "oocyte meiosis" were significantly involved in different stages of testis development and spermatogenesis., Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

Numerous studies have shown that microRNAs (miRNAs) are essential for testicular development and spermatogenesis. In order to further characterise these physiological processes, three immature and three mature testes of the Mongolian horse were collected and six libraries were established. Using small RNA sequencing technology, 531 mature miRNAs were identified, including 46 novel miRNAs without previously ascribed functions. Among the 531 miRNAs, 421 were expressed in both immature and mature libraries, 65 miRNAs were found solely in immature testis libraries and 45 miRNAs were found solely in mature testis libraries. Furthermore, among the miRNAs that were identified in both immature and mature libraries, 107 were significantly differentially expressed (corrected P value (padj)<0.05). Among the miRNAs that were only expressed in immature testes, two miRNAs were differentially expressed, whereas among the miRNAs that were only expressed in mature testes, nine miRNAs were differentially expressed. Comprehensive analysis of miRNA and mRNA expression profiles predicted 107 miRNA-mRNA interaction sites. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the predicted target genes suggested roles of the differentially expressed miRNAs in testicular development and spermatogenesis. These findings identify miRNAs as key factors in the development of the testes and spermatogenesis in the Mongolian horse, which may also help us to understand the mechanisms of fertility in related mammalian species.

Eight horse breeds-Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako and Yonaguni-are native to Japan. Although Japanese native breeds are believed to have originated from ancient Mongolian horses imported from the Korean Peninsula, the phylogenetic relationships among these breeds are not well elucidated. In the present study, we compared genetic diversity among 32 international horse breeds previously evaluated by the Equine Genetic Diversity Consortium, the eight Japanese native breeds and Japanese Thoroughbreds using genome-wide SNP genotype data. The proportion of polymorphic loci and expected heterozygosity showed that the native Japanese breeds, with the exception of the Hokkaido, have relatively low diversity compared to the other breeds sampled. Phylogenetic and cluster analyses demonstrated relationships among the breeds that largely reflect their geographic distribution in Japan. Based on these data, we suggest that Japanese horses originated from Mongolian horses migrating through the Korean Peninsula. The Japanese Thoroughbreds were distinct from the native breeds, and although they maintain similar overall diversity as Thoroughbreds from outside Japan, they also show evidence of uniqueness relative to the other Thoroughbred samples. This is the first study to place the eight native Japanese breeds and Japanese Thoroughbred in context with an international sample of diverse breeds., (© 2019 Stichting International Foundation for Animal Genetics.)

P-element induced wimpy testis-interacting RNAs (piRNAs) are essential for testicular development and spermatogenesis in mammals. Comparative analyses of the molecular mechanisms of spermatogenesis among different organisms are therefore dependent on accurate characterizations of piRNAs. At present, little is known of piRNAs in non-model organisms. Here, we characterize piRNAs in the Mongolian horse, a hardy breed that reproduces under extreme circumstances. A thorough understanding of spermatogenesis and reproduction in this breed may provide insights for the improvement of fecundity and reproductive success in other breeds. We identified 4,936,717 piRNAs and 7,890 piRNA clusters across both testicular developmental stages. Of these, 2,236,377 putative piRNAs were expressed in the mature samples only, and 2,391,271 putative piRNAs were expressed in the immature samples only. Approximately 3,016 piRNA clusters were upregulated in the mature testes as compared to the immature testes, and 4,874 piRNA clusters were downregulated. Functional and pathway analyses indicated that the candidate generating genes of the predicted piRNAs were likely involved in testicular development and spermatogenesis. Our results thus provide information about differential expression patterns in genes associated with testicular development and spermatogenesis in a non-model animal.

Background: Studies on the molecular genetics of horse skin pigmentation have typically focused on very few genes and proteins. In this study, we used Illumina sequencing to determine the global gene expression profiles in horses with white-colored coats and those with black-colored coats, with the goal of identifying novel genes that could regulate horse coat color., Results: Genes encoding ribosomal-associated proteins were highly expressed in horse skin. We found a total of 231 unigenes that were differentially expressed between horses with white coats and horses with black coats; 119 were down-regulated, and 112 were up-regulated. Many of the up-regulated genes in black horses, such as genes related to tyrosine metabolism, may directly regulate dark coat color. Keratin genes, MIA family genes, fatty acid-related genes, and melanoma-associated genes were also differentially regulated, which suggests that they may play important roles in coat color formation., Conclusions: These findings show that the transcription profiles from white and black horse skin provide useful information to understand the genetics underlying the control of skin melanin synthesis in horses, which may enhance our knowledge of human skin diseases, such as melanoma and albinism.

Rabbit hepatitis E virus (HEV) strains have recently been isolated in several areas of China and in the US and France. However, the host range, distribution and zoonotic potential of these HEV strains remain unknown and their propagation in cultured cells has not yet been reported. A total of 211 4-month-old rabbits raised on a farm in Inner Mongolia were tested for the presence of anti-HEV antibodies and HEV RNA. Overall, 121 rabbits (57.3%) tested positive for anti-HEV antibodies, and 151 (71.6%) had detectable HEV RNA. The 174 HEV strains recovered from these viremic rabbits, including two distinct strains each from 23 rabbits, differed from each other by up to 13.6% in a 412-nucleotide (nt) sequence within ORF2, and were 89.3-95.9% identical to the reported rabbit HEV strains in other provinces of China. Three representative Inner Mongolian strains, one each from three phylogenetic clusters, whose entire genomic sequences were determined, shared 79.6-96.7% identities with reported rabbit HEV strains within the entire or 242- to 1349-nt partial genomic sequence. Rabbit HEV strains recovered from liver tissues of rabbits with a high HEV load propagated efficiently in human cell lines (A549 and PLC/PRF/5 cells), suggesting the potential zoonotic risk of rabbit HEV., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Coat color can be used not only in identifying individuals and species, but also in diagnosing certain diseases. The coat color of horse mainly depends on the distribution and proportion of eumelanin and phaeomelanin, generated by melanocytes, which are regulated by the genes such as MC1R, ASIP, KIT, TYRP, and EDNRB. In addition, STX17, MATP, and PMEL17 also play a role in the formation of coat color of horse. In this review, the action mechanism of candidate genes for coat color and association of DNA sequence polymorphism of these candidate genes with color pattern phenotypes and melanoma were summarized in details, which provides efficient theoretical support for horse breeding and control of the horse diseases.

To evaluate the prevalence and characteristics of swine hepatitis E virus (HEV) infection in Inner Mongolia, China, serum samples obtained from 356 2- to 4-month-old pigs on 14 farms in Inner Mongolia were tested for the presence of anti-HEV antibodies and HEV RNA. Overall, 186 pigs (52%) tested positive for anti-HEV antibodies, while 30 pigs (8%) had detectable HEV RNA levels. The 30 HEV isolates recovered from the viremic pigs were phylogenetically classified into genotype 4 and differed from each other by up to 15.3% in a 412 nt sequence within ORF2. The Inner Mongolian swine HEV strains were most similar to human or swine HEV strains isolated in the other provinces of China but differed by 15.9-18.9% from those in Mongolia (formerly known as Outer Mongolia). These results indicate that farm pigs in Inner Mongolia are frequently infected with markedly divergent genotype 4 HEV strains that may be indigenous to China.

To clarify the functions of the equine guttural pouch, the distribution of various immunoglobulin isotypes and subisotypes in the guttural pouch mucosa were examined in healthy horses. IgGa was present in the mucosa of guttural pouch, mucosal lymph nodules and submucosal lymph nodules. IgM was scattered in the mucosal lymph nodules and in the germinal centers of the submucosal lymph nodules. IgGc was recognized only in the submucosal lymph nodules. These immunoglobulin isotypes and subisotypes were found in lymphocytes and plasma cells. On the other hand, IgA was detected in glandular epithelial cells and the surface layer of the mucosal epithelium, as well as in free cells. This finding suggests that IgA is secreted through the glandular epithelium. Based on the above findings, we conclude that the guttural pouch has phylactic ability.

The present study attempted to clarify the characteristics of the guttural pouch mucosa in equines and to evaluate its foreign substance clearance ability. The specimens were collected from nine regions (eight in the guttural pouch mucosa, and one in the nasopharynx mucosa). We first examined the pouch mucosa by light and electron microscopy. We then measured the frequency of goblet cells per 200 epithelial cells, the length of the cilia, the thickness of the epithelial cell layer and lamina propria and statistically analyzed the data. The guttural pouch mucosa consisted of stratified columnar epithelia with brush-like cilia, and there were almost no histological differences between adults and foals. The morphometrical study revealed significant differences in goblet cell frequency (p < 0.001) and the thickness of lamina propria (p < 0.05). By contrast, no statistically significant difference was detected in the length of the cilia or the thickness of the epithelial cell layer. These findings suggest that the guttural pouch mucosa provides foreign substance clearance ability, but that its ability varies among different regions of the epithelium.

The characteristics of the equine auditory tube diverticulum (guttural pouches) were studied in detail by the naked eye and silicon mold method. First, we examined the anatomical relationship between the guttural pouches and their associated bones and muscles. Secondly, a silicon mold was fabricated to clarify the three-dimensional aspect of the guttural pouches, paying a special attention to the distribution of major arteries and nerves surrounding it. Thirdly, the volume of the silicon mold was measured by immersing it in water. The guttural pouches are a pair of pouches located dorso-posteriorly to the posterior pharynx. The pouches had a close contact rostrally with the Os sphenoidale, ventrally with the pharynx and the esophagus, and caudally with the Articulatio atlantoaxialis. The left and right guttural pouches had almost the same capacity in each horse. The A. carotis interna, cranial ganglia of cervical nerves and cervical Truncus sympathicus, as well as the N. vagus, N. glossopharyngeus, N. hypoglossus, and Radices spinales of the N. accessorius, were present in the mucosal crease extending from the roof of the guttural pouches towards the middle of the caudal wall. The N. facialis appeared from the Foramen stylomastoideum ran dorsocaudally along the lateral recess. The N. mandibularis appeared from the Foramen lacerum went over the muscular process of an ear bone, ran along the roof of the lateral recess and finally continued with the rostral side of the guttural pouches. Lymph nodes, scattered on the mucosal surface, appeared as tiny indentations with approximately millet seed size on the silicon surface. The capacity of guttural pouches in adult horses (472 +/- 12.4 cm3) was three-fold larger than that in foals (145 +/- 9.4 cm3).

The domestic horse (Equus caballus) have the large symmetrical guttural pouches (the auditory tube diverticulum) formed by saccate bulge of the auditory tube. In this study, CT examination was carried out in the head of Przewalski's horse (Equus przewalskii), the only true wild horse living at present. As results of the examination, Przewalski's horse possessed the large symmetrical guttural pouches divided into medial and lateral compartments by the stylohyoid bone. Moreover, the right and left guttural pouches meet each other at the median part to form a thin septum. As CT sections get close to the part of the occipital condyle, the lateral compartment disappeared, and the medial compartment gradually became small toward the base of the skull. These results indicate that the nuchal-basal part of the medial compartment is not well-developed as compared with the domestic horse.