Integrated analysis of mRNA and miRNA in testis and cauda epididymidis reveals candidate molecular markers associated with reproduction in Dezhou donkey

Elucidating the Role of Transcriptomic Networks and DNA Methylation in Collagen Deposition of Dezhou Donkey Skin

DNA methylation represents a predominant epigenetic modification with broad implications in various biological functions. Its role is particularly significant in the process of collagen deposition, a fundamental aspect of dermal development in donkeys. Despite its critical involvement, the mechanistic insights into how DNA methylation influences collagen deposition in donkey skin remain limited. In this study, we employed whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to investigate the epigenetic landscape and gene expression profiles in the dorsal skin tissues of Dezhou donkeys across three developmental stages: embryonic (YD), juvenile (2-year-old, MD), and mature (8-year-old, OD). Our analysis identified numerous differentially methylated genes that play pivotal roles in skin collagen deposition and overall skin maturation, including but not limited to COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, GLUL, SFRP2, FOSL1, SERPINE1, MMP1, MMP2, MMP9, and MMP13. Notably, we observed an inverse relationship between gene expression and DNA methylation proximal to transcription start sites (TSSs), whereas a direct correlation was detected in regions close to transcription termination sites (TTSs). Detailed bisulfite sequencing analyses of the COL1A1 promoter region revealed a low methylation status during the embryonic stage, correlating with elevated transcriptional activity and gene expression levels. Collectively, our findings elucidate key genetic markers associated with collagen deposition in the skin of Dezhou donkeys, underscoring the significant regulatory role of DNA methylation. This research work contributes to the foundational knowledge necessary for the genetic improvement and selective breeding of Dezhou donkeys, aiming to enhance skin quality attributes.

ProAKAP4 as a motility long-lasting marker in Catalan donkey spermatozoa

ProAKAP4 is identified within the flagellum of spermatozoa in various mammalian species, serving as a structural protein associated with motility parameters. This investigation focuses on the presence of proAKAP4 in donkey sperm, elucidating its localization, molecular characteristics, and its correlation with motility descriptors and mitochondrial membrane potential. Twelve ejaculates from Catalan donkeys were analyzed in this study. The initial steps involved proAKAP4 sequencing and detection through Western blotting and immunofluorescence. Post-thaw assessments were conducted at 0, 1, and 3 h, encompassing proAKAP4 levels, sperm motility analyzed via Computer-Assisted Sperm Analysis (CASA), and mitochondrial membrane potential determined by flow cytometry using the JC-1 stain. The findings reveal that proAKAP4 in donkeys exhibits a characteristic localization at the principal piece of the flagellum, consistent with observations in other mammals. The molecular weight of proAKAP4 is determined to be 100 kDa. Significantly, a positive correlation (p ≤ 0.05) is established between proAKAP4 concentration and both total and progressive motility. The presence of cryoprotectant is associated with a lower proAKAP4 concentration. Notably, proAKAP4 experiences a substantial decrease (p ≤ 0.05) during the initial hour post-thawing. In conclusion, proAKAP4 is identified in donkey sperm, akin to its presence in other mammals. It exhibits a positive correlation with total and progressive motility, its concentration is notably affected by the presence of cryoprotectant with significant consumption observed during the initial hour following thawing. These findings contribute to our understanding of proAKAP4 dynamics in donkey sperm, providing insights that may have implications for semen preservation and reproductive technologies in equids.

Exploring testicular miRNA profiles during developmental stages in Dezhou donkeys: A preliminary insight

Testicular development and spermatogenesis are complex phenomena controlled by various genetic factors, including miRNA-based post-transcriptional gene expression regulation. Exploring the miRNA expression patterns during testicular development in Dezhou donkeys would enhance our understanding of equine fertility and spermatogenesis. In this investigation, we examined the testicular miRNA profiles at various stages of development. The experimental animals were divided into three groups based on their developmental stages: 2 months old (juvenile: n = 3), 12 months old (adolescent; n = 3) and 24 months old (adult; n = 3) donkeys. Total RNA was extracted from dissected testicles for miRNA sequencing and analysis. In total, 586 miRNAs, including 451 known miRNAs and 135 novel miRNAs, were identified. Among identified miRNAs, 315 displayed age-dependent expression differences. The levels of miRNA expression in the juvenile group were significantly higher than in the adolescent or adult groups. The MiR-483 exhibited the maximum fold change between juvenile and adolescent groups. Several screened genes, including SLC45A4 and TFCP2L1, have been linked to male reproductive pathways in donkeys. In addition, miR-744 was predicted to regulate SPIN2B, a gene implicated in spermatocyte cell cycle progression and genomic integrity of spermatozoa. These results contribute to our comprehension of microRNA regulation during testicular development and spermatogenesis in Dezhou donkeys. The identified microRNAs and their target genes have the potential to serve as biomarkers for evaluating the reproductive capacity of stud donkeys.

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.

A survey report on the donkey original breeding farms in China: Current aspects and future prospective

Introduction

The number of the large-scale donkey breeding farms in China has increased dramatically. However, information regarding the situation of a Chinese donkey population under large-scale donkey breeding farms is limited.

Methods

This survey report was conducted using questionnaires online to investigate the current situation of the donkey original breeding farms in China, in terms of donkey stock, local breeds, reproductive parameters, growth and lactation performance, and future perspectives. China has developed the donkey reserve system based on national, provincial and non-governmental (self-own) donkey original breeding farms.

Results

In the present study, a total of 38 donkey original breeding farms concentrated in Northern of China were studied, and 52% of them keep their donkeys with a stocking density of 100-500 donkeys. China is rich in various local donkey breeds, and 16 local donkey breeds including large-sized, medium-sized and small-sized breeds were collected in our survey. Dezhou donkey are prevalent with a percentage of more than 57% of the total donkeys, while the Cullen donkeys belong to small-sized donkey breeds are scare. The reproductive efficiency and donkey productivity were different across donkey farms, indicating potential differences in management and breeding practices between different donkey original breeding farms. The artificial insemination has been performed in these donkey farms with an average proportion of 73%. Regarding the donkey productivity, the national and provincial donkey original breeding farms showed a higher birthweight and fat content in donkey milk than self-own farms. Furthermore, our results indicate that the donkey breeds with different body size also have important influence on the reproduction parameters and donkey productivity, with the large-sized donkeys had better performance compared to the small-sized donkeys.

Discussion

In summary, our survey provided valuable baseline information on the situation of donkey population dynamics in the donkey original breeding farms. However, further study is required in the future to investigate the factors such as donkey health care, management and nutrition during breeding, fattening and lactation that influence donkey productivity under large-scale farm systems.

The potential of three whole blood microRNAs to predict outcome and monitor treatment response in sarcoid-bearing equids

MicroRNAs (miRNAs) have been proposed as biomarkers for equine sarcoid (ES) disease. In this study, the suitability of three whole blood miRNAs to diagnose ES and to predict and monitor the outcome of therapy was explored. Using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), expression levels of eca-miR-127, eca-miR-379, and eca-miR-432 in whole blood of ES-affected equids before and at least one year after therapy were compared to those of unaffected control equids. Associations of age, sex, species, diagnosis, and therapy outcome with miRNA expression levels were examined using general linear models. In total, 48 ES-affected equids and 47 control equids were recruited. From the affected animals, 31 responded favorably to treatment, and 17 demonstrated a failure of therapy. None of the tested miRNAs were influenced by age. Male equids showed increased expression of eca-miR-127 compared to females and horses showed higher expression levels of eca-miR-379 and eca-miR-432 than donkeys. Eca-miR-127 was confirmed as a diagnostic discriminator between ES-affected and control equids. No difference in miRNA profiles before therapy was found when comparing ES-affected equids with success vs. failure of therapy. Eca-miR-379 and eca-miR-432 decreased over time in horses where therapy was successful, but not in those cases where it failed. Biological variables influence equine whole blood miRNA expression, which may complicate biomarker validation. While none of the tested miRNAs could predict the response to therapy in ES-affected equids and eca-miR-127 showed poor diagnostic accuracy for ES, eca-miR-379 and eca-miR-432 miRNAs might allow refinement of monitoring of success of ES therapy.

Identification of Circular RNAs of Testis and Caput Epididymis and Prediction of Their Potential Functional Roles in 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.

Transcriptional Specificity Analysis of Testis and Epididymis Tissues in Donkey

Donkeys, with high economic value for meat, skin and milk production, are important livestock. However, the current insights into reproduction of donkeys are far from enough. To obtain a deeper understanding, the differential expression analysis and weighted gene co-expression network analysis (WGCNA) of transcriptomic data of testicular and epididymis tissues in donkeys were performed. In the result, there were 4313 differentially expressed genes (DEGs) in the two tissues, including 2047 enriched in testicular tissue and 2266 in epididymis tissue. WGCNA identified 1081 hub genes associated with testis development and 6110 genes with epididymal development. Next, the tissue-specific genes were identified with the above two methods, and the gene ontology (GO) analysis revealed that the epididymal-specific genes were associated with gonad development. On the other hand, the testis-specific genes were involved in the formation of sperm flagella, meiosis period, ciliary assembly, ciliary movement, etc. In addition, we found that eca-Mir-711 and eca-Mir-143 likely participated in regulating the development of epididymal tissue. Meanwhile, eca-Mir-429, eca-Mir-761, eca-Mir-200a, eca-Mir-191 and eca-Mir-200b potentially played an important role in regulating the development of testicular tissue. In short, these results will contribute to functional studies of the male reproductive trait in donkeys.

miRNA-mRNA analysis of sheep adrenal glands reveals the network regulating reproduction

Background

The adrenal gland participates in the process of sheep reproduction. MicroRNAs (miRNAs), endogenous small noncoding RNAs, regulate gene expression at the posttranscriptional level. However, the miRNA-mRNA network profile of adrenal glands relating to reproduction in sheep is still not well-studied. As sheep with FecB^BB genotype show higher lambing number compare with the sheep with FecB⁺⁺ genotype. This research aims to compare gene expression by small RNA-seq in adrenal tissues at follicular (F) and luteal (L) phases in FecB^BB (MM) and FecB⁺⁺ (ww) sheep. After analysis of gene expression, significant differentially expressed microRNAs (DEMs) and corresponding target genes were identified.

Results

A total of 180 miRNAs were found in this study, of which 19 DEMs were expressed in the four comparison groups (MM_F_A vs. MM_L_A, MM_F_A vs. ww_F_A, MM_L_A vs. ww_L_A, ww_F_A vs. ww_L_A). Subsequently, 354 target genes of 19 DEMs were predicted by integrated analysis. Cluster analysis was performed by K_means_cluster, and the expression patterns of these DEMs were separated into four subclusters. Functional analysis of target genes was performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The results indicated that the target genes were involved mainly in the Notch signaling pathway, signal transduction, cell communication, innate immune response and amino acid metabolism. Specifically, the Notch signaling pathway, biosynthetic process and metabolic process of pyrimidine nucleotide and amino acid metabolism appear to play key regulatory roles in the sheep fertility trait. Furthermore, miRNA-mRNA interaction networks were constructed by differentially expressed genes combined with our previous study of transcriptome data. The results showed that several key genes, including TDRD3, ANAPC7, CCNL2, BRD2 and MUT, were related to the transformation from the follicular phase to the luteal phase. PLAC8L1, NFAT5, DDX24 and MBD1 were related to the high fecundity of small tail Han sheep.

Conclusions

In this study, the miRNA transcriptome profile was identified, and miRNA-mRNA interaction networks were constructed in adrenal gland tissue of small tail Han sheep, the interaction between miR-370-3p and its targets were considered to play a major role in the reproduction regulation process. The results enriched the number of known miRNAs in adrenal glands and provided novel ideas and further information to demonstrate posttranscriptional regulation mechanisms at follicular and luteal phases in different genotypes of small tail Han sheep.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-022-01060-y.

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 in vitro digestion and fermentation characteristics of feedstuffs inoculated with cecal or colic fluid of Dezhou donkey

The present study was conducted to evaluate the in vitro dry matter disappearance (IVDMD) and fermentation characteristics of 6 fibrous feedstuffs incubated with donkey cecal or colic microorganisms. The fibrous feeds were corn straw (CS), wheat straw (WS), peanut vine (PNV), peanut shell (PNH), wheat shell (WH) and wheat bran (WB), which are commonly applied in large-scale donkey farms in China. After 48 h fermentation, the highest IVDMD occurred in WB, and the lowest occurred in PNH (P<0.05) regardless what inoculum applied. The IVDMD was positively correlated with OM (R=0.42, P<0.01), CP (R=0.76, P<0.01) and EE (R=0.56, P<0.01), while it was negatively correlated with NDF (R=0.75, P<0.01) and ADF (R=0.79, P<0.01). In terms of volatile fatty acids (VFAs), the greatest net VFA production also occurred in WB (P<0.05). The acetate and branched-chain volatile fatty acid (BCVFA) proportions were greater in the colon culture fluids than in caecum (P<0.05), but the propionate proportions were lower in colon than in caecum (P<0.05). This resulted in an increase in the ratio of acetate to propionate in colon culture fluids. In summary, based on the highest IVDMD, net VFA production and CP content occurring with the lowest contents of both NDF and ADF, WB had the highest nutritive value compared to other fibrous substrates. The extent of feed degradation and fermentation depended mainly on the nature of the incubated feedstuffs. Nevertheless, further study is required to investigate these fibrous feeds on hindgut fermentation and in vivo nutrient digestibility.

Epididymal mRNA and miRNA transcriptome analyses reveal important genes and miRNAs related to sperm motility in roosters

Sperm motility is a crucial trait in chicken production, and the epididymis is an essential organ in the reproductive system. Currently, the molecular mechanisms underlying sperm motility in the epididymis are unclear. In this study, 8 cDNA libraries and eight miRNA libraries were constructed from roosters (4 chickens per group) with diverse sperm motility. After a comparative analysis of epididymal transcriptomes, we detected 84 differentially expressed genes (DEGs) using the edgeR package. Integrated interpretation of DEGs indicated that MMP9, SLN, WT1, PLIN1, and LRRIQ1 are the most promising candidate genes affecting sperm motility in the epididymis of roosters. MiR-146a, mir-135b, and mir-205 could play important regulatory roles in sperm maturation, capacitation, and motility. Additionally, a comprehensive analysis of the mRNA and miRNAs transcriptomes in silico identified a promising gene-miRNA pair miR-135b-HPS5, which may be a vital regulator of sperm motility in the epididymis. Our findings provide novel integrated information of miRNAs and genes that shed light on the regulatory mechanisms of fertility in roosters.

Estimation of Liveweight from Body Measurements through Best Fitted Regression Model in Dezhou Donkey Breed

Dezhou donkey is an excellent local hide, meat and milk breed in Shandong Province. To accelerate the speed of breeding, reproduction and conversation, correlation and multiple regression analysis between body weight (BW) and body size of Dezhou donkey rearing under intensive farms was made by SAS 9.4 software (Statistical Analysis for Windows). A total of 162 donkeys of both gender of age 2 ~ 10 years old were used to investigate the relationships between BW and body dimensional traits (cm) including height of withers, body length; thoracic depth, thoracic girth (TG), thoracic width (TW), circumference of cannon bone (CB), height of rump, rump length (RL) and rump width (RW). The results showed that BW and body measurements have positive and great correlations with R² value ranged from 0.58 to 0.88 (P <0.01). The R² values from the single-parameter equations showed that the TG was highly related to BW (0.72, P < 0.01). The stepwise regression equations were applied to obtain the best prediction equations, and the results indicated that the prediction accuracy for BW was improved with the inclusion of more body measurement variables. The "best fit" models were: BW (kg) = 1.88 × TG + 1.27 × BL + 2.55 × TW + 4.61 × CB + 2.18 × RW + 1.78 × RL - 422.8 (R² = 0.906, P < .01). The predicted BW from the present equations showed the nearest value to the real BW (R² > 0.94, P < .01). In addition, the equations derived to predict the BW of donkeys in Britain, Morocco were less satisfactory for use with the present Dezhou donkey breed because they overestimated or underestimated the BW due to the different donkey breed.