Current status of sperm functional genomics and its diagnostic potential of fertility in bovine (Bos taurus)

Transcriptome Analysis Reveals Spermatogenesis-Related CircRNAs and LncRNAs in Goat Spermatozoa

Mammalian spermatozoa comprises both coding and non-coding RNAs, which are traditionally believed to be a residual of spermatogenesis. The differential expression level of spermatozoal RNAs is also observed between fertile and infertile human, thereby anticipated as potential molecular marker of male fertility. This study investigated the transcriptome profile of goat (Capra hircus) spermatozoa. The sperm transcriptome was analyzed by three different methods viz. RLM-RACE, long-read RNA sequencing (RNAseq) in Nanopore™ platform, and short-read RNAseq in Illumina™ platform. The Illumina™ sequencing discovered 16,604 transcripts with 357 mRNAs having FPKM (fragments per kilobase per million mapped reads) of more than five. The spermatozoal RNA suite included mRNA (94%), rRNA (3%), miscRNA (1%), circRNA (1%), miRNA (1%), etc. This study also predicted circRNAs (127), lncRNAs (655), and imprinted genes (160) that have potential role in male reproduction. The gene ontology analysis revealed the involvement of spermatozoal RNA in regulating male meiosis (TET3, STAT5B), capacitation (ACRBP, CATSPER4), sperm motility (GAS8, TEKT2), spermatogenesis (ADAMTS2, CREB3L4), etc. The spermatozoal RNA were also associated with different biological pathways viz. Wnt signaling pathway, cAMP signaling pathway, AMPK signaling pathway, and MAPK signaling pathways having potential role in spermatogenesis. Overall, this study enlightened the suite of spRNA transcripts in goat and their relevance in male fertility for diagnostic approach.

Protamine 2 and phospholipase C zeta 1 are possible biomarkers for the diagnosis of male subfertility in frozen-thawed stallion semen

Subfertility is one of the main issues in horse breeding and the study of mRNAs in sperm might help in elucidating the reasons that lead to this diagnosis. The present study aims at assessing the differences in the expression of 10 potential candidate genes in stallions of different fertility. Frozen-thawed semen of 29 stallions was included. Each sample was classified into two groups according to pregnancy rates (PR) achieved with this semen: "good fertility" (GF; n = 17; PR ≥ 30 %) or "poor fertility" (PF; n = 12; PR <20 %). All stallions underwent a breeding soundness examination (BSE) before semen production and were only included into the semen cryopreservation program when raw semen characteristics at BSE met minimal requirements. Semen was cryopreserved following European Union regulations and all stallions met the respective health requirements. Each sample was assessed for concentration (NucleoCounter SP-100), motility (CASA), membrane functionality (SYBR-14/PI), mitochondrial membrane potential (JC-1), morphology (SpermacStain), acrosome integrity (SpermacStain), membrane integrity (HOS test) and chromatin integrity (Aniline blue). Sperm RNAs were extracted using the Direct-zol RNA Miniprep Kit (Zymo Research) and RT-qPCR was performed for each target gene. ACTB and RPL32 were included as reference genes (RGs) for normalization. For each variable of each group, mean, standard deviation and SEM were calculated. The difference in gene expression levels between the GF and PF group were analyzed using the Mann-Whitney U test and Spearman's rank correlation. Significant results were considered with p < 0.05. Sperm quality parameters did not differ significantly between the two groups except for concentration, that was significantly higher in GF (p = 0.043). In GF a positive correlation was identified for PRM1/PRM2 with r = +0.6, while PRM1/ACR (r = -0.495), PRM2/ZPBP (r = -0.645) and CRISP3/ACR (r = -0.551) were inversely correlated. In PF direct correlations were registered for PRM1/PRM2 (r = +0.629), PRM1/PRM3 (r = +0.657), PRM2/SPA17 (r = +0.685), SPA17/PLCZ1 (r = +0.786) and PRM3/ACR (r = +0.627). In the total sample (GF + PF), positive correlations were detected for PRM1/PRM2 (r = +0.625), PRM1/PRM3 (r = +0.368); PRM2/SPA17 (r = +0.465), SPA17/PLCZ1 (r = +0.637) and PLCZ1/ZAN (r = +0.587). Only two of the genes considered were differentially expressed in the 2 groups: PRM2 and PLCZ1, that were significantly (p < 0.05) overexpressed in the GF group. Stallions frozen-thawed semen with higher expression levels of PRM2 and PLCZ1 are more likely to belong to animals with a good pregnancy rate. Further studies are needed to investigate the role of sperm transcripts in male subfertility in stallions.

Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (Bos taurus × Bos indicus) bull spermatozoa

Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca2++ ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.

Comparative RNA isolation methods from fresh ejaculated spermatozoa in Sahiwal cattle (Bos indicus) and Murrah buffalo (Bubalus bubalis) bulls for high quality and enhanced RNA yield

Sperm mRNA transcriptional profiling can be used to evaluate the fertility of breeding bulls. The aim of the study was to compare the modified RNA isolation methods for higher RNA yield and quality from freshly ejaculated sperm of cattle and buffalo bulls. Ten fresh ejaculates from each Sahiwal (n = 10 bulls × 10 ejaculates) and Murrah bulls (n = 10 bulls x 10 ejaculates) were used for RNA isolation. From the recovered live sperm, total sperm RNA was isolated by conventional methods (TRIzol, Double TRIzol), membrane-based methods combined with TRIzol (RNeasy + TRIzol) with the addition of β-mercaptoethanol (BME) and Kit (RNeasy mini) methods in fresh semen. Among different isolation methods; the membrane-based modified methods combined with TRIzol (RNeasy + TRIzol) with the addition of β-mercaptoethanol (BME) resulted significantly (p < .05) higher total RNA quantity (300-340 ng/µL) and better purity in different concentrations of spermatozoa viz., 30-40 million, 70-80 million and 300-400 million sperm. The study concluded that the inclusion of BME to the combined membrane-based methods with somatic cell lysis buffer solution was best for constant increased yield and purity of RNA isolation from Sahiwal cattle and Murrah buffalo bull sperm.

Paternal determinants of early embryo development

Existing research has primarily focused on investigating the impacts of the maternal environment, female fertility phenotype, and genetics on pregnancy loss in dairy cattle. Recently, attention has been directed toward understanding the role the sire has on embryo quality and viability. Studies have shown there is a paternal influence on early pregnancy loss, but the specific mechanisms impacting pregnancy establishment and maintenance remain unclear. Despite clear differences that sires have on pregnancy outcomes, there is a lack of evidence regarding specifically how sires influence pregnancy. Sperm characteristics, such as motility, concentration, and morphology, have been extensively studied, but further research is needed to understand what makes one sire more or less fertile than another sire and how this affects pregnancy. To effectively address pregnancy loss, a deeper understanding of the processes involved from fertilisation to blastocyst formation is essential, particularly for understanding early pregnancy loss.

Boar fertility is controlled through systematic changes of mitochondrial protein expression during sperm capacitation

Vigorous activation of mitochondria in spermatozoa during capacitation induces the biological and morphological changes of spermatozoa to acquire fertilizing ability. To in-depth understand the dynamic roles of mitochondrial and male fertility, this study was to identify how the mitochondrial proteins are changed during sperm capacitation and regulate male fertility using boar spermatozoa. The mitochondrial proteins were differentially changed during sperm capacitation according to fertility status, i.e., superior litter size (SL) and normal litter size (NL). Following sperm capacitation, ubiquitin-cytochrome c reductase core protein (UQCRC1) and ATP synthase F1 (ATP5F1) increased in NL, while cytochrome c oxidase subunit 5B (COX5B), and cytochrome c1 (CYC1) proteins decreased. In contrast, only and ubiquinone oxidoreductase core subunit 8 (NDUFS8) protein was increased in SL following capacitation. The protein expression difference value of CYC1, COX5B, and NDUFS8 following sperm capacitation was lower in NL than SL boars. Based on these complicated changes during sperm capacitation, the accuracy for predicting male fertility of NDUFS8 was increased to 87 %. Overall, considering the systematic orchestration of mitochondrial protein expression according to sperm capacitation status, it will be possible to better understand male fertility.

Genome-wide association study reveals candidate markers related to field fertility and semen quality traits in Holstein-Friesian bulls

In vitro assessment of bull semen quality is routinely used in bull semen processing centres in order to ensure that semen destined to be used in the field has passed minimum standards. Despite these stringent quality control checks, individual bulls that pass the quality control checks can still vary in field fertility by up to 25%. A genome-wide association study was undertaken to determine genetic markers associated with prefreeze and post-thaw bull sperm quality traits as well as field fertility. Genome-wide association analysis was performed using a single nucleotide polymorphism (SNP) regression mixed linear model in WOMBAT. Genes within a 250 Kb span of a suggestive (P ≤ 1 × 10^-5) SNP were considered as candidate genes. One SNP was associated with adjusted pregnancy rate, and 21 SNPs were associated across the seven semen quality traits (P ≤ 1 × 10^-5). Functional candidate genes include SIPA1L2 which was associated with adjusted pregnancy rate. This encodes a Rap GTPase-activating protein involved in Rap1 signalling pathway and was previously found to play a role in the process of sperm differentiation. Gene ontology (GO) analysis also identified significantly enriched biological processes involved protein tyrosine kinase activity including genes such as DYRK1A, TEC and TXK that were associated with sperm motility prior to freezing. Another candidate gene associated with post-thaw sperm motility was FHDC1 which coordinates actin filament and microtubule dynamics. The induced 11 GO terms in the ejaculates rejected after freezing trait were related to ATPase, phosphatase and hydrolase activity. These results reveal novel specific genomic regions and candidate genes associated with economically important phenotypes such as field fertility and semen quality traits.

Cryostress induces fragmentation and alters the abundance of sperm transcripts associated with fertilizing competence and reproductive processes in buffalo

The study aimed to assess the influence of cryostress on RNA integrity and functional significance in sperm fertilizing ability. The fresh and post-thawed buffalo sperm (n = 6 each) samples were evaluated for their functional attributes, and sperm total RNA was subjected to transcriptome sequencing followed by validation using real-time PCR and dot blot. Overall, 6911 genes had an expression of FPKM > 1, and among these 431 genes were abundantly expressed (FPKM > 20) in buffalo sperm. These abundantly expressed genes regulate reproductive functions such as sperm motility (TEKT2, SPEM1, and PRM3, FDR = 1.10E-08), fertilization (EQTN, PLCZ1, and SPESP1, FDR = 7.25E-06) and the developmental process involved in reproduction (SPACA1, TNP1, and YBX2, FDR = 7.21E-06). Cryopreservation significantly (p < 0.05) affected the structural and functional membrane integrities of sperm. The expression levels of transcripts that regulate the metabolic activities and fertility-related functions were compromised during cryopreservation. Interestingly, cryostress induces the expression of genes involved (p < 0.05) in chemokine signaling (CX3CL1, CCL20, and CXCR4), G-protein coupled receptor binding (ADRB1, EDN1, and BRS3), translation (RPS28, MRPL28, and RPL18A), oxidative phosphorylation (ND1, ND2, and COX2), response to reactive oxygen species (GLRX2, HYAL2, and EDN1), and immune responses (CX3CL1, CCL26, and TBXA2R). These precociously expressed genes during cryopreservation alter the signaling mechanisms that govern sperm functional competence and can impact fertilization and early embryonic development.

Analyzing the effect of heparin on in vitro capacitation and spermatozoal RNA population in goats

Heparin is a glycosaminoglycan polymer that is commonly used as an anticoagulant. Heparin also induces in vitro capacitation in spermatozoa, although its molecular mechanism is elusive. This study investigated the effect of heparin on in vitro capacitation and spermatozoal RNA (spRNA) population in goats. Goat spermatozoa were treated with 20 μM heparin for 0-6 h and evaluated for motility, capacitation, acrosome reaction, and spRNA population by RNA sequencing (RNA-seq). It was observed that heparin enhanced sperm motility up to 6 h of incubation (p < 0.05). Heparin also induced capacitation and acrosome reaction within 4 h. RNA-seq identified 1254 differentially expressed genes (DEGs) between heparin-treated and control spermatozoa. Most DEGs (1251 nos.) were upregulated and included 1090 protein-coding genes. A few genes (PRND, ITPR1, LLCFC1, and CHRM2) showed >5-fold increased expression in heparin-treated spermatozoa compared to the control. The upregulated genes were found to be involved in cAMP-PKA, PI3-Akt, calcium, MAPK signaling, and oxidative stress pathways. DCFDA staining confirmed the increased oxidative stress in heparin-treated spermatozoa compared to the control (p < 0.05). In conclusion, the results of the present study suggest that heparin enhances sperm motility and induces capacitation by upregulation of the spRNA population and oxidative stress pathway.

Comprehensive analysis of microRNA and metabolic profiles in bovine seminal plasma of different semen quality

Background

Seminal plasma plays a pivotal role in modulating sperm viability and function. However, the underlying mechanisms have not been fully elucidated.

Method

In this study, the bull semen production records of core breeding farms and bull stations in the past 10 years were analyzed.

Results

We found that the semen of 5-year-old bulls collected for the first time is of the best quality (p &lt; 0.05). Despite the bull semen collected under the above conditions, low-quality sperm is still obtained from part of bulls due to individual differences. Interestingly, seminal plasma from normal semen is capable of improving low-quality semen motility. To identify the potential key factors in seminal plasma, the differences in miRNA and metabolite profiles between normal and low-quality seminal plasma were analyzed. We found that 59 miRNAs were differently expressed, including 38 up-regulated and 21 down-regulated miRNAs. Three hundred and ninety-one and 327 significantly different metabolites were identified from the positive and negative ion models, respectively. These multiple miRNAs and metabolites collectively contribute to the motility of sperm, subsequently, affect semen quality.

Discussion

Together, these results not only revealed the critical factors of seminal plasma improving sperm quality but also provided potential miRNA- or metabolite-based biomarkers to identify the high semen quality.

Identification of protein candidates in spermatozoa of water buffalo (Bubalus bubalis) bulls helps in predicting their fertility status

The water buffalo (Bubalus bubalis) is an indispensable part of the Indian dairy sector and in several instances, the farmers incur economic losses due to failed pregnancy after artificial insemination (AI). One of the key factors for the failure of conception is the use of semen from the bulls of low fertilizing potential and hence, it becomes important to predict the fertility status before performing AI. In this study, the global proteomic profile of high fertile (HF) and low fertile (LF) buffalo bull spermatozoa was established using a high-throughput LC-MS/MS technique. A total of 1,385 proteins (≥1 high-quality PSM/s, ≥1 unique peptides, p < 0.05, FDR < 0.01) were identified out of which, 1,002 were common between both the HF and LF groups while 288 and 95 proteins were unique to HF and LF groups respectively. We observed 211 and 342 proteins were significantly high (log Fc ≥ 2) and low abundant (log Fc ≤ 0.5) in HF spermatozoa (p < 0.05). Gene ontology analysis revealed that the fertility associated high abundant proteins in HF were involved in spermatogenesis, sperm motility, acrosome integrity, zona pellucida binding and other associated sperm functions. Besides this, the low abundant proteins in HF were involved in glycolysis, fatty acid degradation and inflammation. Furthermore, fertility related differentially abundant proteins (DAPs) on sperm viz., AKAP3, Sp17, and DLD were validated through Western blotting and immunocytochemistry which was in coherence with the LC-MS/MS data. The DAPs identified in this study may be used as potential protein candidates for predicting fertility in buffaloes. Our findings provide an opportunity in mitigating the economic losses that farmers incur due to male infertility.

Investigating Visual Monitoring of the Scrotum as a Supplementary Tool for Boar Semen Quality Evaluation

Farm animals behavior research uses video cameras, mainly for visual observation and recording. The purpose of this feasibility study was to enrich the predictable methods of boar semen production capacity by correlating sperm variables with the scrotal contractions (SC) frequency and intensity. A video camera was used to record the reaction of the scrotum during ejaculation. The respective collected ejaculates were evaluated and semen parameters, such as viability, morphology, membranes functional integrity and kinematics, were determined. The camera recorded the scrotal contractions/relaxations and the video was handled by the Image Processing Toolbox of Matlab (Mathworks Inc., Natick, MA, USA). The SC intensity was verified as a percentage change in the scrotum size among the video frames of maximum contraction and relaxation. The archived data from the frames were analyzed statistically, using a linear mixed effects model that involved sperm assessed parameters. Correlations of the SC intensity with the average path velocity, VAP (R² = 0.591, p = 0.043) and with the percentage of the cytoplasmic droplets (R² = 0.509, p = 0.036) were noticed. Previous studies reported the positive correlation of VAP with the number of live-born piglets. In conclusion, video monitoring of the boar scrotal function during ejaculation is useful, but more research is needed to establish its appropriateness as a supplementary method for the prognosis of boar ability to produce high-quality semen.

Sperm Transcriptome Analysis Accurately Reveals Male Fertility Potential in Livestock

Nowadays, selection of superior male candidates in livestock as a source of frozen semen based on sperm quality at the cellular level is not considered accurate enough for predicting the potential of male fertility. Sperm transcriptome analysis approaches, such as messenger RNA levels, have been shown to correlate with fertility rates. Using this technology in livestock growth has become the principal method, which can be widely applied to predict male fertility potential in the livestock industry through the analysis of the sperm transcriptome. It provides the gene expression to validate the function of sperm in spermatogenesis, fertilization, and embryo development, as the parameters of male fertility. This review proposes a transcriptomic analysis approach as a high-throughput method to predict the fertility potential of livestock more accurately in the future.

Integrated multi-omics analyses reveals molecules governing sperm metabolism potentially influence bull fertility

Bull fertility is of paramount importance in bovine industry because semen from a single bull is used to breed several thousands of cows; however, so far, no reliable test is available for bull fertility prediction. In the present study, spermatozoa from high- and low-fertility bulls were subjected to high-throughput transcriptomic, proteomic and metabolomic analysis. Using an integrated multi-omics approach the molecular differences between high- and low-fertility bulls were identified. We identified a total of 18,068 transcripts, 5041 proteins and 3704 metabolites in bull spermatozoa, of which the expression of 4766 transcripts, 785 proteins and 33 metabolites were dysregulated between high- and low-fertility bulls. At transcript level, several genes involved in oxidative phosphorylation pathway were found to be downregulated, while at protein level genes involved in metabolic pathways were significantly downregulated in low-fertility bulls. We found that metabolites involved in Taurine and hypotaurine metabolism were significantly downregulated in low-fertility bulls. Integrated multi-omics analysis revealed the interaction of dysregulated transcripts, proteins and metabolites in major metabolic pathways, including Butanoate metabolism, Glycolysis and gluconeogenesis, Methionine and cysteine metabolism, Phosphatidyl inositol phosphate, pyrimidine metabolism and saturated fatty acid beta oxidation. These findings collectively indicate that molecules governing sperm metabolism potentially influence bull fertility.

Identification of differentially expressed long noncoding RNAs in the ovarian tissue of ewes Shal and Sangsari using RNA-seq

Background

The ovary has an important role in reproductive function. Animal reproduction is dominated by numerous coding genes and noncoding elements. Although long noncoding RNAs (LncRNAs) are important in biological activity, little is known about their role in the ovary and fertility.

Methods

Three adult Shal ewes and three adult Sangsari ewes were used in this investigation. LncRNAs in ovarian tissue from two breeds were identified using bioinformatics analyses, and then target genes of LncRNAs were discovered. Target genes were annotated using the DAVID database, and their interactions were examined using the STRING database and Cytoscape software. The expression levels of seven LncRNAs with their target genes were assessed by real‐time PCR to confirm the RNA‐seq.

Results

Among all the identified LncRNAs, 124 LncRNAs were detected with different expression levels between the two breeds (FDR < 0.05). According to the DAVID database, target genes were discovered to be engaged in one biological process, one cellular component, and 21 KEGG pathways (FDR < 0.05). The PES1, RPS9, EF‐1, Plectin, SURF6, CYC1, PRKACA MAPK1, ITGB2 and BRD2 genes were some of the most crucial target genes (hub genes) in the ovary.

Conclusion

These results could pave the way for future efforts to address sheep prolificacy barriers.

Exploring the ovine sperm transcriptome by RNAseq techniques. I Effect of seasonal conditions on transcripts abundance

Understanding the cell molecular changes occurring as a results of climatic circumstances is crucial in the current days in which climate change and global warming are one of the most serious challenges that living organisms have to face. Sperm are one of the mammals’ cells most sensitive to heat, therefore evaluating the impact of seasonal changes in terms of its transcriptional activity can contribute to elucidate how these cells cope with heat stress events. We sequenced the total sperm RNA from 64 ejaculates, 28 collected in summer and 36 collected in autumn, from 40 Manchega rams. A highly rich transcriptome (11,896 different transcripts) with 90 protein coding genes that exceed an average number of 5000 counts were found. Comparing transcriptome in the summer and autumn ejaculates, 236 significant differential abundance genes were assessed, most of them (228) downregulated. The main functions that these genes are related to sexual reproduction and negative regulation of protein metabolic processes and kinase activity. Sperm response to heat stress supposes a drastic decrease of the transcriptional activity, and the upregulation of only a few genes related with the basic functions to maintain the organisms’ homeostasis and surviving. Rams’ spermatozoids carry remnant mRNAs which are retrospectively indicators of events occurring along the spermatogenesis process, including abiotic factors such as environmental temperature.

Sperm Transcripts Associated With Odorant Binding and Olfactory Transduction Pathways Are Altered in Breeding Bulls Producing Poor-Quality Semen

Spermatozoa carries a reservoir of mRNAs regulating sperm functions and fertilizing potential. Although it is well recognized that a considerable proportion of high genetic merit breeding bulls produce poor-quality semen, the transcriptomic alterations in spermatozoa from such bulls are not understood. In the present study, comparative high-throughput transcriptomic profiling of spermatozoa from good and poor-quality semen-producing bulls was carried out to identify the transcripts associated with semen quality. Using next-generation sequencing (NGS), we identified 11,632 transcripts in Holstein Friesian bull spermatozoa; after total hit normalization, a total of 544 transcripts were detected, of which 185 transcripts were common to both good and poor-quality semen, while 181 sperm transcripts were unique to good quality semen, and 178 transcripts were unique to poor-quality semen. Among the co-expressed transcripts, 31 were upregulated, while 108 were downregulated, and 46 were neutrally expressed in poor-quality semen. Bioinformatics analysis revealed that the dysregulated transcripts were predominantly involved in molecular function, such as olfactory receptor activity and odor binding, and in biological process, such as detection of chemical stimulus involved in sensory perception, sensory perception of smell, signal transduction, and signal synaptic transmission. Since a majority of the dysregulated transcripts were involved in the olfactory pathway (85% of enriched dysregulated genes were involved in this pathway), the expression of selected five transcripts associated with this pathway (OR2T11, OR10S1, ORIL3, OR5M11, and PRRX1) were validated using real-time qPCR, and it was found that their transcriptional abundance followed the same trend as observed in NGS; the sperm transcriptional abundance of OR2T11 and OR10S1 differed significantly (p < 0.05) between good and poor-quality semen. It is concluded that poor-quality semen showed altered expression of transcripts associated with olfactory receptors and pathways indicating the relationship between olfactory pathway and semen quality in bulls.

Identification of biomarkers for bull fertility using functional genomics

Prediction of bull fertility is critical for the sustainability of both dairy and beef cattle production. Even though bulls produce ample amounts of sperm with normal parameters, some bulls may still suffer from subpar fertility. This causes major economic losses in the cattle industry because using artificial insemination, semen from one single bull can be used to inseminate hundreds of thousands of cows. Although there are several traditional methods to estimate bull fertility, such methods are not sufficient to explain and accurately predict the subfertility of individual bulls. Since fertility is a complex trait influenced by a number of factors including genetics, epigenetics, and environment, there is an urgent need for a comprehensive methodological approach to clarify uncertainty in male subfertility. The present review focuses on molecular and functional signatures of bull sperm associated with fertility. Potential roles of functional genomics (proteome, small noncoding RNAs, lipidome, metabolome) on determining male fertility and its potential as a fertility biomarker are discussed. This review provides a better understanding of the molecular signatures of viable and fertile sperm cells and their potential to be used as fertility biomarkers. This information will help uncover the underlying reasons for idiopathic subfertility.

Significance and Relevance of Spermatozoal RNAs to Male Fertility in Livestock

Livestock production contributes to a significant part of the economy in developing countries. Although artificial insemination techniques brought substantial improvements in reproductive efficiency, male infertility remains a leading challenge in livestock. Current strategies for the diagnosis of male infertility largely depend on the evaluation of semen parameters and fail to diagnose idiopathic infertility in most cases. Recent evidences show that spermatozoa contains a suit of RNA population whose profile differs between fertile and infertile males. Studies have also demonstrated the crucial roles of spermatozoal RNA (spRNA) in spermatogenesis, fertilization, and early embryonic development. Thus, the spRNA profile may serve as unique molecular signatures of fertile sperm and may play pivotal roles in the diagnosis and treatment of male fertility. This manuscript provides an update on various spRNA populations, including protein-coding and non-coding RNAs, in livestock species and their potential role in semen quality, particularly sperm motility, freezability, and fertility. The contribution of seminal plasma to the spRNA population is also discussed. Furthermore, we discussed the significance of rare non-coding RNAs (ncRNAs) such as long ncRNAs (lncRNAs) and circular RNAs (circRNAs) in spermatogenic events.

Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes

Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.

Proteomic fertility markers in ram sperm

Precise estimation of ram fertility is important for sheep farming to sustain reproduction efficiency and profitability of production. There, however, is no conventional method to accurately predict ram fertility. The objective of this study, therefore, was to ascertain proteomic profiles of ram sperm having contrasting fertility phenotypes. Mature rams (n = 66) having greater pregnancy rates than average (89.4 ± 7.2%) were assigned into relatively-greater fertility (GF; n = 31; 94.5 ± 2.8%) whereas those with less-than-average pregnancy rates were assigned into a lesser-fertility (LF; n = 25; 83.1 ± 5.73%; P = 0.028) group. Sperm samples from the outlier greatest- and least-fertility rams (n = 6, pregnancy rate; 98.4 ± 1.8% and 76.1 ± 3.9%) were used for proteomics assessments utilizing Label-free LC-MS/MS. A total of 997 proteins were identified, and among these, 840 were shared by both groups, and 57 and 93 were unique to GF and LF, respectively. Furthermore, 190 differentially abundant proteins were identified; the abundance of 124 was larger in GF while 66 was larger in LF rams. The GF ram sperm had 79 GO/pathway terms in ten major biological networks while there were 47 GO/pathway terms in six biological networks in sperm of LF rams. Accordingly, differential abundances of sperm proteins between sperm of GF and LF rams were indicative of functional implications of sperm proteome on male fertility. The results of this study emphasize there are potential protein markers for evaluation of semen quality and estimation of ram sperm fertilizing capacity.

Core Microbiome of Slovak Holstein Friesian Breeding Bulls' Semen

Simple Summary

The aim of this study was to characterize the bacterial profile of semen collected from Holstein Friesian breeding bulls via a high-throughput sequencing approach for a 16S rRNA gene variability analysis. A total of 55 fresh semen samples of sexually mature breeding bulls were used in the study. They were gathered from Holstein Friesian breeding bulls at Slovak Biological Services in Nitra, Slovak Republic. To amplify the V4 region of the 16S rRNA bacterial gene, universal primers 515F and 806R enhanced by a 6 bp barcode identification sequence were used. The 16S rRNA high-throughput sequencing strategy was used. Two microbial clusters were identified among the analyzed samples—the first cluster was based on Actinobacteria and Firmicutes, while the second cluster contained a high prevalence of Fusobacteria.

Abstract

Bacterial contamination of semen is an important factor connected to the health status of bulls that may significantly affect semen quality for artificial insemination. Moreover, some important bovine diseases may be transmitted through semen. Up to now, only a very limited number of complex studies describing the semen microbiome of bulls have been published, as many bacteria are hard to cultivate using traditional techniques. The 16S rRNA high-throughput sequencing strategy allows for the reliable identification of bacterial profiles of bovine semen together with the detection of noncultivable bacterial species. Fresh samples from Holstein Friesian breeding bulls (n = 55) were examined for the natural variability in the present bacteria. Semen doses were selected randomly from Slovak Biological Services in Nitra, Slovak Republic. The most predominant phyla within the whole dataset were Firmicutes (31%), Proteobacteria (22%), Fusobacteria (18%), Actinobacteria (13%) and Bacteroidetes (12%). Samples of semen were divided into two separate clusters according to their microbiome compositions using a cording partition around a medoids analysis. Microbiomes of the first cluster (CL1) of samples (n = 20) were based on Actinobacteria (CL1 average = 25%; CL = 28%) and Firmicutes (CL1 = 38%; CL2 = 27%), while the second cluster (CL2; n = 35) contained samples characterized by a high prevalence of Fusobacteria (CL1 = 4%; CL2 = 26%). Some important indicator microbial groups were differentially distributed between the clusters.

Deciphering metabolomic alterations in seminal plasma of crossbred (Bos taurus X Bos indicus) bulls through comparative deep metabolomic analysis

The incidence of sub-fertility is higher in crossbred bulls compared to zebu bulls. In the present study, we analysed the metabolomic profile of seminal plasma from crossbred and zebu bulls and uncovered differentially expressed metabolites between these two breeds. Using a high-throughput LC-MS/MS-based approach, we identified 990 and 1,002 metabolites in crossbred and zebu bull seminal plasma respectively. After excluding the exogenous metabolites, we found that 50 and 68 putative metabolites were unique to crossbred and zebu bull seminal plasma, respectively, whilst 87 metabolites were common to both. After data normalisation, 63 metabolites were found to be dysregulated between crossbred and zebu bull seminal plasma. Observed pathways included Linoleic acid metabolism (observed metabolite was phosphatidylcholine) in crossbred bull seminal plasma whereas inositol phosphate metabolism (observed metabolites were phosphatidylinositol-3,4,5-trisphosphate/inositol 1,3,4,5,6-pentakisphosphate/myo-inositol hexakisphosphate) was observed in zebu bull seminal plasma. Abundance of Tetradecanoyl-CoA was significantly higher, whilst abundance of Taurine was significantly lower in crossbred bull seminal plasma. In conclusion, the present study established the seminal plasma metabolomic profile in crossbred and zebu bulls and suggest that increased lipid peroxidation coupled with low concentrations of antioxidants in seminal plasma might be associated with high incidence of sub-fertility in crossbred bulls.

Germ Cell Drivers: Transmission of Preconception Stress Across Generations

Exposure to stress can accelerate maturation and hasten reproduction. Although potentially adaptive, the trade-off is higher risk for morbidity and mortality. In humans, the intergenerational effects of stress have been demonstrated, but the precise mechanisms are unknown. Strikingly, even if parental stress occurs prior to conception, as adults, their offspring show worse mental and physical health. Emerging evidence primarily from preclinical models suggests that epigenetic programming may encode preconception stress exposures in germ cells, potentially impacting the phenotype of the offspring. In this narrative review, we evaluate the strength of the evidence for this mechanism across animals and humans in both males and females. The strongest evidence comes from studies of male mice, in which paternal preconception stress is associated with a host of phenotypic changes in the offspring and stress-induced changes in the small non-coding RNA content in sperm have been implicated. Two recent studies in men provide evidence that some small non-coding RNAs in sperm are responsive to past and current stress, including some of the same ones identified in mice. Although preliminary evidence suggests that findings from mice may map onto men, the next steps will be (1) considering whether stress type, severity, duration, and developmental timing affect germ cell epigenetic markers, (2) determining whether germ cell epigenetic markers contribute to disease risk in the offspring of stress-exposed parents, and (3) overcoming methodological challenges in order to extend this research to females.

Sperm Functional Genome Associated With Bull Fertility

Bull fertility is an important economic trait in sustainable cattle production, as infertile or subfertile bulls give rise to large economic losses. Current methods to assess bull fertility are tedious and not totally accurate. The massive collection of functional data analyses, including genomics, proteomics, metabolomics, transcriptomics, and epigenomics, helps researchers generate extensive knowledge to better understand the unraveling physiological mechanisms underlying subpar male fertility. This review focuses on the sperm phenomes of the functional genome and epigenome that are associated with bull fertility. Findings from multiple sources were integrated to generate new knowledge that is transferable to applied andrology. Diverse methods encompassing analyses of molecular and cellular dynamics in the fertility-associated molecules and conventional sperm parameters can be considered an effective approach to determine bull fertility for efficient and sustainable cattle production. In addition to gene expression information, we also provide methodological information, which is important for the rigor and reliability of the studies. Fertility is a complex trait influenced by several factors and has low heritability, although heritability of scrotal circumference is high and that it is a known fertility maker. There is a need for new knowledge on the expression levels and functions of sperm RNA, proteins, and metabolites. The new knowledge can shed light on additional fertility markers that can be used in combination with scrotal circumference to predict the fertility of breeding bulls. This review provides a comprehensive review of sperm functional characteristics or phenotypes associated with bull fertility.

Comparative Transcriptomic Analysis of Spermatozoa From High- and Low-Fertile Crossbred Bulls: Implications for Fertility Prediction

Crossbred bulls produced by crossing Bos taurus and Bos indicus suffer with high incidence of infertility/subfertility problems; however, the etiology remains poorly understood. The uncertain predictability and the inability of semen evaluation techniques to maintain constant correlation with fertility demand for alternate methods for bull fertility prediction. Therefore, in this study, the global differential gene expression between high- and low-fertile crossbred bull sperm was assessed using a high-throughput RNA sequencing technique with the aim to identify transcripts associated with crossbred bull fertility. Crossbred bull sperm contained transcripts for 13,563 genes, in which 2,093 were unique to high-fertile and 5,454 were unique to low-fertile bulls. After normalization of data, a total of 776 transcripts were detected, in which 84 and 168 transcripts were unique to high-fertile and low-fertile bulls, respectively. A total of 176 transcripts were upregulated (fold change > 1) and 209 were downregulated (<1) in low-fertile bulls. Gene ontology analysis identified that the sperm transcripts involved in the oxidative phosphorylation pathway and biological process such as multicellular organism development, spermatogenesis, and in utero embryonic development were downregulated in low-fertile crossbred bull sperm. Sperm transcripts upregulated and unique to low-fertile bulls were majorly involved in translation (biological process) and ribosomal pathway. With the use of RT-qPCR, selected sperm transcripts (n = 12) were validated in crossbred bulls (n = 12) with different fertility ratings and found that the transcriptional abundance of ZNF706, CRISP2, TNP2, and TNP1 genes was significantly (p < 0.05) lower in low-fertile bulls than high-fertile bulls and was positively (p < 0.05) correlated with conception rate. It is inferred that impaired oxidative phosphorylation could be the predominant reason for low fertility in crossbred bulls and that transcriptional abundance of ZNF706, CRISP2, TNP2, and TNP1 genes could serve as potential biomarkers for fertility in crossbred bulls.

Semen evaluation: methodological advancements in sperm quality-specific fertility assessment - A review

Assessment of male fertility is based on the evaluation of sperm. Semen evaluation measures various sperm quality parameters as fertility indicators. However, semen evaluation has limitations, and it requires the advancement and application of strict quality control methods to interpret the results. This article reviews the recent advances in evaluating various sperm-specific quality characteristics and methodologies, with the help of different assays to assess sperm-fertility status. Sperm evaluation methods that include conventional microscopic methods, computer-assisted sperm analyzers (CASA), and flow cytometric analysis, provide precise information related to sperm morphology and function. Moreover, profiling fertility-related biomarkers in sperm or seminal plasma can be helpful in predicting fertility. Identification of different sperm proteins and diagnosis of DNA damage has positively contributed to the existing pool of knowledge about sperm physiology and molecular anomalies associated with different infertility issues in males. Advances in methods and sperm-specific evaluation has subsequently resulted in a better understanding of sperm biology that has improved the diagnosis and clinical management of male factor infertility. Accurate sperm evaluation is of paramount importance in the application of artificial insemination and assisted reproductive technology. However, no single test can precisely determine fertility; the selection of an appropriate test or a set of tests and parameters is required to accurately determine the fertility of specific animal species. Therefore, a need to further calibrate the CASA and advance the gene expression tests is recommended for faster and field-level applications.

Evaluation of α5β1 integrin as a candidate marker for fertility in bull sperm samples

With the progressive increase in the use of reproductive biotechnologies in the cattle industry, like artificial insemination and in vitro embryo production, the accurate determination of fertilizing competence of cryopreserved sperm samples is an essential issue. The routine methodology to assess bull sperm quality relies primarily on count, viability and motility of spermatozoa. However, these parameters do not tightly predict the reproductive success of samples. Therefore, identification of complementary markers of sperm functionality to strengthen the predictability of traditional spermogram is desirable to improve livestock reproduction practices. Previous results from our laboratory indicated that α5β1 integrin plays a key role in bovine sperm function and mediates their interaction with the female reproductive tract. Thus, this study aimed to investigate whether the localization of α5β1 held a correlation with fertilizing ability of bovine cryopreserved semen samples. Firstly, we assessed the quality of samples from six different bulls (A-F). We determined motility and viability of sperm samples after thawing and selection. Additionally, we measured the capacitation state of the samples by chlortetracycline (CTC) assay in the presence or absence of heparin, as an indicator of their responsiveness to a capacitating stimulus. Based on these assays, samples were classified being A the bull with the lowest quality and F the bull with the highest quality. Then, we studied the presence and localization of α5β1 integrin. This protein showed a distribution pattern in the acrosomal (A), post-acrosomal (P) and acrosomal + post-acrosomal (A + P) regions with different localization percentages among the studied samples. Next, we determined the fertilizing ability of the samples in in vitro fertilization (IVF) assays and performed correlation analyses between IVF outcome and the routine spermogram parameters or α5β1 integrin localization patterns. When the percentage of cells showing α5β1 integrin was compared to fertilization rate, no correlation was observed. However, the presence of α5β1 integrin in P and A + P regions (PA pattern), positively correlated with IVF rate (p < 0.05). These results suggest that while routine semen analyses failed to predict sperm reproductive competence, integrin localization in post-acrosomal region (PA pattern) showed a positive correlation with IVF outcome, thus posing an attractive marker to predict more accurately the reproductive performance of an individual.

Analysis of long non-coding RNAs in epididymis of cattleyak associated with male infertility

Cattleyak (CY), is a cross breed between cattle and yak (YK), which display equal adaptability to the harsh environment as YK and much higher performances than YK. However, the CY is female fertile and male sterile. Previous studies were conducted on testes tissues to investigate the mechanism of male infertility in CY. There is no systematic research on genes, especially lncRNAs between CY and YK epididymis. In this study, Illumina Hiseq was performed to profile the epididymis transcriptome (lncRNA and mRNA) of CY and YK. In total 18859 lncRNAs were identified, from which lincRNAs 12458, antisense lncRNAs 2345, intronic lncRNAs 3101, and sense lncRNAs 955 respectively. We have identified 345 DE lncRNAs and 3008 DE mRNAs between YK and CY epididymis. Thirteen DEGs were validated by quantitative real-time PCR. Combing with DEG, 14 couples of lncRNAs and their target genes were both DE, and 6 of them including CCDC39, KCNJ16, NECTIN2, MRPL20, PSMC4, and DEFB112 show their potential infertility-related terms such as cellular motility, sperm maturation, sperm storage, cellular junction, folate metabolism, and capacitation. On the other hand, several down-regulated genes such as DEFB124, DEFB126, DEFB125, DEFB127, DEFB129, CES5A, TKDP1, CST3, RNASE9 and CD52 in CY compared to YK were involved in the immune response and sperm maturation. Therefore, comprehensive analysis for lncRNAs and their target genes may enhance our understanding of the molecular mechanisms underlying the process of sperm maturation in CY and may provide important resources for further research.

RNA-Seq analysis reveals functionally relevant coding and non-coding RNAs in crossbred bull spermatozoa

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RNA-Seq analysis was done to characterize the transcriptome of crossbred bull spermatozoa.

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Among the 13,814 transcripts detected, 431 had FPKM > 1 and 13,673 had FPKM > 0 or < 1.

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Coding and non-coding RNAs account for 13,145 (95.15%) and 152 (1.1%), respectively.

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Sperm transcripts were mainly related to ribosome, oxidative phosphorylation and spliceosome pathways.

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qPCR analysis showed individual variations in transcriptional abundance of selected genes.

Sperm, which are believed to be transcriptionally and translationally inactive, synthesize RNA and proteins before there is gradual disappearance of the ribosome during chromatin compaction. Sperm transfer several functionally relevant transcripts to the oocyte, controlling maternal-zygotic transition and embryonic development. The present study was undertaken to profile and analyze sperm transcripts comprehensively using Next Generation Ribonucleic acid sequencing technology in Holstein Friesian x Tharparkar crossbred bulls. The results from global transcriptomic profiling revealed transcripts for 13,814 genes; of which 431 transcripts were expressed with >1 FPKM and 13,383 transcripts were expressed with >0 or <1 FPKM. The abundant mRNA transcripts of crossbred bull sperm were PRM1 and HMGB4. Gene ontology of transcripts with>1 FPKM revealed there was a major involvement in the structural constituent of ribosomes and translation. Results from pathway enrichment indicated the connection between ribosome, oxidative phosphorylation and spliceosome pathways and the transcripts of crossbred bull spermatozoa. The transcriptional abundance of selected genes, validated using RT-qPCR, indicated significant variations between bulls. Collectively, it may be inferred that the transcripts in crossbred bull sperm were heavily implicated in functions such as the structural constituent of ribosomes and translation, and pathways such as ribosome, oxidative phosphorylation and spliceosome. Further studies using larger sample sizes are required to understand the possible implications of transcriptomic variations on semen quality and fertility.

Cryopreservation and its effects on motility and gene expression patterns and fertilizing potential of bovine epididymal sperm

Despite encountering new challenges in using epididymal sperm recovered from cauda epididymides, this accessible and, in some species, worthwhile sample makes inevitable the further development of a suitable cryopreservation protocol. In this study, sperm was recovered from the epididymis of 4°C overnight stored slaughtered bulls' testes and the effects of cryopreservation on the bovine epididymal sperm motility (with CASA) and gene expression patterns (with quantitative Real time-PCR) were evaluated. Moreover the fertilizing potential of cryopreserved epididymal sperm was used in in vitro fertilization (IVF). After freezing and thawing of epididymal sperm, total and slow progressive sperm motility, VCL, VAP, MAD, ALH and BCF were significantly decreased (p < .05), while in the parameters of fast progressive motility, VSL, LIN, WOB and STR there were not any significant variations in the frozen sperm compared to fresh (non-frozen) counterpart. The assessment of abundance of transcripts encoding motility (TSSK6) and fertility (PRM1 and PRM2)-related genes in epididymal sperm, showed that these transcripts were affected by freezing especially in slow progressive motility status (p < .01). Furthermore, cleavage and blastocyst rate did not present any significant differences between bovine embryos produced in vitro by fresh or frozen-thawed epididymal sperm. It can be concluded that epididymal sperm has enough freezability after overnight testes storage, and cryopreservation could not affect the percentage of in vitro produced embryos in spite of the changes of relative abundance of some transcripts and direction progressive motility pattern of sperm.

The role of seminal plasma in the liquid storage of spermatozoa

Ongoing progress in proteomic characterization of seminal plasma has stimulated research on the identification of biomarkers for male fertility and sperm preservability. So far, many studies have evaluated the benefits of reconstituting cryopreserved or sex-sorted semen with seminal plasma. Less information is available about the effect of remaining or added seminal plasma in liquid preserved semen. The interaction between seminal plasma and spermatozoa is species -specific, and within species often complex and ambiguous. This article aims to review the action of seminal plasma on sperm function in preserved semen with a focus on liquid storage. Effects of seminal plasma on sperm traits during in vitro storage are summarized for males from four domestic farm animals, namely the bull, ram, boar and stallion. Special emphasis is placed on the effect of seminal plasma on long-term stored boar semen, including novel data demonstrating the attenuating effect of protective extender on the adverse effect of seminal plasma in some boars.

Genome-wide association study for age at puberty in young Nelore bulls

Selection for bulls that would reach puberty early reduces the generation interval and increases fertility and herd productivity. Despite its economic importance, there are few QTL associated with age at puberty described in the literature. In this study, a weighted single-step genome-wide association study was performed to detect genomic regions and putative candidate genes related to age at puberty in young Nelore bulls. Several protein-coding genes related to spermatogenesis functions were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for age at puberty in Nelore bulls, such as ADAM11, BRCA1, CSNK2A, CREBBP, MEIOC, NDRG2, NECTIN3, PARP2, PARP9, PRSS21, RAD51C, RNASE4, SLX4, SPA17, TEX14, TIMP2 and TRIP13 gene. Enrichment analysis by DAVID also revealed several GO terms related to spermatogenesis such as DNA replication (GO:0006260), male meiosis I (GO:0007141), double-strand break repair (GO:0006302), base excision repair (GO:0006284), apoptotic process (GO:0006915), cell-cell adhesion (GO: 0098609) and focal adhesion (GO:0005925). The heritability for age at puberty shows that this trait can be improved based on traditional EBV selection. Adding genomic information to the system helps to elucidate genes and molecular mechanisms controlling the sexual precocity and could help to predict sexual precocity in Nelore bulls with greater accuracy at younger age, which would speed up the breeding programme for this breed.

Integrated analysis of mRNAs and long noncoding RNAs in the semen from Holstein bulls with high and low sperm motility

Sperm motility is the main index used to assess the quality of bull semen. It may also be used to evaluate the fertility potential of bulls. Protein-coding mRNA and long noncoding RNA (lncRNA) participate in the regulation of spermatogenesis. Here, we employed strand-specific RNA sequencing to profile the semen transcriptome (mRNA and lncRNA) of six paired full-sibling Holstein bulls with divergent sperm motility and to determine the functions of mRNA and lncRNA in sperm motility. Among 20,875 protein-encoding genes detected in semen, 19 were differentially expressed between the high sperm motility group (H: H1, H2, and H3) and low sperm motility group (L: L1, L2, and L3). Of the 11,561 lncRNAs identified in sperm, 2,517 were differentially expressed between the H and L groups. We found that TCONS_00041733 lncRNA targets the node gene EFNA1 (ephrin A1), involved in male reproductive physiology. Our study provides a global mRNA and lncRNA transcriptome of bull semen, as well as novel insights into the regulation of neighboring protein coding by lncRNAs and the influence of mRNAs on sperm motility.