Transcriptome analysis of boar spermatozoa with different freezability using RNA-Seq

Sperm metabolomics identifies freezability markers in Duroc, Landrace, and Large White boars

Cryopreservation of boar semen is widely applied in the conservation of genetic resources and animal breeding to enhance the utilization efficiency of superior boars. However, accurately identifying individuals with good freezing tolerance in boar sperm remains challenging. In this study, based on the differences in sperm motility before and after cryopreservation from 328 boars, we selected six boars each from the Duroc, Landrace, and Large White breeds, and categorized them into poor freezability ejaculates (PFE) and good freezability ejaculates (GFE) groups for sperm metabolomic analysis. A total of 1288 metabolites were identified using both positive and negative ion modes. There were 148 differentially expressed metabolites between the GFE and PFE groups, which were enriched in pathways such as alanine, aspartate and glutamate metabolism; arginine biosynthesis; D-amino acid metabolism; histidine metabolism; beta-alanine metabolism; citrate cycle (TCA cycle); pantothenate and CoA biosynthesis; and pyruvate metabolism. Further analysis, including ROC curve evaluation, identified seven potential biomarkers for sperm cryopreservation. Argininosuccinic acid, asparagine, L-aspartate, fumarate, D-ornithine, DL-serine and histidine were tightly interconnected in a series of amino acids metabolism. In conclusion, our findings imply that differences in certain amino acid biosynthetic pathways contribute to the variations in freezing tolerance of boar sperm.

Integrated analyses of transcriptomes, metabolomes, and proteomes unveil the role of FoXO signaling axis in buck semen cryopreservation

Sperm cryopreservation is a complex process involving gene expression, protein synthesis, membrane stability, and metabolic adaptation. However, molecular alterations in sperm cryopreservation and the mechanisms defending against freezing damage remain poorly understood. This study investigates these changes and defense mechanisms using transcriptomics, proteomics, and metabolomics data. During sperm cryopreservation, the expression level of G protein subunit alpha i3 (GNAI3) was significantly downregulated in post-thaw sperm (P < 0.001), while matrix metallopeptidase 9 (MMP9) was upregulated compared to FS groups (P < 0.01). Additionally, interleukin 6 (IL6) expression in the CS group showed an approximate increase (P < 0.05), whereas ribosomal protein S27a (RPS27A) expression decreased markedly (P < 0.05). Other important molecules such as macrophage stimulating 1 receptor (MST1R), hypoxia-inducible factor 1 subunit alpha (HIF1A), fibroblast growth factor 8 (FGF8), CD9 molecule (CD9), peptidase D (PEPD) and terminal nucleotidyltransferase 5B (TENT5B) also exhibited significant changes in expression (P < 0.05). Moreover, the study revealed the regulatory roles of metabolites such as glucose and glutamic acid during sperm cryopreservation. The involvement of catalase (CAT) protein in antioxidant defense was also noted. The interactions among mRNAs, miRNAs, proteins, and metabolites highlight the critical role of the FoxO signaling pathway in modulating responses to freezing. Our study reveals the molecular regulatory mechanisms of sperm during cryopreservation, emphasizing the importance of the FoxO pathway and specific metabolites in response to cryo-injury. These findings provide deeper insights into the complexity of sperm cryobiology and offer practical guidance for optimizing sperm cryopreservation.

Identification of key genes and variants associated with boar sperm freezability using whole genome resequencing

Cryopreservation induces various cryodamages to the structural or functional aspects of boar sperm, resulting in the deterioration of sperm quality. The extent of cryodamages varies significantly among different individual boars. In our study, 50 boars with either good sperm freezability (GSF) or poor sperm freezability (PSF) were selected from a population of 402 boars. These two groups exhibited significant differences in sperm quality, acrosome integrity, mitochondrial membrane potential, and plasma membrane integrity. Subsequent whole-genome resequencing and FST analysis of GSF and PSF boars uncovered genetic differentiation among 5632 genes. Spermatogenesis, sperm structure, and lipid composition were identified as the potential factors, and 35 genes, such as RNF8, PACRG, CADM1, SPAG16, PPP3CA and MFF, were identified as key candidate genes associated with sperm freezability. Furthermore, by using MassARRAY genotyping and a general linear model, nine variants, including seven single nucleotide polymorphisms (SNPs) and two insertion variants, were found to be significantly correlated with sperm freezability. These variants, located within the candidate genes, represent potential molecular markers for sperm freezability. Our research contributes novel insights into the genetic mechanisms underlying freezability differences in boar sperm and identifies candidate genes and key molecular markers that could be applied in boar breeding practices.

Ferroptosis emerges as the predominant form of regulated cell death in goat sperm cryopreservation

BACKGROUND

Freezing-induced sperm damage, often associated with oxidative stress, can result in regulated cell death. Given that oxidative stress can trigger various forms of regulated cell death, the prevailing form during sperm cryopreservation remains unknown. Our study aimed to investigate this issue using cashmere goats as a model.

RESULTS

We found a significant increase in lyso-phospholipids in frozen-thawed sperm suggested ferroptosis. Assessment of cryopreserved sperm, with or without prior treatment with ferroptosis or apoptosis inhibitors, demonstrated the significant efficacy of ferroptosis inhibitors in reducing freezing damage. This implicates ferroptosis as the primary form of regulated cell death induced during sperm cryopreservation. Additionally, the positive rate of transferrin receptor protein 1 was significantly lower in fresh live sperm (47.8%) than in thawed live sperm (71.5%), and the latter rate was lower than that in dead sperm (82.5%). By contrast, cleaved caspase-3 positivity showed no significant difference between fresh live sperm and thawed live sperm but was notably lower in thawed live sperm than in dead sperm.

CONCLUSIONS

Our findings establish ferroptosis as the dominant regulated cell death form during goat sperm cryopreservation, providing novel insights into freezing-induced sperm damage mechanisms. These findings have significant implications for optimizing cryopreservation protocols and enhancing sperm viability after freezing-thawing.

Development of a novel chimeric lysin to combine parental phage lysin and cefquinome for preventing sow endometritis after artificial insemination

Sow endometritis is usually caused by multiple species of pathogenic bacteria. Numerous isolates from endometritis patients have developed antimicrobial resistance. Thus, novel antibacterial agents and strategies to combat endometritis are needed. A total of 526 bacteria, including Staphylococcus spp. (26.3%), Streptococcus spp. (12.3%), E. coli (28.9%), Enterococcus spp. (20.1%), Proteus spp. (9.5%), and Corynebacterium spp. (2.8%), were isolated from sows with endometritis. We constructed a novel chimeric lysin, ClyL, which is composed of a cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP) catalytic domain from the phage lysin LysGH15 and a cell wall-binding domain (CBD) from the prophage lysin Lys0859. The activities of ClyL and Lys0859 were most pronounced for the Staphylococcus and Streptococcus strains isolated from sow endometritis and bovine mastitis, respectively. ClyL and Lys0859 were combined to create a phage lysin cocktail, which demonstrated a synergistic effect against the coinfection of Staphylococcus and Streptococcus in vitro and in vivo. Furthermore, the combination of phage lysin cocktail and cefquinome had a synergistic bactericidal effect on boar semen that did not influence the activity of sperm. Remarkably, the incidence rate of sow endometritis was 0% (0/7) when the combination of phage lysin cocktail and cefquinome was used in semen via artificial insemination compared with 50% (3/6) when PBS was administered. Overall, the administration of a phage lysin cocktail and cefquinome in semen via artificial insemination is a promising novel strategy to prevent sow endometritis after artificial insemination.

Boar-to-Boar Variations in Quality Characteristics of Sperm from Different Ejaculates Following Freezing-Thawing

The main objective of this study was to investigate boar-to-boar variations in the quality characteristics of sperm from the sperm-rich fractions (SRFs) and whole ejaculates (WEs) following freezing-thawing. Several sperm attributes, such as motility patterns analyzed by the computer-assisted sperm analysis (CASA) system, mitochondrial function, membrane integrity, and DNA fragmentation were used to compare the cryo-survival of sperm from SRFs and WEs from boars with good and poor semen freezability (GSF and PSF, respectively). In this study, boars with post-thaw total motility (TMOT) more than 30% (>30%) were classified as having GSF, while those with post-thaw TMOT less than 30% (<30%) were classified as having PSF. Principal component analysis 1 (PCA1), which is the main component of the sample variation, explained approximately 75% of the variance between the GSF and PSF groups, reaffirming the reliability of post-thaw TMOT as a reliable criterion used to classify the animals. Most of the post-thaw sperm parameters of the SRFs and WEs were positively correlated. Furthermore, scatter plot analyses show stronger relationships between the analyzed post-thaw parameters of the frozen-thawed (FT) sperm of SRFs than those of WEs. Individual boar variations or the sperm source had marked effects on the quality characteristics of FT sperm. The higher TMOT, velocity straight line (VSL), and velocity average path (VAP) of FT sperm were more enhanced in the SRFs compared with the WEs of the PSF group. Furthermore, the mitochondrial function, membrane integrity, and DNA fragmentation of FT sperm were markedly higher in the SRFs than in the WEs, particularly for the poor freezability boars. We suggest that the freezability potential of sperm of the GSF group does not differ significantly between the SRFs and WEs, reaffirming that boar variability is an important factor that affects the cryo-survival of sperm.

A review on the functional roles of trehalose during cryopreservation of small ruminant semen

Sperm cryopreservation is an approach to preserve sperm cells in liquid nitrogen or other cryogenic media for future use in assisted reproductive technologies, such as in vitro fertilization or artificial insemination. Sperm cryopreservation has been extensively used in the dairy industry and has attained excellent results after artificial insemination. However, for small ruminants the application of sperm cryopreservation is limited, due to the poor quality of frozen semen and special characteristics of the reproductive female tract. In order to improve post-thaw semen quality various cryoprotectants are used. Currently, many types of cryoprotectants, such as permeable organic solvents, sugars, antioxidants, and natural or synthetic ice blockers, have been tested on small ruminants' sperm cryopreservation. Among them, trehalose; has shown potential acting as an excellent cryoprotectant for semen freezing. While, the exact roles and action mechanisms of trehalose during cryopreservation remain unclear. In this review, we systematically summarized the present usage status, potential action mechanisms, and future application prospects of trehalose in small-ruminant sperm cryopreservation.

Determinant genetic markers of semen quality in livestock

The reproductive efficiency of livestock is crucial for agricultural productivity and economic sustainability. One critical factor in successful fertilization and the viability of offspring is the quality of semen. Poor semen quality, especially in frozen-thawed semen used in artificial insemination (AI) have been shown to influence conception outcomes, resulting a negative impact on livestock production. Recent advancements in genetic research have identified specific markers linked to semen quality traits in various livestock species, such as cattle, sheep, goats, pigs, buffalo, and equines. These genetic markers are essential in screening males for breeding suitability, which in turn enhances selective breeding programs. Understanding these markers is crucial for improving reproductive performance and increasing productivity in livestock populations. This review offers a comprehensive overview of the genetic markers associated with semen quality in key livestock. It explores the underlying genetic mechanisms and their practical implications in animal breeding and management. The review underscores the importance of integrating genetic insights into breeding strategies to optimize reproductive efficiency and ensure the sustainable development of livestock industries.

Selection and direct biomarkers of reproductive capacity of breeding boars

Efficient management of pig reproduction is paramount for the sustainability and productivity of the global pork industry. Modern artificial insemination (AI) breeding programs have greatly benefited from the integration of advanced selection methods and biomarkers to enhance the reproductive performance of boars. While traditional selection methods have relied soley on boar phenotype, such as growth rate and conformation, modern pig breeding has shifted more and more toward molecular and genetic tools, which are still complemented by phenotypic traits. These methods encompass genomics, transcriptomics, and proteomics. Biomarkers serve as critical indicators of boar reproductive capacity. They can help to identify individuals with superior fertility and aid in the early identification of potential fertility issues, allowing for proactive management strategies. This review summarizes current knowledge of various biomarkers associated with semen quality, sperm function, and overall reproductive fitness in boars. Furthermore, we explore advanced technologies and their potential applications in uncovering novel selection methods and biomarkers for predicting boar fertility. A comprehensive understanding of selection criteria and biomarkers governing boar reproductive capacity is essential for developing effective breeding programs to enhance swine reproductive performance.

Insights into crucial molecules and protein channels involved in pig sperm cryopreservation

Cryopreservation is the most efficient procedure for long-term preservation of mammalian sperm; however, its use is not currently dominant for boar sperm before its use for artificial insemination. In fact, freezing and thawing have an extensive detrimental effect on sperm function and lead to impaired fertility. The present work summarises the basis of the structural and functional impact of cryopreservation on pig sperm that have been extensively studied in recent decades, as well as the molecular alterations in sperm that are related to this damage. The wide variety of mechanisms underlying the consequences of alterations in expression levels and structural modifications of sperm proteins with diverse functions is detailed. Moreover, the use of cryotolerance biomarkers as predictors of the potential resilience of a sperm sample to the cryopreservation process is also discussed. Regarding the proteins that have been identified to be relevant during the cryopreservation process, they are classified according to the functions they carry out in sperm, including antioxidant function, plasma membrane protection, sperm motility regulation, chromatin structure, metabolism and mitochondrial function, heat-shock response, premature capacitation and sperm-oocyte binding and fusion. Special reference is made to the relevance of sperm membrane channels, as their function is crucial for boar sperm to withstand osmotic shock during cryopreservation. Finally, potential aims for future research on cryodamage and cryotolerance are proposed, which might be crucial to minimise the side-effects of cryopreservation and to make it a more advantageous strategy for boar sperm preservation.

Genomic, transcriptomic and epigenomic analysis towards the understanding of porcine semen quality traits. Past, current and future trends

The importance of boar reproductive traits, including semen quality, in the sustainability of pig production system is increasingly being acknowledged by academic and industrial sectors. Research is needed to understand the biology and genetic components underlying these traits so that they can be incorporated into selection schemes and managerial decisions. This article reviews our current understanding of genome biology and technologies for genome, transcriptome and epigenome analysis which now facilitate the identification of causal variants affecting phenotypes more than ever before. Genetic and transcriptomic analysis of candidate genes, Genome-Wide Association Studies, expression microarrays, RNA-Seq of coding and noncoding genes and epigenomic evaluations have been conducted to profile the molecular makeups of pig sperm. These studies have provided insightful information for a several semen-related parameters. Nonetheless, this research is still incipient. The spermatozoon harbors a reduced transcriptome and highly modified epigenome, and it is assumed to be transcriptionally silent for nuclear gene expression. For this reason, the extent to which the sperm's RNA and epigenome recapitulate sperm biology and function is unclear. Hence, we anticipate that single-cell level analyses of the testicle and other male reproductive organs, which can reveal active transcription and epigenomic profiles in cells influencing sperm quality, will gain popularity and markedly advance our understanding of sperm-related traits. Future research will delve deeper into sperm fertility, boar resilience to environmental changes or harsh conditions, especially in the context of global warming, and also in transgenerational inheritance and how the environment influences the sperm transcriptome and epigenome.

RNA Sequencing of Sperm from Healthy Cattle and Horses Reveals the Presence of a Large Bacterial Population

RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and equine sperm cell preparations, low mapping rates to the reference genomes were observed, mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples, which led to a reduced sequencing depth of RNAs of interest. To explore the presence of bacteria, we aligned the unmapped reads to a complete database of bacterial genomes and identified bacteria-associated transcripts which were characterized. This analysis examines the limitations associated with sperm transcriptome profiling by reporting the nature of the RNA sequences among which bacterial RNA was found. These findings can aid researchers in understanding spermatozoal RNA-seq data and pave the way for the identification of molecular markers of sperm performance.

Exploring the full potential of sperm function with nanotechnology tools

Sperm quality is essential to guarantee the success of assisted reproduction. However, selecting high-quality sperm and maintaining it during (cryo)preservation for high efficiency remains challenging in livestock reproduction. A comprehensive understanding of sperm biology allows for better assessment of sperm quality, which could replace conventional sperm analyses used today to predict fertility with low accuracy. Omics approaches have revealed numerous biomarkers associated with various sperm phenotypic traits such as quality, survival during storage, freezability, and fertility. At the same time, nanotechnology is emerging as a new biotechnology with high potential for use in preparing sperm intended to improve reproduction in livestock. The unique physicochemical properties of nanoparticles make them exciting tools for targeting (e.g., sperm damage and sexing) and non-targeting bioapplications. Recent advances in sperm biology have led to the discovery of numerous biomarkers, making it possible to target specific subpopulations of spermatozoa within the ejaculate. In this review, we explore potential biomarkers associated with sperm phenotypes and highlight the benefits of combining these biomarkers with nanoparticles to further improve sperm preparation and technology.

Sperm long non-coding RNAs as markers for ram fertility

It is critical in sheep farming to accurately estimate ram fertility for maintaining reproductive effectiveness and for production profitability. However, there is currently a lack of reliable biomarkers to estimate semen quality and ram fertility, which is hindering advances in animal science and technology. The objective of this study was to uncover long non-coding RNAs (lncRNAs) in sperm from rams with distinct fertility phenotypes. Mature rams were allocated into two groups: high and low fertility (HF; n = 31; 94.5 ± 2.8%, LF; n = 25; 83.1 ± 5.73%; P = 0.028) according to the pregnancy rates sired by the rams (average pregnancy rate; 89.4 ± 7.2%). Total RNAs were isolated from sperm of the highest- and lowest-fertility rams (n = 4, pregnancy rate; 99.2 ± 1.6%, and 73.6 ± 4.4%, respectively) followed by next-generation sequencing of the transcripts. We uncovered 11,209 lncRNAs from the sperm of rams with HF and LF. In comparison to each other, there were 93 differentially expressed (DE) lncRNAs in sperm from the two distinct fertility phenotypes. Of these, 141 mRNAs were upregulated and 134 were downregulated between HF and LF, respectively. Genes commonly enriched for 9 + 2 motile cilium and sperm flagellum were ABHD2, AK1, CABS1, ROPN1, SEPTIN2, SLIRP, and TEKT3. Moreover, CABS1, CCDC39, CFAP97D1, ROPN1, SLIRP, TEKT3, and TTC12 were commonly enriched in flagellated sperm motility and sperm motility. Differentially expressed mRNAs were enriched in the top 16 KEGG pathways. Targets of the differentially expressed lncRNAs elucidate functions in cis and trans manner using the genetic context of the lncRNA locus, and lncRNA sequences revealed 471 mRNAs targets of 10 lncRNAs. This study illustrates the existence of potential lncRNA biomarkers that can be implemented in analyzing the quality of ram sperm and determining the sperm fertility and is used in breeding soundness exams for precision livestock farming to ensure food security on a global scale.

A comprehensive analysis of spermatozoal RNA elements in idiopathic infertile males undergoing fertility treatment

Current approaches to diagnosing male infertility inadequately assess the complexity of the male gamete. Beyond the paternal haploid genome, spermatozoa also deliver coding and non-coding RNAs to the oocyte. While sperm-borne RNAs have demonstrated potential involvement in embryo development, the underlying mechanisms remain unclear. In this study, 47 sperm samples from normozoospermic males undergoing fertility treatment using donor oocytes were sequenced and analyzed to evaluate associations between sperm RNA elements (exon-sized sequences) and blastocyst progression. A total of 366 RNA elements (REs) were significantly associated with blastocyst rate (padj < 0.05), some of which were linked to genes related to critical developmental processes, including mitotic spindle formation and both ectoderm and mesoderm specification. Of note, 27 RE-associated RNAs are predicted targets of our previously reported list of developmentally significant miRNAs. Inverse RE-miRNA expression patterns were consistent with miRNA-mediated down-regulation. This study provides a comprehensive set of REs which differ by the patient's ability to produce blastocysts. This knowledge can be leveraged to improve clinical screening of male infertility and ultimately reduce time to pregnancy.

Factors affecting the success of laparoscopic artificial insemination in sheep

Successful artificial breeding underpins rapid genetic and production gains in animal agriculture. In sheep, artificial insemination with frozen semen is performed via intrauterine laparoscopy as frozen-thawed spermatozoa do not traverse the cervix in sufficient numbers for high fertility and transcervical insemination is anatomically impossible in most ewes. Historically, laparoscopic artificial insemination has always been considered reasonably successful, but recent anecdotal reports of poor fertility place it at risk of warning adoption. Understanding the male, female and environmental factors that influence the fertility of sheep is warranted if the success of artificial insemination is to be improved and genetic progress maximised for the sheep industry. This review details the current practice of laparoscopic AI in sheep. It explores the effects of semen quantity and quality, the ewe, her preparation, and environmental conditions, on the fertility obtained following laparoscopic artificial insemination.

Predicting the cryotolerance of boar sperm through antioxidant stress

High sperm cryotolerance is crucial to the successful cryopreservation of boar sperm. Evaluating the cryotolerance of boar sperm by using a rapid and convenient technique can enhance the commercial viability of these sperm. This study investigated the correlation between sperm parameters for three sample subsets-fresh sperm, sperm with H2O2-induced oxidative damage (hereinafter referred to as H2O2-induced sperm), and frozen-thawed sperm-to identify the potential of these correlations to predict cryotolerance. A total of 64 sperm samples were obtained from 64 Duroc boars. The sperm parameters of the three subsets, where the frozen-thawed sperm were analysed at 30 or 180 min after thawing, were determined, and the coefficients of correlation between these parameters were calculated. The results indicated that H2O2-induced oxidative stress resulted in decreases in various sperm parameters-including total motility (TM), viability (VIA), mitochondrial membrane potential (MMP), and live sperm with MMP (LMP)-but increased their coefficients of variation. Receiver operating characteristic (ROC) curve analysis revealed that the kinematic parameters of the H2O2-induced sperm effectively predicted those of the frozen-thawed boar sperm at 30 min after thawing; the corresponding area under the ROC curve (AUC) was 0.8667 for TM and 0.8733 for progressive motility in the H2O2-induced sperm. For measurement at 180 min after thawing, the sperm membrane and mitochondrial parameters of the H2O2-induced sperm effectively predicted the LMP of the frozen-thawed boar sperm; the corresponding AUC was 0.8489 for VIA, 0.8289 for MMP, and 0.8444 for LMP. To our knowledge, this is the first study to directly establish a strong correlation between post-thaw boar sperm quality and H2O2-induced oxidative stress before freezing. Our proposed technique can serve as a valuable reference for the development of practical applications aimed at enhancing techniques for cryopreserving boar sperm.

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Structural variants (SVs), such as deletions (DELs) and insertions (INSs), contribute substantially to pig genetic diversity and phenotypic variation. Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes, we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes. Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation. Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. We identify that the genotypes of two DELs (296-bp DEL, chr7: 52,172,101-52,172,397; 278-bp DEL, chr18: 23,840,143-23,840,421) located in muscle-specific enhancers are associated with the expression of target genes related to meat quality (FSD2) and muscle fiber hypertrophy (LMOD2 and WASL) in pigs. Our results highlight the role of SVs in domestic porcine evolution, and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

Risk of Sperm Disorders and Impaired Fertility in Frozen-Thawed Bull Semen: A Genome-Wide Association Study

Cryopreservation is a widely used method of semen conservation in animal breeding programs. This process, however, can have a detrimental effect on sperm quality, especially in terms of its morphology. The resultant sperm disorders raise the risk of reduced sperm fertilizing ability, which poses a serious threat to the long-term efficacy of livestock reproduction and breeding. Understanding the genetic factors underlying these effects is critical for maintaining sperm quality during cryopreservation, and for animal fertility in general. In this regard, we performed a genome-wide association study to identify genomic regions associated with various cryopreservation sperm abnormalities in Holstein cattle, using single nucleotide polymorphism (SNP) markers via a high-density genotyping assay. Our analysis revealed a significant association of specific SNPs and candidate genes with absence of acrosomes, damaged cell necks and tails, as well as wrinkled acrosomes and decreased motility of cryopreserved sperm. As a result, we identified candidate genes such as POU6F2, LPCAT4, DPYD, SLC39A12 and CACNB2, as well as microRNAs (bta-mir-137 and bta-mir-2420) that may play a critical role in sperm morphology and disorders. These findings provide crucial information on the molecular mechanisms underlying acrosome integrity, motility, head abnormalities and damaged cell necks and tails of sperm after cryopreservation. Further studies with larger sample sizes, genome-wide coverage and functional validation are needed to explore causal variants in more detail, thereby elucidating the mechanisms mediating these effects. Overall, our results contribute to the understanding of genetic architecture in cryopreserved semen quality and disorders in bulls, laying the foundation for improved animal reproduction and breeding.

Integrated transcriptomics and proteomics assay identifies the role of FCGR1A in maintaining sperm fertilization capacity during semen cryopreservation in sheep

Semen cryopreservation is a promising technology employed in preserving high-quality varieties in animal husbandry and is also widely applied in the human sperm bank. However, the compromised qualities, such as decreased sperm motility, damaged membrane structure, and reduced fertilization competency, have significantly hampered the efficient application of this technique. Therefore, it is imperative to depict various molecular changes found in cryopreserved sperm and identify the regulatory network in response to the cryopreservation stress. In this study, semen was collected from three Chinese Merino rams and divided into untreated (fresh semen, FS) and programmed freezing (programmed freezing semen, PS) groups. After measuring different quality parameters, the ultra-low RNA-seq and tandem mass tag-based (TMT) proteome were conducted in both the groups. The results indicated that the motility (82.63% ± 3.55% vs. 34.10% ± 2.90%, p < 0.05) and viability (89.46% ± 2.53% vs. 44.78% ± 2.29%, p < 0.05) of the sperm in the FS group were significantly higher compared to those in the PS group. In addition, 45 upregulated and 291 downregulated genes, as well as 30 upregulated and 48 downregulated proteins, were found in transcriptomics and proteomics data separately. Moreover, three integrated methods, namely, functional annotation and enrichment analysis, Pearson's correlation analysis, and two-way orthogonal partial least squares (O2PLS) analysis, were used for further analysis. The results suggested that various differentially expressed genes and proteins (DEGs and DEPs) were mainly enriched in leishmaniasis and hematopoietic cell lineage, and Fc gamma receptor Ia (FCGR1A) was significantly downregulated in cryopreserved sperm both at mRNA and protein levels in comparison with the fresh counterpart. In addition, top five genes (FCGR1A, HCK, SLX4, ITGA3, and BET1) and 22 proteins could form a distinct network in which genes and proteins were significantly correlated (p < 0.05). Interestingly, FCGR1A also appeared in the top 25 correlation list based on O2PLS analysis. Hence, FCGR1A was selected as the most potential differentially expressed candidate for screening by the three integrated multi-omics analysis methods. In addition, Pearson's correlation analysis indicated that the expression level of FCGR1A was positively correlated with sperm motility and viability. A subsequent experiment was conducted to identify the biological role of FCGR1A in sperm function. The results showed that both the sperm viability (fresh group: 87.65% ± 4.17% vs. 75.8% ± 1.15%, cryopreserved group: 48.15% ± 0.63% vs. 42.45% ± 2.61%, p < 0.05) and motility (fresh group: 83.27% ± 4.15% vs. 70.41% ± 1.07%, cryopreserved group: 45.31% ± 3.28% vs. 35.13% ± 2.82%, p < 0.05) were significantly reduced in fresh and frozen sperm when FCGR1A was blocked. Moreover, the cleavage rate of embryos fertilized by FCGR1A-blocked sperm was noted to be significantly lower in both fresh (95.28% ± 1.16% vs. 90.44% ± 1.56%, p < 0.05) and frozen groups (89.8% ± 1.50% vs. 82.53% ± 1.53%, p < 0.05). In conclusion, our results revealed that the downregulated membrane protein FCGR1A can potentially contribute to the reduced sperm fertility competency in the cryopreserved sheep sperm.

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.

Review: Evaluation of bull fertility. Functional and molecular approaches

With the term "assisted reproduction technologies" in modern cattle farming, one could imply the collection of techniques that aim at the optimal use of bovine gametes to produce animals of high genetic value in a time- and cost-efficient manner. The accurate characterisation of sperm quality plays a critical role for the efficiency of several assisted reproduction-related procedures, such as sperm processing, in vitro embryo production and artificial insemination. Bull fertility is ultimately a collective projection of the ability of a series of ejaculates to endure sperm processing stress, and achieve fertilisation of the oocyte and production of a viable and well-developing embryo. In this concept, the assessment of sperm functional and molecular characteristics is key to bull fertility diagnostics and prognostics. Among others, functional features linked to sperm plasma membrane, acrosome and DNA integrity are usually assessed as a measure of the ability of sperm to express the phenotypes that will allow them to maintain their homeostasis and orchestrate-in a strict temporal manner-the course of events that will enable the delivery of their genetic content to the oocyte upon fertilisation. Nevertheless, measures of sperm functionality are not always adequate indicators of bull fertility. Nowadays, advancements in the field of molecular biology have facilitated the profiling of several biomolecules in male gametes. The molecular profiling of bovine sperm offers a deeper insight into the mechanisms underlying sperm physiology and, thus, can reveal novel candidate markers for bull fertility prognosis. In this review, the importance of three organelles (the nucleus, the plasma membrane and the acrosome) for the characterisation of sperm fertilising capacity and bull fertility is discussed at functional and molecular levels. In particular, information about sperm head morphometry, chromatin structure, viability as well as the ability of sperm to capacitate and undergo the acrosome reaction are presented in relation to the cryotolerance of male gametes and bull fertility. Finally, major spermatozoal coding and non-coding RNAs, and proteins that are involved in the above-mentioned aspects of sperm functionality are also summarised.

Modulation of long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression in the liver of Beagle dogs by Toxocara canis infection

BACKGROUND

Long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) play crucial roles in regulating various physiological and pathological processes. However, the role of lncRNAs and mRNAs in mediating the liver response during Toxocara canis infection remains incompletely understood.

METHODS

In the present study, the expression profile of lncRNAs and mRNAs was investigated in the liver of Beagle dogs infected by T. canis using high-throughput RNA sequencing.

RESULTS

Compared with the control groups, 876 differentially expressed (DE) lncRNAs and 288 DEmRNAs were identified at 12 h post-infection (hpi), 906 DElncRNAs and 261 DEmRNAs were identified at 24 hpi, and 876 DElncRNAs and 302 DEmRNAs were identified at 36 days post-infection (dpi). A total of 16 DEmRNAs (e.g. dpp4, crp and gnas) were commonly identified at the three infection stages. Enrichment and co-localization analyses identified several pathways involved in immune and inflammatory responses during T. canis infection. Some novel DElncRNAs, such as LNC_015756, LNC_011050 and LNC_011052, were also associated with immune and inflammatory responses. Also, LNC_005105 and LNC_005401 were associated with the secretion of anti-inflammatory cytokines, which may play a role in the healing of liver pathology at the late stage of infection.

CONCLUSIONS

Our data provided new insight into the regulatory roles of lncRNAs and mRNAs in the pathogenesis of T. canis and improved our understanding of the contribution of lncRNAs and mRNAs to the immune and inflammatory response of the liver during T. canis infection.

Effects of BAMBI on luteinized follicular granulosa cell proliferation and steroid hormone production in sheep

Bone morphogenetic protein and activin membrane-bound inhibitor (BAMBI) regulates mammalian ovarian follicle growth and maturation; however, its effect on luteinized granulosa cells (LGCs) in sheep ovarian follicles remains unknown. Here we explored the regulatory role of LGC functions and steroid hormone synthesis by BAMBI. Multiple sequence alignment revealed that the sheep BAMBI gene sequence was relatively conserved. Sheep LGCs were strongly positive for BAMBI. LGC proliferation increased when BAMBI was silenced and decreased when BAMBI was overexpressed. After BAMBI overexpression, the expression of CASP3, CASP8, CASP9, and BAX significantly increased, whereas that of BCL2 and the ratio of BCL2/BAX expression decreased. The opposite was observed after BAMBI silencing. CDKN1A, CCND1, and CCND2 were downregulated with BAMBI overexpression and upregulated with BAMBI silencing. Expression of steroid hormone-related genes (CYP11A1, STAR, and 3BHSD), except CYP19A1, significantly increased after BAMBI overexpression. Moreover, estrogen and progesterone secretion increased after BAMBI overexpression and decreased after BAMBI interference. The effect of the exogenous addition of bone morphogenetic protein 2 (BMP2) on GCs was similar to that of BAMBI overexpression. In conclusion, BAMBI can regulate the proliferation and steroid hormone synthesis of sheep LGCs, and BMP2 can affect LGCs as an activator of BAMBI. These findings provide a basis for further research on the physiological role of BAMBI.

Cryopreservation of Human Spermatozoa: Functional, Molecular and Clinical Aspects

Cryopreservation is an expanding strategy to allow not only fertility preservation for individuals who need such procedures because of gonadotoxic treatments, active duty in dangerous occupations or social reasons and gamete donation for couples where conception is denied, but also for animal breeding and preservation of endangered animal species. Despite the improvement in semen cryopreservation techniques and the worldwide expansion of semen banks, damage to spermatozoa and the consequent impairment of its functions still remain unsolved problems, conditioning the choice of the technique in assisted reproduction procedures. Although many studies have attempted to find solutions to limit sperm damage following cryopreservation and identify possible markers of damage susceptibility, active research in this field is still required in order to optimize the process. Here, we review the available evidence regarding structural, molecular and functional damage occurring in cryopreserved human spermatozoa and the possible strategies to prevent it and optimize the procedures. Finally, we review the results on assisted reproduction technique (ARTs) outcomes following the use of cryopreserved spermatozoa.

Scrutiny of NolA and NodD1 Regulatory Roles in Symbiotic Compatibility Unveils New Insights into Bradyrhizobium guangxiense CCBAU53363 Interacting with Peanut (Arachis hypogaea) and Mung Bean (Vigna radiata)

Bradyrhizobium guangxiense CCBAU53363 efficiently nodulates peanut but exhibits incompatible interaction with mung bean. By comparing the common nod region with those of other peanut bradyrhizobia efficiently nodulating these two hosts, distinctive characteristics with a single nodD isoform (nodD1) and a truncated nolA were identified. However, the regulatory roles of NodD1 and NolA and their coordination in legume-bradyrhizobial interactions remain largely unknown in terms of explaining the contrasting symbiotic compatibility. Here, we report that nolA was important for CCBAU53363 symbiosis with peanut but restricted nodulation on mung bean, while nodD1 was dispensable for CCBAU53363 symbiosis with peanut but essential for nodulation on mung bean. Moreover, nolA exerted a cumulative contribution with nodD1 to efficient symbiosis with peanut. Additionally, mutants lacking nolA delayed nodulation on peanut, and both nolA and nodD1 were required for competitive nodule colonization. It is noteworth that most of the nodulation genes and type III secretion system (T3SS)-related genes were significantly downregulated in a strain 53ΔnodD1nolA mutant compared to wild-type strain CCBAU53363, and the downregulated nodulation genes also had a greater impact than T3SS-related genes on the symbiotic defect of 53ΔnodD1nolA on peanut, which was supported by a more severe symbiotic defect induced by 53ΔnodC than that with the 53ΔnodD1nopP, 53ΔnodD1rhcJ, and 53ΔnodD1ttsI mutants. NolA did not regulate nod gene expression but did regulate the T3SS effector gene nopP in an indirect way. Meanwhile, nolA, nodW, and some T3SS-related genes besides nopP were also demonstrated as new "repressors" that seriously impaired CCBAU53363 symbiosis with mung bean. Taken together, the roles and essentiality of nolA and nodD1 in modulating symbiotic compatibility are sophisticated and host dependent. IMPORTANCE The main findings of this study were that we clarified that the roles and essentiality of nodD1 and nolA are host dependent. Importantly, for the first time, NolA was found to positively regulate T3SS effector gene nopP to mediate incompatibility on mung bean. Additionally, NolA does not regulate nod genes, which are activated by NodD1. nolA exerts a cumulative effect with nodD1 on CCBAU53363 symbiosis with peanut. These findings shed new light on our understanding of coordinated regulation of NodD1 and NolA in peanut bradyrhizobia with different hosts.

Molecular Markers: A New Paradigm in the Prediction of Sperm Freezability

For decades now, sperm cryopreservation has been a pillar of assisted reproduction in animals as well as humans. Nevertheless, the success of cryopreservation varies across species, seasons, and latitudes and even within the same individual. With the dawn of progressive analytical techniques in the field of genomics, proteomics, and metabolomics, new options for a more accurate semen quality assessment have become available. This review summarizes currently available information on specific molecular characteristics of spermatozoa that could predict their cryotolerance before the freezing process. Understanding the changes in sperm biology as a result of their exposure to low temperatures may contribute to the development and implementation of appropriate measures to assure high post-thaw sperm quality. Furthermore, an early prediction of cryotolerance or cryosensitivity may lead to the establishment of customized protocols interconnecting adequate sperm processing procedures, freezing techniques, and cryosupplements that are most feasible for the individual needs of the ejaculate.

Characterization of freezability-associated metabolites in boar semen

Sperm cryopreservation maintains the diversities of porcine genetic resources and improves utilization efficiency of boar semen in artificial insemination practices. Freezability of boar semen presents remarkable differences among individuals. However, metabolic markers for boar semen freezability in both sperm and seminal plasma largely remain unknown. The present study thus aims to determine differences in metabolites of sperm and seminal plasma between poor (PF) and good (GF) freezability semen from a Chinese native pig and screen potential markers for semen freezability. A total of 72,048 metabolites in sperm and 66,551 metabolites in seminal plasma were identified by liquid chromatography-mass spectrometry, respectively. The proportion of lipid molecules among all metabolites in both sperm and seminal plasma was the maximum regardless of negative or positive mode. Furthermore, we identified 21 differentially expressed metabolites (DEMs) in sperm and 185 DEMs in seminal plasma between PF and GF group. Additionally, clustering analysis showed that DEMs in sperm and seminal plasma exhibited significant changes between PF and GF group. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DEMs in sperm were mainly enriched in metabolic pathways of amino acids and caffeine. DEMs in seminal plasma were associated with AMPK and cAMP signaling pathways. Taken together, these results demonstrate that sperm and seminal plasma of native pigs present differential metabolome between PF and GF semen.

Seminal plasma metabolomics analysis of differences in liquid preservation ability of boar sperm

The preservation of semen is pivotal in animal reproduction to ensure successful fertilization and genetic improvement of livestock and poultry. However, investigating the underlying causes of differences in sperm liquid preservation ability and identifying relevant biomarkers remains a challenge. This study utilized liquid chromatography-mass spectrometry (LC-MS) to analyze the metabolite composition of seminal plasma (SP) from two groups with extreme differences in sperm liquid preservation ability. The two groups namely the good liquid preservation ability (GPA) and the poor preservation ability (PPA). The aim was to explore the relationship between metabolite composition in SP and sperm liquid preservation ability, and to identify candidate biomarkers associated with this ability of sperm. The results revealed the identification of 756 metabolites and 70 differentially expressed metabolites (DEM) in the SP from two groups of boar semen with differing liquid preservation abilities at 17 °C. The majority of identified metabolites in the SP belonged to organic acids and derivatives as well as lipids and lipid-like molecules. The DEM in the SP primarily consisted of amino acids, peptides, and analogs. The Kyoto Encyclopedia of Genes and Genomes analysis also demonstrated that the DEM are mainly concentrated in amino acid synthesis and metabolism-related pathways (P < 0.05). Furthermore, eleven key metabolites were identified and six target amino acids were verified, and the results were consistent with the non-targeted metabolic analysis. These findings indicated that amino acids and their associated pathways play a potential role in determining boar sperm quality and liquid preservation ability. D-proline, arginine, L-citrulline, phenylalanine, leucine, DL-proline, DL-serine, and indole may serve as potential biomarkers for early assessment of boar sperm liquid preservation ability. The findings of this study are helpful in understanding the causes and mechanisms of differences in the liquid preservation ability of boar sperm, and provide valuable insights for improving semen quality assessment methods and developing novel extenders or protocols.

Albumin (ALB) and protein disulfide isomerase family A member 4 (PDIA4) are novel markers to predict sperm freezability of Erhualian boar

The frozen semen of Erhualian pig can promote the continuous improvement of commercial pigs, but currently, frozen semen fails to satisfy the practical application requirement. Oxidative damage is one of the crucial factors affecting the quality of frozen semen; besides, there are individual differences in boar sperm freezability. Based on the previous analysis of the proteomic differences of Erhualian boar sperm with different freezability, two differentially abundant proteins (DAPs) in boar sperm, albumin (ALB) and protein disulfide isomerase family A member 4 (PDIA4), were selected as the research objects in the current study. It is assumed that redox-related proteins ALB and PDIA4 can be used as markers to predict Erhualian boar sperm freezability. We cryopreserved the semen of 14 Erhualian boars. According to the difference of frozen semen quality, boars with good and poor freezability ejaculates (GFE and PFE, n = 3) were selected respectively. The relative contents of ALB and PDIA4 in GFE and PFE were analyzed by Western blot, and the localization patterns of ALB and PDIA4 in pre-frozen and frozen-thawed sperm were detected by immunofluorescence. The results showed that the abundances of ALB and PDIA4 in GFE were significantly higher than PFE, and there was a significant correlation between the relative contents of ALB and PDIA4 and frozen-thawed sperm quality parameters. Additionally, the freezing process had no effect on the localization patterns of ALB and PDIA4 in spermatozoa. In conclusion, these results suggest that ALB and PDIA4 are related to boar sperm cryotolerance and may be used as novel freezability markers.

Evaluation of lipidomic change in goat sperm after cryopreservation

The current study aimed to detect the relationship between the spermatozoa cryotolerance and the post-thawed sperm lipidome. Ejaculates from 20 goats, and performed a uniform frozen-thawed procedure in this study. According to the total motility of thawed sperm of goats, semen samples were classified into HF group (High Freezers, n = 8) with >60% total motility and LF group (Low Freezers, n = 8) with < 45% total motility. The lipidomic analysis based on UHPLC-MS/MS was utilized to investigate the relationship between sperm cryotolerance and their lipid metabolites expression. The results showed that the cryotolerance of sperm from different individual goats were in great variation. The total motility of post-thawed sperm in HF group (60.93 ± 2.43%) is significantly higher than that in LF group (34.04 ± 3.41%, P < 0.01). And the post-thawed sperm in HF group exhibited significantly higher plasma membrane (59.06 ± 2.34%) and acrosome integrity (62.93 ± 1.15%) than that in LF group (34.06 ± 4.85%, 44.92 ± 2.19% respectively, P < 0.01). The total of 29 lipid subclasses and 1,133 lipid molecules in the post-thawed goat sperm were identified by lipidomics analysis. The lipid content of thawed sperm in HF group was higher than that in LF group, the lipid profile in HF group was significantly separated from LF group, which indicated that the difference in lipid composition and lipid metabolism mode of sperm between the two groups was existed, especially the expression of phosphatidylcholine and triglyceride molecules. In conclusion, the cryotolerance of sperm from different individual goats were in great variation. Sperm with high cryotolerance may be able to uptake more lipids during cryopreservation. The increase in phosphatidylcholine and triglyceride content of thawed. Sperm may relate to more active lipid anabolic processes.

Coordinated regulation of symbiotic adaptation by NodD proteins and NolA in the type I peanut bradyrhizobial strain Bradyrhizobium zhanjiangense CCBAU51778

Type I peanut bradyrhizobial strains can establish efficient symbiosis in contrast to symbiotic incompatibility induced by type II strains with mung bean. The notable distinction in the two kinds of key symbiosis-related regulators nolA and nodD close to the nodABCSUIJ operon region between these two types of peanut bradyrhizobia was found. Therefore, we determined whether NolA and NodD proteins regulate the symbiotic adaptations of type I strains to different hosts. We found that NodD1-NolA synergistically regulated the symbiosis between the type I strain Bradyrhizobium zhanjiangense CCBAU51778 and mung bean, and NodD1-NodD2 jointly regulated nodulation ability. In contrast, NodD1-NolA coordinately regulated nodulation ability in the CCBAU51778-peanut symbiosis. Meanwhile, NodD1 and NolA collectively contributes to competitive nodule colonization of CCBAU51778 on both hosts. The Fucosylated Nod factors and intact type 3 secretion system (T3SS), rather than extra nodD2 and full-length nolA, were critical for effective symbiosis with mung bean. Unexpectedly, T3SS-related genes were activated by NodD2 but not NodD1. Compared to NodD1 and NodD2, NolA predominantly inhibits exopolysaccharide production by promoting exoR expression. Importantly, this is the first report that NolA regulates rhizobial T3SS-related genes. The coordinated regulation and integration of different gene networks to fine-tune the expression of symbiosis-related genes and other accessory genes by NodD1-NolA might be required for CCBAU51778 to efficiently nodulate peanut. This study shed new light on our understanding of the regulatory roles of NolA and NodD proteins in symbiotic adaptation, highlighting the sophisticated gene networks dominated by NodD1-NolA.

Expression of TXNRD1, HSPA4L and ATP1B1 Genes Associated with the Freezability of Boar Sperm

Cryopreservation is associated with increased oxidative stress, which is responsible for sperm damage. We analyzed the effect of cryopreservation on mRNA and protein expression of thioredoxin reductase 1 (TXNRD1), heat shock protein family A (HSP 70) member 4 like (HSPA4L) and sodium/potassium-transporting ATPase subunit beta-1 (ATP1B1) genes in boar sperm with different freezability. Boars were classified as having good and poor semen freezability (GSF and PSF, respectively), according to the assessment of post-thaw sperm motility. Total RNA was isolated from fresh pre-freeze (PF) and frozen-thawed (FT) sperm from five boars of the GSF and PSF groups, respectively. Quantification of TXNRD1, HSPA4L and ATP1B1 gene expression was performed by RT-qPCR analysis. Proteins extracted from sperm were subjected to Western blotting and SDS-PAGE analyses. Poor freezability ejaculates were characterized by significantly higher relative mRNA expression levels of TXNRD1 and HSPA4L in FT sperm compared with the fresh PF sperm. Furthermore, the relative mRNA expression level of ATP1B1 was significantly higher in the fresh PF sperm of the GSF group. Western blotting analysis revealed significantly higher relative expression of TXNRD1 protein in the fresh PF sperm of the GSF group, while HSPA4L protein expression was markedly increased in FT sperm of the PSF group. Electrophoretic and densitometric analyses revealed a higher number of proteins in the fresh PF and FT sperm of the PSF and GSF groups, respectively. The results of this study indicate that ATP1B1 mRNA expression in the fresh PF sperm is a promising cryotolerance marker, while the variations of TXNRD1 and HSPA4L protein expression in the fresh PF or FT sperm provide useful information that may help to elucidate their biological significance in cryo-damage.

Age-Dependent Variations in Functional Quality and Proteomic Characteristics of Canine (Canis lupus familiaris) Epididymal Spermatozoa

Increased male age is associated with a significant reduction in semen quality. Little is known about the sperm proteome changes resulting from the aging process. This study aimed to investigate the relationship between the functional quality and proteome of epididymal spermatozoa of dogs that were differing in age. The study was conducted on 30 male dogs that were divided into three age groups. G1—12 to 41 months old, G2—42 to 77 months old, and G3—78 to 132 months old. The sperm samples were assessed using a computer-assisted semen analysis (CASA). The epididymal sperm proteins were analyzed using gel electrophoresis (SDS-PAGE), nano-liquid chromatography coupled to quadrupole time of flight mass spectrometry (NanoUPLC-Q-TOF/MS) and bioinformatic tools. The sperm quality parameters were significantly lower in older dogs. NanoUPLC-Q-TOF/MS identification resulted in 865 proteins that were found in the G1, 472 in G2, and 435 in G3. There were seven proteins that were present in all three age groups, and four of them (ACTB, CE10, NPC2, CRISP2) showed significant changes among the studied groups. Age-dependent variations were detected in the sperm proteome composition and were related to important metabolite pathways, which might suggest that several proteins are implicated in sperm maturation and could be potential aging biomarkers.

In Silico Identification of lncRNAs Regulating Sperm Motility in the Turkey (Meleagris gallopavo L.)

Long non-coding RNAs (lncRNAs) are transcripts not translated into proteins with a length of more than 200 bp. LncRNAs are considered an important factor in the regulation of countless biological processes, mainly through the regulation of gene expression and interactions with proteins. However, the detailed mechanism of interaction as well as functions of lncRNAs are still unclear and therefore constitute a serious research challenge. In this study, for the first time, potential mechanisms of lncRNA regulation of processes related to sperm motility in turkey were investigated and described. Customized bioinformatics analysis was used to detect and identify lncRNAs, and their correlations with differentially expressed genes and proteins were also investigated. Results revealed the expression of 863 new/unknown lncRNAs in ductus deferens, testes and epididymis of turkeys. Moreover, potential relationships of the lncRNAs with the coding mRNAs and their products were identified in turkey reproductive tissues. The results obtained from the OMICS study may be useful in describing and characterizing the way that lncRNAs regulate genes and proteins as well as signaling pathways related to sperm motility.

Identification of Genes Related to Squab Muscle Growth and Lipid Metabolism from Transcriptome Profiles of Breast Muscle and Liver in Domestic Pigeon (Columba livia)

Simple Summary

Domestic pigeon is an important small poultry species raised for high-quality meat production. However, the relevant gene associated with meat growth and lipid metabolism during the period from dehulling to marketing are not known. Therefore, we aim to identify genes related to squab muscle growth and lip metabolism from transcriptome profiles of breast muscle and liver in domestic pigeon. In this study, we totally found that 4465 differentially expressed genes (DEGs) identified in the breast muscle and liver libraries, which include 2585 genes that were up-regulated and 2122 genes that were down-regulated. Most genes are involved in cell proliferation and differentiation, lipid metabolism and energy metabolism according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs. We also detected 16 DEGs to verify data from RNA-Seq and qPCR, which were consistent in quantitatively estimating the transcription levels of the tested transcripts by qPCR analysis. The results of this study will lay the foundation for understanding the mechanisms of muscle growth and lipid metabolism in domestic pigeons.

Abstract

The improvements in muscle growth rate and meat quality are the major breeding aims in pigeon industry. Liver and muscle are recognized as important sites for fatty acid metabolism; understanding the role of specific transcripts in the breast muscle and liver might lead to the elucidation of interrelated biological processes. In this study, RNA-Sequencing (RNA-Seq) was applied to compare the transcriptomes of breast muscle and liver tissues among pigeons at five developmental periods (0, 1, 2, 3, 4 weeks post-hatching) to identify candidate genes related to muscle growth and lipid metabolism. There were 3142 differentially expressed genes (DEGs) identified in the breast muscle libraries; 1794 genes were up-regulated while 1531 genes were down-regulated. A total of 1323 DEGs were acquired from the liver libraries, with 791 up-regulated genes and 591 down-regulated genes. By pathway enrichment analysis, a set of significantly enriched pathways were identified for the DEGs, which are potentially involved in cell proliferation and differentiation, lipid metabolism and energy metabolism in pigeon breast muscle and liver. Our results are consistent with previous partial reports from domestic animals and poultry and provide some unidentified genes involved in muscle growth and lipid metabolism. The reliability of the sequencing data was verified through qPCR analysis of 16 genes from eight comparison groups (two genes per group). The findings from this study could contribute to future investigations of muscle growth and lipid metabolism mechanisms and establish molecular approaches to improve muscle growth rate and meat quality in domestic pigeon breeding.

Heat shock protein family D member 1 in boar spermatozoa is strongly related to the litter size of inseminated sows

Background

Sperm quality evaluation is the logical first step in increasing field fertility. Spermatozoa contain cytoplasmic organelles and biomolecules known as sperm-intrinsic factors, which play key roles in sperm maturation, sperm-oocyte fusion, and embryo development. In particular, sperm membrane proteins [e.g., arginine vasopressin receptor 2, beta-actin, prohibitin, and heat shock protein family D member 1 (HSPD1)] and RNA could be used as functional indicators of male fertility. We sought to clarify the effects of differential mRNA expression of selected genes on several fertilisation parameters, including sperm motility, motion kinematics, capacitation, and litter size, in a porcine model.

Results

Our results demonstrated that HSPD1 expression was significantly correlated with male fertility, as measured by the litter size of inseminated sows. The expression of HSPD1 mRNA was linked to sperm motility and other motion kinematic characteristics. Furthermore, HSPD1 had a 66.7% overall accuracy in detecting male fertility, and the high-litter size group which was selected with the HSPD1 marker had a 1.34 greater litter size than the low-litter size group.

Conclusions

Our findings indicate that HSPD1 might be a helpful biomarker for superior boar selection for artificial insemination, which could boost field fertility.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00689-0.

Canine Spermatozoa—Predictability of Cryotolerance

Simple Summary

Semen freezing in dogs is a field of growing interest. The international shipment of cryoconserved semen contributes to the avoidance of long travels and long-term storage of valuable gametes. However, the collection of one semen portion on average results in one to three doses for artificial insemination, which is a poor result in comparison to the outcome in large animals. The costs for the owners are therefore rather high. In individual dogs, the semen quality of raw semen is good; however, it could be suboptimal after thawing. To avoid costly freezing of these low-quality ejaculates, markers of freezability are useful. An abundance of markers are available for large animals, but not for dogs. This review provides an overview on markers for freezability of canine semen.

Abstract

Markers of freezability allow the selection of ejaculates of good freezability. So far, most investigations were conducted in boars, bulls, rams and horses, with high economic interests triggering the efforts. The progress in dogs is comparably slow. A critical evaluation of the methods requires consideration of practicability, with most labs not even possessing a computer assisted sperm analyser (CASA); furthermore, small canine ejaculates mostly do not allow the use of large semen volumes. In dogs, modern markers of freezability no longer assess single membrane constituents or seminal plasma components but comprise tests of cell functionality and adaptability, energy metabolism, cluster analyses of kinetic and morphometric parameters, as well as DNA intactness. Identification of the most efficient combination of tests seems useful. At present, examination by CASA combined with cluster analysis of kinetic subgroups, JC-1 staining and COMET assay or staining with toluidine blue seem most appropriate; however, cell volumetry and other functional tests deserve better attention. A better understanding of spermatozoa energy metabolism might reveal new markers. This review focuses on the requirements and markers of freezability of canine semen, highlighting potential future candidates.

Cryoprotectants-Free Vitrification and Conventional Freezing of Human Spermatozoa: A Comparative Transcript Profiling

Introduction: Spermatozoa cryopreservation is an important technique to preserve fertility for males. This study aimed at exploring the stability of epigenetics information in human spermatozoa, manipulated by two different technologies, freezing and vitrification. Methods: Spermatozoa samples were distributed into three groups: 1. Fresh spermatozoa (control group), 2. Frozen spermatozoa, 3. Vitrified spermatozoa. Epigenetic differences of fresh and cryopreserved spermatozoa were evaluated using high-throughput RNA sequencing. Results: Differentially expressed genes (DEGs) in frozen (1103 genes) and vitrified (333 genes) spermatozoa were evaluated. The bioinformatical analysis identified 8 and 15 significant pathways in groups of frozen and vitrified spermatozoa, respectively. The majority of these pathways are most relevant to immune and infectious diseases. The DEGs of the fertilization process are not detected during vitrification. The freezing process induces more down-regulation of genes and is relevant to apoptosis changes and immune response. Conclusion: Cryopreservation of human spermatozoa is an epigenetically safe method for male fertility preservation. Cryoprotectant-free vitrification can induce more minor biological changes in human spermatozoa, in comparison with conventional freezing.

Relevance of Aquaporins for Gamete Function and Cryopreservation

Simple Summary

The interaction between cells and the extracellular medium is of great importance; changes in medium composition can drive water movement across plasma membranes. Aquaporins (AQPs) are membrane channels involved in the transport of water and some solutes across membranes. When sperm enter the female reproductive tract after ejaculation, they encounter a drastic change in extracellular composition, which leads to water flowing across the plasma membrane. This triggers a series of events that are crucial to allowing fertilization to take place, such as regulation of sperm motility. In the context of assisted reproduction techniques (ART), long-term storage of gametes is sometimes required, and, during cryopreservation, these cells undergo drastic changes in extracellular medium composition. As a result, AQPs are crucial in both sperm and oocytes during this process. Cryopreservation is of considerable importance for fertility preservation in livestock, endangered species and for individuals undergoing certain medical treatments that compromise their fertility. Further research to fully elucidate the roles and underlying mechanisms of AQPs in mammalian sperm is therefore warranted.

Abstract

The interaction between cells and the extracellular medium is of great importance, and drastic changes in extracellular solute concentrations drive water movement across the plasma membrane. Aquaporins (AQPs) are a family of transmembrane channels that allow the transport of water and small solutes across cell membranes. Different members of this family have been identified in gametes. In sperm, they are relevant to osmoadaptation after entering the female reproductive tract, which is crucial for sperm motility activation and capacitation and, thus, for their fertilizing ability. In addition, they are relevant during the cryopreservation process, since some members of this family are also permeable to glycerol, one of the most frequently used cryoprotective agents in livestock. Regarding oocytes, AQPs are very important in their maturation but also during cryopreservation. Further research to define the exact sets of AQPs that are present in oocytes from different species is needed, since the available literature envisages certain AQPs and their roles but does not provide complete information on the whole set of AQPs. This is of considerable importance because, in sperm, specific AQPs are known to compensate the role of non-functional members.

An Exploration of Current and Perspective Semen Analysis and Sperm Selection for Livestock Artificial Insemination

Artificial insemination of livestock has been a staple technology for producers worldwide for over sixty years. This reproductive technology has allowed for the rapid improvement of livestock genetics, most notably in dairy cattle and pigs. This field has experienced continuous improvements over the last six decades. Though much work has been carried out to improve the efficiency of AI, there are still many areas which continue to experience improvement, including semen analysis procedures, sperm selection techniques, sperm sexing technologies, and semen storage methods. Additionally, the use of AI continues to grow in beef cattle, horses, and small ruminants as the technology continues to become more efficient and yield higher pregnancy rates. In this review, AI trends in the various livestock species as well as cutting edge improvements in the aforementioned areas will be discussed at length. Future work will continue to refine the protocols which are used for AI and continue to increase pregnancy rates within all livestock species.

In Silico Analysis of Sperm From Ejaculates with Different Semen Characteristics

Background:

Male infertility is associated with altered characteristics of the sperm within the ejaculate. It is possible to find molecular explanations for the observed phenotypes and their consequences. This study aimed to analyze, using a specialized software, a gene set of transcriptomic data from different types of ejaculates.

Methods:

Data from ejaculate samples categorized as normal, oligospermia, and teratozoospermia were obtained from Gene Expression Omnibus (GEO). After normalization, the data average for each sample category was calculated and analyzed independently using Ingenuity Pathway Analysis (IPA).

Results:

Five important canonical pathways are involved in normal and altered semen samples (Oligospermia and teratozoospermia) except sirtuin signaling and mitochondrial dysfunction pathways. The five most important biological processes are identified in all semen phenotypes, but the only difference is the genes connected with initiation of RNA transcription in oligospermic and asthenospermic samples.

Conclusion:

Surprisingly, different types of ejaculates share many pathways and biological processes; sperm proteomics as a new global approach gives clues for the development of strategies to explain the reason for observed phenotypes of ejaculated spermatozoa, their possible effect on fertility, and for implementing research strategies in the context of infertility diagnosis and treatment.

Transcriptome dynamics in developing testes of domestic cats and impact of age on tissue resilience to cryopreservation

BACKGROUND

Fundamental knowledge of cellular and molecular mechanisms in developing testicular tissues is critical to better understand gonadal biology and responses to non-physiological conditions. The objective of our study was to (1) analyze transcriptome dynamics in developing testis of the domestic cat and (2) characterize age effects on the initial response of the tissue to vitrification. Tissues from adult and juvenile cats were processed for histology, DNA integrity, and RNA sequencing analyses before and after vitrification.

RESULTS

Transcriptomic findings enabled to further characterize juvenile period, distinguishing between early and late juvenile tissues. Changes in gene expression and functional pathways were extensive from early to late juvenile to adult development stages. Additionally, tissues from juvenile animals were more resilient to vitrification compared to adult counterparts, with early juvenile sample responding the least to vitrification and late juvenile sample response being closest to adult tissues.

CONCLUSIONS

This is the first study reporting comprehensive datasets on transcriptomic dynamic coupled with structural analysis of the cat testis according to the age and exposure to cryopreservation. It provides a comprehensive network of functional terms and pathways that are affected by age in the domestic cat and are either enriched in adult or juvenile testicular tissues.

Spermatozoa and seminal plasma small extracellular vesicles miRNAs as biomarkers of boar semen cryotolerance

Freeze boar semen is still the biggest challenge for the swine industry due to the high cold shock sensitivity of boar sperm cells and the variance of post-thaw results among individuals and ejaculates from the same boar. To solve this problem, we investigate if miRNAs present in sperm cells and small extracellular vesicles (EVs) from seminal plasma of raw boar ejaculates can predict high-quality ejaculates after underwent the freeze-thaw process. For this, we obtained miRNAs samples of sperm cells and EVs from raw seminal plasma from 27 ejaculates before the cryopreservation process. Two groups with different freezability considering the analysis post-thaw of structure and sperm functionality were formed: High freezability (HF; n = 04) and low freezability (LF; n = 04). That done, we investigated the miRNAs profile of sperm cells and EVs from seminal plasma in both groups. Three miRNAs were differently abundant in LF ejaculates, being the ssc-miR-503 found in higher levels in sperm cells (P < 0.10). The ssc-miR-130a and ssc-miR-9 most abundant in EVs from seminal plasma (P < 0.10), in LF ejaculates. Through enrichment analysis, it was possible to verify that these miRNAs could be performing modifications in the development of male germ cells and in the production of energy to spermatozoa to maintain their viability and functionality. Therefore, we can demonstrate that ssc-miR-503, ssc-miR-130a, and ssc-miR-9 are related to low sperm cryotolerance in boars semen. So those miRNAs can be used as a biomarker to predict their low ability to tolerate the cryopreservation process.

Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

Background

Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N⁶-methyladenosine (m⁶A) RNA methylation varies in response to stress and has been implicated in multiple important biological processes, including post-transcriptional fate of mRNA, metabolism, and apoptosis. This study aimed to explore whether cryopreservation induces m⁶A modification of mRNAs associated with sperm energy metabolism, cryoinjuries, and freezability.

Results

The mRNA and protein expression of m⁶A modification enzymes were significantly dysregulated in sperm after cryopreservation. Furthermore, m⁶A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. The mRNAs containing highly methylated m⁶A peaks (fts vs. fs) were significantly associated with metabolism and gene expression, while the genes with less methylated m⁶A peaks were primarily involved in processes regulating RNA metabolism and transcription. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis.

Conclusions

Our study is the first to reveal the dynamic m⁶A modification of mRNAs in boar sperm during cryopreservation. These epigenetic modifications may affect mRNA expression and are closely related to sperm motility, apoptosis, and metabolism, which will provide novel insights into understanding of the cryoinjuries or freezability of boar sperm during cryopreservation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07904-8.

Identification and analysis of short open reading frames (sORFs) in the initially annotated noncoding RNA LINC00493 from human cells

Whole transcriptome analyses have revealed that mammalian genomes are massively transcribed, resulting in the production of huge numbers of transcripts with unknown functions (TUFs). Previous research has categorized most TUFs as noncoding RNAs (ncRNAs) because most previously studied TUFs do not encode open reading frames (ORFs) with biologically significant lengths [>100 amino acids (AAs)]. Recent studies, however, have reported that several transcripts harbouring small ORFs that encode peptides shorter than 100 AAs are translated and play important biological functions. Here, we examined the translational capacity of transcripts annotated as ncRNAs in human cells, and identified several hundreds of ribosome-associated transcripts previously annotated as ncRNAs. Ribosome footprinting and polysome profiling analyses revealed that 61 of them are potentially translatable. Among them, 45 were nonnonsense-mediated mRNA decay targets, suggesting that they are productive mRNAs. We confirmed the translation of one ncRNA, LINC00493, by luciferase reporter assaying and western blotting of a FLAG-tagged LINC00493 peptide. While proteomic analysis revealed that the LINC00493 peptide interacts with many mitochondrial proteins, immunofluorescence assays showed that its peptide is mitochondrially localized. Our findings indicate that some transcripts annotated as ncRNAs encode peptides and that unannotated peptides may perform important roles in cells.

Characterization of the Impact of Density Gradient Centrifugation on the Profile of the Pig Sperm Transcriptome by RNA-Seq

RNA-Seq data from human semen suggests that the study of the sperm transcriptome requires the previous elimination from the ejaculates of somatic cells carrying a larger load of RNA. Semen purification is also carried to study the sperm transcriptome in other species including swine and it is often done by density gradient centrifugation to obtain viable spermatozoa from fresh ejaculates or artificial insemination doses, thereby limiting the throughput and remoteness of the samples that can be processed in one study. The aim of this work was to evaluate the impact of purification with density gradient centrifugation by BoviPure^TM on porcine sperm. Four boar ejaculates were purified with BoviPure^TM and their transcriptome sequenced by RNA-Seq was compared with the RNA-Seq profiles of their paired non-purified sample. Seven thousand five hundred and nineteen protein coding genes were identified. Correlation, cluster, and principal component analysis indicated high—although not complete—similarity between the purified and the paired non-purified ejaculates. 372 genes displayed differentially abundant RNA levels between treatments. Most of these genes had lower abundances after purification and were mostly related to translation, transcription and metabolic processes. We detected a significant change in the proportion of genes of epididymal origin within the differentially abundant genes (1.3%) when compared with the catalog of unaltered genes (0.2%). In contrast, the proportion of testis-specific genes was higher in the group of unaltered genes (4%) when compared to the list of differentially abundant genes (0%). No proportion differences were identified for prostate, white blood, lymph node, tonsil, duodenum, skeletal muscle, liver, and mammary gland. Altogether, these results suggest that the purification impacts on the RNA levels of a small number of genes which are most likely caused by the removal of epididymal epithelial cells but also premature germinal cells, immature or abnormal spermatozoa or seminal exosomes with a distinct load of RNAs.

Cellular and Molecular Insights Into the Etiology of Subfertility/Infertility in Crossbred Bulls (Bos taurus × Bos indicus): A Review

Crossbreeding of indigenous cattle (Bos indicus) with improved (Bos taurus) breeds gained momentum and economic relevance in several countries to increase milk production. While production performance of the crossbred offspring is high due to hybrid vigor, they suffer from a high incidence of reproductive problems. Specifically, the crossbred males suffer from serious forms of subfertility/infertility, which can have a significant effect because semen from a single male is used to breed several thousand females. During the last two decades, attempts have been made to understand the probable reasons for infertility in crossbred bulls. Published evidence indicates that testicular cytology indices, hormonal concentrations, sperm phenotypic characteristics and seminal plasma composition were altered in crossbred compared to purebred males. A few recent studies compared crossbred bull semen with purebred bull semen using genomics, transcriptomics, proteomics and metabolomics; molecules potentially associated with subfertility/infertility in crossbred bulls were identified. Nevertheless, the precise reason behind the poor quality of semen and high incidence of sub-fertility/infertility in crossbred bulls are not yet well defined. To identify the underlying etiology for infertility in crossbred bulls, a thorough understanding of the magnitude of the problem and an overview of the prior art is needed; however, such systematically reviewed information is not available. Therefore, the primary focus of this review is to compile and analyze earlier findings on crossbred bull fertility/infertility. In addition, the differences between purebred and crossbred males in terms of testicular composition, sperm phenotypic characteristics, molecular composition, environmental influence and other details are described; future prospects for research on crossbred males are also outlined.