Taking advantage of the use of supervised learning methods for characterization of sperm population structure related with freezability in the Iberian red deer

Extender development for optimal cryopreservation of buck sperm to increase reproductive efficiency of goats

Preservation of sperm significantly contributes to the advancement of assisted reproductive technologies, genetic conservation and improvement efforts, and precision breeding of livestock. This review distills knowledge from the existing information and emerging patterns in the field of buck sperm cryopreservation. The primary focus is on the challenges and opportunities associated with improving extender formulations and freezing techniques in order to enhance the vitality of sperm after thawing and to increase the potential for conception. This review assesses the efficacy and limitations of conventional extenders derived from egg yolk or soybean lecithin, and the adverse impacts of seminal plasma enzymes on sperm quality during the processes of chilling and cryopreservation. Significant progress has been made in the fields of molecular biology namely lipidomics, proteomics, metabolomics, DNA methylation providing valuable knowledge regarding the unique reactions of sperm to cryopreservation. The utilization of the "omics" technologies has shown intricate molecular transformation that occur in sperm during freezing and thawing. Moreover, detection of molecular biomarkers that indicate the quality of sperm and their ability to withstand freezing provides opportunities to choose the best sperm samples for cryopreservation. This, in turn, enhances the results of artificial insemination and genetic conservation endeavors. This review emphasizes the necessity for adopting a comprehensive approach that combines molecular and cellular knowledge with practical methods in the field of sperm cryopreservation to ensure production of goats as major food animals in the global scale.

Bioinformatics on Sperm Subpopulations Using Computer-Assisted Sperm Analysis (CASA)

Computer-aided sperm analysis of motility (CASA-mot) and morphology (CASA-morph) enables the quick acquisition of many parameters on individual spermatozoa. This results in massive datasets apt for exploration using multiparametric tools. Data clustering has been used for decades to identify subpopulations of spermatozoa sharing similar motility patterns or morphological features. There are two main strategies considering the lack of or availability of prior information: unsupervised and supervised clustering. Then, the researcher has a wealth of algorithms for processing the data in both approaches, but one has to be aware that not all of them could be appropriate for dealing with the peculiarities of sperm data. Here, we describe in detail two approaches previously published: the two-step procedure as unsupervised and the support vector machines (SVM) as supervised. Both approaches are widely available in different statistical software, but in the interest of openness in research, specific details are provided for the R statistical environment (open source and non-proprietary platform and packages). This chapter offers strengths, caveats, and suggestions for alternative algorithms.

Artificial intelligence and porcine breeding

Livestock management is evolving into a new era, characterized by the analysis of vast quantities of data (Big Data) collected from both traditional breeding methods and new technologies such as sensors, automated monitoring system, and advanced analytics. Artificial intelligence (A-In), which refers to the capability of machines to mimic human intelligence, including subfields like machine learning and deep learning, is playing a pivotal role in this transformation. A wide array of A-In techniques, successfully employed in various industrial and scientific contexts, are now being integrated into mainstream livestock management practices. In the case of swine breeding, while traditional methods have yielded considerable success, the increasing amount of information requires the adoption of new technologies such as A-In to drive productivity, enhance animal welfare, and reduce environmental impact. Current findings suggest that these techniques have the potential to match or exceed the performance of traditional methods, often being more scalable in terms of efficiency and sustainability within the breeding industry. This review provides insights into the application of A-In in porcine breeding, from the perspectives of both sows (including welfare and reproductive management) and boars (including semen quality and health), and explores new approaches which are already being applied in other species.

Are There Differences between Methods Used for the Objective Estimation of Boar Sperm Concentration and Motility?

Artificial insemination in the swine industry, as in other species, demands adequate semen handling and accurate evaluation for the preparation of seminal doses. Sperm concentration and motility estimates are part of the semen evaluation process and are considered important for maximizing the yield of doses for insemination. In this study, methods were examined for their accuracy in the estimation of boar sperm concentration and motility. Assessments of sperm concentration were carried out using iSperm^®, ISAS^® v1, Open CASA v2, and the Accuread^® photometer. Analyses of sperm motility were performed with iSperm^®, ISAS^® v1, and Open CASA v2 systems. In this study, boar semen samples were collected from 10 healthy males from two genetic lines. There were no relevant differences between sire lines when sperm concentration was assessed. A Bayesian analysis was applied to the four methods used to assess sperm concentration to examine whether there are relevant differences between them. Results suggested differences in the four methods, with a probability of relevance (PR) of 0.86-1.00. The iSperm^® method revealed higher concentration values within the highest posterior density region at 95% confidence interval (HPD_95%) = 167.0, 224.2 M/mL, whereas Open CASA v2 showed the lowest values, with HPD_95% = 99.3, 155.9 M/mL. The iSperm^® demonstrated higher reliability in measuring sperm concentration compared to other methods or devices within the given range of confidence. ANOVAs revealed relevant differences in the three methods of motility estimation. Overall, differences in boar sperm concentration and motility estimates were found using various methods, but further studies are needed for better characterization of these differences.

Characterization of the Germplasm Bank for the Spanish Autochthonous Bull Breed "Asturiana de la Montaña"

Semen cryobanks are critical for preserving autochthonous and rare breeds. Since sperm cryopreservation has been optimized for commercial breeds, non-commercial ones (often endangered) must be characterized to ensure the germplasm's viability. This study reports an investigation of the "Asturiana de la Montaña" breed (AM), a valuable Spanish autochthonous cattle breed adapted to the mountainous Atlantic environment. The survey included cryopreserved semen doses from 40 bulls stored at the Principado de Asturias Germplasm Bank. Data were obtained from the routine fresh semen analysis, CASA (motility), and flow cytometry analyses of fresh and post-thawing semen, and the 56-day non-return-rate (NRR) in heifers and cows (all results as 1st and 3rd quartiles). Fresh samples (artificial vagina) were within the normal range for cattle (4-6 mL, 5-10 × 10⁹/mL; mass motility 5). Post-thawing results showed motility below typical for commercial breeds (total motility 26-43%, progressive 14-28%), with higher values for viability (47-62%). Insemination results showed a good performance for this breed (NRR: 47-56%; higher for heifers). Sperm volume increased with age, with little or no effects on sperm quality. Few associations were found between post-thawing quality or freezability and NRR, LIN being the variable more strongly associated (positively). The AM semen bank shows a good prospect for preserving and disseminating the genetics of this breed. This survey indicates that dedicated research is needed to adapt freezing protocols to this breed, optimizing post-thawing results.

The Quality and Fertilizing Potential of Red Deer (Cervus elaphus L.) Epididymal Spermatozoa Stored in a Liquid State

The aim of this study was to assess the quality and fertilizing potential of red deer epididymal spermatozoa stored in a liquid state for up to 11 days (D11). In Experiment 1, sperm quality was determined. In Experiment 2, the efficiency of in vitro fertilization (IVF) and artificial insemination (AI) of stored sperm were evaluated. An analysis of sperm quality on D5 of storage revealed a decrease (p < 0.05) in motility and morphology, and a higher proportion of apoptotic spermatozoa. On D1, D7 and D10, the total motility of sperm for IVF and AI was determined to be 82.6%, 71.0% and 64.8%, respectively. The results of IVF and AI demonstrated that the fertilizing potential of spermatozoa differs between days of storage. The percentage of blastocysts was higher when oocytes were fertilized on D1 (17.4 %) compared to D7 (8.5%) and D10 sperm (10.5%). Differences were noted in the pregnancy rates of inseminated hinds. The insemination with D1, D7 and D10 sperm led to live births (33% from D7 and D10). The results indicate that the quality of red deer epididymal spermatozoa remains satisfactory during ten days of storage in a liquid state, and that these spermatozoa maintain their fertility potential.

What is the importance of sperm subpopulations?

The study of sperm subpopulations spans three decades. The origin, meaning, and practical significance, however, are less clear. Current technology for assessing sperm morphology (CASA-Morph) and motility (CASA-Mot) has enabled the accurate evaluation of these features, and there are many options for data classification. Subpopulations could occur as a result of the stage of development of each spermatozoon in the subpopulation. Spermatogenesis might contribute to the production of these subpopulations. Insights from evolutionary biology and recent molecular research are indicative of the diversity among male gametes that could occur from unequal sharing of transcripts and other elements through cytoplasmic bridges between spermatids. Sperm cohorts exiting the gonads would contain different RNA and protein contents, affecting the spermatozoon physiology and associations with the surrounding environmental milieu. Subsequently, these differences could affect how spermatozoa interact with the environmental milieu (maturation, mixing with seminal plasma, and interacting with the environmental milieu, or female genital tract and female gamete). The emergence of sperm subpopulations as an outcome of evolution, related to the reproductive strategies of the species, genital tract structures, and copulatory and fertilization processes. This kind of approach in determining the importance of sperm subpopulations in fertilization capacity should have a practical impact for conducting reproductive technologies, inspiring and enabling new ways for the more efficient use of spermatozoa in the medical, animal breeding, and conservation fields. This manuscript is a contribution to the Special Issue in memory of Dr. Duane Garner.

The Effect of Different Extenders on the Quality Characteristics of European Red Deer Epididymal Sperm Stored at 5 °C

The aim of this study was to evaluate the effect of different extenders on the quality of European red deer epididymal sperm stored at 5 °C. Epididymal spermatozoa were collected post mortem from 10 stags and diluted with three extenders (Bovidyl®, BoviFree®, and BioXcell®) and stored at 5 °C. Sperm motility (TMOT), motility parameters (system CASA), plasma membrane integrity (SYBR-14+/PI−), acrosomal membrane integrity (FITC-PNA−/PI−), mitochondrial activity (JC-1/PI), viability, and apoptotic-like changes (YOPRO/PI) were evaluated. The analyses were conducted on the first and successive days of storage (D1−D7). The applied extender, storage time, and the interactions between these factors significantly (p < 0.001) affected most of the analyzed parameters whose values were highest in sperm samples stored in Bovidyl®, regardless of storage time. In Bovidyl®, BoviFree®, and BioXcell® extenders, TMOT values were estimated at 83%, 63%, and 59%, respectively, on D3. The extenders significantly influenced DNA integrity on D7. The percentage of dead sperm increased from D3. The quality of stored sperm cells was significantly influenced by the extenders’ biochemical composition. BoviFree® and BioXcell® contain glycerol which could contribute to deteriorating the quality of spermatozoa stored at 5 °C. Sperm cells stored in the egg yolk-based extender (Bovidyl®) were characterized by the highest viability and functionality.

Cold-Shock Test Is a Practical Method for Selecting Boar Ejaculates Yielding Appropriate Seminal Plasma for Post-Thawing Supplementation

Simple Summary

The pig industry routinely uses artificial insemination with refrigerated semen. Cryopreserved semen has many advantages, but it is not widely used, partly because of unreliable results. The supplementation with seminal plasma (SP) could improve these results, but this fluid also presents variability. We evaluated if a simple cold-shock test (CST) could allow to easily identify the most suitable ejaculates for obtaining SP. Therefore, we tested 63 ejaculates, obtaining SP from the 4 showing higher quality (SPr, cold-shock-resistant) and lower quality (SPs, cold-shock-sensitive) after the CST. SPs and SPr pools supplemented thawed semen (20% SP) from six different boars, incubating at 37 °C and analyzing at times 0, 2, and 4 h. SPr was able to improve post-thawing sperm motility while maintaining viability. SPs had a similar but lower effect. SP in general seemed to stimulate sperm physiology, however decreasing membrane stability, acrosomal integrity, and disulfide bridges in the chromatin. This study supports the suitability of SP for improving thawed semen, with CST-selected ejaculates as preferable for this aim. Artificial insemination trials with thawed semen supplemented with SPr and SPs must validate the practical application of CST.

Abstract

Artificial insemination (AI) with cryopreserved semen is still unreliable for extensive pig industry application. Adding seminal plasma (SP) could improve post-thawing quality, but its suitability could vary. We applied a simple cold-shock test (CST, 5 min at 0 °C) on neat semen for classifying ejaculates (n = 63) as resistant or sensitive, obtaining two SP pools (CST-resistant: SPr, sensitive: SPs). Subsequently, frozen/thawed spermatozoa from six boars were incubated (37 °C) in MR-A® extender (control), 20% SPr, or 20% SPs, and analyzed at 0, 2, and 4 h. SP improved total and progressive motility, with a higher effect for SPr and STR (p < 0.05), decreasing kinematic parameters VCL and VAP, ALH, and BCF. Sperm viability was unaffected. SP increased apoptotic and membrane disorder ratios, and acrosomal damage, not affecting the chromatin structure (DNA fragmentation and immaturity by SCSA), protamination (CMA3), or disulfide levels (mBBr). However, the proportion of spermatozoa with elevated free thiols (disulfide bridges reduction) significantly increased. Results support a stimulatory role of SP on thawed semen, with additional benefits from SPr. The effect of SP and especially SPr after AI should be tested since CST could be a practical test for selecting suitable ejaculates in AI centers.

Melatonin Non-Linearly Modulates Bull Spermatozoa Motility and Physiology in Capacitating and Non-Capacitating Conditions

Bull spermatozoa physiology may be modulated by melatonin. We washed ejaculated spermatozoa free of melatonin and incubated them (4 h, 38 °C) with 0-pM, 1-pM, 100-pM, 10-nM and 1-µM melatonin in TALP-HEPES (non-capacitating) and TALP-HEPES-heparin (capacitating). This range of concentrations encompassed the effects mediated by melatonin receptors (pM), intracellular targets (nM–µM) or antioxidant activity (µM). Treatment effects were assessed as motility changes by computer-assisted sperm analysis (CASA) of motility and physiological changes by flow cytometry. Melatonin effects were more evident in capacitating conditions, with 100 pM reducing motility and velocity (VCL) while increasing a “slow” subpopulation. All concentrations decreased apoptotic spermatozoa and stimulated mitochondrial activity in viable spermatozoa, with 100 pM–1 µM increasing acrosomal damage, 10 nM–1 µM increasing intracellular calcium and 1 pM reducing the response to a calcium-ionophore challenge. In non-capacitating media, 1 µM increased hyperactivation-related variables and decreased apoptotic spermatozoa; 100 pM–1 µM increased membrane disorders (related to capacitation); all concentrations decreased mitochondrial ROS production. Melatonin concentrations had a modal effect on bull spermatozoa, suggesting a capacitation-modulating role and protective effect at physiological concentrations (pM). Some effects may be of practical use, considering artificial reproductive techniques.

Viability longevity and quality of epididymal sperm stored in the liquid state of European red deer (Cervus elaphus elaphus)

The aim of the study was to evaluate viability longevity and quality of liquid-stored epididymal sperm of European red deer (Cervus elaphus elaphus). Sperm samples were recovered from epididymides of 15 mature stags. Samples were diluted to 100 × 10⁶ sperm⁄mL in modified Salomon's extender and stored at 5 °C for 25 days. Sperm were analyzed to determine total motility (TMOT), progressive motility (PMOT) and motion variables [CASA system], acrosomes with normal apical ridges (NAR), viability and acrosomal status (FITC-PNA/PI), plasma membrane integrity (PMI) and mitochondrial membrane potential (MMP) on the first day (D1) and every other day of storage (D3-D25). Data were analyzed using a one-way analysis of variance (ANOVA). Spermatozoa remained motile until D25, whereas TMOT exceeded 60%, NAR and PMI exceeded 80%, FITC-PNA/PI exceeded 75%, and MMP approximated 70% until D11. There was a lesser (P < 0.05) value for these variables on D5 (relative to D1). Furthermore, there was a decrease in values for motility variables as duration of storage increased, excluding amplitude of lateral head displacement, on D3. The results indicate that liquid-stored epididymal sperm of European red deer are characterized as having a long viability (25 days) with a retention of sperm quality for as long as 11 days in the liquid storage state. In vitro or in vivo studies, however, are required to confirm the findings in the present study.

Cryoprotectants synergy improve zebrafish sperm cryopreservation and offspring skeletogenesis

The synergy obtained by the combination of cryoprotectants is a successful strategy that can be beneficial on the optimization of zebrafish sperm cryopreservation. Recently, a protocol was established for this species using an electric ultrafreezer (-150 °C) performing cooling rate (-66 °C/min) and storage within one step. The ultimate objective of sperm cryopreservation is to generate healthy offspring. Therefore, the objective of this study was to select the most adequate cryoprotectant combination, for the previously established protocol, that generate high quality offspring with normal skeletogenesis. Among the permeating cryoprotectant concentrations studied 12.5% and 15% of N,N-dimethylformamide (DMF) yielded high post-thaw sperm quality and hatching rates. For these two concentrations, the presence of bovine serum albumin (10 mg/mL), egg yolk (10%), glycine (30 mM) and bicine (50 mM) was evaluated for post-thaw sperm motility, viability, in vitro fertilization success and offspring skeletal development (30 days post fertilization). Higher concentration of permeating cryoprotectant (15%) decreased the incidence of deformed arches and severe skeletal malformations, which suggests higher capacity to protect the cell against cold stress and DNA damage. Extender containing 15% DMF with Ctrl, Bicine and egg yolk were the non-permeating cryoprotectants with higher post-thaw quality. The use of these compounds results in a reduction in vertebral fusions, compressions and severity of skeletal malformations in the offspring. Therefore, these extender compositions are beneficial for the quality of zebrafish offspring sired by cryopreserved sperm with -66 °C/min freezing rate. To the best of our knowledge, this is the first report on skeletal development of the offspring sired by cryopreserved sperm performed with different freezing media compositions in zebrafish.

Implementation of novel statistical procedures and other advanced approaches to improve analysis of CASA data

Computer-aided sperm analysis (CASA) produces a wealth of data that is frequently ignored. The use of multiparametric statistical methods can help explore these datasets, unveiling the subpopulation structure of sperm samples. In this review we analyse the significance of the internal heterogeneity of sperm samples and its relevance. We also provide a brief description of the statistical tools used for extracting sperm subpopulations from the datasets, namely unsupervised clustering (with non-hierarchical, hierarchical and two-step methods) and the most advanced supervised methods, based on machine learning. The former method has allowed exploration of subpopulation patterns in many species, whereas the latter offering further possibilities, especially considering functional studies and the practical use of subpopulation analysis. We also consider novel approaches, such as the use of geometric morphometrics or imaging flow cytometry. Finally, although the data provided by CASA systems provides valuable information on sperm samples by applying clustering analyses, there are several caveats. Protocols for capturing and analysing motility or morphometry should be standardised and adapted to each experiment, and the algorithms should be open in order to allow comparison of results between laboratories. Moreover, we must be aware of new technology that could change the paradigm for studying sperm motility and morphology.

Computer-assisted system with multiple feature fused support vector machine for sperm morphology diagnosis

Sperm morphology is an important technique in identifying the health of sperms. In this paper we present a new system and novel approaches to classify different kinds of sperm images in order to assess their health. Our approach mainly relies on a one-dimensional feature which is extracted from the sperm's contour with gray level information. Our approach can handle rotation and scaling of the image. Moreover, it is fused with SVM classification to improve its accuracy. In our evaluation, our method has better performance than the existing approaches to sperm classification.

Sperm cell population dynamics in ram semen during the cryopreservation process

Background

Sperm cryopreservation has become an indispensable tool in biology. Initially, studies were aimed towards the development of efficient freezing protocols in different species that would allow for an efficient storage of semen samples for long periods of time, ensuring its viability. Nowadays, it is widely known that an important individual component exists in the cryoresistance of semen, and efforts are aimed at identifying those sperm characteristics that may allow us to predict this cryoresistance. This knowledge would lead, ultimately, to the design of optimized freezing protocols for the sperm characteristics of each male.

Methodology/Principal Findings

We have evaluated the changes that occur in the sperm head dimensions throughout the cryopreservation process. We have found three different patterns of response, each of one related to a different sperm quality at thawing. We have been able to characterize males based on these patterns. For each male, its pattern remained constant among different ejaculates. This latter would imply that males always respond in the same way to freezing, giving even more importance to this sperm feature.

Conclusions/Significance

Changes in the sperm head during cryopreservation process have resulted useful to identify the ability of semen of males for freezing. We suggest that analyses of these response patterns would represent an important tool to characterize the cryoresistance of males when implemented within breeding programs. We also propose follow-up experiments to examine the outcomes of the use of different freezing protocols depending on the pattern of response of males.

Sperm motility patterns in Andalusian donkey (Equus asinus) semen: effects of body weight, age, and semen quality

The aims of this study were to (1) identify sperm subpopulations with specific motion characteristics in fresh Andalusian donkey ejaculates; (2) evaluate the effects of individual donkey and ejaculates within the same donkey on the distribution of the subpopulations found; and (3) explore the relationship between the age and the body weight of donkey donors, the sperm quality parameters, and the sperm subpopulations structure. Sixty ejaculates from 12 Andalusian donkeys (five ejaculates per donkey), ranging in age from 4 to 15 years, were collected. Immediately after collection, sperm characteristics (volume, sperm concentration, objective sperm motility, and sperm morphology) were assessed. Donkeys were evaluated for body weight. Significant (P < 0.05) correlations were established between the body weight of the donkeys and the pH (r = -0.52), sperm motility (percentage of motile spermatozoa: r = -0.31; percentage of progressive motile spermatozoa: r = -0.34), and total sperm abnormalities (r = 0.38). The correlations of the age with the measures of semen quality were low and not significant (P > 0.05). A multivariate clustering procedure separated 65,342 motile spermatozoa into four subpopulations: subpopulation 1, consisting of slow and nonprogressive spermatozoa (15.4%), subpopulation 2, consisting of moderately slow but progressive spermatozoa (35.9%), subpopulation 3, consisting of highly active but nonprogressive spermatozoa (18.5%), and subpopulation 4, consisting of highly active and progressive spermatozoa (30.2%). The distribution of these subpopulations varied significantly (P < 0.05) according to several parameters such as the individual donkey, the ejaculate of the same donkey, the total motility, and the overall sperm concentration. Our results show the existence of four well-defined motile sperm subpopulations in Andalusian donkey ejaculates, and suggest a high heterogeneity in the ejaculate structure in donkey. The relationship between the distribution of the sperm subpopulations and individual donkey, total motility, and sperm concentration shows that the spermatozoa of each have different motility patterns. However, the proportions of sperm subpopulations in the ejaculates did not vary with age and body weight. Finally, the study of discrete subpopulations of motile spermatozoa could lead to a substantial increase in information acquired during donkey semen analysis.