Identifying candidate genes associated with sperm morphology abnormalities using weighted single-step GWAS in a Duroc boar population

Brief biology and pathophysiology of Tekt bundles

Tektins, a family of microtubule-stabilizing proteins, are critical for cilia and flagella assembly in mammals. They maintain doublet microtubule stability and ciliary/flagellar motility. Loss of Tekt1-5 causes microtubule instability, impaired motility, and diseases like infertility, retinal degeneration, Mainzer-Saldino syndrome, and diabetic nephropathy. Pathophysiological stimuli regulate Tektin expression through transcriptional, posttranscriptional, translational, and posttranslational modifications. This review summarizes the latest findings on Tektin functions and their role in diseases.

Genome-Wide Association Study Reveals Novel Loci and Candidate Genes for Birth Weight in Pigs

Birth weight is a key economic trait in pig breeding, affecting pre-weaning survival, growth performance, and overall production efficiency. However, the genetic factors underlying birth weight remain incompletely understood. This study aimed to identify genetic variants associated with birth weight in pigs through a genome-wide association study (GWAS) using 50K SNP genotyping data from 1125 Landrace pigs. Seven significant SNPs linked to birth weight were identified, along with 13 potential candidate genes. To validate these findings, the study population was expanded to include 998 Yorkshire pigs, totaling 2123 individuals. Validation identified two novel SNPs on chromosomes 1 and 16, as well as the previously unreported gene MARCHF11, which was associated with birth weight. These findings enhance the understanding of the genetic architecture underlying birth weight and provide potential targets for molecular marker-assisted selection (MAS). The results offer valuable insights into breeding strategies aimed at improving piglet survival rates and production efficiency. This study underscores the utility of GWAS in identifying key genetic loci for economically important traits in livestock populations.

Identified Candidate Genes of Semen Trait in Three Pig Breeds Through Weighted GWAS and Multi-Tissue Transcriptome Analysis

High-quality semen is an essential factor for the success of artificial insemination, and revealing the genetic structure of pig semen traits helps improve semen quality. This study aimed to identify candidate genes associated with semen traits in three pig breeds (Duroc, Landrace, and Yorkshire) through weighted GWAS and multi-tissue transcriptome analysis. In this study, to identify candidate genes associated with semen traits in Duroc, Landrace, and Yorkshire, we performed weighted GWAS in four traits (sperm motility, sperm progressive motility, sperm abnormality rate, and total sperm count) using 936 pigs and multi-tissue transcriptome analysis using 34 tissues RNA-seq data of 5457 pigs from FarmGTEx. It was found that 16, 9, and 12 significant SNPs associated with semen traits were identified in Duroc, Landrace, and Yorkshire, with corresponding 7, 5, and 7 candidate genes in these three breeds, respectively, which may be involved in mammal spermatogenesis, testicular function, and male fertility. Moreover, we not only found the same candidate gene DNAI2 as in previous studies but also found two new candidate genes PNLDC1 and RSPH3, which were identified simultaneously in both Landrace and Yorkshire. By integrating the GWAS and multi-tissue transcriptome analysis results, we found that candidate genes associated with semen traits of three pig breeds were highly expressed in the testis tissue. The three genotypes of rs320928244 had significant effects on the expression of the DYNLT1 gene in the testis tissue of Landrace. These results together showed that these candidate genes were mainly related to sperm motility defects. This study helps deepen the understanding of the genetic basis of semen traits and provides a theoretical foundation for improving the semen quality of Duroc, Landrace, and Yorkshire breeds.

Assessment of Boar Semen Morphology and Morphometry

The evaluation of sperm morphology is crucial in assessing reproductive health in both humans and animals. In humans, the World Health Organization recognizes the importance of morphology in semen analysis. Similarly, in animal breeding programs, assessing sperm morphology is essential for selecting superior breeding candidates. This review specifically focuses on the pig as a model, given its importance in meat production and as a research model for reproductive biology. Several studies have demonstrated the impact of sperm morphological abnormalities on fertility in pigs, although some studies have reported conflicting results. Understanding the importance of semen morphology evaluation in boar production and describing the changes in semen morphology and evaluation procedures are the main objectives of this review. Factors influencing semen morphological abnormalities, such as breed, age, and environmental conditions, are discussed. Various techniques for assessing sperm morphology, including traditional microscopic evaluation, staining techniques, computer-assisted sperm analysis (CASA), and advanced imaging techniques, are reviewed. The relationships between morphology and other sperm parameters are explored, and the significance of morphology in the production of seminal doses is emphasized. Finally, future directions and challenges in the assessment of boar sperm morphology are discussed, including advances in imaging and analysis techniques, integration of molecular and genetic approaches, standardization of guidelines, and research into fertility outcomes and long-term follow-up studies. By addressing these challenges, improvements in the diagnosis and reproductive outcomes of individuals with abnormal sperm morphology can be achieved.

Effect of Seminal Plasma on the Freezability of Boar Sperm

BACKGROUND

Seminal plasma is an important component of semen and has a significant effect on sperm function. However, the relationship between seminal plasma and sperm freezing capacity has not been fully studied.

PURPOSE

Exploring metabolites and proteins related to the boar sperm freezing capacity in seminal plasma, by metabolomic and proteomic approaches, and directly verifying the protective effect of seminal plasma on the cryopreservation of boar sperm using high and low freezability seminal plasma as base freezing extender.

METHODS

Semen samples were collected from 30 different boars, 11 high and 11 low freezing-resistant boars were selected after freezing 2~4 times, and seminal plasma was selected at the same time. Sperm motility and movement parameters were analyzed using a CASA system. Reproductive hormones (Testosterone, progesterone, estradiol, prolactin, prostaglandin F2α, luteinoid hormone) in seminal plasma were detected by ELISA. Analysis of proteins and metabolites in high and low freezing-resistant seminal plasma by proteomics and metabolomics techniques.

RESULTS

The six reproductive hormones tested were not significantly associated with sperm freezing resistance. A total of 13 differentially expressed metabolites (DEMs) and 38 differentially expressed proteins (DEPs) were identified, while a total of 348 metabolites and 1000 proteins were identified. These DEMs were related to energy metabolism, drugs, or environmental pollutants, while the DEPs were mainly involved in the cytoskeletal dynamics and cell adhesion processes. There were 33 metabolites and 70 proteins significantly associated with mean progress motility (PM) at 10 min and 2 h after thawing. The 70 related proteins were associated with cell division and cycle regulation in gene ontology (GO) terms, as well as KEGG pathways, thermogeneration, and pyruvate metabolism. Using highly freezable boar SP as a base freezing extender made no difference from using lowly freezable boar SP, and both were not as good as the commercial control.

CONCLUSION

There were significant differences in seminal plasma with different freezability, but the similarity was much greater than the difference. The protection effect of seminal plasma is not remarkable, and it does not exhibit superior cryoprotective properties compared to commercial semen cryoelongators.

SIGNIFICANCE

This study provides a deeper understanding of how seminal plasma composition affects sperm freezabilty. It provides potential biomarkers and targets for improving sperm cryopreservation techniques.

Importance and variability of the paternal component in sow reproductive traits

Reproductive traits are an integral part of the goals of the breeding programs that contribute to the economic success of production. Reproductive phenotypes such as litter size, number of piglets born alive, or litter weight at birth are mainly attributed to females. Thus, the maternal components can be found by default in quantitative genetics' animal models. Still, paternal contribution to variance components should not be discarded. In this review, we indicate the importance of paternal effects in pig breeding by describing both the biology and genetics of boars' traits, the use of (non-)genetic service sire effects in quantitative genetic models for traits measured on females, and genes involved in male reproduction. We start by describing the important biological traits of boars that have the most important effect on their reproductive abilities, i.e., sexual maturity, sperm quality, and testes parameters. Then we move to the possible environmental effects that could affect those traits of boars (e.g., feed, temperature). The main part of the review in detail describes the genetics of boars' reproductive traits (i.e., heritability) and their direct effect on reproductive traits of females (i.e., genetic correlations). We then move to the use of both genetic and non-genetic service sire effects in quantitative models estimated as their percentage in the total variance of traits, which vary depending on the breed from 1 to 4.5% or from 1 to 2%, respectively. Finally, we focus on the description of candidate genes and confirmed mutations affecting male reproduction success: IGF2, Tgm8, ESR1, ZSWIM7, and ELMO1. In conclusion, the observed variance of paternal effects in female reproduction traits might come from various attributes of boars including biological and genetic aspects. Those attributes of boars should not be neglected as they contribute to the success of female reproductive traits.

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.

Reproductive physiology of the boar: What defines the potential fertility of an ejaculate?

Despite decades of research and handling of semen for use in artificial insemination (AI) and other assisted reproductive technologies, 5-10% of selected boar sires are still considered sub-fertile, escaping current assessment methods for sperm quality and resilience to preservation. As end-product, the ejaculate (emitted spermatozoa sequentially exposed to the composite seminal plasma, the SP) ought to define the homeostasis of the testes, the epididymis, and the accessory sexual glands. Yet, linking findings in the ejaculate to sperm production biology and fertility is suboptimal. The present essay critically reviews how the ejaculate of a fertile boar can help us to diagnose both reproductive health and resilience to semen handling, focusing on methods -available and under development- to identify suitable biomarkers for cryotolerance and fertility. Bulk SP, semen proteins and microRNAs (miRNAs) have, albeit linked to sperm function and fertility after AI, failed to enhance reproductive outcomes at commercial level, perhaps for just being components of a complex functional pathway. Hence, focus is now on the interaction sperm-SP, comparing in vivo with ex vivo, and regarding nano-sized lipid bilayer seminal extracellular vesicles (sEVs) as priority. sEVs transport fragile molecules (lipids, proteins, nucleic acids) which, shielded from degradation, mediate cell-to-cell communication with spermatozoa and the female internal genital tract. Such interaction modulates essential reproductive processes, from sperm homeostasis to immunological female tolerance. sEVs can be harvested, characterized, stored, and manipulated, e.g. can be used for andrological diagnosis, selection of breeders, and alternatively be used as additives to improve cryosurvival and fertility.

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.

New insights into sperm physiology regulation: Enlightenment from G-protein-coupled receptors

BACKGROUND

G-protein-coupled receptors are critical in many physiological and pathological processes in various organs. Serving as the control panel for sensing extracellular stimuli, G-protein-coupled receptors recognise various ligands, including light, temperature, odours, pheromones, hormones, neurotransmitters, chemokines, etc. Most recently, G-protein-coupled receptors residing in spermatozoa have been found to be indispensable for sperm function.

OBJECTIVE

Here, we have summarised cutting-edge findings on the functional mechanisms of G-protein-coupled receptors that are known to be associated with sperm functions and the activation of their downstream effectors, providing new insights into the roles of G-protein-coupled receptors in sperm physiology.

RESULTS

Emerging studies hint that alterations in G-protein-coupled receptors could affect sperm function, implicating their role in fertility, but solid evidence needs to be continuing excavated with various means. Several members of the G-protein-coupled receptor superfamily, including olfactory receptors, opsins, orphan G-protein-coupled receptors, CXC chemokine receptor 4, CC chemokine receptor 5 and CC chemokine receptor 6 as well as their downstream effector β-arrestins, etc., were suggested to be essential for sperm motility, capacitation, thermotaxis, chemotaxis, Ca2+ influx through CatSper channel and fertilisation capacity.

CONCLUSION

The present review provides a comprehensive overview of studies describing G-protein-coupled receptors and their potential action in sperm function. We also present a critical discussion of these issues, and a possible framework for future investigations on the diverse ligands, biological functions and cell signalling of G-protein-coupled receptors in spermatozoa. Here, the G-protein-coupled receptors and their related G proteins that specifically were identified in spermatozoa were summarised, and provided references valuable for further illumination, despite the evidence that is not overwhelming in most cases.

Genome-Wide Association Study Reveals Novel Candidate Genes Influencing Semen Traits in Landrace Pigs

Artificial insemination plays a crucial role in pig production, particularly in enhancing the genetic potential of elite boars. To accelerate genetic progress for semen traits in pigs, it is vital to understand and identify the underlying genetic markers associated with desirable traits. Herein, we genotyped 1238 Landrace boars with GeneSeek Porcine SNP50 K Bead chip and conducted genome-wide association studies to identify genetic regions and candidate genes associated with 12 semen traits. Our study identified 38 SNPs associated with the analyzed 12 semen traits. Furthermore, we identified several promising candidate genes, including HIBADH, DLG1, MED1, APAF1, MGST3, MTG2, and ZP4. These candidate genes have the potential function to facilitate the breeding of boars with improved semen traits. By further investigating and understanding the roles of these genes, we can develop more effective breeding strategies that contribute to the overall enhancement of pig production. The results of our study provide valuable insights for the pig-breeding industry and support ongoing research efforts to optimize genetic selection for superior semen traits.

Genome-Wide Association Analysis of Semen Characteristics in Piétrain Boars

Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen characteristics. These traits comprise sperm morphology and sperm motility under different temporal and thermal storage conditions, in addition to standard semen quality parameters. Two consecutive samples of the fourth and fifth ejaculates from the same boar were comprehensively analyzed in a genotyped Piétrain boar population. A total of 13 genomic regions on different chromosomes were identified that contain single-nucleotide polymorphisms significantly associated with these traits. Subsequent analysis of the genomic regions revealed candidate genes described to be involved in spermatogenesis, such as FOXL3, GPER1, PDGFA, PRKAR1B, SNRK, SUN1, and TSPO, and sperm motility, including ARRDC4, CEP78, DNAAF5, and GPER1. Some of these genes were also associated with male fertility or infertility in mammals (e.g., CEP78, GPER1). The analyses based on these laboriously determined and valuable phenotypes contribute to a better understanding of the genetic background of male fertility traits in pigs and could prospectively contribute to the improvement of sperm quality through breeding approaches.

Animal board invited review: An update on the methods for semen quality evaluation in swine - from farm to the lab

Pig breeding is mainly conducted through artificial insemination with liquid-stored semen. It is, therefore, crucial to ensure that sperm quality is over the standard thresholds, as reduced sperm motility, morphology or plasma membrane integrity are associated with reduced farrowing rates and litter sizes. This work aims to summarise the methods utilised in farms and research laboratories to evaluate sperm quality in pigs. The conventional spermiogram consists in the assessment of sperm concentration, motility and morphology, which are the most estimated variables in farms. Yet, while the determination of these sperm parameters is enough for farms to prepare seminal doses, other tests, usually carried out in specialised laboratories, may be required when boar studs exhibit a decreased reproductive performance. These methods include the evaluation of functional sperm parameters, such as plasma membrane integrity and fluidity, intracellular levels of calcium and reactive oxygen species, mitochondrial activity, and acrosome integrity, using fluorescent probes and flow cytometry. Furthermore, sperm chromatin condensation and DNA integrity, despite not being routinely assessed, may also help determine the causes of reduced fertilising capacity. Sperm DNA integrity can be evaluated through direct (Comet, transferase deoxynucleotide nick end labelling (TUNEL) and its in situ nick variant) or indirect tests (Sperm Chromatin Structure Assay, Sperm Chromatin Dispersion Test), whereas chromatin condensation can be determined with Chromomycin A3. Considering the high degree of chromatin packaging in pig sperm, which only have protamine 1, growing evidence suggests that complete decondensation of that chromatin is needed before DNA fragmentation through TUNEL or Comet can be examined.

Identification of New Candidate Genes Related to Semen Traits in Duroc Pigs through Weighted Single-Step GWAS

Semen traits play a key role in the pig industry because boar semen is widely used in purebred and crossbred pigs. The production of high-quality semen is crucial to ensuring a good result in artificial insemination. With the wide application of artificial insemination in the pig industry, more and more attention has been paid to the improvement of semen traits by genetic selection. The purpose of this study was to identify the genetic regions and candidate genes associated with semen traits of Duroc boars. We used weighted single-step GWAS to identify candidate genes associated with sperm motility, sperm progressive motility, sperm abnormality rate and total sperm count in Duroc pigs. In Duroc pigs, the three most important windows for sperm motility-sperm progressive motility, sperm abnormality rate, and total sperm count-explained 12.45%, 9.77%, 15.80%, and 12.15% of the genetic variance, respectively. Some genes that are reported to be associated with spermatogenesis, testicular function and male fertility in mammals have been detected previously. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. We found a common candidate gene, STRA8, in sperm motility and sperm progressive motility, and common candidate genes ZSWIM7, TEKT3 and UBB in sperm motility and sperm abnormality rate, which confirms the hypothesis of gene pleiotropy. Gene network enrichment analysis showed that STRA8, UBB and CATSPER1 were enriched in the common biological process and participated in male meiosis and spermatogenesis. The SNPs of candidate genes can be given more weight in genome selection to improve the ability of genome prediction. This study provides further insight into the understanding the genetic structure of semen traits in Duroc boars.

Identification and functional characterization of developmental-stage-dependent piRNAs in Tibetan sheep testes

The core function of the testes is to produce sperms, which is the prerequisite for maintaining male fertility. PIWI-interacting RNAs (piRNAs) are a class of non-coding small RNAs that are mainly enriched in the reproductive organ and play a key role in germ cell development and spermatogenesis. However, the expression and function of piRNAs in the testes of Tibetan sheep, a domestic animal endemic to the Tibetan Plateau, remain unknown. In this study, we evaluated the sequence structure, expression profile, and potential function of piRNAs in testicular tissues from Tibetan sheep at different developmental stages (3 months, 1 year, and 3 years of age, respectively) by small RNA sequencing. Of the identified piRNAs, the sequence lengths of 24-26 nt and 29 nt dominate. Most piRNA sequences begin with uracil and have a distinct ping-pong structure which mainly distributes in exons, repeat regions, introns, and other unannotated regions of the genome. The piRNAs in the repeat region are primarily derived from the retrotransposons: long terminal repeats, long interspersed nuclear elements, and short interspersed elements. These piRNAs constitute 2,568 piRNA clusters, which mainly distribute on chromosomes 1, 2, 3, 5, 11, 13, 14, and 24, and of these clusters, a total of 529 piRNA clusters were differentially expressed in at least two age groups. Most of the piRNAs were expressed in a low abundance in the testes of developing Tibetan sheep. A total of 41,552 and 2,529 differential piRNAs were identified in testes from 3 months vs. 1 year, and 1 year vs. 3 years, respectively, presenting significantly increased abundance for most piRNAs in 1 year and 3 years compared with 3 months. The functional evaluation of the target genes showed that the differential piRNAs are mainly involved in regulating gene expression, transcription, protein modification, and cell development during spermatogenesis and testicular development. In conclusion, this study focused on the sequence structure and expression characteristics of piRNAs in the testis of Tibetan sheep and provided new insights into the functional mechanism of piRNAs in testicular development and spermatogenesis of sheep.

Whole-Genome Profile of Greek Patients with Teratozοοspermia: Identification of Candidate Variants and Genes

Male infertility is a global health problem that affects a large number of couples worldwide. It can be categorized into specific subtypes, including teratozoospermia. The present study aimed to identify new variants associated with teratozoospermia in the Greek population and to explore the role of genes on which these were identified. For this reason, whole-genome sequencing (WGS) was performed on normozoospermic and teratozoospermic individuals, and after selecting only variants found in teratozoospermic men, these were further prioritized using a wide range of tools, functional and predictive algorithms, etc. An average of 600,000 variants were identified, and of them, 61 were characterized as high impact and 153 as moderate impact. Many of these are mapped in genes previously associated with male infertility, yet others are related for the first time to teratozoospermia. Furthermore, pathway enrichment analysis and Gene ontology (GO) analyses revealed the important role of the extracellular matrix in teratozoospermia. Therefore, the present study confirms the contribution of genes studied in the past to male infertility and sheds light on new molecular mechanisms by providing a list of variants and candidate genes associated with teratozoospermia in the Greek population.

PELP1 is overexpressed in lung cancer and promotes tumor cell malignancy and resistance to tyrosine kinase inhibitor drug

Proline, glutamate, and leucine-rich protein 1 (PELP1) are involved in several cancers, but little is known about PELP1 in lung cancer. In this study, PELP1 expression was evaluated in 305 lung cancer (NSCLC) specimens to explore the role of PELP1 in lung cancer. After silencing PELP1, the proliferation, migration, invasion of tumor cells, PELP1 in relation to cell cycle and signaling pathways were evaluated, and whole-genome exons were analyzed. PELP1 is overexpressed in lung cancer, PELP1 expression correlated with squamous carcinoma, smoking, and wild-type EGFR status (all Ps<0.001) but associated with lung cancer-specific survival (P > 0.05). Silencing significantly inhibited lung cancer cell proliferation, migration, and invasion (P < 0.05) and promoted high sensitivity of lung cancer cells to tyrosine kinase inhibitor (TKI) gefitinib. PELP1-silenced cells showed downregulated phosphorylated MAPK, cyclinD1, CDK2, and upregulated RB (P < 0.05) but no change in AKT. In PELP1-silenced lung cancer cells, 140 genes were upregulated, and 143 genes were downregulated. Furthermore, the number of T regulatory cell was higher in lung adenocarcinoma with pelp1 high-expression and pelp1 expression was negatively correlated with CD274 (PDL-1) and CTLA4. Therefore, PELP1 plays an important role in the malignant behavior of NSCLC and could be a potential therapeutic target.

TCFL5 deficiency impairs the pachytene to diplotene transition during spermatogenesis in the mouse

Spermatogenesis is a complex, multistep process during which spermatogonia give rise to spermatozoa. Transcription Factor Like 5 (TCFL5) is a transcription factor that has been described expressed during spermatogenesis. In order to decipher the role of TCFL5 during in vivo spermatogenesis, we generated two mouse models. Ubiquitous removal of TCFL5 generated by breeding TCFL5^fl/fl with SOX2-Cre mice resulted in sterile males being unable to produce spermatozoa due to a dramatic alteration of the testis architecture presenting meiosis arrest and lack of spermatids. SYCP3, SYCP1 and H1T expression analysis showed that TCFL5 deficiency causes alterations during pachytene/diplotene transition resulting in a meiotic arrest in a diplotene-like stage. Even more, TCFL5 deficient pachytene showed alterations in the number of MLH1 foci and the condensation of the sexual body. In addition, tamoxifen-inducible TCFL5 knockout mice showed, besides meiosis phenotype, alterations in the spermatids elongation process resulting in aberrant spermatids. Furthermore, TCFL5 deficiency increased spermatogonia maintenance genes (Dalz, Sox2, and Dmrt1) but also increased meiosis genes (Syce1, Stag3, and Morc2a) suggesting that the synaptonemal complex forms well, but cannot separate and meiosis does not proceed. TCFL5 is able to bind to the promoter of Syce1, Stag3, Dmrt1, and Syce1 suggesting a direct control of their expression. In conclusion, TCFL5 plays an essential role in spermatogenesis progression being indispensable for meiosis resolution and spermatids maturation.

Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs

Simple Summary

Copy number variation (CNV) is a type of variant that may influence meat quality of, for example intramuscular fat (IMF). In this study, a genome-wide association study (GWAS) was then performed between CNVs and IMF in a pig F2 resource population. A total of 19 CNVRs were found to be significantly associated with IMF. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.

Abstract

Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.

Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs

Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.

Identification of new semen trait-related candidate genes in Duroc boars through genome-wide association and weighted gene co-expression network analyses

Semen traits are crucial in commercial pig production since semen from boars is widely used in artificial insemination for both purebred and crossbred pig production. Revealing the genetic architecture of semen traits potentially promotes the efficiencies of improving semen traits through artificial selection. This study is aimed to identify candidate genes related to the semen traits in Duroc boars. First, we identified the genes that were significantly associated with three semen traits, including sperm motility (MO), sperm concentration (CON), and semen volume (VOL) in a Duroc boar population through a genome-wide association study (GWAS). Second, we performed a weighted gene co-expression network analysis (WGCNA). A total of 2, 3, and 20 single-nucleotide polymorphisms were found to be significantly associated with MO, CON, and VOL, respectively. Based on the haplotype block analysis, we identified one genetic region associated with MO, which explained 6.15% of the genetic trait variance. ENSSSCG00000018823 located within this region was considered as the candidate gene for regulating MO. Another genetic region explaining 1.95% of CON genetic variance was identified, and, in this region, B9D2, PAFAH1B3, TMEM145, and CIC were detected as the CON-related candidate genes. Two genetic regions that accounted for 2.23% and 2.48% of VOL genetic variance were identified, and, in these two regions, WWC2, CDKN2AIP, ING2, TRAPPC11, STOX2, and PELO were identified as VOL-related candidate genes. WGCNA analysis showed that, among these candidate genes, B9D2, TMEM145, WWC2, CDKN2AIP, TRAPPC11, and PELO were located within the most significant module eigengenes, confirming these candidate genes' role in regulating semen traits in Duroc boars. The identification of these candidate genes can help to better understand the genetic architecture of semen traits in boars. Our findings can be applied for semen traits improvement in Duroc boars.

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model

A combined Genotyping By Sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) protocol was used to identify—in parallel—genetic variation (Genomic-Wide Association Studies (GWAS) and epigenetic differences of Differentially Methylated Regions (DMR) in the genome of spermatozoa from the porcine animal model. Breeding boars with good semen quality (n = 11) and specific and well-documented differences in fertility (farrowing rate, FR) and prolificacy (litter size, LS) (n = 7) in artificial insemination programs, using combined FR and LS, were categorized as High Fertile (HF, n = 4) or Low Fertile (LF, n = 3), and boars with Unknown Fertility (UF, n = 4) were tested for eventual epigenetical similarity with those fertility-proven. We identified 165,944 Single Nucleotide Polymorphisms (SNPs) that explained 14–15% of variance among selection lines. Between HF and LF individuals (n = 7, 4 HF and 3 LF), we identified 169 SNPs with p ≤ 0.00015, which explained 58% of the variance. For the epigenetic analyses, we considered fertility and period of ejaculate collection (late-summer and mid-autumn). Approximately three times more DMRs were observed in HF than in LF boars across these periods. Interestingly, UF boars were clearly clustered with one of the other HF or LF groups. The highest differences in DMRs between HF and LF experimental groups across the pig genome were located in the chr 3, 9, 13, and 16, with most DMRs being hypermethylated in LF boars. In both HF and LF boars, DMRs were mostly hypermethylated in late-summer compared to mid-autumn. Three overlaps were detected between SNPs (p ≤ 0.0005, n = 1318) and CpG sites within DMRs. In conclusion, fertility levels in breeding males including FR and LS can be discerned using methylome analyses. The findings in this biomedical animal model ought to be applied besides sire selection for andrological diagnosis of idiopathic sub/infertility.

A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine

BACKGROUND

Genetic pressure in animal breeding is sparking the interest of breeders for selecting elite boars with higher sperm quality to optimize ejaculate doses and fertility rates. However, the molecular basis of sperm quality is not yet fully understood. Our aim was to identify candidate genes, pathways and DNA variants associated to sperm quality in swine by analysing 25 sperm-related phenotypes and integrating genome-wide association studies (GWAS) and RNA-seq under a systems biology framework.

RESULTS

By GWAS, we identified 12 quantitative trait loci (QTL) associated to the percentage of head and neck abnormalities, abnormal acrosomes and motile spermatozoa. Candidate genes included CHD2, KATNAL2, SLC14A2 and ABCA1. By RNA-seq, we identified a wide repertoire of mRNAs (e.g. PRM1, OAZ3, DNAJB8, TPPP2 and TNP1) and miRNAs (e.g. ssc-miR-30d, ssc-miR-34c, ssc-miR-30c-5p, ssc-miR-191, members of the let-7 family and ssc-miR-425-5p) with functions related to sperm biology. We detected 6128 significant correlations (P-value ≤ 0.05) between sperm traits and mRNA abundances. By expression (e)GWAS, we identified three trans-expression QTL involving the genes IQCJ, ACTR2 and HARS. Using the GWAS and RNA-seq data, we built a gene interaction network. We considered that the genes and interactions that were present in both the GWAS and RNA-seq networks had a higher probability of being actually involved in sperm quality and used them to build a robust gene interaction network. In addition, in the final network we included genes with RNA abundances correlated with more than four semen traits and miRNAs interacting with the genes on the network. The final network was enriched for genes involved in gamete generation and development, meiotic cell cycle, DNA repair or embryo implantation. Finally, we designed a panel of 73 SNPs based on the GWAS, eGWAS and final network data, that explains between 5% (for sperm cell concentration) and 36% (for percentage of neck abnormalities) of the phenotypic variance of the sperm traits.

CONCLUSIONS

By applying a systems biology approach, we identified genes that potentially affect sperm quality and constructed a SNP panel that explains a substantial part of the phenotypic variance for semen quality in our study and that should be tested in other swine populations to evaluate its relevance for the pig breeding sector.

Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm's response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

Gene Polymorphisms in Boar Spermatozoa and Their Associations with Post-Thaw Semen Quality

Genetic markers have been used to assess the freezability of semen. With the advancement in molecular genetic techniques, it is possible to assess the relationships between sperm functions and gene polymorphisms. In this study, variant calling analysis of RNA-Seq datasets was used to identify single nucleotide polymorphisms (SNPs) in boar spermatozoa and to explore the associations between SNPs and post-thaw semen quality. Assessment of post-thaw sperm quality characteristics showed that 21 boars were considered as having good semen freezability (GSF), while 19 boars were classified as having poor semen freezability (PSF). Variant calling demonstrated that most of the polymorphisms (67%) detected in boar spermatozoa were at the 3’-untranslated regions (3’-UTRs). Analysis of SNP abundance in various functional gene categories showed that gene ontology (GO) terms were related to response to stress, motility, metabolism, reproduction, and embryo development. Genomic DNA was isolated from sperm samples of 40 boars. Forty SNPs were selected and genotyped, and several SNPs were significantly associated with motility and membrane integrity of frozen-thawed (FT) spermatozoa. Polymorphism in SCLT1 gene was associated with significantly higher motility and plasma membrane integrity of FT spermatozoa from boars of the GSF group compared with those of the PSF group. Likewise, polymorphisms in MAP3K20, MS4A2, and ROBO1 genes were significantly associated with reduced cryo-induced lipid peroxidation and DNA damage of FT spermatozoa from boars of the GSF group. Candidate genes with significant SNP associations, including APPL1, PLBD1, FBXO16, EML5, RAB3C, OXSR1,PRICKLE1, and MAP3K20 genes, represent potential markers for post-thaw semen quality, and they might be relevant for future improvement in the selection procedure of boars for cryopreservation. The findings of this study provide evidence indicating that polymorphisms in genes expressed in spermatozoa could be considered as factors associated with post-thaw semen quality.

Weighted single-step GWAS identified candidate genes associated with semen traits in a Duroc boar population

BACKGROUND

In the pig production industry, artificial insemination (AI) plays an important role in enlarging the beneficial impact of elite boars. Understanding the genetic architecture and detecting genetic markers associated with semen traits can help in improving genetic selection for such traits and accelerate genetic progress. In this study, we utilized a weighted single-step genome-wide association study (wssGWAS) procedure to detect genetic regions and further candidate genes associated with semen traits in a Duroc boar population. Overall, the full pedigree consists of 5284 pigs (12 generations), of which 2693 boars have semen data (143,113 ejaculations) and 1733 pigs were genotyped with 50 K single nucleotide polymorphism (SNP) array.

RESULTS

Results show that the most significant genetic regions (0.4 Mb windows) explained approximately 2%~ 6% of the total genetic variances for the studied traits. Totally, the identified significant windows (windows explaining more than 1% of total genetic variances) explained 28.29, 35.31, 41.98, and 20.60% of genetic variances (not phenotypic variance) for number of sperm cells, sperm motility, sperm progressive motility, and total morphological abnormalities, respectively. Several genes that have been previously reported to be associated with mammal spermiogenesis, testes functioning, and male fertility were detected and treated as candidate genes for the traits of interest: Number of sperm cells, TDRD5, QSOX1, BLK, TIMP3, THRA, CSF3, and ZPBP1; Sperm motility, PPP2R2B, NEK2, NDRG, ADAM7, SKP2, and RNASET2; Sperm progressive motility, SH2B1, BLK, LAMB1, VPS4A, SPAG9, LCN2, and DNM1; Total morphological abnormalities, GHR, SELENOP, SLC16A5, SLC9A3R1, and DNAI2.

CONCLUSIONS

In conclusion, candidate genes associated with Duroc boars' semen traits, including the number of sperm cells, sperm motility, sperm progressive motility, and total morphological abnormalities, were identified using wssGWAS. KEGG and GO enrichment analysis indicate that the identified candidate genes were enriched in biological processes and functional terms may be involved into spermiogenesis, testes functioning, and male fertility.