Identification of key genes affecting sperm motility in chicken based on whole-transcriptome sequencing

Gut-testis axis in roosters: Lactiplantibacillus plantarum supplementation improves reproductive performance

Probiotics are widely used in poultry farming and industry, as they offer numerous health and performance benefits for birds. Probiotic Lactobacilli maintain gut microbiota balance, aid nutrient utilization, boost the immune system, increase stress resistance and serve as antibiotic alternatives. However, their impact on male reproductive function is not yet fully understood. This study investigated the effect of a novel probiotic strain, Lactiplantibacillus plantarum SNI3 (LbSNI3), on the reproductive performance of roosters. Twenty adult roosters were used. LbSNI3 was administered orally (dose: 2 × 107 CFU/animal/day) for 7 weeks to half of the animals. Control birds (10) received sterile tap water vehicle. Ejaculate volume, sperm concentration, sperm motility, number of IPVL penetration holes and testosterone plasma concentration have been measured weekly. Testis weight, dimensions and histology have been determined at the end of the experiment. mRNA levels of select genes, involved in spermatogenesis and sperm motility, oxidative and steroid synthesis have been measured in the testis samples by qRT-PCR. Total antioxidant capacity, superoxide dismutase (SOD) enzyme activity and malondialdehyde (MDA) levels were also analyzed. LbSNI3 administration increased the ejaculate volume, sperm concentration and the number of penetration holes, resulting in a significant improvement in the reproductivity index. In contrast, testosterone levels were not statistically different in control versus LbSNI3-treated groups. At the end of the experiment, testis size, the area, and the lumen of seminiferous tubuli were increased in LbSNI3-treated roosters. The testicular expression of Gpx1, Sepw1, Dio2, Birc5 and Rec8 genes was elevated following oral administration of LbSNI3. Total antioxidant activity, SOD activity significantly increased, while MDA concentration decreased, indicating enhanced antioxidant capacity in the testis. LbSNI3 produces a bacterial metabolite, γ-glutamyl-glutamate, which enters the glutathione cycle and strengthens the testicular defense mechanisms against oxidative stress. In conclusion, oral administration of probiotic LbSNI3 enhances antioxidant defense mechanisms in the testis, leading to increased reproductive index in adult roosters. This effect may be mediated through the gut-testis axis and could be utilized to improve productivity in the livestock industry.

Integrated omics reveals the regulatory role of PKCα in Sertoli cell proliferation and apoptosis through the MAPK/ERK signaling pathway in goose testis

Testicular development is essential for reproductive performance in geese, as the testes are the primary organs for sperm production and play a pivotal role in egg-laying physiology. Despite their importance, genes, proteins, and pathways regulating goose testicular development are poorly understood. This study employed integrative transcriptomic and proteomic analysis methods to identify critical regulators of testicular development in geese across three reproductive periods. Additionally, the role of PKCα in Sertoli cell proliferation via the MAPK/ERK pathway was evaluated at the cellular level. A total of 8,921 differentially expressed genes and 1,866 differentially expressed proteins were identified, revealing key pathways such as FOXO, MAPK, PPAR, and Hedgehog that regulate testicular development. Both omics correlation analysis and signal pathway regulation network results show the importance of MAPK in this process, while cellular experiment revealed that PKCα affects proliferation and apoptosis of Sertoli cells through the MAPK/ERK signaling pathway. The findings revealed that PKCα downregulation reduced the expression of genes associated with both cell proliferation and apoptosis, resulting in a diminished activity of Sertoli cells. This study compared testicular transcriptomes and proteomes of Hungarian and Jilin white geese, identifying key genes, proteins, and pathways critical for reproduction. These findings advance our understanding of molecular mechanisms underlying testicular development and provide insights to enhance gander reproductive performance.

Transcriptome analysis of testis and epididymis identifies key genes and pathways regulating gander sperm motility

Sperm motility is a critical indicator of semen quality and determines the reproduction performance in male poultry. However, compared to chickens and ducks, very little is known about the physiological basis of varying levels of sperm motility as well the underlying regulatory mechanisms in geese. To address this, in the present study, a systematic comparison of semen quality parameters and histomorphological characteristics and genome-wide transcriptomic profiles of testes and epididymis were performed in ganders with high and low sperm motility. Our results showed that the size, weight, and organ index of bilateral testes and epididymis of ganders from high sperm motility (HSM) group tended to be higher (P > 0.05) than those of ganders from low sperm motility (LSM) group, implying better reproductive organ development in HSM. The ejaculate volume, sperm density, sperm viability, and semen quality factor of the ganders were observed to be significantly higher in HSM than in LSM (P < 0.01), and the opposite was seen in sperm deformity rate (P < 0.01). Moreover, the ganders in HSM showed significantly higher testicular seminiferous epithelial thickness and seminiferous tubule diameter (P < 0.05), higher number of Sertoli cells (SC), spermatids (Sd), and spermatozoa (Sa, P < 0.05), as well as greater diameter and area of epididymal proximal efferent ductule (PED, P < 0.05) than those in LSM. Comparative transcriptomic analysis identified 1,828 and 483 differentially expressed genes (DEGs) in the testis and epididymis of ganders between HSM and LSM, respectively. Functional enrichment analysis revealed that these DEGs were significantly enriched in the Wnt signaling, Apelin signaling, melanogenesis, and GnRH signaling pathways. The protein-protein interaction network analysis further highlighted the hub genes. The testicular DEGs including PLCB1, PLCB2, WNT11, WNT4, and LRP6 were identified to regulate sperm motility through the Wnt signaling pathway, while the epididymal DEGs including WNT3A, WNT9B, SOX2, and SOX10 could affect sperm motility by regulating epididymal cellular proliferation and differentiation. These data provided new insights into the regulatory mechanisms of male poultry reproductive organ development and sperm quality and would be helpful for developing molecular approaches in the genetic improvement of goose fertility.

Genome-Wide Analysis of Genetic Predispositions Linked to Damaged Membranes and Impaired Fertility as Indicators of Compromised Sperm-Egg Interaction Mechanisms in Frozen-Thawed Rooster Semen

BACKGROUND

Cryopreservation cannot be widely used for rooster sperm due to high incidences of cryoinjury, including damage to sperm membranes. Thus, cryopreserved rooster sperm has limited use due to low sperm motility and reduced fertilizing ability, which disrupts the mechanisms involved in sperm-egg interactions. Previously, we used an Illumina 60K single-nucleotide polymorphism (SNP) array to search for genes associated with rooster sperm quality, before and after freeze-thawing. As a continuation of these genome-wide association studies (GWAS), the present investigation used a denser 600K SNP chip. Consequently, the screen depth was expanded by many markers for cryo-resistance in rooster sperm while more candidate genes were identified. Thus, our study aimed to identify genome-wide associations with ejaculate quality indicators, including those concerning sperm membrane damage.

METHODS

We selected sperm quality indicators after freezing-thawing using samples from a proprietary cryobank collection created to preserve generative and germ cells of rare and endangered breeds of chickens and other animal species. A total of 258 ejaculates from 96 roosters of 16 different breeds were analyzed. Moreover, 96 respective DNA samples were isolated for genotyping using a 600K Affymetrix® Axiom® high-density genotyping array.

RESULTS

In total, 31 SNPs and 26 candidate genes were associated with characteristics of sperm membrane damage, progressive motility, and sperm cell respiration induction using 2,4-dinitrophenol. In particular, we identified the ENSGALG00000029931 gene as a candidate for progressive motility, PHF14 and ARID1B for damaged sperm membranes, and KDELR3, DDX17, DMD, CDKL5, DGAT2, ST18, FAM150A, DIAPH2, MTMR7, NAV2, RAG2, PDE11A, IFT70A, AGPS, WDFY1, DEPDC5, TSC1, CASZ1, and PLEKHM2 for sperm cell respiration induction.

CONCLUSIONS

Our findings provide important information for understanding the genetic basis of sperm membrane integrity and other traits that can potentially compromise the mechanisms involved in sperm-egg interactions. These findings are relevant to the persistence of fertility after thawing previously frozen rooster semen.

Molecular mechanisms underlying age-dependent effects of rearing system on the goose testicular development and semen quality

As an important non-genetic factor, the rearing system has significant effects on male poultry reproductive system development. However, compared with other poultry such as chickens and ducks, less is known about the effects and mechanisms of rearing system on the gander reproductive organ development and semen quality. In the present study, the testicular morphological, histological, and transcriptomic responses of three goose breeds to the two dryland rearing systems (i.e., cage rearing system, CRS and net-floor mixed rearing system, MRS) were systematically analyzed and compared. Results from histomorphological analysis demonstrated that the effects of rearing system on the gander testicular development were age-dependent, and moreover, the CRS may be more conducive than MRS to the testicular development and semen quality during the period from post-hatch week 10 to week 43. At week 30, compared to Sichuan White goose (SW), the rearing system showed more pronounced effects on the testicular size, weight, and organ index of Gang goose (GE) and Landes goose (LD). However, such effects were mitigated in LD and even reversed in GE at week 43. Meanwhile, most testicular histological parameters of three goose breeds were higher under MRS than under CRS at week 30, while the converse was seen in some histological parameters of either GE or LD at week 43. Moreover, the semen quality was generally better under CRS than under MRS at week 43. Through comparative transcriptomics analysis, the Wnt signaling pathway together with several involved hub genes were identified to have important roles in mediating the effects of rearing system on the goose testicular development. Moreover, the metabolism-related, cell cycle, and Wnt signaling pathways could be partially responsible for differences in the goose breed-related testicular development and semen quality under CRS, where a number of genes involved in meiosis could have crucial roles. These results would not only provide novel insights into the effects and mechanisms of rearing system on male poultry reproductive performance, but they would also be helpful for the optimization and selection of dryland rearing systems in male geese.

Exploring the molecular basis of efficient feed utilization in low residual feed intake slow-growing ducks based on breast muscle transcriptome

Residual feed intake (RFI) has recently gained attention as a key indicator of feed efficiency in poultry. In this study, 800 slow-growing ducks with similar initial body weights were reared in an experimental facility until they were culled at 42 d of age. Thirty high RFI (HRFI) and 30 low RFI (LRFI) birds were selected to evaluate their growth performance, carcass characteristics, and muscle development. Transcriptome and weighted gene co-expression correlation network analyses of pectoral muscles were conducted on six LRFI and six HRFI ducks. The results revealed that selecting for LRFI significantly reduced feed consumption (P < 0.05) and improved feed efficiency without affecting the growth performance, slaughter rate, or meat quality of ducks (P > 0.05). Moreover, compared with HRFI ducks, LRFI ducks had a lower pectoral muscle fat content (P < 0.05), larger muscle fiber diameter and area (P < 0.05), and lower muscle fiber density (P < 0.05). There were significant differences in gene expression between LRFI and HRFI ducks, with 102 upregulated and 258 downregulated genes, which were enriched in the PPAR signaling pathway, adipocytokine signaling pathway, actin cytoskeleton regulation, ECM-receptor interaction, and focal adhesion. The expression of genes associated with fat and energy metabolism, including ACSL6, PCK1, APOC3, HMGCS2, PRKAG3, and G6PC1, was downregulated in LRFI ducks, and weighted gene co-expression correlation network analysis identified PRKAG3 as a hub gene. Our findings indicate that reduced mitochondrial energy metabolism may contribute to the RFI of slow-growing ducks, with PRKAG3 playing a pivotal role in this biological process. These findings provide novel insights into the molecular changes underlying RFI variation in slow-growing ducks.

microRNA as an Important Mediator in the Regulation of Male Gallus gallus domesticus Reproduction: Current State of the Problem

During all periods of male ontogenesis, physiological processes responsible for the correct functioning of reproductive organs and spermatogenesis are under the influence of various factors (neuro-humoral, genetic, and paratypical). Recently, the attention of researchers has increasingly turned to the study of epigenetic factors. In scientific publications, one can increasingly find references to the direct role of microRNAs, small non-coding RNAs involved in post-transcriptional regulation of gene expression, in the processes of development and functioning of reproductive organs. Although the role of microRNAs in the reproduction of mammals, including humans, has been intensively studied, this area of knowledge in birds remains under-researched and limited to single experiments. This is likely due to the unique features of embryogenesis and the structure of the avian reproductive system. This review summarizes the current state of knowledge on the role of microRNAs in avian reproduction. Insight into the molecular basis of spermatogenesis in Gallus gallus domesticus is provided. Data on the functions and mechanisms by which microRNAs influence the processes of growth, development, and formation of rooster germ cells that determine the necessary morphofunctional qualitative characteristics of mature spermatozoa are summarized. Particular attention is paid to miRNA biogenesis as an important step affecting the success of spermatogenesis, as well as the role of miRNAs in avian sex differentiation during early embryogenesis. The modern literature sources systematized in this review, revealing the questions about the role of miRNAs in the reproductive function of birds, create a theoretical basis and define new perspectives and directions for further research in this field.

Whole transcriptome sequencing of testis and epididymis reveals genes associated with sperm development in roosters

BACKGROUND

Chickens play a crucial role as the primary global source of eggs and poultry, and the quality of rooster semen significantly impacts poultry reproductive efficiency. Therefore, it is imperative to comprehend the regulatory mechanisms underlying sperm development.

RESULTS

In this study, we established transcriptome profiles of lncRNAs, miRNAs, and mRNAs in 3 testis tissues and 3 epididymis tissues from "Jing Hong No.1" roosters at 24, 35, and 64 weeks of age. Using the data, we conducted whole transcriptome analysis and constructed a ceRNA network. We detected 10 differentially expressed mRNAs (DEmRNAs), 33 differentially expressed lncRNAs (DElncRNAs), and 10 differentially expressed miRNAs (DEmiRNAs) in the testis, as well as 149 DEmRNAs, 12 DElncRNAs, and 10 DEmiRNAs in the epididymis. These genes were found to be involved in cell differentiation and development, as well as various signaling pathways such as GnRH, MAPK, TGF-β, mTOR, VEGF, and calcium ion pathways. Subsequently, we constructed two competing endogenous RNA (ceRNA) networks comprising DEmRNAs, DElncRNAs, and DEmiRNAs. Furthermore, we identified four crucial lncRNA-mRNA-miRNA interactions that govern specific biological processes in the chicken reproductive system: MSTRG.2423.1-gga-miR-1563-PPP3CA and MSTRG.10064.2-gga-miR-32-5p-GPR12 regulating sperm motility in the testis; MSTRG.152556.1-gga-miR-9-3p-GREM1/THYN1 governing immunomodulation in the epididymis; and MSTRG.124708.1-gga-miR-375-NDUFB9/YBX1 controlling epididymal sperm maturation and motility.

CONCLUSIONS

Whole transcriptome sequencing of chicken testis and epididymis screened several key genes and ceRNA regulatory networks, which may be involved in the regulation of epididymal immunity, spermatogenesis and sperm viability through the pathways of MAPK, TGF-β, mTOR, and calcium ion. These findings contribute to our comprehensive understanding of the intricate molecular processes underlying rooster spermatogenesis, maturation and motility.

Comprehensive analysis of the differential expression of mRNAs, lncRNAs, and miRNAs in Zi goose testis with high and low sperm mobility

Sperm mobility (SM) is an objective index for measuring sperm motility; however, the mechanisms underlying its regulation in geese remain unclear. The present study sought to elucidate the genetic mechanism underlying SM traits in Zi geese (Anser cygnoides L.). To this end, three successive experiments were performed. In Experiment I, SM was determined in 40 ganders; the 3 ganders with the highest mobility and three with the lowest mobility were assigned to the high and low sperm mobility rank (SMR) groups, respectively. In Experiment II, the differences in fertility between the two SMR groups were assessed within two breeding flocks comprising the selected six ganders from Experiment I and 30 females (each flock had 3 ganders and 15 females). In Experiment III, the testes of the 6 ganders were harvested for histological observation and whole-transcriptome sequencing. Results revealed better fertility, well-developed seminiferous tubules, and abundant mature sperm in the high-SMR-flock compared to those of the low-SMR-flock (89 vs. 81%) (P < 0.05). Differential expression (DE) analysis identified 76 mRNAs, 344 lncRNAs, and 17 miRNAs between the SMR groups, with LOC106049708, XPNPEP3, GNB3, ADCY8, PRKAG3, oha-miR-182-5p, and ocu-miR-10b-5p identified as key mRNAs and miRNAs contributing to SM. Enrichment analysis implicated these DE RNAs in pathways related to ATP binding, cell metabolism, apelin signaling, Wnt signaling, and Adherens junctions. Additionally, competing endogenous RNA (ceRNA) networks comprising 9 DE mRNAs, 17 DE miRNAs, and 169 DE lncRNAs were constructed. Two ceRNA network pathways (LOC106049708-oha-miR-182-5p-MSTRG.2479.6 and PRKAG3-ocu-miR-10b-5p-MSTRG.9047.14) were identified as key regulators of SM in geese. These findings offer crucial insights into the identification of key genes and ceRNA pathways influencing sperm mobility in geese.

Signaling pathways and regulatory networks in quail skeletal muscle development: insights from whole transcriptome sequencing

Quail, as an advantageous avian model organism due to its compact size and short reproductive cycle, holds substantial potential for enhancing our understanding of skeletal muscle development. The quantity of skeletal muscle represents a vital economic trait in poultry production. Unraveling the molecular mechanisms governing quail skeletal muscle development is of paramount importance for optimizing meat and egg yield through selective breeding programs. However, a comprehensive characterization of the regulatory dynamics and molecular control underpinning quail skeletal muscle development remains elusive. In this study, through the application of HE staining on quail leg muscle sections, coupled with preceding fluorescence quantification PCR of markers indicative of skeletal muscle differentiation, we have delineated embryonic day 9 (E9) and embryonic day 14 (E14) as the start and ending points, respectively, of quail skeletal muscle differentiation. Then, we employed whole transcriptome sequencing to investigate the temporal expression profiles of leg muscles in quail embryos at the initiation of differentiation (E9) and upon completion of differentiation (E14). Our analysis revealed the expression patterns of 12,012 genes, 625 lncRNAs, 14,457 circRNAs, and 969 miRNAs in quail skeletal muscle samples. Differential expression analysis between the E14 and E9 groups uncovered 3,479 differentially expressed mRNAs, 124 lncRNAs, 292 circRNAs, and 154 miRNAs. Furthermore, enrichment analysis highlighted the heightened activity of signaling pathways related to skeletal muscle metabolism and intermuscular fat formation, such as the ECM-receptor interaction, focal adhesion, and PPAR signaling pathway during E14 skeletal muscle development. Conversely, the E9 stage exhibited a prevalence of pathways associated with myoblast proliferation, exemplified by cell cycle processes. Additionally, we constructed regulatory networks encompassing lncRNA‒mRNA, miRNA‒mRNA, lncRNA‒miRNA-mRNA, and circRNA-miRNA‒mRNA interactions, thus shedding light on their putative roles within quail skeletal muscle. Collectively, our findings illuminate the gene and non-coding RNA expression characteristics during quail skeletal muscle development, serving as a foundation for future investigations into the regulatory mechanisms governing non-coding RNA and quail skeletal muscle development in poultry production.