Transcriptome analysis and identification of age-associated fertility decreased genes in hen uterovaginal junction

Identification of genes associated with sperm storage capacity in hens at different times after insemination by RNA-seq and Ribo-seq

BACKGROUND

Sperm storage capacity (SSC) determines the duration of fertility in hens and is an important reproduction trait that cannot be ignored in production. Currently, the genetic mechanism of SSC is still unclear in hens. Therefore, to explore the genetic basis of SSC, we analyzed the uterus-vagina junction (UVJ) of hens with different SSC at different times after insemination by RNA-seq and Ribo-seq.

RESULTS

Our results showed that 589, 596, and 527 differentially expressed genes (DEGs), 730, 783, and 324 differentially translated genes (DTGs), and 804, 625, and 467 differential translation efficiency genes (DTEGs) were detected on the 5th, 10th, and 15th days after insemination, respectively. In transcription levels, we found that the differences of SSC at different times after insemination were mainly reflected in the transmission of information between cells, the composition of intercellular adhesion complexes, the regulation of ion channels, the regulation of cellular physiological activities, the composition of cells, and the composition of cell membranes. In translation efficiency (TE) levels, the differences of SSC were mainly related to the physiological and metabolic activities in the cell, the composition of the organelle membrane, the physiological activities of oxidation, cell components, and cell growth processes. According to pathway analysis, SSC was related to neuroactive ligand-receptor interaction, histidine metabolism, and PPAR signaling pathway at the transcriptional level and glutathione metabolism, oxidative phosphorylation, calcium signaling pathway, cell adhesion molecules, galactose metabolism, and Wnt signaling pathway at the TE level. We screened candidate genes affecting SSC at transcriptional levels (COL4A4, MUC6, MCHR2, TACR1, AVPR1A, COL1A1, HK2, RB1, VIPR2, HMGCS2) and TE levels(COL4A4, MUC6, CYCS, NDUFA13, CYTB, RRM2, CAMK4, HRH2, LCT, GCK, GALT). Among them, COL4A4 and MUC6 were the key candidate genes differing in transcription, translation, and translation efficiency.

CONCLUSIONS

Our study used the combined analysis of RNA-seq and Ribo-seq for the first time to investigate the SSC and reveal the physiological processes associated with SSC. The key candidate genes affecting SSC were screened, and the theoretical basis was provided for the analysis of the molecular regulation mechanism of SSC.

The sperm storage capacity in hens was correlated with the morphological differences of the oviduct and uterus-vagina junction

The fertilization rate is an important index to evaluate the reproductive capacity of hens, which is mainly affected by semen quality, timing of artificial insemination (AI), and the ability to store sperm. A high sperm storage (SS) capacity can extend the interval, reduce the frequency, and decrease the labor costs of AI. However, relatively few studies have investigated the SS capacity of hens. Therefore, the aims of the present study were to identify factors influencing the SS capacity of Guangxi partridge chickens and to explore the impact of the sperm count in different sections of the oviduct and sperm storage tubules (SSTs), in addition to the number and surface area of SSTs on SS capacity at different time points after AI. We found that SS capacity was positively correlated to the egg production rate (P < 0.01) and body length (P < 0.05). On post-AI days 5, 10, and 15, the sperm count was higher in uterus-vagina junction (UVJ) than the magnum, isthmus, and infundibulum (P < 0.01), but gradually decreased over time. Also, the duration of SS and the sperm count of the UVJ was greater in the high SS group than the low SS group (P < 0.05). Histopathological analysis of the UVJ showed that the number and surface area of the SSTs (P < 0.01), as well as the proportion of SSTs containing sperm, were greater in the high SS group at all time points post AI (P < 0.01), while the proportion of SSTs containing sperm gradually decreased over time. Collectively, these results highlight the potential for selective breeding of SS capacity and show that SS capacity is related to laying performance and body length of Guangxi partridge hens. In addition, SS capacity was positively correlated to the surface area of SSTs and the proportion containing sperm. A greater sperm count stored in the UVJ was correlated to more sperm transported to the infundibulum and subsequent greater SS capacity of hens.

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

Turkey hen sperm storage tubule transcriptome response to artificial insemination and the presence of semen

Introduction: Sperm storage within the uterovaginal junction (UVJ) of avian species occurs in specialized structures termed sperm storage tubules (SSTs) and allows for prolonged storage of semen, though the molecular mechanisms involved in semen preservation are not well understood. Little work has been done examining how function of the SSTs is impacted by insemination and by semen present in the SSTs. Methods: Transcriptome analysis was performed on isolated SSTs from turkey hens receiving no insemination (control), sham-insemination, or semen-insemination at three timepoints (D1, D30, and D90 post-insemination). Bioinformatic and functional annotation analyses were performed using CLC Genomics Workbench, Database for Annotation, Visualization, and Integrated Discovery (DAVID), and Ingenuity Pathway Analysis (IPA). Pairwise comparisons and k-medoids cluster analysis were utilized to decipher differential expression profiles in the treatment groups. Results: The SST transcriptome of the semen inseminated group exhibited the greatest differences within the group, with differences detectable for up to 90 days post insemination, while control and sham-inseminated groups were more similar. In the semen-inseminated samples, upregulation of pathways relating to classical and non-classical reproductive signaling, cytoskeletal remodeling, physiological parameters of the local UVJ environment, and cellular metabolism was observed. In the sham-inseminated samples, upregulation of immune pathways and non-reproductive endocrine hormones was observed. Discussion: This work provides insights into the molecular level changes of the SST in response to insemination as well as to the presence of semen. Results from this study may have direct implications on fertility rates as well as potential strategies for avian semen cryopreservation protocols.

The construction of a testis transcriptional cell atlas from embryo to adult reveals various somatic cells and their molecular roles

BACKGROUND

The testis is a complex organ that undergoes extensive developmental changes from the embryonic stage to adulthood. The development of germ cells, which give rise to spermatozoa, is tightly regulated by the surrounding somatic cells.

METHODS

To better understand the dynamics of these changes, we constructed a transcriptional cell atlas of the testis, integrating single-cell RNA sequencing data from over 26,000 cells across five developmental stages: fetal germ cells, infants, childhood, peri-puberty, and adults. We employed various analytical techniques, including clustering, cell type assignments, identification of differentially expressed genes, pseudotime analysis, weighted gene co-expression network analysis, and evaluation of paracrine cell-cell communication, to comprehensively analyze this transcriptional cell atlas of the testis.

RESULTS

Our analysis revealed remarkable heterogeneity in both somatic and germ cell populations, with the highest diversity observed in Sertoli and Myoid somatic cells, as well as in spermatogonia, spermatocyte, and spermatid germ cells. We also identified key somatic cell genes, including RPL39, RPL10, RPL13A, FTH1, RPS2, and RPL18A, which were highly influential in the weighted gene co-expression network of the testis transcriptional cell atlas and have been previously implicated in male infertility. Additionally, our analysis of paracrine cell-cell communication supported specific ligand-receptor interactions involved in neuroactive, cAMP, and estrogen signaling pathways, which support the crucial role of somatic cells in regulating germ cell development.

CONCLUSIONS

Overall, our transcriptional atlas provides a comprehensive view of the cell-to-cell heterogeneity in the testis and identifies key somatic cell genes and pathways that play a central role in male fertility across developmental stages.

Uterine microbial communities and their potential role in the regulation of epithelium cell cycle and apoptosis in aged hens

BACKGROUND

Alterations of the uterine microbiome are closely associated with various intrauterine diseases and physiological conditions, which are well-established in mammals. However, as representative oviparous animals, the research on the uterine microbial ecosystem and its functions with physiological homeostasis is limited in chickens. Additionally, continuous egg-laying disrupts the oviducal immune defenses of aged hens, susceptible to pathogen invasion, causing poor egg quality and food-borne infections in humans. Here, we investigated aging-related changes in the oviduct microbial colonization and transmission from the gut to eggs and their roles in a hen model.

RESULTS

The results of 16S rDNA sequencing showed significant differences in the oviduct microbial composition between young (38 weeks) and aged (77 weeks) laying hens. SourceTracker analysis further revealed differences in the effects of microbial transmission on the oviducal microbiota between young and aged hens. Enhanced barrier defense with cell apoptosis suppression and cell cycle arrest of the uterus were observed in aged hens reducing microbial transmission from the lower to upper reproductive tract. In addition, a total of 361 significantly differential metabolites were identified using metabolomics in the aged uterine microbiota, especially in products of amino acid metabolism and biosynthesis of various secondary metabolites, which might have essential effects on cell apoptosis by regulating immune responses and cell cycle. Notably, antibiotics disrupted uterine microbiota by dietary intervention and direct perfusion did not retard aging-related physiological changes but further aggravated aging processes by disrupting the cell cycle and apoptosis.

CONCLUSIONS

The microbiota continuum along the reproductive tract in aged birds differs from that in young birds, especially with a significant shift in the uterus. The aged uterine microbiota probably contributes to the regulation of cell cycle and apoptosis by microbial metabolites primarily involved in amino acid metabolism and biosynthesis of various secondary metabolites. These findings provide new insights into the roles of the reproductive tract microbiota in regulating the cell programming of the aged host, contributing to the exploration of the microbiome as a target for diagnosing aging health status and therapy for gynecological diseases in women. Video Abstract.

Transcriptome analysis of the uterovaginal junction containing sperm storage tubules in heat-stressed breeder hens

Sperm storage tubules (SSTs) in the uterovaginal junction (UVJ) of the oviduct are major sites of sperm storage after artificial insemination or mating. Female birds may regulate sperm motility in the UVJ. Heat stress can decrease the reproductive ability of broiler breeder hens. However, its effects on UVJ remain unclear. Changes in gene expression aid in understanding heat stress-affected molecular mechanisms. Herein, we wanted to conduct a comparative transcriptomic analysis to identify the differentially expressed genes (DEGs) in the UVJ of breeder hens under thermoneutral (23°C) and heat stress (36°C for 6 h) conditions. The results indicated that cloacal temperatures and respiratory rates were significantly increased in heat-stressed breeder hens (P < 0.05). Total RNA was extracted from the hen UVJ tissues containing SSTs after heat exposure. Transcriptome analysis identified 561 DEGs, including 181 upregulated DEGs containing heat shock protein (HSP) transcripts and 380 downregulated DEGs containing immune-related genes, such as interleukin 4-induced 1, radical S-adenosyl methionine domain containing 2, and 2'-5'-oligoadenylate synthetase like, in heat-stressed hens. Gene Ontology analysis revealed the significantly enriched terms involving HSPs. Kyoto Encyclopedia of Genes and Genomes analysis identified 9 significant pathways, including the protein processing in endoplasmic reticulum (11 genes including HSPs), neuroactive ligand-receptor interaction (13 genes including luteinizing hormone/choriogonadotropin receptor), biosynthesis of amino acids (4 genes including tyrosine aminotransferase), ferroptosis (3 genes including heme oxygenase 1), and nitrogen metabolism (carbonic anhydrase [CA]-12 and CA6) pathways. Protein-protein interaction network analysis of DEGs revealed 2 large networks, one containing upregulated HSPs and the other containing downregulated interferon-stimulating genes. Overall, heat stress inhibits innate immunity in the UVJ tissues of broiler chickens, and heat-stressed chickens protect their cells by increasing the expression levels of HSPs. The identified genes are potential candidates for further exploration of the UVJ in heat-stressed hens. The identified molecular pathways and networks increase our understanding of the sperm storage reservoirs (UVJ containing SSTs) within the reproductive tract and may be used to prevent heat stress-induced fertility loss in breeder hens.

Transcriptome identification of genes associated with uterus-vagina junction epithelial folds formation in chicken hens

The development regulation of the uterine-vaginal junction (UVJ) epithelial folds during the sexual maturation of female birds played crucial roles in the adults' sperm storage duration and fertilization capability. However, there is a lack of studies on it in the breeding field of laying hens. In this study, White Leghorn was used for the morphological and developmental studies. According to the morphological characteristics, the development of the UVJ epithelial folds was classified into 4 stages (morphological stage T1-T4). Significant individual differences were observed simultaneously, which is one of the factors leading to the adults' UVJ morphological differences. Bulk RNA-seq suggested the different regulations of UVJ epithelial folds were classified into 3 stages (developmental stage S1-S3). Genes enriched in cell proliferation, differentiation, polarity, migration, adhesion and junction were supposed to regulate UVJ epithelial fold formation. Single-cell RNA-sequencing (scRNA-seq) showed significant differences between different types of cells within UVJ at the developmental stage S2. Immunohistochemical studies confirmed that the different proliferation rates between the epithelium and nonepithelium were one of the key factors leading to the formation of UVJ epithelial folds. Genes in the TGF-beta and WNT pathways may play roles in regulating the proliferation and differentiation of epithelium. Some factors, such as CHD2, CDC42, and carbonic anhydrases, were important participants in forming UVJ epithelial folds. This study will provide new thoughts on the differential regulation of fertilization traits from the developmental biology perspective.

Sperm storage by females across the animal phyla: A survey on the occurrence and biomolecules involved in sperm storage

Long-term sperm storage by females in various regions of the oviduct is documented across many invertebrate and vertebrate species. Although, many reports emphasize on the histology, histochemistry and ultrastructural features of sperm storage, very little is known about the mechanisms underlying the sperm storage. The current review documents the occurrence of sperm storage by females in a wide array of invertebrate and vertebrate species. This review also provides an insight on the presence of various molecular factors of the sperm storage tubules presumably responsible for the prolonged sperm storage with an emphasis on a model reptile, the Indian garden lizard, Calotes versicolor which contains a unique approximately 55-kDa protein in its utero-vaginal lavage and found to inhibit washed epididymal sperm motility in a concentration and time-dependent manner in a reversible fashion.

Transcriptome analysis and identification of genes associated with individual fertilization rate differences in hen infundibulum

1. Fertilisation rate is closely related to the reproductive performance and economic status of chicken laying breeders. In this study, two flocks (n = 1,029 in population I and n = 358 in population II) in the later laying period were used for investigating the individual differences among population fertilisation rates (FRs).2. The funnel and distal parts of the infundibulum were collected from nine individuals (five with low FR and four with high FR from population II) and RNA-sequencing (RNA-seq) method was used to investigate the transcriptome differences in fertilisation. Differences in fertilisation regulation were investigated by comparing the different parts (funnel and distal) of the infundibulum between the low FR and high FR groups.3. There were notable individual FR differences in both categories. Some individuals had a relative high FR (≥90%) for a long time (>5 days after AI), contrarily, some individuals lost the ability to fertilise eggs in a very short time.4. Differentially expressed genes (DEGs), such as DUSP7, PPP1R3B, FYB, OVA, OVALX and OVALY may be associated with sperm functional regulation, fertilisation and early-stage fertilised ovum development processes. DEGs such as AVBD1, AVBD2, AVBD6, NFATC2 and BANK1 indicated a severe immune response to sperm survival and fertilisation in the oviduct.5. The results suggested that individual differences should be considered in the breeding and reproduction process. The DEGs identified in this study may promote our understanding of different fertilisation regulation in laying breeders.

Transcriptomic and Metabolomic Profile Analysis of Muscles Reveals Pathways and Biomarkers Involved in Flavor Differences between Caged and Cage-Free Chickens

The cage-free system has gained a lot of interest in recent years because it can offer chickens more freedom and is easier to manage compared with free-range rearing systems, but few studies have focused on the effect of the cage-free rearing system on meat quality and flavor. In this study, 44 Jianghan chickens were reared in caged or cage-free systems to explore the effect of different rearing systems on meat-eating quality. Sensory evaluation of cooked muscles showed that the leg muscle aroma, juiciness, and flavor intensity significantly improved by the cage-free rearing. The cage-free hens had significantly lower body weight, abdominal fat percentage, and meat fat content, but higher meat moisture content. The cage-free group had brighter breast muscle and redder leg muscle color 24 h after slaughter. Transcriptomic and metabolomic profile analysis of the leg muscle samples showed that the cage-free rearing changed biosynthesis pathways associated with glycogen metabolism, lipid and fatty acid biosynthesis and transport, muscle cellular type, and cellular components, which were related to raw meat quality. Different rearing systems also resulted in differences in glycolipid metabolism, lipid metabolism, and altered levels of intramuscular fat content and other flavor precursors. Pathways such as glycerolipid metabolism, adipocytokine signaling, and metabonomic pathways such as linoleic acid, glycerophospholipid, arginine, proline, and β-alanine metabolism may be responsible for the meat quality and flavor change.

Characteristics of the Mating Behavior of Domesticated Geese from Anser cygnoides and Anser anser

Mating behavior is a critically important component of poultry reproduction. Here, a total of 135 geese were selected, specifically, Sichuan white geese (Anser cygnoides), Zhedong white geese (Anser cygnoides), and Hungarian geese (Anser anser) (300-day-old), and the mating behavior was monitored daily from 6:00 a.m. to 6:00 p.m. during the 20-day observation period. The results showed that the mating process included mounting, female cooperation, and successful copulation. Overall, the three breeds preferred mating on land. More than thirty percent of the mating time was primarily concentrated from 4:00 p.m. to 6:00 p.m. in domesticated geese from Anser cygnoides, the corresponding values for Sichuan white geese and Zhedong white geese were 32.0% and 33.3%, respectively. The mating of the Hungarian geese usually took place in the morning. In addition, the frequency of successful copulation of Sichuan white geese and Zhedong white geese were 2.31 and 1.94 times per day, significantly greater than that of Hungarian geese (0.89 times). Furthermore, a significant positive correlation between successful copulation and laying rates (r = 0.985) or fertilization rates (r = 0.992) was observed in Hungarian geese. Taken together, the mating behaviors among the different breeds were mainly reflected in time preference and successful copulation frequency.

Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production

Egg production is an important economic trait and a key indicator of reproductive performance in ducks. Egg production is regulated by several factors including genes. However the genes involved in egg production in duck remain unclear. In this study, we compared the ovarian transcriptome of high egg laying (HEL) and low egg laying (LEL) ducks using RNA-Seq to identify the genes involved in egg production. The HEL ducks laid on average 433 eggs while the LEL ducks laid 221 eggs over 93 weeks. A total of 489 genes were found to be significantly differentially expressed out of which 310 and 179 genes were up and downregulated, respectively, in the HEL group. Thirty-eight differentially expressed genes (DEGs), including LHX9, GRIA1, DBH, SYCP2L, HSD17B2, PAR6, CAPRIN2, STC2, and RAB27B were found to be potentially related to egg production and folliculogenesis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that DEGs were enriched for functions related to glutamate receptor activity, serine-type endopeptidase activity, immune function, progesterone mediated oocyte maturation and MAPK signaling. Protein-protein interaction network analysis (PPI) showed strong interaction between 32 DEGs in two distinct clusters. Together, these findings suggest a mix of genetic and immunological factors affect egg production, and highlights candidate genes and pathways, that provides an understanding of the molecular mechanisms regulating egg production in ducks and in birds more broadly.

Transcriptome analysis of inseminated sperm storage tubules throughout the duration of fertility in the domestic turkey, Meleagris gallopavo

Sperm storage tubules (SST) are specialized invaginations of the oviductal epithelium that permit avian species to store spermatozoa for extended periods of time, without compromising sperm fertilization capacity. The molecular and physiological mechanisms behind sperm storage tubule differentiation, sperm protection, and regression remain largely unknown, but most likely have potential implications for substantially improving hen fertility, sperm storage, and semen cryopreservation in commercial poultry species. RNA sequencing was performed on sperm storage tubules isolated from the epithelium of the uterovaginal junction (UVJ) from hens at d 1, 7, 30, 60, and 90 postinsemination (n = 4 per timepoint). Read mapping and differential expression analysis were performed using CLC Genomics Workbench. A total of 2,340 differentially expressed genes were subjected to pathway analysis through Ingenuity Pathway Analysis (IPA). Through functional annotation of differentially expressed genes during early, peak, and late egg production, novel insights regarding the role of innate and acquired immune response to sperm, lipid synthesis and transfer, steroid hormone signalling, cytoskeletal reorganization, and regulation of ion homeostasis in SST were obtained. Additionally, potential pathways were identified that could be involved with suppressing sperm motility while sperm reside within the SST. Upstream analysis identified potential regulatory roles for 18 upstream regulators that could modulate sperm storage tubule function, including suppression of sperm motility. Understanding sperm storage tubule function throughout the laying cycle, especially with regards to sperm preservation may allow for the development of industry-based protocols for semen storage and cryopreservation that mimic the sperm preservation capabilities of SST and improve fertility.