Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

Integrative Meta-Analysis: Unveiling Genetic Factors in Meat Sheep Growth and Muscular Development through QTL and Transcriptome Studies

OBJECTIVE

The study aimed to investigate the effects of castration on performance, carcass characteristics, and meat quality in sheep, as well as explore the expression of key genes related to metabolic pathways and muscle growth following castration.

METHODS

A meta-analysis approach was utilized to analyze data from multiple studies to compare the performance, carcass characteristics, and meat quality of castrated sheep (wethers) with intact rams. Additionally, protein-protein interaction (PPI) networks, differential gene expression (DEG) interactions, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify molecular mechanisms associated with fat metabolism and muscle development in sheep tails.

RESULTS

The analysis revealed that castrated sheep (wethers) exhibited improved average daily gain, increased tenderness, lower backfat thickness, and a tendency for greater loin muscle area compared to intact rams. This suggests that castration promotes faster growth and results in leaner carcasses with potentially higher muscle content. Furthermore, the identification of downregulated DEGs like ACLY, SLC27A2, and COL1A1 and upregulated DEGs such as HOXA9, PGM2L1, and ABAT provides insights into the molecular mechanisms underlying fat deposition and muscle development in sheep.

CONCLUSIONS

The findings support the practice of castration in sheep production as it enhances growth performance, leads to leaner carcasses with higher muscle content, and improves meat tenderness. The identified changes in gene expression offer valuable insights for further research into understanding the impact of castration on muscle development and fat metabolism in sheep. This meta-analysis contributes to the knowledge of molecular mechanisms involved in fat deposition in sheep, opening avenues for future investigations in livestock fat metabolism research.

Identification and functional analysis of ovarian lncRNAs during different egg laying periods in Taihe Black-Bone Chickens

Introduction: Long non-coding RNA (lncRNA) refers to a category of non-coding RNA molecules exceeding 200 nucleotides in length, which exerts a regulatory role in the context of ovarian development. There is a paucity of research examining the involvement of lncRNA in the regulation of ovary development in Taihe Black-Bone Chickens. In order to further investigate the egg laying regulation mechanisms of Taihe Black-Bone Chickens at different periods, transcriptome analysis was conducted on the ovarian tissues at different laying periods. Methods: This study randomly selected ovarian tissues from 12 chickens for RNA-seq. Four chickens were selected for each period, including the early laying period (102 days, Pre), the peak laying period (203 days, Peak), and the late laying period (394 days, Late). Based on our previous study of mRNA expression profiles in the same ovarian tissue, we identified three differentially expressed lncRNAs (DE lncRNAs) at different periods and searched for their cis- and trans-target genes to draw an lncRNA-mRNA network. Results and discussion: In three groups of ovarian tissues, we identified 136 DE lncRNAs, with 8 showing specific expression during the early laying period, 10 showing specific expression during the peak laying period, and 4 showing specific expression during the late laying period. The lncRNA-mRNA network revealed 16 pairs of lncRNA-target genes associated with 7 DE lncRNAs, and these 14 target genes were involved in the regulation of reproductive traits. Furthermore, these reproductive-related target genes were primarily associated with signaling pathways related to follicle and ovary development in Taihe Black-Bone Chickens, including cytokine-cytokine receptor interaction, TGF-beta signaling pathway, tyrosine metabolism, ECM-receptor interaction, focal adhesion, neuroactive ligand-receptor interaction, and cell adhesion molecules (CAMs). This study offers valuable insights for a comprehensive understanding of the influence of lncRNAs on poultry reproductive traits.

Astaxanthin Improved the Quality of Hu Ram Semen by Increasing the Antioxidant Capacity and Mitochondrial Potential and Mitigating Free Radicals-Induced Oxidative Damage

The objective of this research was to investigate the effect of astaxanthin supplementations of semen extender on the quality of Hu ram semen after up to five days of preservation at 4 °C. Semen samples were collected from five healthy Hu rams using an artificial vagina during breeding season (April to August 2023) and diluted with a basic extender supplemented with control (0), 1 µM, 2 µM, 3.5 µM, or 4.5 µM of AXT. Overall, 170 semen ejaculate samples (34 repetitions) from five healthy Hu rams were used in our research study. The results revealed that the addition of AXT (3.5 µM) significantly (p ≤ 0.05) increased the sperm kinematic indexes (T.M%, P.M%, MAD%, STR%, and LIN %), sperm viability, plasma membrane integrity, acrosome integrity, total antioxidant content (T-AOC), and mitochondrial membrane potential (MMP) of the Hu rams spermatozoa after up to five days of preservation at 4 °C. Contrary to that, the addition of the best concentration of AXT (3.5 µM) to the semen extender significantly (p ≤ 0.05) reduced the reactive oxygen species (ROS) and malondialdehyde (MDA) concentration of Hu ram semen. In conclusion, the results of the current study indicate that the addition of a semen extender with AXT improves the quality of Hu ram spermatozoa by increasing the total antioxidant capacity (T-AOC) and mitochondrial membrane potential (MMP). On the other hand, reducing free radicals induced oxidative (ROS) and per oxidative (MDA) damage to Hu ram semen.

Comparative analysis of alternative splicing events in skeletal muscle of different sheep

This paper aims to investigate the relationship between genes with alternative splicing (AS) events and breed-specific differences in muscle development in two breeds of sheep. RNA-seq was utilized to identify genes with AS between Small-tailed Han sheep and Dorset sheep. The gene lists of differentially spliced genes were identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted on these genes. In this study, 299 genes with 356 AS indicated significant differences between two diffrerent breeds. There are differences in 31 genes with 35 AS. Cassette, alt5' and alt3' exhibited the highest levels of enrichment across various significant levels. GO and KEGG enrichment analysis demonstrated a significant correlation between Wnt, TGF-beta, Notch and MAPK signaling pathways and the development of muscle in sheep. These findings indicate that genes with AS are linked to variations in muscle development in sheep. These results offer significant scientific and practical implications for improving the quality of sheep meat.

Transcriptome Analysis Reveals the Profile of Long Non-Coding RNAs during Myogenic Differentiation in Goats

The long non-coding RNAs (lncRNAs) are emerging as essential regulators of the growth and development of skeletal muscles. However, little is known about the expression profiles of lncRNAs during the proliferation and differentiation of skeletal muscle satellite cells (MuSCs) in goats. In this study, we investigate potential regulatory lncRNAs that govern muscle development by performing lncRNA expression profiling analysis during the proliferation (cultured in the growth medium, GM) and differentiation (cultured in the differentiation medium, DM1/DM5) of MuSCs. In total, 1001 lncRNAs were identified in MuSC samples, and 314 differentially expressed (DE) (FDR < 0.05, |log2FC| > 1) lncRNAs were screened by pairwise comparisons from three comparison groups (GM-vs-DM1, GM-vs-DM5, DM1-vs-DM5). Moreover, we identified the cis-, trans-, and antisense-regulatory target genes of DE lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these target genes were significantly enriched in muscle development-related GO terms and KEGG pathways. In addition, the network of interactions between DE lncRNAs and their target genes was identified, which included well-known myogenesis regulators such as Myogenic differentiation 1 (MyoD), Myogenin (MyoG), and Myosin heavy chain (MyHC). Meanwhile, competing endogenous RNA (ceRNA) network analysis showed that 237 DE lncRNAs could bind to 329 microRNAs (miRNAs), while miRNAs could target 564 mRNAs. Together, our results provide a genome-wide resource of lncRNAs that may contribute to myogenic differentiation in goats and lay the groundwork for future investigation into their functions during skeletal muscle development.

Comparison of alternative splicing (AS) events in adipose tissue of polled dorset versus small tail han sheep

Background

During the alternative splicing (AS), the exons of primary transcripts are spliced in various arrangements, resulting in structurally and functionally distinct mRNAs and proteins. This study aimed to examine genes with AS events from Small Tail Han sheep and Dorset sheep to explore the mechanism of adipose developments.

Methods

This study identified the genes with AS events in adipose tissues of two different sheep with next-generation sequencing. In this paper, genes with significantly different AS events were performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.

Results

364 genes with 411 A S events showed significant differences in adipose tissues between the two breeds; 108 genes with 120 A S events were extremely significant differences between the two breeds. We identified several novel genes that are related with adipose growth and development. The results of KEGG and GO analysis indicated that oocyte meiosis, mitogen-activated protein kinase (Wnt), mitogen-activated protein kinase (MAPK) signaling pathway, etc. Were closely related to the adipose tissue developments.

Conclusions

This paper revealed that the genes with AS events are important for adipose tissues in sheep, exploring the mechanisms of AS events associated with adipose tissue developments in sheep of different breeds.

Whole genome sequencing revealed genetic diversity, population structure, and selective signature of Panou Tibetan sheep

BACKGROUND

The detection of selective traits in different populations can not only reveal current mechanisms of artificial selection for breeding, but also provide new insights into phenotypic variation in new varieties and the search for genes associated with important traits. Panou sheep is a cultivated breed of Tibetan sheep in China with stable genetic performance, consistent appearance and fast growth and development after decades of artificial selection and cultivation. Due to long-term adaptation to the high altitude, cold and hypoxic environment in the plateau area, they may have formed a unique gene pool that is different from other Tibetan sheep breeds. To explore the genetic resources of Panou sheep, we used next-generation sequencing technology for the first time to investigate the genome-wide population structure, genetic diversity, and candidate signatures of positive selection in Panou sheep.

RESULTS

Comparative genomic analysis with the closely related species Oula sheep (a native breed of Tibetan sheep in China) was used to screen the population selection signal of Panou sheep. Principal component analysis and neighbor joining tree showed that Panou sheep and Oula sheep had differences in population differentiation. Furthermore, analyses of population structure, they came from the same ancestor, and when K = 2, the two populations could be distinguished. Panou sheep exhibit genetic diversity comparable to Oula sheep, as shown by observed heterozygosity, expected heterozygosity and runs of homozygosity. Genome-wide scanning using the Fst and π ratio methods revealed a list of potentially selected related genes in Panou sheep compared to Oula sheep, including histone deacetylase 9 (HDAC9), protein tyrosine kinase 2 (PTK2), microphthalmia-related transcription factor (MITF), vesicular amine transporter 1 (VAT1), trichohyalin-like 1 (TCHHL1), amine oxidase, copper containing 3 (AOC3), interferon-inducible protein 35 (IFI35).

CONCLUSIONS

The results suggest that traits related to growth and development and plateau adaptation may be selection targets for the domestication and breeding improvement of Tibetan sheep. This study provides the fundamental footprints for Panou sheep breeding and management.

Identification of differentially expressed genes and signaling pathways in Gaoyou duck ovary at different physiological stages

Introduction

Gaoyou duck is famous in China and abroad for its good production of double-yolk eggs. However, there has been no systematic research on the egg-laying characteristics of the Gaoyou duck, which limits the development and utilization of breed resource.

Methods

To identify the essential genes related to ovarian development, the transcriptome profiles of the ovaries of Gaoyou ducks at different physiological stages were analyzed. The transcriptome profiles of the ovaries of Gaoyou ducks at 150 d (before laying), 240 d (egg laying) and 500 d (nesting) were constructed, and the differentially expressed genes (DEGs) underwent GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses.

Results

The 6 randomly selected DEGs were verified by real-time fluorescent quantitative PCR that their relative expression was consistent with the transcriptional expression profile. Furthermore, KEGG analysis found that 8 candidate signaling pathways were essential for ovarian development, including the MAPK signaling pathway, Progesterone-mediated oocyte maturation, Cell adhesion molecules (CAMs), NOD-like receptor signaling pathway, ECM-receptor interaction, Focal adhesion, TGF-beta signaling path-way and Phagosome. Finally, 5 key DEGs were identified to participate in ovarian development, including TGIF1, TGFBR2, RAF1, PTK2 and FGF10.

Discussion

Our findings reveal the mechanisms under-lying the molecular regulation of related genes in Gaoyou duck ovarian development.

Identification and characterization of unique and common lncRNAs and mRNAs in the pituitary, ovary, and uterus of Hu sheep with different prolificacy

LncRNAs are regarded as regulators in various animal reproductive physiological processes. However, the regulation of lncRNAs in the reproductive organ development of Hu sheep with different prolificacy remains unknown. Herein, numerous tissue-unique and -common differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs), and fecundity-unique DELs and DEGs were identified among different comparison groups at horizontal and vertical levels. Moreover, the tissue-unique and -common, and fecundity-unique female reproduction-associated DEGs and DELs were screened, and the interaction networks were constructed. Furthermore, MSTRG.43442.1 was mainly present in the cytoplasm of tested cells. The key genes ADAMTS1 and DCN were mainly localized in the granulosa cells, pituitary cells and/or endometrial epithelial cells of ovary, pituitary and/or uterus. Overall, this study identified large numbers of unique and common DELs and DEGs in the female reproductive organs of Hu sheep with different prolificacy and provided new insights into understanding the regulation of Hu sheep fecundity.

LncRNA-412.25 activates the LIF/STAT3 signaling pathway in ovarian granulosa cells of Hu sheep by sponging miR-346

Although long non-coding RNAs (lncRNAs) are reported to regulate follicular development and reproductive disease pathogenesis, the underlying mechanisms have not been elucidated. In this study, lncRNA expression profiling of different-sized healthy follicles from Hu sheep with different prolificacy revealed 50 613 lncRNAs. Numerous lncRNAs were differentially expressed among different comparison groups. This study characterized one novel transcript, lncRNA-412.25 (from healthy follicles with a diameter of >5 mm), which was predominantly expressed in the high prolificacy group and localized to the cytoplasm of granulosa cells (GCs). LncRNA-412.25 knockdown promoted and inhibited Hu sheep GC apoptosis and proliferation, respectively. Interestingly, lncRNA-412.25 could directly bind to miR-346, which can target the gene of leukemia inhibitory factor (LIF). Knockdown of lncRNA-412.25 promoted GC apoptosis by downregulating LIF expression, where this effect was attenuated by miR-346. Moreover, the miR-346 inhibitor mitigated the lncRNA-412.25 knockdown-induced downregulation of phosphorylated protein of signal transducer and activator of transcription 3 (STAT3), which was validated using immunofluorescence analysis. Our results demonstrated that lncRNA-412.25 regulates GC proliferation and apoptosis in Hu sheep by binding to miR-346 and then activating the LIF/STAT3 pathway. These findings provide novel insights into the mechanisms underlying prolificacy in sheep.

CircRNAs in Xiang pig ovaries among diestrus and estrus stages

BACKGROUND

The fecundity of sows is a trait of major economic in pig industry. The molecular regulation of estrus cycles can affect the fecundity of female animals. Compared with the other pig breeds, Xiang pig exhibits the special estrus behaviors. CircRNAs are thought to involve in regulation of multiple biological processes. However, the potential roles of circRNAs in ovary regulation on Xiang pig estrus are largely unknown.

RESULTS

8,937 circRNAs were identified from eight libraries constructed from the ovarian samples of Xiang pig at estrus and diestrus stages by RNA sequencing method. Of which, 1,995 were high confidence circRNAs detected at least two junction reads in each ovary sample and seven circRNAs were validated by RT-PCR method. Furthermore, we identified 290 upregulated and 15 downregulated circRNAs in estrus ovaries. These differentially expressed circRNAs (DECs) derived from 273 host genes. And 207 miRNAs were identified to be targets sponged by 156 DECs with 432 binding sites, containing more than one miRNA binding site in each circRNA. Function enrichment analysis revealed that the host genes and the targets of miRNAs sponged by DECs were enriched in several reproduction-related signaling pathways, such as ovarian steroidogenesis, oocyte maturation, circadian rhythm, estrogen signaling pathway, GnRH signaling pathway, circadian entrainment, and oocyte meiosis. The circRNA-miRNA-mRNA networks revealed that 153 miRNAs interacting with 122 DECs and 86 miRNAs interacting with 84 DECs were involved in ovarian functions and ovarian circadian entrainment and circadian rhythm respectively. The DEC-miRNA-DEG (differentially expressed gene, DEG) networks associated with reproduction-related signaling pathways contained 22 DECs,18 miRNAs and 7 DEGs. 22 DECs were recognized as hub circRNAs during the estrus phase of Xiang pigs.

CONCLUSIONS

The circRNAs that function as miRNA sponges could play a key role in post-transcriptional regulation of gene expression during Xiang pig's estrus cycle.

Chlorogenic Acid Improves Quality of Chilled Ram Sperm by Mitigating Oxidative Stress

Simple Summary

Sheep sperm is extremely sensitive to reactive oxygen species (ROS) and can produce a large amount of ROS during chilling storage, leading to a decline in semen quality. Adding antioxidants is an important method to improve semen quality. Chlorogenic acid (CGA) is a kind of plant extract with an antioxidant capacity, which can effectively eliminate free radicals and improve the antioxidant capacity of semen. However, its role in the chilling storage of Hu ram semen is not clear. Therefore, CGA with different concentrations was added to chilling storage extender to investigate its effect on chilled ram sperm. The results of this study revealed that CGA with proper concentration had a positive effect on chilled Hu ram sperm and 0.8 mg/mL CGA had the best effect.

Abstract

The purpose of this study was to investigate whether the addition of chlorogenic acid (CGA) to a sheep semen extender could improve the quality of chilled sheep sperm. Ejaculates (n = 80) were collected from five Hu rams with an artificial vagina. The ejaculates were mixed and divided into five equal parts, diluted with a CGA-free Tris–egg yolk extender (control), or supplemented with 0.2, 0.4, 0.8, and 1.2 mg/mL. The sperm kinematic parameters (viability, progressive motility), functional integrity of plasma membrane and acrosome, adenosine triphosphate (ATP) concentration and antioxidant parameters (Catalase (CAT), Superoxide dismutase (SOD) activity, total antioxidant capacity (T-AOC), ROS level and Malondialdehyde (MDA) content) were evaluated during storage of the semen. The results indicated that: PM, plasmatic membrane integrity and acrosomal integrity in 0.8 mg/mL CGA were higher (p < 0.05) from day 1 to 5. The ROS level in CGA groups was lower than the control (p < 0.05). CAT, SOD, ATP, and T-AOC were highest at 0.8 mg/mL concentration within 1 to 5 days. The above results indicated that the right concentration of CGA improved the quality of Hu ram sperm during chilling storage.

Effects of Paper Mulberry Silage on the Growth Performance, Rumen Microbiota and Muscle Fatty Acid Composition in Hu Lambs

Paper mulberry (Broussonetia papyrifera) is widely ensiled to feed sheep in southwestern China, as unconventional woody forage. Feeding lambs with paper mulberry silage (PMS) may improve certain feeding characteristics, thereby affecting the growth performance and meat quality. The aim of this study is to investigate the effects of four diets of PMS on growth performance, rumen microbial composition, and muscle fatty acids profile in Hu lambs. The results showed that 30% and 40% PMS increased the dry matter intake and average daily gain of Hu lambs compared to the control group. PMS30 and PMS40 increased the content of C24:1, and PMS40 increased the content of C20:5n-3. The content of microbial protein (MCP) was higher in PMS40 than in others, but PMS30 and PMS40 reduced the total volatile fatty acid in rumen. PMS30 significantly increased the ratio of acetic acid to propionic acid. The abundance of ruminal Christensenellaceae_R-7_group and norank_f_Eubacterium_coprostanoligenes_group was significantly higher in PMS30 and PMS40 groups. Moreover, Christensenellaceae_R-7_group had a significant positive correlation with n3-polyunsaturated fatty acid. PMS40 might lead to a relatively high content of unsaturated fatty acids in longissimus dorsi muscle by increasing the relative abundance of Christensenellaceae_R-7_group in rumen.

Insight Into Pituitary lncRNA and mRNA at Two Estrous Stages in Small Tail Han Sheep With Different FecB Genotypes

The pituitary is a remarkably dynamic organ with roles in hormone (FSH and LH) synthesis and secretion. In animals with the FecB (fecundity Booroola) mutation, the pituitary experiences hormone fluctuations during the follicular-luteal transition, which is implicated in the expression and regulation of many genes and regulators. Long non-coding RNAs (lncRNAs) are a novel type of regulatory factors for the reproductive process. Nevertheless, the expression patterns of lncRNAs and their roles in FecB-mediated follicular development and ovulation remain obscure. Thus, we profiled the pituitary transcriptome during the follicular (F, 45 h after evacuation vaginal sponges) and luteal (L, 216 h after evacuation vaginal sponges) phases in FecB-mutant homozygous (BB) and wild-type (WW) Small Tail Han sheep. We identified 78 differentially expressed genes (DEGs) and 41 differentially expressed lncRNAs (DELs) between BB_F and BB_L, 32 DEGs and 26 DELs between BB_F and WW_F, 16 DEGs and 29 DELs between BB_L and WW_L, and 50 DEGs and 18 DELs between WW_F and WW_L. The results of real-time quantitative PCR (RT-qPCR) correlated well with the transcriptome data. In both the follicular and luteal phases, DEGs (GRID2, glutamate ionotropic receptor delta type subunit 2; ST14, ST14 transmembrane serine protease matriptase) were enriched in hormone synthesis, secretion, and action. MSTRG.47470 and MSTRG.101530 were the trans-regulated elements of ID1 (inhibitor of DNA binding 3, HLH protein) and the DEG ID3 (inhibitor of DNA binding 3, HLH protein), and EEF2 (eukaryotic translation elongation factor 2), respectively; these factors might be involved in melatonin and peptide hormone secretion. In the FecB-mediated follicular phase, MSTRG.125392 targeted seizure-related 6 homolog like (SEZ6L), and MSTRG.125394 and MSTRG.83276 targeted the DEG KCNQ3 (potassium voltage-gated channel subfamily Q member 3) in cis, while MSTRG.55861 targeted FKBP4 (FKBP prolyl isomerase 4) in trans. In the FecB-mediated luteal phase, LOC105613905, MSTRG.81536, and MSTRG.150434 modulated TGFB1, SMAD3, OXT, respectively, in trans. We postulated that the FecB mutation in pituitary tissue elevated the expression of certain genes associated with pituitary development and hormone secretion. Furthermore, this study provides new insights into how the pituitary regulates follicular development and ovulation, illustrated by the effect of the FecB mutation.