Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle

Analysis of genetic diversity and selection signatures on the Zhashi Brown goat through whole genome sequencing data

The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province in southern China and boasts a rich history. The goats exhibit exceptional traits, including heat and insect resistance, strong reproductive capabilities and superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole-genome resequencing on 21 Zhashi Brown goats. Additionally, we performed a joint analysis using published whole-genome data from 119 goats, including Chengdu Brown goat, Matou goat, Wuxue goat, Xiangdong Black goat, Qaidam Cashmere goat, Ujumqin Cashmere goat and Shanbei Cashmere goat. The results revealed that the Zhashi Brown goat is genetically more pure than other Southern Chinese goat breeds. Furthermore, the genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity and inbreeding coefficient) of the Zhashi Brown goat's genome is at a low level among the eight breeds, indicating the need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide diversity, integrated haplotype score, the fixation index and cross-population extended haplotype homozygosity, we systematically scanned selective signals within the genomic landscape of Zhashi Brown goat. The outcomes underscore strong selection signals associated with genes implicated in immune response, heat tolerance, reproductive performance and meat quality. These findings make a significant contribution to our understanding of the genetics framework associated with adaptive traits in Zhashi Brown goat. Furthermore, this study explores the genetic diversity of the Zhashi Brown goat, which may contribute to the theoretical framework for conserving its genetic resources, while the identified trait-associated variations could inform future strategies to optimize selective breeding programs.

Comprehensive characterization of lncRNA N6-methyladenosine modification dynamics throughout bovine skeletal muscle development

BACKGROUND

N6-methyladenosine (m6A) methylation is a key epigenetic modification that can modulate gene expression and strongly affect mammalian developmental processes. However, the genome-wide methylation of long non-coding RNAs (lncRNAs) and its implications for the development of skeletal muscle remain poorly understood. Bovine skeletal muscle samples from five developmental stages were analyzed in this study to establish lncRNA methylome and transcriptomic maps.

RESULTS

Globally, 59.67% of lncRNAs in skeletal muscle with m6A modifications, and this percentage decreased progressively during development. lncRNA expression levels were positively associated with the number of m6A peaks, with lncRNAs possessing 3 or more peaks showing significantly higher expression levels than those with 1 or 2 peaks. Specific lncRNAs involved in skeletal muscle development were identified through two analytical approaches. The first approach employed weighted gene co-expression network analysis (WGCNA) of transcriptomic data to identify correlations between annotated lncRNAs and growth-related traits, resulting in 21 candidate hub lncRNAs. The intersection of these 21 hub lncRNAs with 151 differentially methylated lncRNAs (DM-lncRNAs) identified 10 shared candidate lncRNAs. The second approach integrated MeRIP-seq and RNA-seq data to identify 36 lncRNAs that were both differentially m6A modified and differentially expressed (dme-lncRNAs). GO and KEGG enrichment analyses of cis-target genes associated with these dme-lncRNAs identified eight candidate lncRNAs. Combining the results from the two approaches identified 16 key m6A-modified lncRNAs likely involved in skeletal muscle development.

CONCLUSIONS

These findings highlight the regulatory and functional significance of dynamic lncRNA methylation in skeletal muscle development.

Understanding lncRNAs: key regulators of myogenesis and lipogenesis in farm animals

Long non-coding RNAs (lncRNAs) are RNA molecules exceeding 200 nucleotides in length. Recent studies have demonstrated their involvement in regulating gene expression and various biological processes. Among these, myogenesis and lipogenesis are particularly important because of their direct effects on muscle development and fat deposition in farm animals. These processes are crucial for determining meat quality, growth rates, and overall economic value in animal husbandry. Although the specific mechanisms through which lncRNAs influence these pathways are still under investigation, further research into their roles in muscle and fat development is crucial for optimizing farm animal breeding strategies. Here, we review the characteristics of lncRNAs, including their biogenesis, localization, and structures, with a particular focus on their association with myogenesis and adipogenesis. This review seeks to establish a theoretical foundation for enhancing farm animal production. In particular, focusing on lncRNAs may reveal how these molecules can enhance the economic traits of farm animals, thereby contributing to the optimization of farm animal breeding processes.

Long non-coding RNA (LncRNA) and epigenetic factors: their role in regulating the adipocytes in bovine

Investigating the involvement of long non-coding RNAs (lncRNAs) and epigenetic processes in bovine adipocytes can provide valuable new insights into controlling adipogenesis in livestock. Long non-coding RNAs have been associated with forming chromatin loops that facilitate enhancer-promoter interactions during adipogenesis, as well as regulating important adipogenic transcription factors like C/EBPα and PPARγ. They significantly influence gene expression regulation at the post-transcriptional level and are extensively researched for their diverse roles in cellular functions. Epigenetic modifications such as chromatin reorganization, histone alterations, and DNA methylation subsequently affect the activation of genes related to adipogenesis and the progression of adipocyte differentiation. By investigating how fat deposition is epigenetically regulated in beef cattle, scientists aim to unravel molecular mechanisms, identify key regulatory genes and pathways, and develop targeted strategies for modifying fat deposition to enhance desirable traits such as marbling and meat tenderness. This review paper delves into lncRNAs and epigenetic factors and their role in regulating bovine adipocytes while focusing on their potential as targets for genetic improvement to increase production efficiency. Recent genomics advancements, including molecular markers and genetic variations, can boost animal productivity, meeting global demands for high-quality meat products. This review establishes a foundation for future research on understanding regulatory networks linked to lncRNAs and epigenetic changes, contributing to both scholarly knowledge advancement and practical applications within animal agriculture.

Scans for Signatures of Selection in Genomes of Wagyu and Buryat Cattle Breeds Reveal Candidate Genes and Genetic Variants for Adaptive Phenotypes and Production Traits

Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and FST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds.

A newly identified lncRNA lnc000100 regulates proliferation and differentiation of cattle skeletal muscle cells

Cattle skeletal muscle development is a complex and highly coordinated biological process mediated by a series of myogenic regulators, which plays a critical role in beef yield and quality. Long non-coding RNAs (lncRNAs) have been shown to regulate skeletal muscle development. However, the molecular mechanism by which lncRNAs regulate skeletal muscle development is largely unknown. We performed transcriptome analysis of muscle tissues of adult and embryo Angus cattle to investigate the mechanism by which lncRNA regulates skeletal muscle development between adult and embryo cattle. A total of 37,115 candidate lncRNAs were detected, and a total of 1,998 lncRNAs were differentially expressed between the muscle tissue libraries of adult and embryo cattle, including 1,229 up-regulated lncRNAs and 769 down-regulated lncRNAs (adult cattle were the control group). We verified the expression of 7 differentially expressed lncRNAs by quantitative real-time PCR (RT-qPCR), and analysed the tissue expression profile of lnc000100, which is down-regulated in the longest dorsal muscle during foetal life and which is highly specifically expressed in muscle tissue. We found that the interference of lnc000100 significantly inhibited cell proliferation and promoted cell differentiation. Lnc000100 was located in the nucleus by RNA-FISH. Our research provides certain resources for the analysis of lncRNA regulating cattle skeletal muscle development, and may also provide new insights for improving beef production and breed selection.

Integrated analysis of lncRNA and mRNA for the apoptosis of porcine ovarian granulosa cells after polyphenol resveratrol treatment

Resveratrol (RES) is a non-flavonoid polyphenol compound that can be involved in follicular development and ovulation. However, the mechanism by which resveratrol regulates the apoptosis of porcine ovarian granulosa cells (POGCs) through long non-coding RNA (lncRNA) is poorly understood. We generated POGCs models of different doses of RES (0, 25, 50, 75, and 100 μM). It was observed that the cell viability was the highest in the 50 μM group, and the highest apoptosis rates were recorded in the 100 μM group. Therefore, a control group (n = 3, 0 μM RES group), a low RES group (n = 3, 50 μM RES group), and a high RES group (n = 3, 100 μM RES group) of POGCs were created for next RNA sequencing. Gene Ontology (GO) indicated that differentially expressed lncRNAs associated with apoptotic process were highly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of lncRNA target genes found that the Wnt signaling pathway and PI3K-Akt signaling pathway were both enriched. Furthermore, we constructed lncRNA-mRNA networks related to Metabolic and Cell Apoptosis, respectively. In the networks, five key-lncRNAs were screened, which may play a significant role in the process of POGCs metabolism and apoptosis. Furthermore, we focused on the function of a lnc-GAM (lncRNA associated with Granulosa cells Apoptosis and Metabolism) and verified that lnc-GAM could influence cell apoptosis in POGCs development by affecting the mRNA expression of apoptosis-related markers, and also affects the secretion of steroid hormones and related genes expression in POGCs cultured in vitro. Our study provides seminal data and important new insights into the regulation of reproductive mechanisms in porcine and other female mammals.

Genetic polymorphisms of muscular fitness in young healthy men

The effects of genetic polymorphisms on muscle structure and function remain elusive. The present study tested for possible associations of 16 polymorphisms (across ten candidate genes) with fittness and skeletal muscle phenotypes in 17- to 37-year-old healthy Caucasian male endurance (n = 86), power/strength (n = 75) and team athletes (n = 60), and non-athletes (n = 218). Skeletal muscle function was measured with eight performance tests covering multiple aspects of muscular fitness. Along with body mass and height, the upper arm and limb girths, and maximal oxygen uptake were measured. Genotyping was conducted on DNA extracted from blood. Of the 16 polymorphisms studied, nine (spanning seven candidate genes and four gene families/signalling pathways) were independently associated with at least one skeletal muscle fitness measure (size or function, or both) measure and explained up to 4.1% of its variation. Five of the studied polymorphisms (activin- and adreno-receptors, as well as myosine light chain kinase 1) in a group of one to three combined with body height, age and/or group explained up to 20.4% of the variation of muscle function. ACVR1B (rs2854464) contributed 2.0-3.6% to explain up to 14.6% of limb proximal girths. The G allele (genotypes AG and GG) of the ACVR1B (rs2854464) polymorphism was significantly overrepresented among team (60.4%) and power (62.0%) athletes compared to controls (52.3%) and endurance athletes (39.2%), and G allele was also most consistently/frequently associated with muscle size and power. Overall, the investigated polymorphisms determined up to 4.1% of the variability of muscular fitness in healthy young humans.