Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus

Relationships Among Growth, Carcass Characteristics, and Myf5 Myf6, MyoD, and MyoG Genes Expression Level in Saanen Male Kids with Varying Slaughter Weights

The objective of this study was to determine the relationship between the MRF gene family members and slaughter characteristics in Saanen kids with varying slaughter weights. Twenty male kids of the Turkish Saanen breed were individually fattened for 60 days after weaning under an intensive management system. The kids were divided into two groups: low slaughter weight (L; n = 11; ≤29 kg) and high slaughter weight (H; n = 13; >29) at the end of the fattening. After slaughter, muscle samples from Longissimus-dorsi (LD) and Semitendinosus (ST) muscles were obtained. Carcass characteristics were higher in H than in L kids (p < 0.05). Myogenic Factor 5 gene expression level in the LD muscle of H kids was higher (p < 0.05) than that of L kids. A similar trend was observed regarding Myogenic Factor 6 and Myoblast Determination Factor gene expression levels in the LD muscle (p < 0.05). Also, the Myogenin gene expression level of H kids was higher than that of L kids in both muscles (p < 0.05). There were positive correlations among the slaughter weight, carcass characteristics, and some MRF gene expression levels in both muscles (p < 0.05) that the higher gene expression increases the weight and affects the carcass characteristics. The study results suggest that the difference in slaughter weight at the end of fattening in Saanen kids may be due to the expression level of myogenic regulatory factor (MRF) genes. Fattening performance and MRF genes may have a positive correlation.

Molecular signatures diversity unveiled through a comparative transcriptome analysis of longissimus dorsi and psoas major muscles in Hanwoo cattle

This study investigates the transcriptome-level alterations that influence production traits and early fattening stage myogenesis in Hanwoo cattle, specifically focusing on the highly prized Longissimus dorsi (LD) and Psoas major (PM) skeletal muscles, which hold significant commercial value. We conducted RNA sequencing analysis on LD and PM muscles from 14 Hanwoo steers (n = 7, each group) at the age of 10 months, all fed the same diet. Our results unveiled a total of 374 and 206 up-regulated differentially expressed genes (DEGs) in LD and PM muscles, respectively, with statistical significance (p < 0.05) and a log2fold change ≥ 1. Genes governing muscle development processes, such as PAX3, MYL3, COL11A1, and MYL6B, were found to be expressed at higher levels in both tissues. Conversely, genes regulating lipid metabolism, including FABP3, FABP4, LEP, ADIPOQ, and PLIN1, exhibited higher expression in the PM muscle. Functional enrichment analysis revealed a tissue-specific response, as PM muscle showed increased lipid metabolism allied pathways, including the PPAR signaling pathway and regulation of lipolysis in adipocytes, while LD was characterized by growth and proliferative processes. Our findings validate the presence of a muscle-dependent transcription and co-expression pattern that elucidates the transcriptional landscape of bovine skeletal muscle.

Genomic signatures reveal selection in Chinese and European domesticated geese

The Swan goose and Greylag goose are species of geese native to East Asia and Europe, respectively, and are widely believed to be the ancestors of Chinese and European domesticated geese. The Yili goose (YL) and European domestic geese originated from the Greylag goose, but the history of domestication is unclear. In this study, we sequenced and analyzed the genome of the YL goose and the Hortobagy goose to combine with other previously sequenced goose populations for in-depth analysis. The population genetic variations in Stone geese, East Zhejiang White Geese, Taihu geese and Zi geese were also identified and compared. The results showed that admixture gene flow existed in the YL geese population, which was introgressed by Chinese geese, suggesting that gene flow events were frequent and widespread among domesticated geese. Further selected sweep analysis identified candidate genes and metabolic pathways that may be related to the differences in morphology. Several genes such as TGFBR3L, CMYA5, FOXD1, ARHGEF28 and SUCLG2 are associated with growth, reproduction and fertility traits. The results of this study will help to understand the genetic characteristics of domestic geese and the genes affecting important traits and provide a basis for the improved breed of domestic geese.

CircGUCY2C regulates cofilin 1 by sponging miR-425-3p to promote the proliferation of porcine skeletal muscle satellite cells

Circular ribonucleic acids (or circRNAs) are an emerging class of endogenous noncoding RNAs that are involved in physiological and pathological processes. Increasing evidence suggests that circRNAs play an important regulatory role in skeletal muscle development and meat quality regulation. In this study, it was found that circGUCY2C exhibits a high expression level in the longissimus dorsi muscle. It shows resistance to RNase R and additionally promotes the mRNA expression of cyclin-dependent kinase 2 (CDK2) and proliferating cell nuclear antigen (PCNA). Specifically, it was observed that the overexpression of circGUCY2C could promote the transition of porcine skeletal muscle satellite cells into the S and G2 phases of the cell cycle and that it regulates the proliferation of porcine skeletal muscle satellite cells. In contrast, miR-425-3p plays the opposite role and has an inhibitory effect on the proliferation of porcine skeletal muscle satellite cells. MiR-425-3p has been described as a target of circGUCY2C; consequently, the depletion of miR-425-3p promoted the proliferation of porcine skeletal muscle satellite cells. CFL1 (cofilin 1) is a target of miR-425-3p, and circGUCY2C upregulated CFL1 expression by inhibiting miR-425-3p. Collectively, our research outcomes demonstrate that circGUCY2C significantly influences the proliferation of porcine skeletal muscle satellite cells by selectively targeting the miR-425-3p-CFL1 axis, and our work partially clarified the role of circGUCY2C in porcine skeletal muscle satellite cells. Thus, the study provides new insight into the function of circGUCY2C and adds to the knowledge of the post-transcriptional regulation of pork quality.

An Exploratory Data Analysis from Ovine and Bovine RNA-Seq Identifies Pathways and Key Genes Related to Cervical Dilatation

The present study developed a review and exploration of data in public and already validated repositories. The main objective was to identify the pathways involved in ruminants' cervical dilatation, which are conserved between cattle and sheep in the follicular and luteal phases of the reproductive cycle. In cattle, 1961 genes were more differentially expressed in the follicular phase and 1560 in the luteal phase. An amount of 24 genes were considered exclusively expressed from these. A total of 18 genes were in the follicular phase and 6 genes were in the luteal phase. In sheep, 2126 genes were more differentially expressed in the follicular phase and 2469 genes were more differentially expressed in the luteal phase. Hoxb genes were identified in both species and are correlated with the PI3K/Akt pathway. PI3K/Akt was also found in both cattle and sheep, appearing prominently in the follicular and luteal phases of both species. Our analyses have pointed out that the PI3K/Akt pathway and the Hoxb genes appear in prominence in modulating mechanisms that involve estrus alterations in the cervix. PI3K/Akt appears to be an important pathway in the cervical relaxation process.

Bovine HOXA11 Gene Identified from RNA-Seq: mRNA Profile Analysis and Genetic Variation Detection Using ME Method and Their Associations with Carcass Traits

The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10^-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10^-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10^-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.

Association of HOXC8 Genetic Polymorphisms with Multi-Vertebral Number and Carcass Weight in Dezhou Donkey

An increase in the number of vertebrae can significantly affect the meat production performance of livestock, thus increasing carcass weight, which is of great importance for livestock production. The homeobox gene C8 (HOXC8) has been identified as an essential candidate gene for regulating vertebral development. However, it has not been researched on the Dezhou donkey. This study aimed to verify the Dezhou donkey HOXC8 gene's polymorphisms and assess their effects on multiple vertebral numbers and carcass weight. In this study, the entire HOXC8 gene of the Dezhou donkey was sequenced, SNPs at the whole gene level were identified, and typing was accomplished utilizing a targeted sequencing genotype detection technique (GBTS). Then, a general linear model was used to perform an association study of HOXC8 gene polymorphism loci, multiple vertebral numbers, and carcass weight for screening candidate markers that can be used for molecular breeding of Dezhou donkeys. These findings revealed that HOXC8 included 12 SNPs, all unique mutant loci. The HOXC8 g.15179224C>T was significantly negatively associated with carcass weight (CW) and lumbar vertebrae length (LL) (p < 0.05). The g.15179674G>A locus was shown to be significantly positively associated with the number of lumbar vertebrae (LN) (p < 0.05). The phylogenetic tree constructed for the Dezhou donkey HOXC8 gene and seven other species revealed that the HOXC8 gene was highly conserved during animal evolution but differed markedly among distantly related animals. The results suggest that HOXC8 is a vital gene affecting multiple vertebral numbers and carcass weight in Dezhou donkeys, and the two loci g.15179224C>T and g.15179674G>A may be potential genetic markers for screening and breeding of new strains of high-quality and high-yielding Dezhou donkeys.

Blood Transcriptome Profiling Links Immunity to Disease Severity in Myotonic Dystrophy Type 1 (DM1)

The blood transcriptome was examined in relation to disease severity in type I myotonic dystrophy (DM1) patients who participated in the Observational Prolonged Trial In DM1 to Improve QoL- Standards (OPTIMISTIC) study. This sought to (a) ascertain if transcriptome changes were associated with increasing disease severity, as measured by the muscle impairment rating scale (MIRS), and (b) establish if these changes in mRNA expression and associated biological pathways were also observed in the Dystrophia Myotonica Biomarker Discovery Initiative (DMBDI) microarray dataset in blood (with equivalent MIRS/DMPK repeat length). The changes in gene expression were compared using a number of complementary pathways, gene ontology and upstream regulator analyses, which suggested that symptom severity in DM1 was linked to transcriptomic alterations in innate and adaptive immunity associated with muscle-wasting. Future studies should explore the role of immunity in DM1 in more detail to assess its relevance to DM1.

Adiponectin Influences FGF2 in the Developing Porcine Corpus Luteum

Luteal angiogenesis is regulated by pro-angiogenic hormones including fibroblast growth factor 2 (FGF2) and angiopoietin 1 (Ang1), which are regulated by the adipokine leptin during development. Another adipokine, adiponectin, exhibits an inverse relationship with leptin and has been identified in the CL. Therefore, it is hypothesized that adiponectin will influence pro-angiogenic hormones in the developing porcine CL. Crossbred sows were randomly allocated to one of two days of the estrous cycle, day 5 (D5; n = 4) or day 7 (D7; n = 5) for CL collection. Tissue was processed for immunohistochemical localization of adiponectin receptor 2 (AdipoR2), gene expression of FGF2, Ang1, leptin, AdipoR2, and cell culture for adiponectin treatment. The expression of AdipoR2 tended (p = 0.09) to be higher in D7 lutea and was more prevalently localized to the cell surface of large and small luteal cells than in D5 tissue. Adiponectin influenced (p ≤ 0.05) FGF2, leptin, and AdipoR2 gene expression relative to the dose and day (D5 or D7). Collectively, the evidence supports the supposition that adiponectin influences angiogenic factors in the developing CL.

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.

miR-301a inhibits adipogenic differentiation of adipose-derived stromal vascular fractions by targeting HOXC8 in sheep

MicroRNAs (miRNAs) regulate adipogenic differentiation in stromal vascular fractions (SVFs) through post-transcriptional regulation of transcription factors and other functional genes. miR-301 and the homeobox C8 (HOXC8) gene are involved in lipid homeostasis; however, their roles in the adipogenic differentiation of ovine SVFs are unknown. Here, we explored the effects of miR-301 and HOXC8 on adipogenic differentiation in ovine SVFs and the regulatory role of miR-301a in HOXC8 expression. Additionally, we evaluated the effect of miR-301a and HOXC8 on the mRNA abundance of adipogenic markers and the ability of ovine SVFs to accumulate lipids. We found that miR-301a regulates adipogenic differentiation in ovine SVFs by directly targeting the 3'-untranslated region of HOXC8, resulting in significant downregulation of the HOXC8 mRNA and protein. Moreover, miR-301a overexpression suppressed adipogenic differentiation in ovine SVFs and significantly inhibited the expression of adipogenesis-related genes-including adiponectin, C/EBPα, PPARγ, and FABP4. Conversely, HOXC8 overexpression in ovine SVFs increased the accumulation of lipid droplets and remarkably promoted the expression of adipogenic markers. Taken together, our results indicate that miR-301a attenuates the adipogenic differentiation of ovine SVFs by targeting HOXC8. These findings improve our understanding of the mechanism of lipid accumulation and metabolism in sheep.

Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle

The Warner-Bratzler shear force (WBSF) and myofibrillar fragmentation index (MFI) are complementary methodologies used to measure beef tenderness. Longissimus thoracis samples from the 20 most extreme bulls (out of 80 bulls set) for WBSF (tender (n = 10) and tough (n = 10)) and MFI (high (n = 10) and low (n = 10)) traits were collected to perform transcriptomic analysis using RNA-Sequencing. All analysis were performed through CLC Genomics Workbench. A total of 39 and 27 transcripts for WBSF and MFI phenotypes were DE, respectively. The possible DE novel mRNA isoforms, for WBSF and MFI traits, are myosin encoders (e.g. MYL1 and MYL6). In addition, we identified potential mRNA isoforms related to genes affecting the speed fibers degradation during the meat aging process. The DE novel transcripts are transcripted by genes with biological functions related to oxidative process, energy production and striated muscle contraction. The results suggest that the identified mRNA isoforms could be used as potential candidate to select animals in order to improve meat tenderness.

DNA methylomic homogeneity and heterogeneity in muscles and testes throughout pig adulthood

DNA methylome pattern is significantly different among tissues, ages, breeds, and genders. We assessed 20 methylome and transcriptome data in longissimus dorsi (LD) or testicles from Bamaxiang (BMX) and Large White pigs (LW) by deep sequencing technology. We identified ~55.7M CpGs and 5.30M, 0.20M, 1.20M, and 0.16M differential CpGs (P<0.01) between tissues, ages, breeds, and genders, respectively. Interestingly, 7.54% of differentially methylated regions (DMRs) are co-localized with promoters, which potentially regulate gene expression. RNA-seq analysis revealed that 23.42% CpGs are significantly correlated with gene expression (mean |r|=0.58, P<0.01), most of which are enriched in tissue-specific functions. Specially, we also found that the methylation levels in promoters of 655 genes were strongly associated with their expression levels (mean |r|=0.66, P<0.01). In addition, differentially methylated CpGs (DMCpGs) between breeds in HOXC gene cluster imply important regulatory roles in myocytes hypertrophy and intermuscular fat (IMF) deposition. Dramatically, higher similarity of methylation pattern was observed within pedigree than across pedigrees, which indicates the existence of heritable methylation regions. In summary, a part of CpGs in promoter can change its methylation pattern and play a marked regulatory function in different physiological or natural environments.

Gene regulation could be attributed to TCF3 and other key transcription factors in the muscle of pubertal heifers

Puberty is a whole-body event, driven by the hypothalamic integration of peripheral signals such as leptin or IGF-1. In the process of puberty, reproductive development is simultaneous to growth, including muscle growth. To enhance our understanding of muscle function related to puberty, we performed transcriptome analyses of muscle samples from six pre- and six post-pubertal Brahman heifers (Bos indicus). Our aims were to perform differential expression analyses and co-expression analyses to derive a regulatory gene network associate with puberty. As a result, we identified 431 differentially expressed (DEx) transcripts (genes and non-coding RNAs) when comparing pre- to post-pubertal average gene expression. The DEx transcripts were compared with all expressed transcripts in our samples (over 14,000 transcripts) for functional enrichment analyses. The DEx transcripts were associated with "extracellular region," "inflammatory response" and "hormone activity" (adjusted p < .05). Inflammatory response for muscle regeneration is a necessary aspect of muscle growth, which is accelerated during puberty. The term "hormone activity" may signal genes that respond to progesterone signalling in the muscle, as the presence of this hormone is an important difference between pre- and post-pubertal heifers in our experimental design. The DEx transcript with the highest average expression difference was a mitochondrial gene, ENSBTAG00000043574 that might be another important link between energy metabolism and puberty. In the derived co-expression gene network, we identified six hub genes: CDC5L, MYC, TCF3, RUNX2, ATF2 and CREB1. In the same network, 48 key regulators of DEx transcripts were identified, using a regulatory impact factor metric. The hub gene TCF3 was also a key regulator. The majority of the key regulators (22 genes) are members of the zinc finger family, which has been implicated in bovine puberty in other tissues. In conclusion, we described how puberty may affect muscle gene expression in cattle.

Transcriptomic Profile of Primary Culture of Skeletal Muscle Cells Isolated from Semitendinosus Muscle of Beef and Dairy Bulls

The aim of the study was to identify differences in the transcriptomic profiles of primary muscle cell cultures derived from the semitendinosus muscle of bulls of beef breeds (Limousin (LIM) and Hereford (HER)) and a dairy breed (Holstein-Friesian (HF)) (n = 4 for each breed). Finding a common expression pattern for proliferating cells may point to such an early orientation of the cattle beef phenotype at the transcriptome level of unfused myogenic cells. To check this hypothesis, microarray analyses were performed. The analysis revealed 825 upregulated and 1300 downregulated transcripts similar in both beef breeds (LIM and HER) and significantly different when compared with the dairy breed (HF) used as a reference. Ontological analyses showed that the largest group of genes were involved in muscle organ development. Muscle cells of beef breeds showed higher expression of genes involved in myogenesis (including erbb-3, myf5, myog, des, igf-1, tgfb2) and those encoding proteins comprising the contractile apparatus (acta1, actc1, myh3, myh11, myl1, myl2, myl4, tpm1, tnnt2, tnnc1). The obtained results confirmed our hypothesis that the expression profile of several groups of genes is common in beef breeds at the level of proliferating satellite cells but differs from that observed in typical dairy breeds.