Novel Insights into the Differences in Nutrition Value, Gene Regulation and Network Organization between Muscles from Pasture-Fed and Barn-Fed Goats

Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds

BACKGROUND

Mutton quality is closely related to genetic variants and gene expression alterations during growth and development, resulting in differences in nutritional values, flavor, and odor.

RESULTS

We first evaluated and compared the composition of crude protein, crude fat, cholesterol, amino acid (AA), and fatty acid (FA) in the longissimus dorsi muscle of Guizhou black goats (GZB, n = 5) and Yunshang black goats (YBG, n = 6). The contents of cholesterol and FA related to odor in GZB were significantly lower than that in YBG, while the concentrations of umami amino acids and intramuscular fat were significantly higher in GZB. Furthermore, structural variants (SVs) in the genomes of GZB (n = 30) and YBG (n = 11) were explored. It was found that some regions in Chr 10/12/18 were densely involved with a large number of SVs in the genomes of GZB and YBG. By setting FST ≥ 0.25, we got 837 stratified SVs, of which 25 SVs (involved in 12 genes, e.g., CORO1A, CLIC6, PCSK2, and TMEM9) were limited in GZB. Functional enrichment analysis of 14 protein-coding genes (e.g., ENPEP, LIPC, ABCA5, and SLC6A15) revealed multiple terms and pathways related with metabolisms of AA, FA, and cholesterol. The SVs (n = 10) obtained by the whole genome resequencing were confirmed in percentages of 36.67 to 86.67% (n = 96) by PCR method. The SVa and SVd polymorphisms indicated a moderate negative correlation with HMGCS1 activity (n = 17).

CONCLUSION

This study is the first to comprehensively reveal potential SVs related to mutton nutritional values, flavor, and odor based on genomic compare between two black goat breeds with closely genetic relationship. The SVs generated in this study provide a data resource for deeper studies to understand the genomic characteristics and possible evolutionary outcomes with better nutritional values, flavor and extremely light odor.

Unveiling the role of circRBBP7 in myoblast proliferation and differentiation: A novel regulator of muscle development

Muscle development is a multistep process regulated by diverse gene networks, and circRNAs are considered novel regulators mediating myogenesis. Here, we systematically analyzed the role and underlying regulatory mechanisms of circRBBP7 in myoblast proliferation and differentiation. Results showed that circRBBP7 has a typical circular structure and encodes a 13 -kDa protein. By performing circRBBP7 overexpression and RNA interference, we found that the function of circRBBP7 was positively correlated with the proliferation and differentiation of myoblasts. Using RNA sequencing, we identified 1633 and 532 differentially expressed genes (DEGs) during myoblast proliferation or differentiation, respectively. The DEGs were found mainly enriched in cell cycle- and skeletal muscle development-related pathways, such as the MDM2/p53 and PI3K-Akt signaling pathways. Further co-IP and IF co-localization analysis revealed that VEGFR-1 is a target of circRBBP7 in myoblasts. qRT-PCR and WB analysis further confirmed the positive correlation between VEGFR-1 and circRBBP7. Moreover, we found that in vivo transfection of circRBBP7 into injured muscle tissues significantly promoted the regeneration and repair of myofibers in mice. Therefore, we speculate that circRBBP7 may affect the activity of MDM2 by targeting VEGFR-1, altering the expression of muscle development-related genes by mediating p53 degradation, and ultimately promoting myoblast development and muscle regeneration. This study provides essential evidence that circRBBP7 can serve as a potential target for myogenesis regulation and a reference for the application of circRBBP7 in cattle genetic breeding and muscle injury treatment.

Multi-omics reveal the effects and regulatory mechanism of dietary neutral detergent fiber supplementation on carcass characteristics, amino acid profiles, and meat quality of finishing pigs

This study aimed to reveal the effects and regulatory mechanism of dietary NDF on the performance of pigs by multi-omics analysis. Results showed that 16 % dietary NDF significantly improved meat quality, increased flavor amino acid content, and reduced backfat thickness and the feed-to-gain ratio. 16S rDNA sequencing showed that 16 % NDF significantly increased the abundance of Akkermansia, Lachnoclostridium, and Ruminococcus. Transcript analysis showed that genes related to muscle development and lipid metabolism were significantly modified. Metabonomic analysis showed that 16 % NDF significantly increased amino and fatty acid related metabolites. Correlation analysis suggested that 16 % NDF treatment may alter the gut microbiota and metabolites, regulate the expression of genes related to lipid and amino metabolism, and ultimately affect the flavor and performance of pigs. This study provides a novel understanding about the effect and regulatory mechanism of NDF supplements on the finishing pigs and a relevant reference for the improvement of diet formulation.

Genome-Wide Detection of Copy Number Variations and Their Potential Association with Carcass and Meat Quality Traits in Pingliang Red Cattle

Copy number variation (CNV) serves as a significant source of genetic diversity in mammals and exerts substantial effects on various complex traits. Pingliang red cattle, an outstanding indigenous resource in China, possess remarkable breeding value attributed to their tender meat and superior marbling quality. However, the genetic mechanisms influencing carcass and meat quality traits in Pingliang red cattle are not well understood. We generated a comprehensive genome-wide CNV map for Pingliang red cattle using the GGP Bovine 100K SNP chip. A total of 755 copy number variable regions (CNVRs) spanning 81.03 Mb were identified, accounting for approximately 3.24% of the bovine autosomal genome. Among these, we discovered 270 potentially breed-specific CNVRs in Pingliang red cattle, including 143 gains, 73 losses, and 54 mixed events. Functional annotation analysis revealed significant associations between these specific CNVRs and important traits such as carcass and meat quality, reproduction, exterior traits, growth traits, and health traits. Additionally, our network and transcriptome analysis highlighted CACNA2D1, CYLD, UBXN2B, TG, NADK, and ITGA9 as promising candidate genes associated with carcass weight and intramuscular fat deposition. The current study presents a genome-wide CNV map in Pingliang red cattle, highlighting breed-specific CNVRs, and transcriptome findings provide valuable insights into the underlying genetic characteristics of Pingliang red cattle. These results offer potential avenues for enhancing meat quality through a targeted breeding program.

Integrated Metabolomics and Transcriptomics Analyses Reveal the Candidate Genes Regulating the Meat Quality Change by Castration in Yudong Black Goats (Capra hircus)

Yudong black goats (YDGs) are a local breed in southwest China that possess unique meat qualities and produce a high meat yield, making them ideal models for studying goat meat quality. Castration may decrease off-odors, significantly change metabolites and improve meat quality. Using multi-omics techniques, this study focused on Yudong black goat wethers (YDW, n = 4) and Yudong black bucks (YDB, n = 4). The findings revealed that 33 differentially expressed genes (DEGs) and 279 significantly changed metabolites (SCMs) influenced goat meat quality by affecting fat accumulation and lipolysis regulatory processes. Herein, several candidate genes (IGF1, TNNT2, PPP2R2C, MAPK10 and VNN1, etc.) were identified that play a role in regulating meat quality, non-castrated and castrated, alongside a series of metabolites that may serve as potential meat quality biomarkers. Lipids (triglycerides, oxidized lipids_5-iso PGF2VI, ceramide (t18:1/36:2(2OH)) and Carnitine C20:5, etc.) were significantly higher in the castrated goats. These results revealed that lipids and hydrophilic metabolites were affected by castration, which might be beneficial in terms of goat meat quality. This study aimed to investigate the differences in meat quality between uncastrated and castrated male goats and the possible molecular regulatory mechanisms.

Feeding regimens affecting carcass and quality attributes of sheep and goat meat - A comprehensive review

Sheep and goats can efficiently convert low quality forage into high-quality meat which contains specific nutrients and quality traits. Carcass traits and quality attributes of sheep and goat meat depend upon several factors and one of most effective strategies amongst these is feeding regimens. In this review, the major aspects of feeding regimens affecting growth rate, carcass traits and quality attributes of sheep and goat meat are thoroughly discussed, with a particular focus on physical-chemical composition, flavor profile, and fatty acid (FA) profile. Grazing lambs and kids receiving concentrate or under stall-feeding systems had greater average daily gain and carcass yield compared with animals reared on pasture only. However, growth rate was higher in lambs/kids grazing on pastures of improved quality. Moreover, the meat of grazing lambs receiving concentrate had more intense flavor, intramuscular fat (IMF) content, and unhealthy FA composition, but comparable color, tenderness, juiciness, and protein content compared to that of lambs grazed on grass only. In contrast, meat of concentrate-fed lambs had more intense color, greater tenderness and juiciness, IMF and protein contents, and lower flavor linked to meat. Additionally, the meat of kids grazed on concentrate supplementation had higher color coordinates, tenderness, IMF content and unhealthy FA composition, whereas juiciness and flavor protein content were similar. In contrast, kids with concentrate supplementation had superior color coordinates, juiciness, IMF content and unhealthy FA composition, but lower tenderness and flavor intensity compared to pasture-grazed kids. Thus, indoor-finished or supplemented grazing sheep/goats had higher growth rate and carcass quality, higher IMF content and unhealthy FA composition compared to animals grazed on grass only. Finally, supplementation with concentrate increased flavor intensity in lamb meat, and improved color and tenderness in kid meat, whereas indoor-fed sheep/goats had improved color and juiciness as well as reduced flavor compared to pasture-grazed animals.

Expression Variation of CPT1A Induces Lipid Reconstruction in Goat Intramuscular Precursor Adipocytes

Intramuscular fat (IMF) deposition is one of the most important factors affecting meat quality and is closely associated with the expression of carnitine palmitoyl transferase 1A (CPT1A) which facilitates the transfer of long-chain fatty acids (LCFAs) into the mitochondria. However, the role of how CPT1A regulates the IMF formation remains unclear. Herein, we established the temporal expression profile of CPT1A during the differentiation of goat intramuscular precursor adipocytes. Functionally, the knockdown of CPT1A by siRNA treatment significantly increased the mRNA expression of adipogenic genes and promoted lipid deposition in goat intramuscular precursor adipocytes. Meanwhile, a CPT1A deficiency inhibited cell proliferation and promoted cell apoptosis significantly. CPT1A was then supported by the overexpression of CPT1A which significantly suppressed the cellular triglyceride deposition and promoted cell proliferation although the cell apoptosis also was increased. For RNA sequencing, a total of 167 differential expression genes (DEGs), including 125 upregulated DEGs and 42 downregulated DEGs, were observed after the RNA silencing of CPT1A compared to the control, and were predicted to enrich in the focal adhesion pathway, cell cycle, apoptosis and the MAPK signaling pathway by KEGG analysis. Specifically, blocking the MAPK signaling pathway by a specific inhibitor (PD169316) rescued the promotion of cell proliferation in CPT1A overexpression adipocytes. In conclusion, the expression variation of CPT1A may reconstruct the lipid distribution between cellular triglyceride deposition and cell proliferation in goat intramuscular precursor adipocyte. Furthermore, we demonstrate that CPT1A promotes the proliferation of goat adipocytes through the MAPK signaling pathway. This work widened the genetic regulator networks of IMF formation and delivered theoretical support for improving meat quality from the aspect of IMF deposition.

Review of Feeding Systems Affecting Production, Carcass Attributes, and Meat Quality of Ovine and Caprine Species

Growth rate, carcass attributes, and meat quality traits of small ruminants (i.e., sheep and goats) depend on various factors, among which the feeding system is one of the most important factors. However, how feeding systems affect these parameters differ between sheep and goats. Therefore, this review aimed to evaluate the differences in how different feeding systems affect the growth performance, carcass characteristics, and meat quality of sheep and goats. It also explored the effects of a new finishing strategy-time-limited grazing with supplements on these traits. Compared with stalled feeding, finishing lambs/kids on pasture-only feed reduced the average daily gain (ADG) and carcass yield, while supplemented-grazing lambs/kids had near-equivalent or higher ADG and carcass attributes. Pasture-grazing increased the meat flavor intensity and healthy fatty acid content (HFAC) of lamb/kid meat. Supplemental grazing lambs had comparable or superior meat sensory attributes and increased meat protein and HFAC compared to stall-fed ones. In contrast, supplemental grazing only improved the meat color of kids but had little effect on other meat qualities. Moreover, time-limited grazing with supplemental concentrates increased the carcass yield and meat quality in lamb meat. Overall, the effects of different feeding systems on growth performance and carcass traits were comparable between sheep and goats but differed in terms of the meat quality.

Comparative evolutionary and molecular genetics based study of Buffalo lysozyme gene family to elucidate their antibacterial function

Lysozyme is used as a food preservative, biological medicine, and infant food additive as a natural anti-infective chemical having bactericidal activity and abundantly secreted in mammals' milk, saliva, etc. We systematically analyzed the 16 coding LYZ genes (C and G-type) in buffalo and cattle to elucidate their evolutionary perspective thoroughly by evaluating an evolutionary relationship, motif patterning, physicochemical attributes, gene, and protein structure, as well as the functional role of the mammary gland-specific expressed buffalo and cattle LYZ genes precisely while considering expression levels difference and the interaction sites variation with bacteria envisaged the potential ability of buffalo LYZ protein with enhanced antibacterial effect. Thus, we speculated that the buffalo mammary glands expressed lysozyme has good antibacterial activity. This study on the buffalo lysozyme gene family not only provides comprehensive insights into the genetic architecture and their antibacterial effect but also offers a theoretical basis for the development of new veterinary drugs and animal health care for mastitis, as well as a new molecular genetic basis to study food or medical lysozyme.