A ratiometric fluorescence probe for bisulfite detection in live cells and meat samples.

The development of reliable probe technology for the detection of bisulfite (HSO3-) in situ in food and biological samples is contributing significantly to food quality and safety assurance as well as community health. In this work, a responsive probe, EHDI, is developed for ratiometric fluorescence detection of HSO3- in aqueous solution, meat samples, and living cells. The probe is designed based on the HSO3- triggered 1,4-addition of electron deficit C = C bond of EHDI. As a result of this specific 1,4-addition, the π-conjugation system was destructed, resulting in blue shifts of the emission from 687 to 440 nm and absorption from 577 to 355 nm. The probe has good water solubility, high sensitivity and selectivity, allowing it to be used for imaging of HSO3- internalization and production endogenously. The capability of probe EHDI for HSO3- was then validated by traditional HPLC technology, enabling accurately detect HSO3- in beef samples. The successful development of this probe thus offers a new tool for investigating HSO3- in situ in food and biological conditions.

Transcriptomic analysis of the longissimus thoracis muscle in pigs has identified molecular regulatory patterns associated with meat quality.

Meat quality is a critical aspect of pig breeding. In addition to genetics, meat quality is also influenced by nutritional and environmental factors. In this study, three pig breeds, Shengxianhua, Jiaxing, and Qinglian Black (SXH, JXB and QLB), were used as experimental animals. Transcriptional analysis was performed on the longissimus thoracis (LT) muscle to investigate variations in intramuscular fat (IMF), inosine monophosphate (IMP), amino acids, and muscle fiber morphology across different breeds. Ingenuity canonical pathway analysis (IPA) identified biological processes and key driver genes related to metabolism and muscle development. Additionally, weighted gene co-expression network analysis (WGCNA) revealed gene modules associated with IMP. KEGG and GO analyses identified specific biological processes and signaling pathways related to IMP, including the Oxidative Phosphorylation pathway and rRNA Metabolic Processes. These findings provide novel insights into the molecular regulatory mechanisms underlying meat quality variations among pig breeds.

Transcriptomic analysis of different intramuscular fat contents on the flavor of the longissimus dorsi tissues from Guangling donkey.

BACKGROUND: In this study, researchers aimed to explore the impact of intramuscular fat (IMF) concentration on the flavor of donkey meat, specifically in the longissimus dorsi muscle of Guangling donkeys. The internal volatile organic compounds that cause the flavor differences between donkey muscles are not clear at present. Transcriptomic technologies were utilized to analyze gene expression and its relationship to donkey meat flavor. METHOD: Thirty Guangling donkeys had their IMF content evaluated in the longissimus dorsi muscle. Based on IMF content, 16 donkeys of similar ages were divided into two groups: low-fat (L) and high-fat (H). Headspace solid-phase microextraction Gas chromatography-mass spectrometry (HS-SPME-GC-MS) and headspace solid phase microextraction mass spectrometry were used to identify potential flavor components that differed between the two groups. RESULTS: Five key volatile substances were identified, and WGCNA and KEGG analysis was conducted to analyze the genes associated with these substances. The results showed that pathways like PPAR signaling, nucleotide excision repair, glucagon signaling, arachidonic acid metabolism, and glycolysis/glycogenesis were involved in lipid deposition. Additionally, a gene-gene interaction network map was constructed, highlighting the importance of hub genes such as EEF2, DDX49, GAP43, SNAP25, NDUFS8, MRPS11, RNASEH2A, POLR2E, POLR2C and ALB in regulating key flavor substances. CONCLUSION: This study provided valuable insights into the regulation of genes and protein expression related to flavor substances in donkey meat. It also deepened understanding of the influence of IMF on flavor and laid a foundation for future molecular breeding improvements in Guangling donkeys.

Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies.

BACKGROUND: Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities. RESULTS: By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues. CONCLUSIONS: Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.

Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance.

BACKGROUND: The transcriptome and metabolome dissection of the skeletal muscle of high- and low- growing individuals from a crossbred population of the indigenous Chongming white goat and the Boer goat were performed to discover the potential functional differentially expressed genes (DEGs) and differential expression metabolites (DEMs). RESULTS: A total of 2812 DEGs were detected in 6 groups at three time stages (3,6,12 Month) in skeletal muscle using the RNA-seq method. A DEGs set containing seven muscle function related genes (TNNT1, TNNC1, TNNI1, MYBPC2, MYL2, MHY7, and CSRP3) was discovered, and their expression tended to increase as goat muscle development progressed. Seven DEGs (TNNT1, FABP3, TPM3, DES, PPP1R27, RCAN1, LMOD2) in the skeletal muscle of goats in the fast-growing and slow-growing groups was verified their expression difference by reverse transcription-quantitative polymerase chain reaction. Further, through the Liquid chromatography-mass spectrometry (LC-MS) approach, a total of 183 DEMs in various groups of the muscle samples and these DEMs such as Queuine and Keto-PGF1α, which demonstrated different abundance between the goat fast-growing group and slow-growing group. Through weighted correlation network analysis (WGCNA), the study correlated the DEGs with the DEMs and identified 4 DEGs modules associated with 18 metabolites. CONCLUSION: This study benefits to dissection candidate genes and regulatory networks related to goat meat production performance, and the joint analysis of transcriptomic and metabolomic data provided insights into the study of goat muscle development.

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.

Transcriptomic analysis reveals differentially expressed genes associated with meat quality in Chinese Dagu chicken and AA+ broiler roosters.

BACKGROUND: With the improvement of living standards, the quality of chicken has become a significant concern. Chinese Dagu Chicken (dual-purpose type) and Arbor Acres plus broiler (AA+ broiler) (meat-type) were selected as the research subjects in this study, the meat quality of the breast and leg muscles were measured. However, the molecular mechanism(s) underlying regulation of muscle development are not yet fully elucidated. Therefore, finding molecular markers or major genes that regulate muscle quality has become a crucial breakthrough in chicken breeding. Unraveling the molecular mechanism behind meat traits in chicken and other domestic fowl is facilitated by identifying the key genes associated with these developmental events. Here, a comparative transcriptomic analysis of chicken meat was conducted on breast muscles (BM) and leg muscles (LM) in AA+ broilers (AA) and Dagu chicken (DG) to explore the differences in their meat traits employing RNA-seq. RESULTS: Twelve cDNA libraries of BM and LM from AA and DG were constructed from four experimental groups, yielding 14,464 genes. Among them, Dagu chicken breast muscles (DGB) vs AA+ broilers breast muscles (AAB) showed 415 upregulated genes and 449 downregulated genes, Dagu chicken leg muscles (DGL) vs AA+ broilers leg muscles (AAL) exhibited 237 upregulated genes and 278 downregulated genes, DGL vs DGB demonstrated 391 upregulated genes and 594 downregulated genes, and AAL vs AAB displayed 122 upregulated genes and 154 downregulated genes. 13 genes, including nine upregulated genes (COX5A, COX7C, NDUFV1, UQCRFS1, UQCR11, BRT-1, FGF14, TMOD1, MYOZ2) and four downregulated genes (MYBPC3, MYO7B, MTMR7, and TNNC1), were found to be associated with the oxidative phosphorylation signaling pathway. Further analysis revealed that the differentially expressed genes (DEGs) from muscle were enriched in various pathways, such as metabolic pathways, oxidative phosphorylation, carbon metabolism, glycolysis, extracellular matrix-receptor interaction, biosynthesis of amino acids, focal adhesion, vascular smooth muscle contraction, and cardiac muscle contraction, all of which are involved in muscle development and metabolism. This study also measured the meat quality of the breast and leg muscles from the two breeds, which demonstrated superior overall meat quality in Chinese Dagu Chicken compared to the AA+ broiler. CONCLUSIONS: Our findings show that the meat quality of dual-purpose breeds (Chinese Dagu chicken) is higher than meat-type (AA+ broiler), which may be related to the DEGs regulating muscle development and metabolism. Our findings also provide transcriptomic insights for a comparative analysis of molecular mechanisms underlying muscle development between the two breeds, and have practical implications for the improvement of chicken breeding practices.

Machine Learning-Assisted Portable Microplasma Optical Emission Spectrometer for Food Safety Monitoring.

To meet the needs of food safety for simple, rapid, and low-cost analytical methods, a portable device based on a point discharge microplasma optical emission spectrometer (µPD-OES) was combined with machine learning to enable on-site food freshness evaluation and detection of adulteration. The device was integrated with two modular injection units (i.e., headspace solid-phase microextraction and headspace purge) for the examination of various samples. Aromas from meat and coffee were first introduced to the portable device. The aroma molecules were excited to specific atomic and molecular fragments at excited states by room temperature and atmospheric pressure microplasma due to their different atoms and molecular structures. Subsequently, different aromatic molecules obtained their own specific molecular and atomic emission spectra. With the help of machine learning, the portable device was successfully applied to the assessment of meat freshness with accuracies of 96.0, 98.7, and 94.7% for beef, pork, and chicken meat, respectively, through optical emission patterns of the aroma at different storage times. Furthermore, the developed procedures can identify beef samples containing different amounts of duck meat with an accuracy of 99.5% and classify two coffee species without errors, demonstrating the great potential of their application in the discrimination of food adulteration. The combination of machine learning and µPD-OES provides a simple, portable, and cost-effective strategy for food aroma analysis, potentially addressing field monitoring of food safety.

Comparison of competitive and sandwich immunochromatographic analysis in the authentication of chicken in meat products.

Cheap chicken meat is often used as an undeclared substitute in meat products. In this study, two formats of the immunochromatographic assay (ICA) of immunoglobulins of class Y (IgY) as a biomarker for chicken authentication were developed. In both competitive ICA (cICA) and sandwich ICA (sICA), gold nanoparticles (GNP) were conjugated with anti-species antibodies. A simple procedure of sample preparation, which took only 30 min, was proposed. Test systems demonstrated high sensitivity and rapidity: visual limits of detection of IgY and assay durations were 12/14 ng/mL and 10/15 min for cICA and sICA, respectively. The absence of cross-reactivity with the mammalian species confirmed the high specificity of the test systems. Good applicability of the assays was confirmed for the detection of chicken in raw meat mixtures: as low as 3% and 0.2% (w/w) of chicken could be revealed in beef and pork by cICA and sICA, respectively. The influence of heat processing of meat-based products on immune recognition and, consequently, the analytical performance of the test systems was revealed. It was shown that sICA is preferable for the detection of IgY even in thermally processed meat. The proposed ICAs can be recommended for rapid on-site control of meat products' composition.

Determination of succinic acid and lactic acid in pigs' serum, intestinal contents, and meat by ultrahigh-performance liquid chromatography-tandem mass spectrometry.

RATIONALE: Succinic acid and lactic acid have been associated with diarrhea in weaned piglets. The level of succinic acid and lactic acid in serum, meat, and intestinal contents is important to elucidate the mechanism of diarrhea in weaned piglets. METHODS: A facile method was developed for the quantification of succinic acid and lactic acid in pigs' serum, intestinal contents, and meat using ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC/MS/MS). The serum samples underwent protein precipitation with methanol. The meat and intestinal contents were freeze-dried and homogenized using a tissue grinding apparatus. Methanol-water mixture (80:20, v/v) was used for homogenizing the meat, while water was used for homogenizing the intestinal contents. An additional step of protein precipitation with acetonitrile was required for the intestinal contents. The resulting solution was diluted with water before being analyzed by UHPLC/MS/MS. Separation of succinic acid and lactic acid could be achieved within 3 min using a Kinetic XB-C18 column. RESULTS: The coefficients of variation for peak areas of succinic acid and lactic acid were less than 5.0%. The established method demonstrated good linearity as indicated by correlation coefficients exceeding 0.996. Additionally, satisfactory recoveries ranging from 88.58% to 108.8% were obtained. The detection limits (RS/N = 3) for succinic acid and lactic acid were determined to be 0.75 ng/mL and 0.02 µg/mL, respectively. CONCLUSION: This method exhibited high sensitivity, simplicity in operation, and small sample weight, making it suitable for quantitative determination of succinic acid and lactic acid in pigs' serum, intestinal contents, and meat. The method developed will provide valuable technical support in studying the metabolic mechanisms of succinic acid and lactic acid in pigs.

Effects of antibacterial peptides from Brevibacillus texasporus on growth performance, meat quality and gut health of cultured largemouth bass (Micropterus salmoides).

The aim of this study was to investigate the effects of antibacterial peptides from Brevibacillus texasporus (BT) on the growth performance, meat quality and gut health of cultured largemouth bass (Micropterus salmoides). Largemouth bass (36.17 ± 1.52 g) were divided into 2 groups and each group was fed with diets supplemented with or without 200 ppm of BT peptides for 130 days. The results showed that BT peptides had no significant influences on growth performance and body indexes, but significantly enhanced total antioxidant capacity and lysozyme content in the serum. Moreover, digestive enzymes activities and intestinal villous height were also prominently increased. From meat quality aspect, no significant differences were found in nutritional components, amino acid composition, fatty acid composition and texture property, except the values of hardness, gumminess and γ-linolenic acid (C18:3n6) were remarkably increased after BT peptides intervention. Finally, the results of gut microbiota and short chain fatty acids revealed that BT peptides significantly decreased the relative abundances of harmful bacteria such as genus Acinetobacter and Pseudomonas, and increased the production of short chain fatty acids. In conclusion, this study confirmed that BT peptides could be used to improve the health of largemouth bass, which provided novel insights into the application of antimicrobial peptides in aquacultures.

Rapid Analysis of Estrogens in Meat Samples by High Performance Liquid Chromatography with Fluorescence Detection.

A novel reagent named 4-(N-methyl-1,3-dioxo-benzoisoquinolin-6-yl-oxy)benzene sulfonyl chloride (MBIOBS-Cl) for the determination of estrogens in food samples by high-performance liquid chromatography (HPLC) with fluorescence detection has been developed. Estrogens could be easily labeled by MBIOBS-Cl in Na2CO3-NaHCO3 buffer solution at pH 10.0. The complete labeling reaction for estrogens could be accomplished within five minutes, the corresponding derivatives exhibited strong fluorescence with the maximum excitation and emission wavelengths at 249 nm and 443 nm, respectively. The derivatization conditions, such as the molar ratio of reagent to estrogens, derivatization time, pH, temperature, and buffers were optimized. Derivatives were sufficiently stable to be efficiently analyzed by HPLC with a reversed-phase Agilent ZORBAX 300SB-C18 column with a good baseline resolution. Excellent linear correlations were obtained for all estrogen derivatives with correlation coefficients greater than 0.9998. Ultrasonic-Assisted extraction was used to optimize the extraction of estrogens from meat samples with a recovery higher than 82%. The detection limits (LOD, S/N = 3) of the method ranged from 0.95 to 3.3 µg· kg-1. The established method, which is fast, simple, inexpensive, and environment friendly, can be successfully applied for the detection of four steroidal estrogens from meat samples with little matrix interference.

Use of a commercial tissue dissociation system to detect Salmonella-contaminated poultry products.

Successful detection of bacterial pathogens in food can be challenging due to the physical and compositional complexity of the matrix. Different mechanical/physical and chemical methods have been developed to separate microorganisms from food matrices to facilitate detection. The present study benchmarked a commercial tissue digestion system that applies both chemical and physical methods to separate microorganisms from tissues against stomaching, a standard process currently utilized by commercial and regulatory food safety laboratories. The impacts of the treatments on the physical properties of the food matrix were characterized along with the compatibility of the methods with downstream microbiological and molecular detection assays. The results indicate the tissue digestion system can significantly reduce the average particle size of the chicken sample relative to processing via a stomacher (P < 0.001) without adversely affecting either real-time PCR (qPCR) or plate counting assays, which are typically used to detect Salmonella. Furthermore, inoculated chicken treated with the GentleMACS resulted in a significant increase (P < 0.003) in the qPCR's detection capabilities relative to stomached controls. Cohen kappa (κ) coefficient and McNemar's test indicate the plating assays and PCR results agree with measurements obtained via the 3 M Molecular Detection System as defined in the MLG standard (κ > 0.62; P > 0.08). Collectively, the results demonstrate that the technique enables detection of pathogens in meat at lower levels of contamination using current industry standard technologies.

Associations between the rumen microbiota and carcass merit and meat quality in beef cattle.

The rumen microbiota is important for energy and nutrient acquisition in cattle, and therefore its composition may also affect carcass merit and meat quality attributes. In this study, we examined the associations between archaeal and bacterial taxa in the rumen microbiota of beef cattle and 12 different attributes, including hot carcass weight (HCW), dressing percentage, ribeye area (REA), intramuscular fat content, marbling score, fat thickness, yield grade, moisture content, purge loss, and shear force. There were significant correlations between the relative abundance of certain archaeal and bacterial genera and these attributes. Notably, Selenomonas spp. were positively correlated with live weight and HCW, while also being negatively correlated with purge loss. Members of the Christensenellaceae R-7, Moryella, and Prevotella genera exhibited positive and significant correlations with various attributes, such as dressing percentage and intramuscular fat content. Ruminococcaceae UCG-001 was negatively correlated with live weight, HCW, and dressing percentage, while Acidaminococcus and Succinivibrionaceae UCG-001 were negatively correlated with intramuscular fat content, moisture content, and marbling score. Overall, our findings suggest that specific changes in the rumen microbiota could be a valuable tool to improve beef carcass merit and meat quality attributes. Additional research is required to better understand the relationship between the rumen microbiota and these attributes, with the potential to develop microbiome-targeted strategies for enhancing beef production. KEY POINTS: • Certain rumen bacteria were associated with carcass merit and meat quality • Moryella was positively correlated with intramuscular fat in beef carcasses • Acidaminococcus spp. was negatively correlated with marbling and intramuscular fat.

Plasma activated water effects on behavior, performance, carcass quality, biochemical changes, and histopathological alterations in quail.

BACKGROUND: Plasma-activated water (PAW) is an innovative promising technology which could be applied to improve poultry health. The current study investigated the effects of drinking water supply with PAW on quail behaviour, performance, biochemical parameters, carcass quality, intestinal microbial populations, and internal organs histopathology. A total of 54 twenty-one-day-old Japanese quail chicks were randomly allotted to three treatments provided with PAW at doses 0, 1 ml (PAW-1), and 2 ml (PAW-2) per one litter drinking water. Each treatment contained 6 replicates (3 birds/ cage; one male and two females). RESULTS: The results clarified that there were no significant (P > 0.05) changes in behaviour, and performance. For the biochemical indicators, the PAW-1 group showed significantly higher serum H2O2, total protein and globulin levels compared with the other groups (P = 0.015, < 0.001, and 0.019; respectively). PAW groups had significantly lower serum creatinine and urea levels than the control (P = 0.003). For the carcass quality, the internal organs relative weight between different treatments was not changed. In contrast, there was a significant increase in the meat colour, taste, and overall acceptance scores in PAW groups compared with the control one (P = 0.013, 0.001, and < 0.001; respectively). For the intestinal microbial population, lactobacilli count was significantly higher in PAW-2 compared with the control group (P = 0.014), while there were no changes in the total bacterial count between different treatment groups. Moreover, mild histological changes were recorded in the intestine, liver, and spleen of PAW groups especially PAW-2 compared with the control one. CONCLUSIONS: PAW offered benefits, such as reducing creatine and urea levels, improving meat characteristics, and increasing lactobacilli count, all of which are crucial for sustainable quail farming. Therefore, further research is needed.

Effects of high dietary inclusion of Arthrospira platensis, either extruded or supplemented with a super-dosing multi-enzyme mixture, on broiler growth performance and major meat quality parameters.

BACKGROUND: This investigation assessed the effects of high dietary inclusion of Spirulina (Arthrospira platensis) on broiler chicken growth performance, meat quality and nutritional attributes. For this, 120 male broiler chicks were housed in 40 battery brooders (three birds per brooder). Initially, for 14 days, a standard corn and soybean meal diet was administered. Subsequently, from days 14 to 35, chicks were assigned to one of the four dietary treatments (n = 10 per treatment): (1) control diet (CTR); (2) diet with 15% Spirulina (SP); (3) diet with 15% extruded Spirulina (SPE); and (4) diet with 15% Spirulina plus a super-dosing enzymes supplement (0.20% pancreatin extract and 0.01% lysozyme) (SPM). RESULTS: Throughout the experimental period, both SP and SPM diets resulted in decreased final body weight and body weight gain compared to control (p < 0.001), with the SPE diet showing comparable results to CTR. The SPE diet prompted an increase in average daily feed intake (p = 0.026). However, all microalga treatments increased the feed conversion ratio compared to CTR. Dietary inclusion of Spirulina notably increased intestinal content viscosity (p < 0.010), which was mitigated by the SPM diet. Spirulina supplementation led to lower pH levels in breast meat 24 h post-mortem and heightened the b* colour value in both breast and thigh meats (p < 0.010). Furthermore, Spirulina contributed to an increased accumulation of total carotenoids, n-3 polyunsaturated fatty acids (PUFA), and saturated fatty acids (SFA), while diminishing n-6 PUFA, thus altering the n-6/n-3 and PUFA/SFA ratios favourably (p < 0.001). However, it also reduced zinc concentration in breast meat (p < 0.001). CONCLUSIONS: The findings indicate that high Spirulina levels in broiler diets impair growth due to increased intestinal viscosity, and that extrusion pre-treatment mitigates this effect. Despite reducing digesta viscosity, a super-dosing enzyme mix did not improve growth. Data also indicates that Spirulina enriches meat with antioxidants and n-3 PUFA but reduces α-tocopherol and increases saturated fats. Reduced zinc content in meat suggests the need for Spirulina biofortification to maintain its nutritional value.

Identification of circRNA-associated ceRNA networks in the longissimus dorsi of yak under different feeding systems.

BACKGROUND: Yaks (Bos grunniens), prized for their ability to thrive in high-altitude environments, are indispensable livestock in the plateau region. Modifying their feeding systems holds significant promise for improving their growth and meat quality. Tenderness, a key determinant of yak meat quality and consumer appeal, is demonstrably influenced by dietary regimen. Indoor feeding regimes have been shown to enhance tenderness by lowering shear stress and optimizing pH values. CircRNAs, well-known modulators of circulatory function, also play a crucial role in skeletal muscle development across various animal species. However, their functional significance in yak skeletal muscle remains largely unexplored. RESULTS: In this study, we identified a total of 5,534 circRNAs within the longissimus dorsi muscle, and we found 51 differentially expressed circRNAs (20 up-regulated and 31 down-regulated) between the two feeding groups. Constructing a comprehensive ceRNA network illuminated intricate regulatory mechanisms, with PGP and circRNA_0617 converging on bta-miR-2285q, mirrored by KLF15/circRNA_0345/bta-miR-20b and CTSF/circRNA_0348/bta-miR-146a. These findings shed light on the potential of circRNAs to influence yak muscle development and meat quality, offering valuable insights for future research. CONCLUSIONS: This investigation unraveled a complex interaction network between circRNAs、mRNAs and miRNAs in yak skeletal muscle. We further elucidated the target genes regulated by these target genes within the network, offering valuable insights into the potential regulatory mechanisms governing muscle development and meat quality-related traits in yaks.

A network-based approach to understanding gene-biological processes affecting economically important traits of Nelore cattle.

This study aimed to build gene-biological process networks with differentially expressed genes associated with economically important traits of Nelore cattle from 17 previous studies. The genes were clustered into three groups by evaluated traits: group 1, production traits; group 2, carcass traits; and group 3, meat quality traits. For each group, a gene-biological process network analysis was performed with the differentially expressed genes in common. For production traits, 37 genes were found in common, of which 13 genes were enriched for six Gene Ontology (GO) terms; these terms were not functionally grouped. However, the enriched GO terms were related to homeostasis, the development of muscles and the immune system. For carcass traits, four genes were found in common. Thus, it was not possible to functionally group these genes into a network. For meat quality traits, the analysis revealed 222 genes in common. CSRP3 was the only gene differentially expressed in all three groups. Non-redundant biological terms for clusters of genes were functionally grouped networks, reflecting the cross-talk between all biological processes and genes involved. Many biological processes and pathways related to muscles, the immune system and lipid metabolism were enriched, such as striated muscle cell development and triglyceride metabolic processes. This study provides insights into the genetic mechanisms of production, carcass and meat quality traits of Nelore cattle. This information is fundamental for a better understanding of the complex traits and could help in planning strategies for the production and selection systems of Nelore cattle.

Smartphone-based digital phenotyping for genome-wide association study of intramuscular fat traits in longissimus dorsi muscle of pigs.

Intramuscular fat (IMF) content and distribution significantly contribute to the eating quality of pork. However, the current methods used for measuring these traits are complex, time-consuming and costly. To simplify the measurement process, this study developed a smartphone application (App) called Pork IMF. This App serves as a rapid and portable phenotyping tool for acquiring pork images and extracting the image-based IMF traits through embedded deep-learning algorithms. Utilizing this App, we collected the IMF traits of the longissimus dorsi muscle in a crossbred population of Large White × Tongcheng pigs. Genome-wide association studies detected 13 and 16 SNPs that were significantly associated with IMF content and distribution, respectively, highlighting NR2F2, MCTP2, MTLN, ST3GAL5, NDUFAB1 and PID1 as candidate genes. Our research introduces a user-friendly digital phenotyping technology for quantifying IMF traits and suggests candidate genes and SNPs for genetic improvement of IMF traits in pigs.

Genome-wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons.

Selective breeding of meat pigeons is primarily based on growth traits, especially muscle mass (MM). Identification of functional genes and molecular markers of growth and slaughter traits through a genome-wide association study (GWAS) will help to elucidate the underlying molecular mechanisms and provide a theoretical basis for the selective breeding of meat pigeons. The phenotypic data of body weight (BW) and body size (BS) of 556 meat pigeons at 52 and 80 weeks of age were collected. In total, 160 434 high-quality single nucleotide polymorphism sites were obtained by restriction site-associated DNA sequencing. The GWAS analysis revealed that MSTN, IGF2BP3 and NCAPG/LCORL were important candidate genes affecting the growth traits of meat pigeons. IGF2BP3 and NCAPG/LCORL were highly correlated to BW and BS, which are related to overall growth and development, while MSTN was associated with pectoral thickness and BW. Phenotypic association validation with the use of two meat pigeon populations found that the MSTN mutation c.C861T determines the MM. These results provide new insights into the genetic mechanisms underlying phenotypic variations of growth traits and MM in commercial meat pigeons. The identified markers and genes provide a theoretical basis for the selective breeding of meat pigeons.