Transcriptomic and metabolomic profiling of the Longissimus thoracis muscle insights into variations in meat quality between Hainan Black and Nubian Black goats

It is deemed that meat quality of kids' is better than that of adults' for Hainan black goat. Generally, meat quality is affected by many indicators, such as intramuscular fat (IMF) content, muscle fiber diameter and shear force. It is indicated that long non-coding RNAs (lncRNAs) play essential roles in meat quality of goats. However, it is unclear whether and how lncRNAs and genes play their roles in meat quality of Hainan Black goats. Here, we firstly compared the meat quality between two-month-old kids (kids) and adult goats (adults). Then, the lncRNA-seq and RNA-seq data were integrated and analyzed to explore the potential functions of lncRNAs and genes. The results showed that adults' IMF content and muscle fiber diameter were extremely significantly higher than that of kids (P<0.01). For the sequenced data, average 84,970,398, and 83,691,250 clean reads were obtained respectively for Kids and adults, among which ~96% were mapped to the reference genome of goats. Through analyzing, 18,242 goat annotated genes, 1,429 goat annotated lncRNAs and 2,967 novel lncRNAs were obtained. Analysis of differential expression genes (DEGs) and lncRNAs (DELs) showed that 328 DEGs and 98 DELs existed between kids and adults. Furthermore, functional enrichment analysis revealed that a number of DEGs and DELs were mainly associated with IMF. Primarily, DGAT2 expressed higher in adults than that in kids and CPT1A expressed higher in kids than that in adults. Both of them were overlapped by DEGs and targets of DELs, suggesting the two DEGs and the DELs targeted by the two DEGs might be the potential regulators of goat IMF deposition. Taken together, our results provide basic support for further understanding the function and mechanism of lncRNAs and genes in meat quality of Hainan black goats.

Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.

Effect of feeding regime during finishing on lamb welfare, production performance and meat quality

Heritability and genetic correlation estimates for performance, meat quality and quantitative skeletal muscle fiber traits in broiler

This study comprehensively explored muscle fibre characteristics and expression patterns of myosin heavy chain (MyHC) family in skeletal muscles of Large White and Mashen pigs exhibiting differences in muscle fibre development in postnatal muscle growth. Muscle fibre density and diameter were analysed using haematoxylin and eosin staining. The expression patterns of MyHCI, MyHCIIa, MyHCIIx and MyHCIIb were detected by quantitative real-time polymerase chain reaction. The muscle fibre diameter increased and density decreased gradually with aging. In individuals of the same age, the muscle fibre diameter was significantly lower and density was significantly higher in Mashen than in Large White pigs. The MyHCI expression increased, whereas that of MyHCIIa first increased and then decreased. The expression of MyHCI and MyHCIIa was significantly higher in Mashen. The expression of MyHCIIx and MyHCIIb decreased with increasing age; their expression was significantly lower in Mashen pigs. Muscle fibre diameter was negatively correlated with MyHCI expression and positively correlated with MyHCIIx and MyHCIIb expression (except the expression of MyHCI in psoas major). Muscle fibre diameter, muscle fibre density, and MyHCs expression follow certain patterns in skeletal muscles. These results provide valuable information for understanding the molecular mechanism responsible for pig growth performance and meat quality.

Development of myofibers and muscle transcriptomic analysis in growing Yili geese

Studies exploring the transcriptome of stress and its effects on meat quality are very limited, particularly in goats. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats/treatment): (1) transported for 180 min, (2) transported for 30 min, or (3) held in pens (control) to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Blood samples were collected before and after treatment, and meat samples were collected after humane slaughter for stress hormone, meat quality (Longissimus dorsi), and transcriptomic analysis. Plasma epinephrine concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group; however, norepinephrine concentrations were not affected by the treatment. Muscle glycogen concentrations (15 min postmortem) were lower (P < 0.01) in both 30 min and 180 min groups compared to the control group. Calpastatin levels were higher (P < 0.01) in 180 min and 30 min groups than the control group. Warner–Bratzler shear force values of loin chops were the highest in the 180 min group (4 ± 0.15, kg), lowest in the control group (3.51 ± 0.10, kg), and intermediate in the 30 min group (3.78 ± 0.09, kg; P < 0.01) both at day 1 and day 6 aging time. Additionally, desmin levels of day 6 samples were lowest in the control group, highest in 180 min group, and intermediate in 30 min group (P < 0.05). RNA-seq results showed that a total of 10,633 genes were differentially expressed (5194 up regulated; 5439 down regulated) among all comparisons (blood and day 1 and day 6 muscle samples). Among these differentially expressed genes (DEGs), KLF9, AMPK, FOXO3, PTX3, GADD45, PTPN1, CASP7, MAPK4, HSPA12A, and JAK-STAT were probably associated with the effects of stress on skeletal muscle proteins and involved in biological process such as cellular response to corticosteroid stimulus, endoplasmic reticulum stress, insulin resistance, DNA repair, apoptosis, MAPK cascade and regulation of proteolysis. The KEGG analysis revealed that AMPK and JAK-SAT signaling pathways and autophagy were among the top 20 enriched pathways in our treatment comparisons. The results provide an understanding of the genes and pathways involved in stress responses and related changes in postmortem muscle metabolism and meat quality characteristics in goats.

The magnitude of physiological responses to a stressor can vary among individual goats within a herd; however, whether these differences can differentially affect meat quality is not known. This study was conducted to determine the influence of the magnitude of epinephrine response (ER) to acute stress on muscle metabolome and meat quality in goats. Male Spanish goats (6 mo old) were transported for 180min. (N = 75 goats; 25 goats/d) to impose stress. Blood samples were obtained after transport for analysis of physiological responses. Goats were slaughtered using humane procedures and samples were collected for muscle metabolomics and meat quality analyses. The data obtained from blood and muscle/meat analysis were then categorized based on epinephrine concentrations into low (LE), medium (ME), and high (HE) ER groups (n = 12/ER group). The physiological and meat quality variables were analyzed as a Completely Randomized Design in SAS, and metabolomics data were analyzed using R software. Plasma glucose concentrations were significantly high in the HE group, low in the LE group, and intermediate in the ME group (P < 0.05). However, leukocyte counts and cortisol, norepinephrine, blood urea nitrogen, and creatine concentrations were not different among the ER groups. Muscle (Longissimus dorsi) glycogen concentrations (15min postmortem) were significantly higher (P < 0.05) in the ME and LE groups than in the HE group. However, postmortem Longissimus muscle pH and temperature (15min and 24h), 24h calpastatin and desmin levels, and rib chop color (L*, a*, and b*), cooking loss, and Warner-Bratzler shear force values were unaffected by ER. Targeted metabolomics analysis of Longissimus muscle (15min) revealed that diacyl phosphatidylcholines (C38:0; 40:6) and sphingomyelin (C20:2) were significantly different (P < 0.05) among the ER groups, with the concentrations of these metabolites being consistently high in the LE group. These differential muscle metabolite concentrations suggest that ER can influence biochemical pathways associated with cell membrane integrity and signaling. ER had a significant effect on dopamine concentrations, with the levels increasing with increasing levels of ER. The results indicate that differences in epinephrine reactivity can influence selected physiological responses and muscle metabolites; however, it does not significantly influence meat quality attributes.

Differential expression of lipid metabolism-related genes and myosin heavy chain isoform genes in pig muscle tissue leading to different meat quality

Simple SummarySkeletal muscle development and meat quality are key traits of considerable importance to consumers and farmers. In the past, second-generation sequencing technology has been used to study genes regulating muscle development and meat quality. However, with the limitation of read length, goat transcriptome was constructed mainly on the basis of the merging of short reads, resulting in an insufficient understanding of goat transcriptome structures. Identification of full-length transcript structure was still a challenge. Therefore, in this study, a hybrid sequencing was conducted that combined the long-reading character of third-generation sequencing with the quantification ability of second-generation sequencing. By comparing the longissimus dorsi and biceps femoris muscles, genes and transcript isoforms regulating meat quality and muscle development of goat were identified. A large number of novel loci and isoforms were identified in the goats. Functional annotation of these genes showed that they were associated with skeletal muscle development and lipid metabolism.Domestic goats are commonly reared for meat and milk production in several regions of the world. However, the genetic mechanism underlying muscle development and meat quality of goats is limited. Therefore, the aim of this study was to identify known and novel genes regulating muscle development and meat quality of goats using second- and third-generation sequencing technologies. To achieve this, the meat quality and transcriptomes of longissimus dorsi (LD) and biceps femoris (BF) muscle tissues of Lingqiu Greyback goats were examined and compared. Differentially expressed genes (DEGs) and isoforms (DEIs) were functionally annotated. Results showed that 45,574 full-length transcripts covering 18,491 loci were characterized, and 12,566 genes were co-expressed in all samples. Differential expression analysis identified 231 DEGs, including 45 novel genes in the LD and BF muscles of the goats. Additionally, 1173 DEIs were found, in which 642 novel isoforms were identified in this study. Functional annotation and pathway analysis of the DEGs and DEIs revealed that some of them were associated with muscle growth and lipid metabolism. Overall, the findings of this study contribute to the understanding of the transcriptomic diversity underlying meat quality and muscle development of goat.

In order to understand the histological differences between different beef types and their correlation with meat quality traits, six cattle (Holstein cattle and Xilin buffalo) were selected for meat quality traits and histological morphological determination. The results showed that: in terms of muscle fiber diameter, Xilin buffalo >Longlin scalper >Holstein cattle, the density of muscle fibers is the opposite; TypeImuscle fiber proportion ,Xilin buffalo >Holstein cattle >Longlin scalpers showed significant differences among each other (P<0.05); II type A muscle fiber proportion Westwood Xilin buffalo >Longlin scalpers , no significant difference, but ii type A and B ii muscle fiber proportion is put in bigger difference, the alkaline type A muscle fiber ratio is relatively high acid dyeing, ii type B muscle fiber ratio was lower than those of acid dyeing. The diameter of muscle fiber was significantly correlated with marbling, tenderness, pH and intramuscular fat. Type i muscle fiber proportion and marble, intramuscular fat and tender degree of positive correlation, while ii B in proportion to the muscle fibers and pH2 has significant negative correlation.

This study was conducted to unravel the variation in meat quality between tender (psoas major, PM) and less tender (longissimus lumborum, LL) muscles of Indian water buffaloes (Bubalus bubalis). PM and LL were subjected to physicochemical analysis, ultrastructural study and proteome characterization using two‐dimensional gel electrophoresis (2‐DE) and mass spectrometry. Higher (P &lt; 0.05) muscle fiber diameter and Warner–Bratzler shear force was observed in LL, whereas higher (P &lt; 0.05) water‐holding capacity and myofibrillar protein extractability was observed in PM. Transmission electron microscopy revealed higher (P &lt; 0.05) sarcomere length in PM compared with LL. Proteome analysis using 2‐DE revealed 123 differentially abundant proteins in PM and LL. The MALDI‐TOF‐TOF MS analysis of selected protein spots from LL and PM with significant (P &lt; 0.05) differences identified the proteins mainly consisting of calcium‐transporting ATPase.Practical ApplicationsOwing to its low fat, low cholesterol and other healthier attributes, meat produced from water buffaloes has gained increased popularity in several Asian and African countries. Tenderness, which is considered to be the most important attribute of meat quality and a trait highly valued by consumers, varies substantially between muscles. In spite of advancements in optimizing tenderness, an unacceptable level of variation does exist. Findings from the present study illustrate the basis of tenderness variability in psoas major and longissimus lumborum muscles of Indian water buffaloes. Our results indicated complex nature of tenderness development and demonstrated a significant variation in biochemical parameters, ultrastructure and proteome expression. Understanding the variation in texture between muscles is a logical first step to develop strategies for better utilization and for delivering highly palatable product to consumers. This study suggests the necessity to develop muscle‐specific tenderization strategies to minimize the variation between tender and less tender muscles.

The aim of this study was to evaluate the relationship between temperament in Nellore bulls with carcass and meat quality traits. In total, 1,400 bulls were studied, and temperament was assessed using two measurements: movement score (MOV) and flight speed test (FS). Both MOV and FS were measured at two time points, with background (MOVb and FSb) temperament measured at yearling age, ~550 d after birth, and the preslaughter (MOVps and FSps) temperament measured at the end of the feedlot period. The change of temperament resulting in an increase or decrease in reactivity was also used to measure meat quality. The traits used to define carcass and meat quality included carcass bruises (BRU), hot carcass weight (HCW, kg), ribeye area (REA, cm2), backfat thickness (BFT, cm), marbling score (MS), meat pH after thawing (pH), presence or absence of dark cutters, color parameters of luminosity (L*), redness (a*) and yellowness (b*), cooking loss (CL, %), and Warner-Bratzler shear force (WBSF, kg). A principal component (PC) analysis was initially applied to the carcass and meat quality traits, followed by logistic regression models and linear mixed models to evaluate the effects of temperament on carcass and meat quality. The risks of carcass bruises and dark cutters did not differ as a function of any temperament trait (P > 0.05). In turn, animals classified as high MOVb (reactive) had lower PC3 values (P = 0.05), CL (P = 0.02), and tended to have lower MS (P = 0.08). In addition, animals classified as high FSb (faster and reactive cattle) produced carcasses with smaller REA (P < 0.01), higher meat pH (P < 0.01), lower color gradients (L*, P = 0.04; b*, P < 0.01), and lower PC1 and PC4 scores (P < 0.01) when compared with the low FSb class. For preslaughter temperament, high MOVps was related to lower color a* (P = 0.04), whereas high FSps was related to lower HCW, MS, and PC2 (P < 0.01) than the calmer ones (low FSps). The reduction in MOV was related to more tender meat, and the reduction in FS to heavier carcass and brighter meat. We conclude that excitable temperament in Nellore cattle may have negative effects in some of the carcass and meat quality attributes assessed, mainly those related to muscle deposition on carcass and color gradients. Measurement of temperament before the cattle entered the feedlot was a better predictor of carcass and meat quality traits, compared with temperament assessment at the end of the feeding period.

Amylose plays important role in body health. It is controversial whether changing dietary amylose/amylopectin ratio (DAR) will improve meat quality in growing-finishing pigs. A total of 48 Duroc×Landrace×Large White castrated male pigs (initial body weight 49.8±2.8kg) were randomly allotted to two treatments, and fed ad libitum either with a low DAR diet (LR, amylose/amylopectin: 12/88) or a high DAR diet (HR, amylose/amylopectin: 30/70) for 68days. Feed intake was recorded every day, body weight was weighed at 46th and 68th day to calculate average daily gain (ADG), average daily feed intake (ADFI) and Feed:gain ratio. Blood was collected at -30min (fasting 12hr), 60, 90, 120, 180min postprandial at 64th day and then serum was obtained by centrifugation of blood at 1,500×g at 4°C. After pigs were slaughtered, samples such as longissimus dorsi, iliopsoas and semitendinosus were collected. Density, diameter and types of muscle fibres were analysed. Results showed that ADG, ADFI, Feed:Gain ratio, cross-sectional area of longissimus dorsi muscle, backfat thickness, colour scores were not affected by DAR. Ingestion of LR diet increased the fasting glucose (p<0.05) and insulin (p<0.05) concentrations in serum. The drip loss and firmness were decreased significantly in LR vs. HR animals (p<0.05). Densities of muscle fibre in longissimus dorsi, iliopsoas and semitendinosus were greater in LR pigs (p<0.05). Moreover, ingestion of LR diet significantly increased myosin heavy chain (MyHC) IIa mRNA level and decreased MyHC IIb gene expression in longissimus dorsi muscle (LM) (p<0.05). Therefore, intake of diet low in amylose/amylopectin ratio induces a better meat quality (lower drip loss and lower firmness), which could attribute to smaller myofibres, a shift to slower and/or more oxidative fibres.

Meat quality is influenced by factors such as age, breed, slaughter weight, and nutrition. This study investigated the growth performance, slaughter performance, and meat quality of ducks across different breeds and ages. Results indicated that at the same age, significant differences in body weight were observed among breeds (p < 0.05), with the weight ranking in descending order as follows: Cherry Valley ducks (C) > Wuqin 10 meat ducks (W) > Mianyang Partridge ducks (M) > Liancheng White ducks (L). A comparison of the same breed across different ages revealed that the pectoral muscle ratio tended to increase with age, whereas the leg muscle ratio showed the opposite trend; however, total meat production gradually rose. At all three growth stages, C ducks exhibited higher body weight and meat yield than the other breeds. W ducks demonstrated excellent meat quality traits and appropriate meat production, with indices such as shear force, water-holding capacity, and fat content all higher than those of the other breeds. L ducks and M ducks had relatively lower body weight and meat production compared to the other breeds, yet their shear force and water-holding capacity were superior to those of C ducks. The analysis of meat quality at different times showed that across all breeds, shear force, meat color, muscle fiber diameter, crude protein content, and fat content increased with age, while drip loss rate and muscle fiber density decreased. A comprehensive multi-index evaluation model for duck meat quality under different breeds was established, along with a four-factor principal component model (Z1, Z2, Z3, Z4). Using the comprehensive ranking equation K, the meat quality performance of different breeds at various ages, in descending order, was as follows: 63-day-old W > 90-day-old M > 63-day-old C > 90-day-old L > 63-day-old M > 90-day-old C > 63-day-old L > 90-day-old W > 42-day-old C > 42-day-old W. This study not only provides a theoretical basis for evaluating meat quality traits in different duck breeds but also offers insights for breed selection and age-related quality optimization.