Unveiling the mix-up: investigating species and unauthorized tissues in beef-based meat products.

Customers are very concerned about high-quality products whose provenance is healthy. The identification of meat authenticity is a subject of growing concern for a variety of reasons, including religious, economic, legal, and public health. Between March and April of 2023, 150 distinct marketable beef product samples from various retailers in El-Fayoum, Egypt, were gathered. There were 30 samples of each of the following: luncheon, kofta, sausage, burger, and minced meat. Every sample underwent a histological investigation as well as subjected to a standard polymerase chain reaction (PCR) analysis to identify meat types that had not been stated by Egyptian regulations. According to the obtained data, the meat products under scrutiny contained a variety of unauthorized tissues which do not match Egyptian regulations. Furthermore, the PCR results indicated that the chicken, camels, donkeys, and pigs derivatives were detected in 60%, 30%, 16%, and 8% of examined samples, respectively. In conclusion, besides displaying a variety of illegal tissues, the majority of the meat items under examination were tainted with flesh from many species. As a result, it is crucial to regularly inspect these products before they are put on the market to ensure that they comply with the law and don't mislead customers Furthermore, it is advisable for authorities to implement rigorous oversight of food manufacturing facilities to ensure the production of safe and wholesome meat.

Effect on prime animal beef merit from breeding solely for lighter dairy cows.

As the proportion of prime carcasses originating from dairy herds increases, the focus is shifting to the beef merit of the progeny from dairy herds. Several dairy cow total merit indexes include a negative weight on measures of cow size. However, there is a lack of knowledge on the effect of genetic selection, solely for lighter or smaller-sized dairy cows, on the beef performance of their progeny. Therefore, the objective of this study was to quantify the genetic correlations among cow size traits (i.e., cow BW, cow carcass weight [CW]), cow BCS, cow carcass conformation (CC), and cow carcass fat cover (CF), as well as the correlations between these cow traits and a series of beef performance slaughter-related traits (i.e., CW, CC, CF, and age at slaughter [AS]) in their progeny. After data editing, there were 52,950 cow BW and BCS records, along with 57,509 cow carcass traits (i.e., CW, CC, and CF); carcass records from 346,350 prime animals along with AS records from 316,073 prime animals were also used. Heritability estimates ranged from moderate to high (0.18-0.62) for all cow and prime animal traits. The same carcass trait in cows and prime animals were strongly genetically correlated with each other (0.76-0.85), implying that they are influenced by very similar genomic variants. Selecting exclusively for cows with higher BCS (i.e., fatter) will, on average, produce more conformed prime animal carcasses, owing to a moderate genetic correlation (0.30) between both traits. Genetic correlations revealed that selecting exclusively for lighter BW or CW cows will, on average, result in lighter prime animal carcasses of poor CC, while also delaying slaughter age. Nonetheless, selective breeding through total merit indexes should be successful in breeding for smaller dairy cows and desirable prime animal carcass traits concurrently, because of the nonunity genetic correlations between the cow and prime animal traits; this will help to achieve a more ethical, environmentally sustainable, and economically viable dairy-beef industry.

Validation of two laboratory methods for beef intramuscular fat quantification.

Many studies on beef nutritional qualities require the quantification of intramuscular fat. To reduce the sample amount, solvent use and time of analysis, two alternative methods to the Folch et al. (1957) reference method were studied: a miniaturised Folch's method and a near-infrared spectroscopic method. Performances and acceptability limits were evaluated with accuracy profiles for each of the methods. Equations to correct bias between the alternative and reference methods were calculated. Uncertainties associated with measurements were determined, and the validity domains were defined. From a previous set of studies, the ability of each method to discriminate samples from bovines of different breeds or receiving diverse treatments was tested. The validity domain of the miniaturised Folch's method ranged from 1.9 to 13.8 g of total lipids/100 g of tissue, and that of the near-infrared spectroscopic method ranged from 4.8 to 13.8 g of total lipids/100 g of tissue, with less than 20% difference from the reference method's results. Thus, the two alternative methods could be used depending on the research objectives: the miniaturised Folch's method could be used for detailed quantification of intramuscular fat and the near-infrared spectroscopic method for a quick classification of a large number of muscles. The precise knowledge of uncertainties associated with each measurement was determined, and perfect continuity with the results obtained so far with the reference Folch's method was confirmed.

An open-access computer image analysis (CIA) method to predict meat and fat content from an android smartphone-derived picture of the bovine 5th-6th rib.

Marbling and rib composition are important attributes related to carcass yields and values, beef quality, consumer satisfaction and purchasing decisions. An open-access computer image analysis method based on a fresh beef rib image captured under nonstandardized and uncontrolled conditions was developed to determine the intramuscular, intermuscular and total fat content. For this purpose, cross-section images of the 5th-6th rib from 130 bovine carcasses were captured with a Galaxy S8 smartphone. The pictures were analyzed with a program developed using ImageJ open source software. The 17 processed image features that were obtained were mined relative to gold standard measures, namely, intermuscular fat, total fat and muscles dissected from a rib and weighed, and intramuscular fat content (IMF - marbling) determined by the Soxhlet method. The best predictions with the lowest prediction errors were obtained by the sparse partial least squares method for both IMF percent and rib composition and from a combination of animal and image analysis features captured from the caudal face of the 6th rib captured on a table. These predictions were more accurate than those based on animal and image analysis features captured from the caudal face of the 5th rib on hanging carcasses. The external-validated prediction precision was 90% for IMF and ranged from 71 to 86% for the total fat, intermuscular and muscle rib weight ratios. Therefore, an easy, low-cost, user-friendly and rapid method based on a smartphone picture from the 6th rib of bovine carcasses provides an accurate method for fat content determination.

Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle.

Copy number variation (CNV) represents a major source of genetic variation, which may have potentially large effects, including alternating gene regulation and dosage, as well as contributing to gene expression and risk for normal phenotypic variability. We carried out a comprehensive analysis of CNV based on whole genome sequencing in Chinese Simmental beef cattle. Totally, we found 9313 deletion and 234 duplication events, covering 147.5 Mb autosomal regions. Within them, 257 deletion events of high frequency overlapped with 193 known RefGenes. Among these genes, we observed several genes were related to economically important traits, like residual feed intake, immune responding, pregnancy rate and muscle differentiation. Using a locus-based analysis, we identified 11 deletions and 1 duplication, which were significantly associated with three traits including carcass weight, tenderloin and longissimus muscle area. Our sequencing-based study provided important insights into investigating the association of CNVs with important traits in beef cattle.

Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection.

BACKGROUND: While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. RESULTS: We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. CONCLUSIONS: In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

Long-range linkage disequilibrium in French beef cattle breeds.

BACKGROUND: Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d'Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. RESULTS: We computed linkage disequilibrium (r2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. CONCLUSIONS: We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

BACKGROUND: Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. RESULTS: Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. CONCLUSIONS: We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

Effects of Green Tea Powder, Pomegranate Peel Powder, Epicatechin and Punicalagin Additives on Antimicrobial, Antioxidant Potential and Quality Properties of Raw Meatballs.

Alternative technologies, which have been developed in order to meet the consumers' demand for nourishing and healthy meat and meat products, are followed by the food industry. In the present study, it was determined, using the HPLC method, that green tea contains a high level of epicatechin (EP) under optimal conditions and that pomegranate peel contains a high level of punicalagin (PN). Green tea, pomegranate peel, EP and PN were added to meatballs at different concentrations in eight groups. The antioxidant capacities of extracts were measured. The antimicrobial activity was examined for 72 h using three different food pathogens. The highest level of antimicrobial activity was achieved in the 1% punicalagin group, whereas the minimum inhibition concentration (L. monocytogenes, S. typhimurium) was found to be 1.87 mg/mL. A statistically significant decrease was found in FFA, POV and TBARS levels of meatballs on different days of storage (p < 0.05). When compared to the control group, the bioactive compounds preserved the microbiological and chemical properties of meatballs during storage at +4 °C (14 days). It was concluded that the extracts with high EP and PN concentrations can be used as bio-preservative agents for meat and meat products.

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits.

BACKGROUND: Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated. RESULTS: The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold of P-value < 10-5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3'UTR variants, 5'UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3'UTR variants, 5'UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits. CONCLUSIONS: The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.

Multiple omics analysis reveals that high fiber diets promote gluconeogenesis and inhibit glycolysis in muscle.

BACKGROUND: Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, the underlying mechanisms are still not entirely clear. RESULTS: In this study, to investigate the mechanisms that impact meat quality in twin sheep fed either with high fiber low protein (HFLP) forage (Ceratoides) or low fiber high protein (LFHP) forage (alfalfa) diets, multi omics techniques were utilized for integration analysis based on the feed nutritional value and the sheep microbiome, transcriptome, metabolome, and fatty acid profile. Results showed that the production performance and the muscle components of lambs were significantly affected by feeds. The essential fatty acid (linoleic acid and arachidonic acid) content of the muscle, based on gas chromatography-mass spectrometry analysis, was increased when lambs were fed with HFLP. The microbes in the lambs' rumen fed a HFLP diet were more diverse than those of the LFHP fed group. Besides, the ratio of Bacteroidetes and Firmicutes in the rumen of the sheep fed a LFHP diet was 2.6 times higher than that of the HFLP fed group. Transcriptome analysis of the muscle revealed that the genes related to glucose metabolic processes and fatty acid biosynthesis were significantly differentially expressed between the two groups. Potential cross talk was found between the sfour omics data layers, which helps to understand the mechanism by which feedstuffs affect meat quality of lambs. CONCLUSION: Feed systems may affect the epigenetic regulation of genes involved in the glucose metabolic pathway. HFLP feeds could induce gluconeogenesis to maintain glucose levels in blood, resulting in decreased fat content in muscle. The multiple omics analysis showed that the microbiota structure is significantly correlated with the metabolome and gene expression in muscle. This study laid a theoretical foundation for controlling the nutrient intake of sheep; it suggested that its fatty acid spectrum modifications and the removal of meat quality detrimental material could guide sheep feeding for functional mutton.

Use of gene expression profile to identify potentially relevant transcripts to myofibrillar fragmentation index trait.

The myofibrillar fragmentation index (MFI) is an indicative trait for meat tenderness. Longissimus thoracis muscle samples from the 20 most extreme bulls (out of 80 bulls set) for MFI (high (n = 10) and low (n = 10) groups) trait were used to perform transcriptomic analysis, using RNA Sequencing (RNA-Seq). An average of 24.616 genes was expressed in the Nellore muscle transcriptome analysis. A total of 96 genes were differentially expressed (p value ≤ 0.001) between the two groups of divergent bulls for MFI. The HEBP2 and BDH1 genes were overexpressed in animals with high MFI. The MYBPH and MYL6, myosin encoders, were identified. The differentially expressed genes were related to increase mitochondria efficiency, especially in cells under oxidative stress conditions, and these also were related to zinc and calcium binding, membrane transport, and muscle constituent proteins, such as actin and myosin. Most of those genes were involved in metabolic pathways of oxidation-reduction, transport of lactate in the plasma membrane, and muscle contraction. This is the first study applying MFI phenotypes in transcriptomic studies to identify and understand differentially expressed genes for beef tenderness. These results suggest that differences detected in gene expression between high and low MFI animals are related to reactive mechanisms and structural components of oxidative fibers under the condition of cellular stress. Some genes may be selected as positional candidate genes to beef tenderness, MYL6, MYBPH, TRIM63, TRIM55, TRIOBP, and CHRNG genes. The use of MFI phenotypes could enhance results of meat tenderness studies.

Meat color is determined not only by chromatic heme pigments but also by the physical structure and achromatic light scattering properties of the muscle.

Meat color is important for consumer acceptability, with excessively dark meat often associated with consumer rejection. It is determined chromatically by pigment content (measured by hue and chroma) and achromatically by scattering of light by the microstructure (measured by lightness), the latter of which has received minimal research focus. This review discusses the individual components of the meat microstructure that cause differences in achromatic contributions to color. Differences in achromatic light scattering between light and dark extremes of meat color are most likely explained by structural attributes within the muscle cell. These differences are proposed to arise from variations in (a) transverse shrinkage of the structural lattice of the myofilaments, myofibrils, and muscles fibers, (b) longitudinal shrinkage of the sarcomere, and (c) different protein composition of the surrounding medium (sarcoplasm and extracellular space). These are discussed at a mechanistic level, in relation to six parameters of the muscle cell: (a) protein surface charge altering the myofilament spacing, (b) protein solubility, (c) sarcoplasmic protein binding to myofilaments and myofibrils, (d) integrity of the cytoskeleton and cell adhesion proteins, (e) sarcomere integrity and myofibrillar proteins, and (f) myosin denaturation and rigor bond modification. New data are presented to support the proposed role of structural elements in muscle causing achromatic light scattering and their contribution to the surface color of meat. In addition, the relationships between lightness and water holding capacity and pH are explored and the economic impact of dark meat for the meat industry is discussed.

Effects of rumen-protected oil supplementation on finishing grazing beef cattle.

The objective of this study was to evaluate the effects of rumen-protected oil (soybean and palm oil) in supplements for beef cattle during the fattening phase in pastures on the intake and digestibility of nutrients, animal performance, and carcass characteristics. Forty-eight noncastrated male Nellore cattle (15 ± 2 months and 389.5 ± 20 kg of body weight) were used in a completely randomized design to evaluate the following treatments: protein-energy supplement (PES) without rumen-protected oil (control: CO), PES containing palm rumen-protected oil (PRPO), PES containing soybean rumen-protected oil (SRPO), and PES containing a mixture of soybean and palm rumen-protected oil (SPRPO). The study lasted 112 days, and there was a decrease in crude protein intake (P < 0.05) and an increase in ether extract intake (P < 0.05) when rumen-protected oil was included in the supplements. In comparison to the palm rumen-protected oil supplement, the soybean rumen-protected oil supplement promoted a lower average daily gain (ADG) (P < 0.05); however, regardless of the rumen-protected oil source, an increase in the fat thickness of the subcutaneous tissue was observed. In addition, there was no difference in carcass gain (P > 0.05) regardless of oil source. Rumen-protected oil is a tool to increase the finishing of pasture-finished young beef cattle in the dry season.

miRNA transcriptome comparison between muscle and adipose tissues indicates potential miRNAs associated with intramuscular fat in Chinese swamp buffalo.

The amount of intramuscular fat (IMF) affects the tenderness and juiciness of beef and is an important indicator of beef quality. A few miRNAs involved in IMF deposition have been identified in other livestock. However, in the buffalo, the association between miRNA and IMF has not been reported and the miRNA expression profile remains poorly understood. In this study, small RNA sequencing was performed to characterize the miRNA expression pattern in muscle and adipose tissues using the Illumina platform. A total of 108 differentially expressed (DE) miRNAs were identified, including 98 known miRNAs and 10 novel miRNAs. A qRT-PCR experiment confirmed the quality of the DE analysis. Eight DE miRNAs showed high expression in adipose tissue and a considerable expression level in muscle tissue. Functional enrichment indicated that bta-miR-148a, bta-miR-143, bta-miR-10b, bta-let-7i, bta-let-7f, bta-let-7b, bta-miR-30a-5p, and bta-miR-100 were significantly associated with adipogenesis, suggesting these as candidate regulators for IMF deposition in buffalo. However, further functional validation is required. This is the first characterization of the miRNA expression profile in the muscle and adipose tissues of buffalo. These results provide information for the identification of miRNAs with potential effects on IMF deposition in buffalo.

Analysis of a large dataset reveals haplotypes carrying putatively recessive lethal and semi-lethal alleles with pleiotropic effects on economically important traits in beef cattle.

BACKGROUND: In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals. METHODS: In this paper, we searched for haplotypes that carry putatively recessive lethal or semi-lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production. RESULTS: We found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, - €3.11, and - €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype. CONCLUSIONS: We analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.

More animals than markers: a study into the application of the single step T-BLUP model in large-scale multi-trait Australian Angus beef cattle genetic evaluation.

Multi-trait single step genetic evaluation is increasingly facing the situation of having more individuals with genotypes than markers within each genotype. This creates a situation where the genomic relationship matrix ([Formula: see text]) is not of full rank and its inversion is algebraically impossible. Recently, the SS-T-BLUP method was proposed as a modified version of the single step equations, providing an elegant way to circumvent the inversion of the [Formula: see text] and therefore accommodate the situation described. SS-T-BLUP uses the Woodbury matrix identity, thus it requires an add-on matrix, which is usually the covariance matrix of the residual polygenic effet. In this paper, we examine the application of SS-T-BLUP to a large-scale multi-trait Australian Angus beef cattle dataset using the full BREEDPLAN single step genetic evaluation model and compare the results to the application of two different methods of using [Formula: see text] in a single step model. Results clearly show that SS-T-BLUP outperforms other single step formulations in terms of computational speed and avoids approximation of the inverse of [Formula: see text].

Differential Transcriptome Analysis of Early Postnatal Developing Longissimus Dorsi Muscle from Two Pig Breeds Characterized in Divergent Myofiber Traits and Fatness.

Meat quality traits (MQTs) are very important in the porcine industry, which are mainly determined by skeletal muscle fiber composition, extra-muscular and/or intramuscular fat content. To identify the differentially expressed candidate genes affecting the meat quality traits, first we compared the MQTs and skeletal muscle fiber characteristics in the longissimus dorsi muscle (LDM) of the Northeast Min pig (NM) and the Changbaishan wild boar (CW) with their body weight approaching 90 kg. The significant divergences in the skeletal muscle fiber phenotypes and fatness traits between the two porcine breeds established an ideal model system for further identifying potential key functional genes that dominated MQTs. Further, a transcriptome profile analysis was performed using the Illumina sequencing method in early postnatal developing LDM from the two breeds at the ages of 42 days. Comparative analysis between these two cDNA libraries showed that there were 17,653 and 22,049 unambiguous tag-mapped sense transcripts detected from NM and CW, respectively. 4522 differentially expressed genes (DEGs) were revealed between the two tissue samples, of them, 4176 genes were found as having been upregulated and 346 genes were identified as having been downregulated in the NM library. By pathway enrichment analysis, a set of significantly enriched pathways were identified for the DEGs, which are potentially involved in myofiber development, differentiation and growth, lipogenesis and lipolysis in porcine skeletal muscle. The expression levels of 30 out of the DEGs were validated by real-time quantitative reverse transcriptase PCR (qRT-PCR) and the observed result was consistent noticeably with the Illumina transcriptome profiles. The findings from this study can contribute to future investigations of skeletal muscle growth and development mechanism and to establishing molecular approaches to improve meat quality traits in pig breeding.

Effects of active immunization against porcine Sox6 on meat quality and myosin heavy chain isoform expression in growing-finishing pigs.

A feeding trial for 91 days was conducted to investigate effects of active immunization against porcine Sox6 (pSox6) on meat quality and myosin heavy chain (MyHC) isoform expression in growing-finishing pigs. Twenty-four castrated Duroc × Landrace × Yarkshire pigs were randomly divided into three groups: (1) Control group; (2) 1 mg/head pSox6 active immunity group; (3) 4 mg/head pSox6 active immunity group (4 mg/head group). The results showed that pigs in 4 mg/head group had a greater a* (Redness) and a higher marbling score, while no significant effect was observed in L* (Lightness), b* (Yellowness), intramuscular fat and cooking loss. Muscle succinic dehydrogenase activity in pSox6 active immunization groups was significantly increased, and muscle lactate dehydrogenase activity was significantly reduced. Meanwhile, active immunization against pSox6 upregulated the mRNA expression of MyHC I, while no effect was observed on the mRNA expressions of MyHC IIa, MyHC IIx, MyHC IIb. In addition, pigs in the 4 mg/head group exhibited lower Sox6 mRNA level and higher MyHC I protein level, while no significant influence was observed on MyHC IIb protein level. Together, our data imply that active immunization against pSox6 could improve the pork quality and promote the MyHC I expression in growing-finishing pigs.

Effects of long-term microalgae supplementation on muscle microstructure, meat quality and fatty acid composition in growing pigs.

We investigated the effects of long-term microalgae supplementation (7% in a piglet diet and 5% in a fattening diet) on muscle microstructure and meat quality, including fatty acid composition in female Landrace pigs (n = 31). The major effects were muscle-specific increases in n-3 and n-6 polyunsaturated fatty acids (PUFA) concentrations, resulting in increased accumulation of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Carcass traits and meat quality of longissimus thoracis muscle were not affected by the microalgae diet with the exception of reduced drip loss (p = 0.01) and increased protein proportion (p = 0.04). In addition, the microalgae diet resulted in a shift to a more oxidative myofibre type composition in semitendinosus but not longissimus thoracis muscle. In conclusion, microalgae supplementation offers a unique opportunity to enhance essential n-3 PUFA contents in pig meat. The results support small but coordinated changes in skeletal muscle phenotypic appearance and functionality.