Insights into the influence of diet and genetics on feed efficiency and meat production in sheep

Feed costs and carcass yields affect the profitability and sustainability of sheep production. Therefore, it is crucial to select animals with a higher feed efficiency and high-quality meat production. This study focuses on the impact of dietary and genetic factors on production traits such as feed efficiency, carcass quality, and meat quality. Diets promote optimal sheep growth and development and provide sufficient protein can lead to higher-quality meat. However, establishing an optimized production system requires careful consideration and balance of dietary parameters. This includes ensuring adequate protein intake and feeding diets with higher intestinal absorption rates to enhance nutrient absorption in the gut. The study identifies specific genes, such as Callipyge, Calpastatin, and Myostatin, and the presence of causal mutations in these genes, as factors influencing animal growth rates, feed efficiency, and meat fatty acid profiles. Additionally, variants of other reported genes, including PIGY, UCP1, MEF2B, TNNC2, FABP4, SCD, FASN, ADCY8, ME1, CA1, GLIS1, IL1RAPL1, SOX5, SOX6, and IGF1, show potential as markers for sheep selection. A meta-analysis of reported heritability estimates reveals that residual feed intake (0.27 ± 0.07), hot carcass weight (0.26 ± 0.05), dressing percentage (0.23 ± 0.05), and intramuscular fat content (0.45 ± 0.04) are moderately to highly heritable traits. This suggests that these traits are less influenced by environmental factors and could be improved through genetic selection. Additionally, positive genetic correlations exist between body weight and hot carcass weight (0.91 ± 0.06), dressing percentage (0.35 ± 0.15), and shear force (0.27 ± 0.24), indicating that selecting for higher body weight could lead to favorable changes in carcass quality, and meat quality.

Genome-Wide Search for Associations with Meat Production Parameters in Karachaevsky Sheep Breed Using the Illumina BeadChip 600 K

In a group of Karachaevsky rams, a genome-wide associations analysis of single nucleotide polymorphisms (SNPs) with live parameters of meat production was performed. We used for genotyping the Ovine Infinium HD BeadChip 600 K, which consists of points to detection of 606,000 polymorphisms. A total of 12 SNPs was found to be significantly associated with live meat quality parameters of the corpus and legs and ultrasonic traits. In this case, 11 candidate genes were described, the polymorphic variants of which can change in sheep body parameters. We found SNPs in the exons, introns, and other regions of some genes and transcripts: CLVS1, EVC2, KIF13B, ENSOART00000000511.1, KCNH5, NEDD4, LUZP2, MREG, KRT20, KRT23 and FZD6. The described genes involved in the metabolic pathways of cell differentiation, proliferation and apoptosis are connected with the regulation of the gastrointestinal, immune and nervous systems. In known productivity genes (MSTN, MEF2B, FABP4, etc.), loci were not found to be a significant presence of influence on the meat productivity of the Karachaevsky sheep phenotypes. Our study confirms the possible involvement of the identified candidate genes in the formation of the phenotypes of productivity traits in sheep and indicates the need for new research into candidate genes structure in point to detect their polymorphisms.

Genetic variation of CAST gene in Local Karnobat and Karnobat merino sheep breeds

Karnobat sheep plays an important role in the development of sheep breeding in Southeastern region of Bulgaria. They are valuable source of genetic material. The aim of present experiment was to determine the allele variation of CAST gene in Local Karnobat and Karnobat Merino sheep breeds. A total of 60 blood samples were collected – 30 per breed. DNA was extracted and genotypes of all animals were identified by means of PCR-RFLP technique. The restriction reactions were accomplished by specific enzyme MspI. As expected both breeds were characterized with low level of genetic diversity due to the fact that mostly maintaining selection has been implemented. In Local Karnobat sheep breed was identified only one heterozygous individual from all 30. In Karnobat merino were identified allele M with frequency 0,97 and allele N with frequency 0,03. Genotypes MM and MN were revealed with frequencies 0,93 and 0,07, respectively. According to the statistical analysis both breeds were in HWE equilibrium.

Identification of polymorphisms in the MSTN and ADRB3 genes associated with growth and ultrasound carcass traits in Kajli sheep

The aim of this investigation was to find single nucleotide polymorphisms (SNPs) in the myostatin (MSTN) and the beta-3 adrenergic receptor (ADRB3) genes associated with growth and ultrasound carcass traits in Kajli sheep. The five growth traits were birth weight (BWT-EBV), 120-day weight (120DWT-EBV), 180-day weight (180DWT-EBV), 270-day weight (270DWT-EBV), and 365-day weight (365DWT-EBV). The three ultrasound carcass traits were width (WLD) and depth of longissimus dorsi (DLD) and back fat thickness (BFT). The analysis of the MSTN sequence revealed one non-synonymous substitution (c.197T > A) in exon 1, one single nucleotide substitution (c.373 + 18G > T) in intron 1, and one synonymous substitution (c.861T > A) in exon 3. However, there were four single nucleotide synonymous substitutions (c.130C > T, c.294C > G, c.579G > T, and c.654C > G) in exon 1 of the ADRB3 gene. All the SNPs in the MSTN gene, except for c.373 + 18G > T, were in Hardy-Weinberg Equilibrium (HWE). Conversely, none of the SNPs found in ADRB3 were in HWE. Two of the MSTN SNPs (c.197T > A and c.373 + 18G > T) had significant associations with all evaluated growth and ultrasound carcass traits. The SNPs c.130C > T and c.294C > G in ADRB3 were significantly associated with 180DWT-EBV. Collectively, these findings indicate that several SNPs in the studied genes were significantly related to growth and carcass traits in Kajli sheep.

Changes of Metabolites and Gene Expression under Different Feeding Systems Associated with Lipid Metabolism in Lamb Meat

The effects of the different feeding systems, graze feeding (GSF), time-limited graze feeding (GF), and stall-feeding (SF)) on the fatty acid content, metabolites, and genes expression of the longissimus dorsi (LD) in Tan lambs were investigated in the present study. Thirty-nine 4-month-old male Tan lambs with similar body weight (24.91 ± 1.74 kg) were selected and divided into the three feeding systems (n = 13) randomly. Lambs were slaughtered after 83 days of the feeding trails, and LD muscle samples were collected for further analysis. The results indicated that different feeding systems have no significant effect on short-chain fatty acids in Tan lambs (p > 0.05). However, the total saturated fatty acids (∑SFA) and monounsaturated fatty acids (∑MUFA) in the GSF and GF groups were lower than those in the SF group (p < 0.001). The total polyunsaturated fatty acids (∑PUFA) in the GSF group were higher than those in the GF and SF groups (p < 0.001). Moreover, in the comparison of both GF vs GSF groups and SF vs GSF groups, metabolomic analysis showed that metabolites such as cis-(6,9,12)-linolenic acid, arachidic acid, acetylcarnitine, and L-carnitine with lower concentration were significantly enriched in the biosynthesis of unsaturated fatty acid pathway (p < 0.05), but metabolites such as phosphorylcholine, glycerophosphocholine, cytidine 5'-diphosphocholine, and glycerol-3-phosphate with higher concentrations were enriched in the glycerophospholipid metabolism pathway. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of the results indicated that in the comparison of the GSF group with the SF group, differentially expressed genes (DEGs) such as LIPC, ERFE, FABP3, PLA2R1, LDLR, and SLC10A6, were enriched in the steroid biosynthesis and cholesterol metabolism pathways. In addition, differential metabolites and genes showed a significant correlation with the content of ∑SFA, ∑MUFA, and ∑PUFA in lamb meat (p < 0.05). These findings demonstrated that the feeding system was an important factor in regulating fatty acid content by affecting lipid-metabolism-related metabolites and gene expression in muscle, and graze-feeding system provided lamb meat with higher ∑PUFA content than time-limited-grazing and stall-feeding systems.

Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

Simple Summary

Skeletal muscle mass is an important economic trait, and muscle development and growth is a crucial factor to supply enough meat for human consumption. Thus, understanding (candidate) genes regulating skeletal muscle development is crucial for understanding molecular genetic regulation of muscle growth and can be benefit the meat industry toward the goal of increasing meat yields. During the past years, significant progress has been made for understanding these mechanisms, and thus, we decided to write a comprehensive review covering regulators and (candidate) genes crucial for muscle development and growth in farm animals. Detection of these genes and factors increases our understanding of muscle growth and development and is a great help for breeders to satisfy demands for meat production on a global scale.

Abstract

Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.

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.

Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus

Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes such as growth, development, and reproduction of animals. Here, we used RNA-seq technology to study the expression profile of lncRNAs in the anterior pituitary of sheep during estrus and anestrus. In this study, we identified a total of 995 lncRNAs, of which 335 lncRNAs were differentially expressed in two states (including 38 up-regulated and 297 down-regulated lncRNAs). RT-qPCR verified the expression levels of several lncRNAs. Target predictive analysis revealed that these lncRNAs can act in cis or trans and regulate the expression of genes involved in the regulation of sheep estrus. Target gene enrichment analysis of differentially expressed lncRNAs indicates that these lncRNAs can regulate sheep estrus by regulating hormone metabolism and energy metabolism. Through our research, we provide the expression profile of lncRNAs in the pituitary of sheep, which provides a valuable resource for further understanding of the genetic regulation of seasonal estrus in sheep from the perspective of lncRNAs.

Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep

Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep (MG)) breed and the STH breed were selected to measure production performance and meat quality. We used 14 indexes of production performance and meat quality, which in the MG × STH population showed significant differences compared to the STH breed. Subsequently, the longissimusdorsi from the two sheep were subjected to comparative transcriptomic analyses to identify differentially expressed genes (DEGs) related to production performance and meat quality. A total of 874 DEGs were identified between the two sheep groups. A total of 110 unique DEGs related to sheep production performance and meat quality were selected as the candidate DEGs. We found 6 production-performance-related and 30 meat-quality-related DEGs through a correlation analysis, including SPARC, ACVRL1, FNDC5 and FREM1. The expression levels of 11 DEGs were validated by real-time PCR, and the results were in accordance with the results of the comparative transcriptomic and correlation analyses. These results will assist in understanding sheep heterosis and molecular marker-assisted selection.

Dietary supplementation with Essential-oils-cobalt for improving growth performance, meat quality and skin cell capacity of goats

Essential oils (EO) are secondary metabolites usually made up of terpenoids and phenylpropanoids and have antimicrobial properties. However, the feeding effects of EO-Cobalt (EOC) on the performance of goats are largely unknown. Herein we investigated and reported the effects of dietary EOC (0, 52, and 91 mg daily) on fiber producing cashmere goats. We determined the resulting phenotypes including live growth, carcass weight, meat quality, and cashmere fiber traits. We show that dietary supplement of EOC significantly promoted average daily gain (P < 0.05), and significantly improved carcass weight, and meat and hair fiber quality (P < 0.05). We further conducted RNA-seq using skin and liver tissues from each group to assess the molecular mechanism conferring these phenotypic changes. A total of 191 differentially expressed genes were found in the skin tissues (0 vs 91 mg), while 1,127 DEGs were found in livers. Analyses of liver samples for differential gene action and functional prediction found that EOC stimulated physiological changes in the body’s immune system at both blood and cell levels. Our results demonstrated the potential of using EO-based feed ingredient to improve animal growth performance, meat quality and fiber quality, and further illustrated the molecular basis that contribute to phenotypes at physiological levels.