Gene expression patterns during intramuscular fat development in cattle

A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle

Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.

Molecular and Cellular Mechanisms of Intramuscular Fat Development and Growth in Cattle

Intramuscular fat, also referred to as marbling fat, is the white fat deposited within skeletal muscle tissue. The content of intramuscular fat in the skeletal muscle, particularly the longissimus dorsi muscle, of cattle is a critical determinant of beef quality and value. In this review, we summarize the process of intramuscular fat development and growth, the factors that affect this process, and the molecular and epigenetic mechanisms that mediate this process in cattle. Compared to other species, cattle have a remarkable ability to accumulate intramuscular fat, partly attributed to the abundance of sources of fatty acids for synthesizing triglycerides. Compared to other adipose depots such as subcutaneous fat, intramuscular fat develops later and grows more slowly. The commitment and differentiation of adipose precursor cells into adipocytes as well as the maturation of adipocytes are crucial steps in intramuscular fat development and growth in cattle. Each of these steps is controlled by various factors, underscoring the complexity of the regulatory network governing adipogenesis in the skeletal muscle. These factors include genetics, epigenetics, nutrition (including maternal nutrition), rumen microbiome, vitamins, hormones, weaning age, slaughter age, slaughter weight, and stress. Many of these factors seem to affect intramuscular fat deposition through the transcriptional or epigenetic regulation of genes directly involved in the development and growth of intramuscular fat. A better understanding of the molecular and cellular mechanisms by which intramuscular fat develops and grows in cattle will help us develop more effective strategies to optimize intramuscular fat deposition in cattle, thereby maximizing the quality and value of beef meat.

Differential expressions of FASN, SCD, and FABP4 genes in the ribeye muscle of omega-3 oil-supplemented Tattykeel Australian White lambs

BACKGROUND

The concept of the functional nutritional value of health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) is becoming a phenomenon among red meat consumers globally. This study examined the expressions of three lipogenic genes (fatty acid binding protein 4, FABP4, fatty acid synthase, FASN; and stearoyl-CoA desaturase, SCD) in the ribeye (Longissimus thoracis et lumborum) muscle of Tattykeel Australian White (TAW) lambs fed fortified omega-3 diets and correlations with fatty acids. To answer the research question, "are there differences in the expression of lipogenic genes between control, MSM whole grain and omega-3 supplemented lambs?", we tested the hypothesis that fortification of lamb diets with omega-3 will lead to a down-regulation of lipogenic genes. Seventy-five six-month old TAW lambs were randomly allocated to the (1) omega-3 oil-fortified grain pellets, (2) unfortified grain pellets (control) or (3) unfortified MSM whole grain pellets diet supplements to generate three treatments of 25 lambs each. The feeding trial lasted 47 days.

RESULTS

From the Kruskal-Wallis test, the results showed a striking disparity in lipogenic gene expression between the three dietary treatments in which the FABP4 gene was significantly up-regulated by 3-folds in the muscles of lambs fed MSM Milling (MSM) whole grain diet compared to the omega-3 and control diets. A negative correlation was observed between FASN gene expression and intramuscular fat (IMF), eicosapentaenoic acid (EPA), total polyunsaturated fatty acids (PUFA), omega-6 polyunsaturated fatty acids (n-6 PUFA) and monounsaturated fatty acids (MUFA). The FABP4 gene expression was positively correlated (P < 0.05) with EPA and docosahexaenoic acid (DHA).

CONCLUSION

Taken together, this study's results suggest that FABP4 and FASN genes perform an important role in the biosynthesis of fatty acids in the ribeye muscle of TAW lambs, and supplementary diet composition is an important factor influencing their expressions.

Characteristics of Transcriptome and Metabolome Concerning Intramuscular Fat Content in Beijing Black Pigs

To study the characteristics of genes and metabolites related to intramuscular fat (IMF) content with less influence by breed background and individual differences, the skeletal muscle samples from 40 Beijing black pigs with either high or low IMF content were used to perform transcriptome and metabolome analyses. About 99 genes (twofold-change) were differentially expressed. Up-regulated genes in the high IMF pigs were mainly related to fat metabolism. The key genes in charge of IMF deposition are ADIPOQ, CIDEC, CYP4B1, DGAT2, LEP, OPRL1, PLIN1, SCD, and THRSP. KLHL40, TRAFD1, and HSPA6 were novel candidate genes for the IMF trait due to their high abundances. In the low IMF pigs, the differentially expressed genes involved in virus resistance were up-regulated. About 16 and 18 differential metabolites (1.5 fold-change) were obtained in the positive and negative modes, respectively. Pigs with low IMF had weaker fatty acid oxidation due to the down-regulation of various carnitines. Differentially expressed genes were more important in determining IMF deposition than differential metabolites because relatively few differential metabolites were obtained, and they were merely the products under the physiological status of diverged IMF content. This study provided valuable information for further studies on IMF deposition.

IMF deposition ceRNA network analysis and functional study of HIF1a in yak

The concentration of intramuscular fat (IMF) is a crucial determinant of yak meat quality. However, the molecular mechanisms that regulate IMF in yak remain largely elusive. In our study, we conducted transcriptome sequencing on the longissimus dorsi muscle tissues of yaks with varying IMF contents. We then filtered differentially expressed genes (DEGs), microRNAs (DEMs), and long non-coding RNAs (DELs) to elucidate potential regulatory pathways of adipogenesis in yaks. Overall, our research sheds light on an array of potential mRNAs and noncoding RNAs implicated in IMF deposition and elaborates on the role of HIF1α in yaks. These findings contribute valuable insights that can serve as a guide for further research into the molecular mechanisms governing IMF deposition.

Early Weaning Possibly Increases the Activity of Lipogenic and Adipogenic Pathways in Intramuscular Adipose Tissue of Nellore Calves

This study aimed to evaluate by wide-expression profile analysis how early weaning at 120 days can alter the skeletal muscle metabolism of calves supplemented with a concentrated diet until the growth phase. Longissimus thoracis muscle samples were obtained by biopsy from two groups of calves, early weaned (EW; n = 8) and conventionally weaned (CW; n = 8) at two different times (120 days of age-T1 [EW] and 205 days of age-T2 [CW]). Next, differential gene expression analysis and functional enrichment of metabolic pathways and biological processes were performed. The results showed respectively 658 and 165 differentially expressed genes when T1 and T2 were contrasted in the early weaning group and when early and conventionally weaned groups were compared at T2. The FABP4, SCD1, FASN, LDLR, ADIPOQ, ACACA, PPARD, and ACOX3 genes were prospected in both comparisons described above. Given the key role of these differentially expressed genes in lipid and fatty acid metabolism, the results demonstrate the effect of diet on the modulation of energy metabolism, particularly favoring postnatal adipogenesis and lipogenesis, as well as a consequent trend in obtaining better quality cuts, as long as an environment for the maintenance of these alterations until adulthood is provided.

Characterization of Type I and Type III Collagen in the Intramuscular Connective Tissue of Wuzhumuqin Sheep

Intramuscular connective tissue (IMCT) collagen is an important factor in meat quality. This study analyzed the characteristics of type I and III collagen in the IMCT of the semitendinosus (SD) and longissimus dorsi (LD) of Wuzhumuqin sheep at different growth stages (6, 9, 12, and 18 months). Utilizing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier transform infrared spectroscopy (FTIR), collagen types I and III were successfully isolated and shown to contain an intact triple helix structure. Immunofluorescence revealed that these collagens were located in the endomysium and perimysium. Collagen-related genes were significantly expressed in sheep aged 9 and 12 months. The amino acid content increased with age in type I collagen whereas it decreased in type III collagen. Furthermore, type III collagen contained more hydroxyproline (Hyd) than type I collagen. Differential scanning calorimetry (DSC) revealed that the thermal stability of collagen increased with age, accompanied by a decrease in solubility. Semitendinosus muscle had more collagen cross-linkages than LD muscle due to the high pyridinoline (Pyr) content in the endomysium. Finally, a correlation analysis highlighted the multiple correlations between characteristics in different types of collagen during sheep growth. In summary, the collagen characteristics in the IMCT of sheep were impacted by collagen type, muscle type, and age. Furthermore, the various correlations between these characteristics may play an important role in the development of IMCT.

Lipid metabolism mRNA expression and cellularity of intramuscular adipocytes within the Longissimus muscle of Angus- and Wagyu-sired cattle fed for a similar days on feed or body weight endpoint

This study investigates intramuscular (IM) adipocyte development in the Longissimus muscle (LM) between Wagyu- and Angus-sired steers compared at a similar age and days on feed (D) endpoint or similar body weight (B) endpoint by measuring IM adipocyte cell area and lipid metabolism mRNA expression. Angus-sired steers (AN, n = 6) were compared with steers from two different Wagyu sires (WA), selected for either growth (G) or marbling (M), to be compared at a similar days on feed (DOF; 258 ± 26.7 d; WA-GD, n = 5 and WA-MD, n = 5) in Exp. 1 or body weight (BW; 613 ± 18.0 kg; WA-GB, n = 4 and WA-MB, n = 5) in Exp. 2, respectively. In Exp. 1, WA-MD steers had a greater (P ≤ 0.01) percentage of IM fat in the LM compared with AN and WA-GD steers. In Exp. 2, WA-MB steers had a greater (P ≤ 0.01) percentage of IM fat in the LM compared with AN and WA-GB steers. The distribution of IM adipocyte area was unimodal at all biopsy collections, with IM adipocyte area becoming progressively larger as cattle age (P ≤ 0.01) and BW increased (P ≤ 0.01). Peroxisome proliferator activated receptor delta (PPARd) was upregulated earlier for WA-MD and WA-MB cattle compared with other steers at a similar DOF and BW (P ≤ 0.02; treatment × biopsy interaction). Peroxisome proliferator activated receptor gamma was upregulated (PPARg) at a lesser BW for WA-MB steers (P = 0.09; treatment × biopsy interaction), while WA-MD steers had a greater (P ≤ 0.04) overall mean PPARg mRNA expression compared with other steers. Glycerol-3-phosphate acyltransferase, lipin 1, and hormone sensitive lipase demonstrated mRNA expression patterns similar to PPARg and PPARd or CCAAT enhancer binding protein beta, which emphasizes their importance in marbling development and growth. Additionally, WA-MD and WA-MB steers often had a greater early mRNA expression of fatty acid transporters (fatty acid transport protein 1; P < 0.02; treatment × biopsy interaction) and binding proteins (fatty acid binding protein 4) compared with other steers. Cattle with a greater marbling propensity appear to upregulate adipogenesis at a younger chronological and physiological maturity through PPARd, PPARg, and possibly adipogenic regulating compounds, lysophosphatidic acid, and diacylglycerol. These genes and compounds could be used as potential markers for marbling propensity of cattle in the future.

Long-stranded non-coding RNAs temporal-specific expression profiles reveal longissimus dorsi muscle development and intramuscular fat deposition in Tianzhu white yak

The process of muscle development and intramuscular fat (IMF) deposition is quite complex and controlled by both mRNAs and ncRNAs. Long-stranded non-coding RNAs (LncRNAs) are involved in various biological processes in mammals while also playing a critical role in muscle development and fat deposition. In the present study, RNA-Seq was used to comprehensively study the expression of lncRNAs and mRNAs during muscle development and intramuscular fat deposition in postnatal Tianzhu white yaks at three stages, including 6 mo of age (calve, n = 6), 30 mo of age (young cattle, n = 6) and 54 mo of age (adult cattle, n = 6). The results indicated that a total of 2,101 lncRNAs and 20,855 mRNAs were screened across the three stages, of which the numbers of differential expression (DE) lncRNAs and DE mRNAs were 289 and 1,339, respectively, and DE lncRNAs were divided into eight different expression patterns based on expression trends. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that some DE mRNAs overlapped with target genes of lncRNAs, such as NEDD4L, SCN3B, AGT, HDAC4, DES, MYH14, KLF15 (muscle development), ACACB, PCK2, LIPE, PIK3R1, PNPLA2, and MGLL (intramuscular fat deposition). These DE mRNAs were significantly enriched in critical muscle development and IMF deposition-related pathways and GO terms, such as AMPK signaling pathway, PI3K-Akt signaling pathway, PPAR signaling pathway, etc. In addition, lncRNA-mRNA co-expression network analysis revealed that six lncRNAs (MSTRG.20152.2, MSTRG.20152.3, XR_001351700.1, MSTRG.8190.1, MSTRG.4827.1, and MSTRG.11486.1) may play a major role in Tianzhu white yak muscle development and lipidosis deposition. Therefore, this study enriches the database of yak lncRNAs and could help to further explore the functions and roles of lncRNAs in different stages of muscle development and intramuscular fat deposition in the Tianzhu white yak.

Effect of grain inclusion rates in diets provided to early-weaned calves and steroidal implants utilization on growth performance and carcass characteristics of beef steers

One hundred and twenty-one Angus × SimAngus-crossbred steers (body weight (BW) = 159 ± 22 kg) were used to evaluate the effects of different grain inclusion (GI) rates in diets provided to early-weaned calves and steroidal implants (SI) utilization on growth performance and carcass characteristics, particularly intramuscular fat deposition, of beef steers. The experiment was conducted as a randomized complete block design with a 2 × 2 factorial arrangement of treatments, consisting of two GI rates (35% vs. 58%, dry matter (DM) basis), each one associated or not to steroidal implant utilization (no implants vs. 80 mg trenbolone acetate (TA) + 16 mg estradiol followed by 120 mg TA + 24 mg of estradiol). After being early-weaned (124 ± 14 d of age), steers were offered an average of 4.5 kg/d (DM basis) of a concentrate-based diet with a greater or lesser GI rate for 60 d. After being fed a concentrate-based diet with different GI rates for 60 d, steers were fed a common backgrounding diet for 56 d and subsequently fed a common high-grain diet until harvested at a constant final BW (620 kg). Steers were not implanted until the beginning of the backgrounding phase and then re-implanted when initiating the finishing phase. Data were analyzed using PROC MIXED in SAS. There were no GI × SI interactions (P ≥ 0.62) for any of the growth performance parameters throughout the experimental period. Implanted steers tended to have a greater average daily gain (P = 0.10) during the finishing phase than nonimplanted steers. For the 12th rib fat thickness and yield grade (YG), a GI × SI interaction (P = 0.03) and a tendency for a GI × SI interaction (P = 0.10) was detected, respectively. Nonimplanted steers fed diets with greater GI rates presented the greatest 12th rib fat thickness and tended to have the greatest YG among treatments. No other interactions (P ≥ 0.33) were observed for the hot carcass weight, Longissimus muscle (LM) area, quality grade, marbling score, and kidney-pelvic-heart fat content. Steers fed diets with lesser GI rates tended to have a greater LM area than steers fed diets with greater GI rates (P = 0.10). Results from this experiment indicate that varying GI rates in diets provided to early-weaned calves and subsequent implantation with steroidal hormones did not affect marbling deposition.

RNA-Seq Analysis Identifies Differentially Expressed Genes in the Longissimus dorsi of Wagyu and Chinese Red Steppe Cattle

Meat quality has a close relationship with fat and connective tissue; therefore, screening and identifying functional genes related to lipid metabolism is essential for the production of high-grade beef. The transcriptomes of the Longissimus dorsi muscle in Wagyu and Chinese Red Steppe cattle, breeds with significant differences in meat quality and intramuscular fat deposition, were analyzed using RNA-seq to screen for candidate genes associated with beef quality traits. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the 388 differentially expressed genes (DEGs) were involved in biological processes such as short-chain fatty acid metabolism, regulation of fatty acid transport and the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In addition, crystallin alpha B (CRYAB), ankyrin repeat domain 2 (ANKRD2), aldehyde dehydrogenase 9 family member A1 (ALDH9A1) and enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) were investigated for their effects on intracellular triglyceride and fatty acid content and their regulatory effects on genes in lipogenesis and fatty acid metabolism pathways. This study generated a dataset from transcriptome profiling of two cattle breeds, with differing capacities for fat-deposition in the muscle, and revealed molecular evidence that CRYAB, ANKRD2, ALDH9A1 and EHHADH are related to fat metabolism in bovine fetal fibroblasts (BFFs). The results provide potential functional genes for maker-assisted selection and molecular breeding to improve meat quality traits in beef cattle.

Transcriptome Profile Reveals Genetic and Metabolic Mechanisms Related to Essential Fatty Acid Content of Intramuscular Longissimus thoracis in Nellore Cattle

Beef is a source of essential fatty acids (EFA), linoleic (LA) and alpha-linolenic (ALA) acids, which protect against inflammatory and cardiovascular diseases in humans. However, the intramuscular EFA profile in cattle is a complex and polygenic trait. Thus, this study aimed to identify potential regulatory genes of the essential fatty acid profile in Longissimus thoracis of Nellore cattle finished in feedlot. Forty-four young bulls clustered in four groups of fifteen animals with extreme values for each FA were evaluated through differentially expressed genes (DEG) analysis and two co-expression methodologies (WGCNA and PCIT). We highlight the ECHS1, IVD, ASB5, and ERLIN1 genes and the TF NFIA, indicated in both FA. Moreover, we associate the NFYA, NFYB, PPARG, FASN, and FADS2 genes with LA, and the RORA and ELOVL5 genes with ALA. Furthermore, the functional enrichment analysis points out several terms related to FA metabolism. These findings contribute to our understanding of the genetic mechanisms underlying the beef EFA profile in Nellore cattle finished in feedlot.

Transcriptomic profile of longissimus thoracis associated with fatty acid content in Nellore beef cattle

The beef fatty acid (FA) profile has the potential to impact human health, and displays polygenic and complex features. This study aimed to identify the transcriptomic FA profile in the longissimus thoracis muscle in Nellore beef cattle finished in feedlot. Forty-four young bulls were sampled to assess the beef FA profile by considering 14 phenotypes and including differentially expressed genes (DEG), co-expressed (COE), and differentially co-expressed genes (DCO) analyses. All samples (n = 44) were used for COE analysis, whereas 30 samples with extreme phenotypes for the beef FA profile were used for DEG and DCO. A total of 912 DEG were identified, and the polyunsaturated (n = 563) and unsaturated ω-3 (n = 346) FA sums groups were the most frequently observed. The COE analyses identified three modules, of which the blue module (n = 1776) was correlated with eight of 14 FA phenotypes. Also, 759 DCO genes were listed, and the oleic acid (n = 358) and monounsaturated fatty acids sum (n = 120) were the most frequent. Furthermore, 243 and 13, 319 and seven, and 173 and 12 gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were enriched respectively for the DEG, COE, and DCO analyses. Combining the results, we highlight the unexplored GIPC2, ASB5, and PPP5C genes in cattle. Besides LIPE and INSIG2 genes in COE modules, the ACSL3, ECI1, DECR2, FITM1, and SDHB genes were signaled in at least two analyses. These findings contribute to understand the genetic mechanisms underlying the beef FA profile in Nellore beef cattle finished in feedlot.

Main regulatory factors of marbling level in beef cattle

The content of intramuscular fat (IMF), that determines marbling levels is considered as one of the vital factors influencing beef sensory quality including tenderness, juiciness, flavour and colour. The IMF formation in cattle commences around six months after conception, and continuously grows throughout the life of the animal. The accumulation of marbling is remarkably affected by genetic, sexual, nutritional and management factors. In this review, the adipogenesis and lipogenesis process regulated by various factors and genes during fetal and growing stages is briefly presented. We also discuss the findings of recent studies on the effects of breed, gene, heritability and gender on the marbling accumulation. Various research reported that feeding during pregnancy, concentrate to roughage ratios and the supplementation or restriction of vitamin A, C, and D are crucial nutritional factors affecting the formation and development of IMF. Castration and early weaning combined with high energy feeding are effective management strategies for improving the accumulation of IMF. Furthermore, age and weight at slaughter are also reviewed because they have significant effects on marbling levels. The combination of several factors could positively affect the improvement of the IMF deposition. Therefore, advanced strategies that simultaneously apply genetic, sexual, nutritional and management factors to achieve desired IMF content without detrimental impacts on feed efficiency in high-marbling beef production are essential.

Effects of Dietary Protein Concentration on Lipid Metabolism Gene Expression and Fatty Acid Composition in 18-23-Month-Old Hanwoo Steers

The present study evaluated the influence of dietary protein level on growth performance, fatty acid composition, and the expression of lipid metabolic genes in intramuscular adipose tissues from 18- to 23-month-old Hanwoo steers, representing the switching point of the lean-to-fat ratio. Forty steers with an initial live weight of 486 ± 37 kg were assigned to one of two treatment groups fed either a concentrate diet with 14.5% CP and or with 17% CP for 6 months. Biopsy samples of intramuscular tissue were collected to analyze the fatty acid composition and gene expression at 23 months of age. Throughout the entire experimental period, all steers were restrained twice daily to allow individual feeding. Growth performance, blood metabolites, and carcass traits, according to ultrasonic measurements, were not affected by the experimental diets. The high-protein diet significantly increased the expression of intramuscular PPARα (p < 0.1) and LPL (p < 0.05) but did not affect genes involved in fatty acid uptake (CD36 and FABP4) nor lipogenesis (ACACA, FASN, and SCD). In addition, it downregulated intramuscular VLCAD (p < 0.01) related to lipogenesis but also GPAT1 (p = 0.001), DGAT2 (p = 0.016), and SNAP23 (p = 0.057), which are involved in fatty acid esterification and adipocyte size. Hanwoo steers fed a high-protein diet at 18-23 months of age resulted in a relatively lower lipid turnover rate than steers fed a low-protein diet, which could be responsible for shortening the feeding period.

Effect of plane of nutrition in early life on the transcriptome of visceral adipose tissue in Angus heifer calves

Adipose tissue represents not only an important energy storage tissue but also a major endocrine organ within the body, influencing many biochemical systems including metabolic status, immune function and energy homeostasis. The objective of this study was to evaluate the effect of an enhanced dietary intake during the early calfhood period on the transcriptome of visceral adipose tissue. Artificially reared Angus × Holstein-Friesian heifer calves were offered either a high (HI, n = 15) or moderate (MOD, n = 15) plane of nutrition from 3 to 21 weeks of life. At 21 weeks of age all calves were euthanized, visceral adipose harvested and samples subsequently subjected to mRNA sequencing. Plane of nutrition resulted in the differential expression of 1214 genes within visceral adipose tissue (adj. p < 0.05; fold change > 1.5). Differentially expressed genes were involved in processes related to metabolism and energy production. Biochemical pathways including Sirtuin signalling (adj. p < 0.0001) and the adipogenesis pathways (adj. p = 0.009) were also significantly enriched, indicating greater metabolic processing and adipogenesis in the calves on the high plane of nutrition. Results from this study identify novel genes regulating the molecular response of visceral adipose tissue to an improved plane of nutrition during early calfhood.

Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India

The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats. A clear demarcation could be observed between the breeds in terms of expression of genes associated with lipid metabolism (FASN, SCD, THRSP, DGAT2 and FABP3). Most significant genes with high connectivity identified by gene co-expression network analysis were associated with triacylglycerol biosynthesis pathway in Barbari goat. Highly interactive genes identified in Changthangi goat were mainly associated with muscle fibre type. This study provides an insight into the differential expression of genes in longissimus thoracis muscles between Barbari and Changthangi goats that are adapted to and reared in different agro-climatic regions.

Difference in developmental dynamics between subcutaneous and abdominal adipose tissues in goose (Anser Cygnoides)

Goose (Anas cygnoides), as a typical species domesticated from a migratory bird, has maintained the capability of depositing excess lipid and preferentially accumulating fat within the abdomen and subcutaneous, which not only leads to decrease in yield of meat product, but also affects the feed conversion rate. Here, an experiment was conducted to examine the difference in developmental dynamics between subcutaneous (SAT) and abdominal adipose tissues (AAT) in goose. The results showed that SAT could be clearly observed at embryonic days (E) 15, whereas AAT were clearer until E20. Although the weights of SAT and AAT showed a significant rising with advancing age (P < 0.05), their gains were not completely uniform, and more adipose deposited preferentially toward AAT after birth (P < 0.05). Additionally, a clear expansion in adipocyte size was observed in AAT and SAT during embryonic stages (P < 0.05). The average adipocyte area in AAT continued to increase after birth (P < 0.05), while the cell areas in SAT were relatively invariable (P > 0.05). Furthermore, the expression levels of FABP4/aP2, ACSL1 and PPARγ were much higher in SAT than in AAT, whereas relative higher expression level of IL-6 was observed in the AAT during embryonic stages. After birth, the more expression of LPL and PPARα were detected in AAT than did in SAT (P < 0.05), whereas greater ATGL expression was in SAT (P < 0.05). Taken together, these findings suggest that AAT may display greater fat storage capacity than SAT accompanied by changes in cell area and lipogenic capacity. Considering that there is disparity in the individual adipose tissues, we suggested that careful consideration for the precise interventions used to control SAT or AAT deposition in meat-producing animals to improve feed efficiency.

Intramuscular collagen characteristics and expression of related genes in skeletal muscle of cull cows receiving a high-energy diet

We aimed to investigate differences in the synthesis and metabolism of intramuscular collagen in the Longissimus thoracis (LT) muscle between heifers and cull-cows fed high-energy diet. Ten cull-cows, (74.9 ± 3.2 months age, weighing 536 ± 14.55 kg) and ten heifers (18.4 ± 3.2 months age, weighting 310.5 ± 14.5 kg) were fed with high-energy diets for 150 days. The total collagen content did not differ between treatments. Greater collagen solubility was observed in heifers than cull-cows, although no differences in lysyl oxidase activity were observed between treatments. No differences were observed for mRNA expression of CO1A1, MMP2, MMP9 and TIMP2 between treatments. However, cull-cows presented greater mRNA expression of COL3A1, TIMP1 and TIMP3 than heifers. Our data give no indication that feeding a high-energy diet to cull-cows decreases the concentration of intramuscular collagen in the LT muscle or increases its solubility in respect to the collagen solubility in LT muscles from heifers on the same diet.

Subcutaneous and intramuscular fat transcriptomes show large differences in network organization and associations with adipose traits in pigs

Subcutaneous fat (SCF) and intramuscular fat (IMF) deposition is relevant to health in humans, as well as meat production and quality in pigs. In this study, we generated RNA sequence data for 122 SCF, 120 IMF, and 87 longissimus dorsi muscle (LDM) samples using 155 F₆ pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds. The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F₆ pigs. We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity, and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF, containing genes that were associated with the immune process and DNA double-strand repair, respectively. We identified 215 SCF genes related to kinase inhibitor activity, mitochondrial fission, and angiogenesis, and 90 IMF genes related to lipolysis and fat cell differentiation, displayed a tissue-specific association with back fat thickness and IMF content, respectively. We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissue-dependent predictability for the two adipose traits. Alternative splicing of genes was also found to be associated with SCF or IMF deposition, but the association was much less extensive than that based on expression levels. This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition. These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

BACKGROUND

Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12).

RESULTS

We identified a total of 26,247 genes and 6935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.

CONCLUSIONS

Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.

MiR-26b-5p regulates the preadipocyte differentiation by targeting FGF21 in goats

MicroRNAs are a class of highly conserved and widely distributed non-coding RNAs. It is known that miR-26b has a high abundance in adipose tissue and is considered to be an effective regulator of adipogenesis. However, it is unclear whether miR-26b-5p, the product of miR-26b precursor, has the same effect as miR-26b. In the present study, we explored the potential role of miR-26b-5p in preadipocyte differentiation of goats. We found that the expression of miR-26b-5p had dramatic change during goat intramuscular preadipocyte differentiation. Transfection and RT-qPCR revealed that overexpression of miR-26b-5p increased the level of adipogenic marker genes and lipid accumulation in goat preadipocyte, suggesting that miR-26b-5p positively regulates goat preadipocyte differentiation. Furthermore, bioinformatics analysis and dual fluorescein reporter assays were performed to predict and validate the targets of miR-26b-5p. The results showed that miR-26b-5p has a binding site in the 3'UTR of FGF21 and overexpression of miR-26b-5p significantly down-regulated the expression of FGF21 mRNA. Luciferase activity assays confirmed that miR-26b-5p is a positive regulator of goat intramuscular preadipocyte via targeting FGF21. These findings provide reference for further revealing of the regulatory networks of goat fat metabolism and contribute to a better understanding of intramuscular fat deposition in goats.

NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks

A classic problem in computational biology is the identification of altered subnetworks: subnetworks of an interaction network that contain genes/proteins that are differentially expressed, highly mutated, or otherwise aberrant compared with other genes/proteins. Numerous methods have been developed to solve this problem under various assumptions, but the statistical properties of these methods are often unknown. For example, some widely used methods are reported to output very large subnetworks that are difficult to interpret biologically. In this work, we formulate the identification of altered subnetworks as the problem of estimating the parameters of a class of probability distributions that we call the Altered Subset Distribution (ASD). We derive a connection between a popular method, jActiveModules, and the maximum likelihood estimator (MLE) of the ASD. We show that the MLE is statistically biased, explaining the large subnetworks output by jActiveModules. Based on these insights, we introduce NetMix, an algorithm that uses Gaussian mixture models to obtain less biased estimates of the parameters of the ASD. We demonstrate that NetMix outperforms existing methods in identifying altered subnetworks on both simulated and real data, including the identification of differentially expressed genes from both microarray and RNA-seq experiments and the identification of cancer driver genes in somatic mutation data.

Differential Gene Expression in Longissimus Dorsi Muscle of Hanwoo Steers-New Insight in Genes Involved in Marbling Development at Younger Ages

The Korean Hanwoo breed possesses a high capacity to accumulate intramuscular fat, which is measured as a marbling score in the beef industry. Unfortunately, the development of marbling is not completely understood and the identification of differentially expressed genes at an early age is required to better understand this trait. In this study, we took muscle samples from 12 Hanwoo steers at the age of 18 and 30 months. From the contrast between age and marbling score, we identified in total 1883 differentially expressed genes (FDR < 0.05 and logarithm fold change ≥ 1.5) with 782 genes up-regulated and 1101 down-regulated. Differences in gene expression were higher between the ages x marbling groups rather than between high and low marbling groups. At 18 months of age, the genes SLC38A4, ABCA10, APOL6, and two novel genes (ENSBTAG00000015330 and ENSBTAG00000046041) were up-regulated in the high marbling group. From the protein–protein interaction network analysis, we identified unique networks when comparing marbling scores between different ages. Nineteen genes (AGT, SERPINE1, ADORA1, FOS, LEP, FOXO1, FOXO3, ADIPOQ, ITGA1, SDC1, SDC4, ITGB3, ITGB4, CXCL10, ACTG2, MX1, EDN1, ACTA2, and ESPL1) were identified to have an important role in marbling development. Further analyses are needed to better understand the role of these genes.

Effect of Heat Stress on Dairy Cow Performance and on Expression of Protein Metabolism Genes in Mammary Cells

Simple Summary

Environmental temperatures are increasing, and consequent global warming also has negative effects on dairy cattle farms, which may result in reduced production and poorer milk quality. The protein content of casein, in particular, is important in influencing the coagulation properties of milk and, therefore, the production and quality of cheese. The aim of this study was to assess the effect of heat stress on animal performance and on the expression of selected genes involved in milk protein metabolism. Eight dairy cows were kept under thermoneutral conditions for 8 days. The same animals were then maintained under mild heat stress conditions for an additional 8 days. The results of this study revealed that mild heat stress reduced the feed intake and performance of dairy cows in terms of milk and protein yield, but not the expression of the target genes involved in milk protein metabolism, such as those coding for caseins.

Abstract

The aim of this study was to assess the effect of heat stress on dairy cow performance and on the expression of selected genes involved in milk protein metabolism. Eight Italian Holstein Friesian cows were kept under thermoneutral conditions (temperature–humidity index (THI) < 72, CON) for 8 days and under mild heat stress conditions (72 < THI < 78, HS) for an additional 8 days. The rectal temperature, feed intake, and milk yield were recorded during the last 3 days of the CON and HS periods. During the same time period, milk samples were collected to assess the composition and expression of selected genes involved in milk protein metabolism. Gene expression analyses were performed on somatic cells from milk, which are representative of mammary tissue. In terms of dairy cow performance, HS resulted in lower milk and protein yields and feed intake but higher rectal temperature than for CON (p < 0.05). Under HS, there were greater abundances of HSPA1A (p < 0.05) and BCL2 (p < 0.05), compared to CON, but similar levels of CSN2 (p > 0.05), CSN3 (p > 0.05), HSPA8 (p > 0.05), and STAT5B (p > 0.05) mRNA. Mild heat stress reduced the performance of dairy cows without affecting the expression of genes coding for caseins.

Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits

Intramuscular fat (IMF) content and its composition affect the quality of meat. Selection for IMF generated a correlated response on its fatty acid composition. The increase of IMF content is associated with an increase of its saturated (SFA) and monounsaturated (MUFA) fatty acids, and consequently a decrease of polyunsaturated fatty acids (PUFA). We carried out a genome wide association study (GWAS) for IMF composition on two rabbit lines divergently selected for IMF content, using a Bayes B procedure. Association analyses were performed using 475 individuals and 90,235 Single Nucleotide Polymorphisms (SNPs). The main objectives were to identify genomic regions associated with the IMF composition and to generate a list of candidate genes. Genomic regions associated with the intramuscular fatty acid composition were spread across different rabbit chromosomes (OCU). An important region at 34.0-37.9 Mb on OCU1 was associated with C14:0, C16:0, SFA, and C18:2n6, explaining 3.5%, 11.2%, 11.3%, and 3.2% of the genomic variance, respectively. Another relevant genomic region was found to be associated at 46.0-48.9 Mb on OCU18, explaining up to 8% of the genomic variance of MUFA/SFA. The associated regions harbor several genes related to lipid metabolism, such as SCD, PLIN2, and ERLIN1. The main genomic regions associated with the fatty acids were not previously associated with IMF content in rabbits. Nonetheless, MTMR2 is the only gene that was associated with both the IMF content and composition in rabbits. Our study highlighted the polygenic nature of the fatty acids in rabbits and elucidated its genetic background.

Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo

BACKGROUND

In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important driver that affects IMF deposition.

RESULTS

To reveal the intrinsic factors responsible for the low IMF content of buffalo, mRNA expression patterns in muscle and adipose tissue between buffalo and cattle were characterized by RNA sequencing analysis. The IMF content in Nanyang cattle was higher than that in Xinyang buffalo. A total of 1566 mRNAs expressed in adipose tissue showed differential expression between the longissimus dorsi muscles of buffalo and cattle. Functional annotation suggested a difference in the glycolysis/gluconeogenesis pathway between the two species. The results of RT-qPCR analysis and gain-of-function experiments confirmed the positive association between the IMF content and phosphoenolpyruvate carboxykinase 1 (PCK1) expression in buffalo. In both mouse C2C12 cells and cultured bovine myocytes, the activity of the PCK1 promoter in buffalo is lower than that in cattle. However, in mouse 3T3-L1 adipocytes and cultured bovine adipocytes, the activity of PCK1 in buffalo promoter is higher than that in cattle.

CONCLUSIONS

These results indicate the important role of PCK1 in buffalo IMF deposition and illustrate the differences between buffalo and cattle promoter activity that drive PCK1 expression. This research helps to establish a foundation for further studies investigating IMF deposition in buffalo.

The Effects of Age at Weaning and Length of Lipid Supplementation on Growth, Metabolites, and Marbling of Young Steers

Simple Summary

Consumers value quality beef and producers are starting to look at the ways production decisions affect the long-term performance of the animals. Early weaning is a production option in many beef cattle production environments. We are looking at the addition of rumen by-pass lipids in addition to early weaning to increase the marbling of steers. The supplementation of rumen protected lipids’ increased plasma concentrations of fatty acids. Supplementation of rumen-protected lipids improved carcass quality of young steers by increasing marbling scores and lipid concentration of steaks without negatively impacting dressing percentage. Therefore, a combination of early weaning and rumen by-pass lipid supplementation can be used as management practices to meet current consumer demands.

Abstract

The objective of this study was to determine how weaning age, days on supplements, and lipid supplementation affected the growth and marbling deposition of steers. Steers from a single sire were early weaned (n = 24) at 150 ± 11 days of age or traditionally weaned (n = 24) at 210 ± 11 days of age. Steers were assigned to control (n = 12/weaning group) or an isocaloric, isonitrogenous rumen by-pass lipid (RBL, n = 12/weaning group) for either 45 (n = 6/treatment) or 90 (n=6/treatment) days then harvested. Steer body weight (BW) was recorded on days −14 and −7, then BW and blood samples were collected on days 0, 22, 45, 66, and 90. The right rib section of each animal was collected for proximate analysis. Longissimus dorsi from RBL steers had increased lipids compared with control steers (3.6 ± 0.2 vs. 2.4 ± 0.2% on a wet basis; p < 0.0001). Steers fed for 90 days had greater (p = 0.02) concentrations of Longissimus dorsi lipid (3.3 ± 0.2%) than those fed for 45 days (2.7 ± 0.2%). There was a weaning age by treatment by days on feed interaction for intramuscular adipocyte diameter (p = 0.02) in which early weaned RBL fed for 90 days steers had an increased adipocyte diameter compared to the early weaned control fed for 90 and early weaned fed for 45 days steers with all other treatment groups as intermediates. Supplementation of RBL increased concentrations of C18:2, C20:4, and total fatty acids on days 45 and 90 (p ≤ 0.05). Data show that RBL supplementation increased the marbling content of the Longissimus dorsi. Furthermore, a longer period of supplementation resulted in increased adipose diameter.

Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction

This study evaluated the potential of a panel of 20 protein biomarkers, quantified by Reverse Phase Protein Array (RPPA), to explain and predict two important meat quality traits, these being beef tenderness assessed by Warner-Bratzler shear force (WBSF) and the intramuscular fat (IMF) content (also termed marbling), in a large database of 188 Protected Designation of Origin (PDO) Maine-Anjou cows. Thus, the main objective was to move forward in the progression of biomarker-discovery for beef qualities by evaluating, at the same time for the two quality traits, a list of candidate proteins so far identified by proteomics and belonging to five interconnected biological pathways: (i) energy metabolic enzymes, (ii) heat shock proteins (HSPs), (iii) oxidative stress, (iv) structural proteins and (v) cell death and protein binding. Therefore, three statistical approaches were applied, these being Pearson correlations, unsupervised learning for the clustering of WBSF and IMF into quality classes, and Partial Least Squares regressions (PLS-R) to relate the phenotypes with the 20 biomarkers. Irrespective of the statistical method and quality trait, seven biomarkers were related with both WBSF and IMF, including three small HSPs (CRYAB, HSP20 and HSP27), two metabolic enzymes from the oxidative pathway (MDH1: Malate dehydrogenase and ALDH1A1: Retinal dehydrogenase 1), the structural protein MYH1 (Myosin heavy chain-IIx) and the multifunctional protein FHL1 (four and a half LIM domains 1). Further, three more proteins were retained for tenderness whatever the statistical method, among which two were structural proteins (MYL1: Myosin light chain 1/3 and TNNT1: Troponin T, slow skeletal muscle) and one was glycolytic enzyme (ENO3: β-enolase 3). For IMF, two proteins were, in this trial, specific for marbling whatever the statistical method: TRIM72 (Tripartite motif protein 72, negative) and PRDX6 (Peroxiredoxin 6, positive). From the 20 proteins, this trial allowed us to qualify 10 and 9 proteins respectively as strongly related with beef tenderness and marbling in PDO Maine-Anjou cows.

Molecular signatures of muscle growth and composition deciphered by the meta-analysis of age-related public transcriptomics data

The lean-to-fat ratio is a major issue in the beef meat industry from both carcass and meat production perspectives. This industrial perspective has motivated meat physiologists to use transcriptomics technologies to decipher mechanisms behind fat deposition within muscle during the time course of muscle growth. However, synthetic biological information from this volume of data remains to be produced to identify mechanisms found in various breeds and rearing practices. We conducted a meta-analysis on 10 transcriptomic data sets stored in public databases, from the longissimus thoracis of five different bovine breeds divergent by age. We updated gene identifiers on the last version of the bovine genome (UCD1.2), and the 715 genes common to the 10 studies were subjected to the meta-analysis. Of the 238 genes differentially expressed (DEG), we identified a transcriptional signature of the dynamic regulation of glycolytic and oxidative metabolisms that agrees with a known shift between those two pathways from the animal puberty. We proposed some master genes of the myogenesis, namely MYOG and MAPK14, as probable regulators of the glycolytic and oxidative metabolisms. We also identified overexpressed genes related to lipid metabolism (APOE, LDLR, MXRA8, and HSP90AA1) that may contribute to the expected enhanced marbling as age increases. Lastly, we proposed a transcriptional signature related to the induction (YBX1) or repression (MAPK14, YWAH, ERBB2) of the commitment of myogenic progenitors into the adipogenic lineage. The relationships between the abundance of the identified mRNA and marbling values remain to be analyzed in a marbling biomarkers discovery perspectives.

High-energy diet improves growth performance, meat quality and gene expression related to intramuscular fat deposition in finishing yaks raised by barn feeding

This research aimed to investigate the effects of dietary energy concentration (combined net energy, Nemf) on growth performance and meat quality of yaks raised by barn feeding. In all, 30 male yaks (3‐year old and 114.57 ± 21.56 kg of body weight) were allocated to one of three isonitrogenous dietary treatments that had different Nemf concentrations (low 3.72 MJ/kg, middle 4.52 MJ/kg and high 5.32 MJ/kg, respectively). The yaks were fed for 120 days. The results showed that the final weight, average daily gain, dressing percentage, backfat thickness and loin muscle area were significantly improved (p < .05) with the increase in dietary energy concentration. However, an opposite trend of feed:gain ratio, cooking loss, driage, shear force and moisture content was found. A significant improvement (p < .05) of intramuscular fat content was observed in the high‐energy group. Additionally, the proportion of polyunsaturated fatty acid was increased (p < .05) at the expense of the saturated fatty acids. The mRNA expressions of lipogenic genes fatty acid synthase, acetyl‐CoA carboxylase, sterol regulatory element‐binding protein 1, stearoyl‐CoA desaturase, peroxisome proliferator‐activated receptor γ, lipoprotein lipase and heart fatty acid‐binding proteins increased (p < .05) in a dose‐dependent manner. However, the mRNA expressions of lipolytic genes carnitine palmitoyltransferase‐1 and hormone‐sensitive lipase correspondingly decreased (p < .05) with increased dietary energy level. In summary, the growth performance, meat production and meat quality improvement of finishing yaks can be achieved by increasing the dietary energy concentration. The intramuscular fat accumulation of yaks was achieved through up‐regulation of intramuscular lipogenic gene expression as well as fatty acid transport gene expression and down‐regulation of lipolytic gene expression by promoting dietary energy concentration.

Genome-Wide Identification of Discriminative Genetic Variations in Beef and Dairy Cattle via an Information-Theoretic Approach

Analyzing the associations between genotypic changes and phenotypic traits on a genome-wide scale can contribute to understanding the functional roles of distinct genetic variations during breed development. We performed a whole-genome analysis of Angus and Jersey cattle breeds using conditional mutual information, which is an information-theoretic method estimating the conditional independency among multiple factor variables. The proposed conditional mutual information-based approach allows breed-discriminative genetic variations to be explicitly identified from tens of millions of SNP (single nucleotide polymorphism) positions on a genome-wide scale while minimizing the usage of prior knowledge. Using this data-driven approach, we identified biologically relevant functional genes, including breed-specific variants for cattle traits such as beef and dairy production. The identified lipid-related genes were shown to be significantly associated with lipid and triglyceride metabolism, fat cell differentiation, and muscle development. In addition, we confirmed that milk-related genes are involved in mammary gland development, lactation, and mastitis-associated processes. Our results provide the distinct properties of Angus and Jersey cattle at a genome-wide level. Moreover, this study offers important insights into discovering unrevealed genetic variants for breed-specific traits and the identification of genetic signatures of diverse cattle breeds with respect to target breed-specific properties.

Transcriptome changes associated with fat deposition in the longissimus thoracis of Korean cattle following castration

The castration of bulls increases the intramuscular fat (IMF) content in skeletal muscle. However, the biological processes of IMF accumulation in skeletal muscle after castration are not completely understood at the molecular level. This study examined the global transcriptomic changes in the longissimus thoracis muscle (LT) of bulls following castration using RNA sequencing (RNA-Seq) and identified new genes or pathways associated with beef quality. Ten bulls and 10 steers castrated at 6 months of age were slaughtered at 26 and 32 months of age respectively. For transcriptome analysis, six LT samples from three bulls and three steers were selected based on age, carcass weight, carcass quantity and beef quality grades. Using RNA-Seq, transcriptomic profiles of the LT were compared between bulls and steers. In all, 640 of the 18,027 genes identified through RNA-Seq were differentially expressed genes (DEGs) between bulls and steers. Pathway analysis of these 640 DEGs showed significant (p < .05) changes in seven Kyoto Encyclopedia of Genes and Genomes pathways, and the most significant terms were complement and coagulation cascade pathways. The transcriptomic expression patterns of 10 genes in the complement and coagulation cascades were validated using all animals through quantitative real-time polymerase chain reaction analysis. In conclusion, transcriptome changes associated with the complement and coagulation cascade pathways provide novel insights into understanding molecular mechanisms responsible for IMF accumulation following castration in beef cattle.

The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak

Background

The Intramuscular fat (IMF) content in meat products, which is positively correlated with meat quality, is an important trait considered by consumers. The regulation of IMF deposition is species specific. However, the IMF-deposition-related mRNA and non-coding RNA and their regulatory network in yak (Bos grunniens) remain unknown. High-throughput sequencing technology provides a powerful approach for analyzing the association between transcriptome-related differences and specific traits in animals. Thus, the whole transcriptomes of yak muscle and adipose tissues were screened and analyzed to elucidate the IMF deposition-related genes. The muscle tissues were used for IMF content measurements.

Results

Significant differences were observed between the 0.5- and 2.5-year-old yaks. Several mRNAs, miRNAs, lncRNAs and circRNAs were generally expressed in both muscle and adipose tissues. Between the 0.5- and 2.5-year-old yaks, 149 mRNAs, 62 miRNAs, 4 lncRNAs, and 223 circRNAs were differentially expressed in muscle tissue, and 72 mRNAs, 15 miRNAs, 9 lncRNAs, and 211 circRNAs were differentially expressed in adipose tissue. KEGG annotation revelved that these differentially expressed genes were related to pathways that maintain normal biological functions of muscle and adipose tissues. Moreover, 16 mRNAs, 5 miRNAs, 3 lncRNAs, and 5 circRNAs were co-differentially expressed in both types of tissue. We suspected that these co-differentially expressed genes were involved in IMF-deposition in the yak. Additionally, LPL, ACADL, SCD, and FASN, which were previously shown to be associated with the IMF content, were identified in the competing endogenous RNA (ceRNA) regulatory network that was constructed on the basis of the IMF deposition-related genes. Three ceRNA subnetworks also revealed that TCONS-00016416 and its target SIRT1 “talk” to each other through the same miR-381-y and miR-208 response elements, whereas TCONS-00061798 and its target PRKCA, and TCONS-00084092 and its target LPL “talk” to each other through miR-122-x and miR-499-y response elements, respectively.

Conclusion

Taken together, our results reveal the potential mRNA and noncoding RNAs involved in IMF deposition in the yak, providing a useful resource for further research on IMF deposition in this animal species.

GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: The regulation of beef quality by resident progenitor cells1

The intramuscular adipose tissue deposition in the skeletal muscle of beef cattle is a highly desired trait essential for high-quality beef. In contrast, the excessive accumulation of crosslinked collagen in intramuscular connective tissue contributes to beef toughness. Recent studies revealed that adipose tissue and connective tissue share an embryonic origin in mice and may be derived from a common immediate bipotent precursor in mice and humans. Having the same linkages in the development of adipose tissue and connective tissue in beef, the lineage commitment and differentiation of progenitor cells giving rise to these tissues may directly affect beef quality. It has been shown that these processes are regulated by some key transcription regulators and are subjective to epigenetic modifications such as DNA methylation, histone modifications, and microRNAs. Continued exploration of relevant regulatory pathways is very important for the identification of mechanisms influencing meat quality and the development of proper management strategies for beef quality improvement.

Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle

The identification of biological processes related to the regulation of complex traits is a difficult task. Commonly, complex traits are regulated through a multitude of genes contributing each to a small part of the total genetic variance. Additionally, some loci can simultaneously regulate several complex traits, a phenomenon defined as pleiotropy. The lack of understanding on the biological processes responsible for the regulation of these traits results in the decrease of selection efficiency and the selection of undesirable hitchhiking effects. The identification of pleiotropic key-regulator genes can assist in developing important tools for investigating biological processes underlying complex traits. A multi-breed and multi-OMICs approach was applied to study the pleiotropic effects of key-regulator genes using three independent beef cattle populations evaluated for fertility traits. A pleiotropic map for 32 traits related to growth, feed efficiency, carcass and meat quality, and reproduction was used to identify genes shared among the different populations and breeds in pleiotropic regions. Furthermore, data-mining analyses were performed using the Cattle QTL database (CattleQTLdb) to identify the QTL category annotated in the regions around the genes shared among breeds. This approach allowed the identification of a main gene network (composed of 38 genes) shared among breeds. This gene network was significantly associated with thyroid activity, among other biological processes, and displayed a high regulatory potential. In addition, it was possible to identify genes with pleiotropic effects related to crucial biological processes that regulate economically relevant traits associated with fertility, production and health, such as MYC, PPARG, GSK3B, TG and IYD genes. These genes will be further investigated to better understand the biological processes involved in the expression of complex traits and assist in the identification of functional variants associated with undesirable phenotypes, such as decreased fertility, poor feed efficiency and negative energetic balance.

Effects of alleles in crossbred pigs estimated for genomic prediction depend on their breed-of-origin

BACKGROUND

This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, and how these are related to estimated effects for purebred performance.

RESULTS

SNP-allele substitution effects were estimated for a commonly used SNP panel using a genomic best linear unbiased prediction model with breed-specific partial relationship matrices. Estimated breeding values for purebred and crossbred performance were converted to SNP-allele effects by breed-of-origin. Differences between purebred and crossbred, and between breeds-of-origin were evaluated by comparing percentage of variance explained by genomic regions for back fat thickness (BF), average daily gain (ADG), and residual feed intake (RFI). From ten regions explaining most additive genetic variance for crossbred performance, 1 to 5 regions also appeared in the top ten for purebred performance. The proportion of genetic variance explained by a genomic region and the estimated effect of a haplotype in such a region were different depending upon the breed-of-origin. To illustrate underlying mechanisms, we evaluated the estimated effects across breeds-of-origin for haplotypes associated to the melanocortin 4 receptor (MC4R) gene, and for the MC4Rsnp itself which is a missense mutation with a known effect on BF and ADG. Although estimated allele substitution effects of the MC4Rsnp mutation were very similar across breeds, explained genetic variance of haplotypes associated to the MC4R gene using a SNP panel that does not include the mutation, was considerably lower in one of the breeds where the allele frequency of the mutation was the lowest.

CONCLUSIONS

Similar regions explaining similar additive genetic variance were observed across purebred and crossbred performance. Moreover, there was some overlap across breeds-of-origin between regions that explained relatively large proportions of genetic variance for crossbred performance; albeit that the actual proportion of variance deviated across breeds-of-origin. Results based on a missense mutation in MC4R confirmed that even if a causal locus has similar effects across breeds-of-origin, estimated effects and explained variance in its region using a commonly used SNP panel can strongly depend on the allele frequency of the underlying causal mutation.

Timing of Exposure to High-Concentrates versus High-Quality Forages on Growth and Marbling Deposition in Steers

Forty Angus-cross steers (280 ± 21.4 kg BW, 8 mo.) were used to examine the effects of exposure to 2 diets [high concentrate diets (CONC) versus high quality forages (FOR)] during 2 time periods [early (EARLY; at 30-d post weaning) or late (LATE; just prior to slaughter)] on animal growth, marbling deposition and tenderness. Steers were blocked by weight and randomly assigned to four dietary treatments: 1) CONC-FOR, 2) CONC-CONC, 3) FOR-CONC, or 4) FOR-FOR. Exposure to CONC during the EARLY or LATE period increased (P < 0.05) growth and fat deposition compared to FOR-FOR. Hot carcass weight was greater (P < 0.05) for CONC-CONC and FOR-CONC steers than FOR-FOR and CONC-FOR due to changes in dressing percent. Marbling score was greater (P < 0.05) for CONC-CONC and CONC-FOR compared to FOR-FOR. Exposure to CONC during the EARLY period (CONC-FOR and CONC-CONC) increased (P < 0.05) n-6 polyunsaturated fatty acids (PUFA) deposition in longissimus muscle (LM) and subcutaneous adipose tissue (SQ); whereas, exposure to CONC during the LATE period (CONC-CONC and FOR-CONC) reduced (P < 0.05) n-3 PUFA, trans-11 octadecenoic acid and cis-9 trans-11 isomer of conjugated linoleic acid (CLA). Warner-Bratzler shear force at d 2 and 7 of postmortem aging in ribeye steaks from CONC-CONC and FOR-CONC was greater (P < 0.05) than FOR-FOR and CONC-FOR. Lipogenic gene expression was up-regulated (P < 0.05) and lipolytic gene expression was downregulated (P < 0.06) in SQ from CONC-CONC and FOR-CONC compared to FOR-FOR. Overall, exposure to CONC in both periods increased growth rate and marbling deposition but LATE exposure had the greatest impact on adipose lipogenesis and lipolysis, fatty acid composition, and tenderness.

Effect of dietary nitrogen level and source on mRNA expression of urea transporters in the rumen epithelium of fattening bulls

This paper aims to study the effect of the dietary treatments on mRNA expression of urea transporter B (UT-B) and some aquaporins (AQP) in rumen epithelium of Italian Simmental young bulls. Eighty animals allocated to 16 pens were fed from about 500 to 650 kg body weight with four experimental diets, which resulted from the combination of two crude protein levels (125 and 110 g/kg dry matter, diets M and L, respectively) and two nitrogen sources (soybean meal (SBM) or SBM partly replaced by an isonitrogenous mixture of corn and urea; diets -U and +U, respectively). At slaughtering samples of blood and rumen epithelium were collected from six bulls for each diet. Blood samples were analysed for haematological parameters and quantitative PCR was carried out on the mRNA extracted from the rumen epithelium samples. The bulls fed diets M had lower plasma concentrations of aspartate aminotransferase than those receiving diets L (78.9 vs. 88.3 U/l, p = 0.04). Plasma urea was higher (p = 0.03) for diets M and lower for diets +U (2.0 vs. 2.5 and 1.73 vs. 2.00 mmol/l, respectively, in M and L diets, p = 0.04). The effect of dietary treatments on rumen UT expression were limited to AQP3, which was down regulated (p = 0.01) in diets +U. Finally, a high positive correlation (R2 = 0.871) between the expressions of AQP7 and AQP10 was found. In conclusion, the AQP3 appears very responsive to dietary treatments and therefore it is a candidate to be further studied in rumen metabolism experiments. The close relationship between mRNA expression of AQP7 and AQP10 indicates a similar function of these two proteins.

Novel genetic polymorphisms associated with carcass traits in grazing Texel sheep

Improving meat production traits has increased its importance in sheep breeding. We report novel associations of SNP present in genes related to lipid metabolism and growth with several carcass traits in purebred Texel lambs. Expected progeny differences (EPD) predictions from 461 animals from the Central Progeny Testing of Texel breed in Uruguay were used for the association analysis. Live weights at different stages, ultrasound and post-mortem traits were analyzed. Markers in several genes were associated with growth, carcass and meat quality traits. Among others: PPARGC1A with valuable cuts weight, hot carcass weight and carcass fatness; DGAT1 with live weights, fat thickness, rib-eye area and shoulder weight; CAST with birth weight and fat thickness; GHR with birth weight and carcass fatness, and GHRHR with live weights and fat thickness. Genotypic effects ranged from 0.035 to 0.923 (DGAT1 vs. weaning weight) units of phenotypic SD. Most of the associations described are novel in sheep breeding, deserving further analyses.

RNA-Seq Analysis Reveals a Positive Role of HTR2A in Adipogenesis in Yan Yellow Cattle

In this study, we performed high throughput RNA sequencing at the primary bovine preadipocyte (Day-0), mid-differentiation (Day-4), and differentiated adipocyte (Day-9) stages in order to characterize the transcriptional events regulating differentiation and function. The preadipocytes were isolated from subcutaneous fetal bovine adipose tissues and were differentiated into mature adipocytes. The adipogenic characteristics of the adipocytes were detected during various stages of adipogenesis (Day-0, Day-4, and Day-9). We used RNA sequencing (RNA-seq) to investigate a comprehensive transcriptome information of adipocytic differentiation. Compared to the pre-differentiation stage (Day-0), 2510 genes were identified as differentially expressed genes (DEGs) at the mid-differentiation stage (Day-4). We found 2446 DEGs in the mature adipocytic stage relative to the mid-differentiation stage. Some adipogenesis-related transcription factors, CCAAT-enhancer-binding protein α (C/EBPα) and peroxisome proliferator-activated receptor γ (PPARγ) were differentially expressed at Day-0, Day-4, and Day-9. We further investigated the adipogenic function of 5-hydroxytryptamine receptor 2A (HTR2A) in adipogenesis. Overexpression of HTR2A stimulated the differentiation of preadipocytes, and knockdown of HTR2A had opposite effects. Furthermore, functional enrichment analysis of DEGs revealed that the PI3K-Akt signaling pathway was the significantly enriched pathway, and HTR2A regulated adipogenesis by activating or inhibiting phosphorylation of phospho-AKT (Ser473). In summary, the present study provides the first comparative transcription of various periods of adipocytes in cattle, which presents a solid foundation for further study into the molecular mechanism of fat deposition and the improvement of beef quality in cattle.

Beef tenderness and intramuscular fat proteomic biomarkers: muscle type effect

Tenderness and intramuscular fat content are key attributes for beef sensory qualities. Recently some proteomic analysis revealed several proteins which are considered as good biomarkers of these quality traits. This study focuses on the analysis of 20 of these proteins representative of several biological functions: muscle structure and ultrastructure, muscle energetic metabolism, cellular stress and apoptosis. The relative abundance of the proteins was measured by Reverse Phase Protein Array (RPPA) in five muscles known to have different tenderness and intramuscular lipid contents: Longissimus thoracis (LT), Semimembranosus (SM), Rectus abdominis (RA), Triceps brachii (TB) and Semitendinosus (ST). The main results showed a muscle type effect on 16 among the 20 analyzed proteins. They revealed differences in protein abundance depending on the contractile and metabolic properties of the muscles. The RA muscle was the most different by 11 proteins differentially abundant comparatively to the four other muscles. Among these 11 proteins, six were less abundant namely enolase 3 (ENO3), phosphoglucomutase 1 (PGK1), aldolase (ALDOA), myosin heavy chain IIX (MyHC-IIX), fast myosin light chain 1 (MLC1F), triosephosphate isomerase 1 (TPI1) and five more abundant: Heat shock protein (HSP27, HSP70-1A1, αB-crystallin (CRYAB), troponin T slow (TNNT1), and aldolase dehydrogenase 1 (ALDH1A1). Four proteins: HSP40, four and a half LIM domains protein 1 (FHL1), glycogen phosphorylase B (PYGB) and malate dehydrogenase (MDH1) showed the same abundance whatever the muscle. The correlations observed between the 20 proteins in all the five muscles were used to construct a correlation network. The proteins the most connected with the others were in the following order MyHC-IIX, CRYAB, TPI1, PGK1, ALDH1A1, HSP27 and TNNT1. This knowledge is important for understanding the biological functions related to beef tenderness and intramuscular fat content.

Effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein-Friesian bulls

Background

Adipose tissue is a major endocrine organ and is thought to play a central role in the metabolic control of reproductive function in cattle. Plane of nutrition during early life has been shown to influence the timing of puberty in both male and female cattle, though the exact biological mechanisms involved are currently unknown. The aim of this study was to investigate the effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein-Friesian bulls to identify possible downstream effects on reproductive physiology.

Results

Holstein-Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n = 10) or low (n = 10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.08 and 0.57 kg/day for the high and low plane of nutrition treatments, respectively. At 126 days of age, the bulls were euthanized, subcutaneous adipose tissue samples were harvested and RNAseq analysis was performed. There were 674 genes differentially expressed in adipose tissue of calves on the low compared with the high plane of nutrition (P < 0.05; FDR < 0.05; fold change > 2.0). High plane of nutrition positively altered the expression of genes across an array of putative biological processes but the most dominant cellular processes affected were cellular energy production and branched chain amino acid degradation. A high plane of nutrition caused upregulation of genes such as leptin (LEP) and adiponectin (ADIPOQ), which are known to directly affect reproductive function.

Conclusions

These results provide an insight into the effect of augmenting the plane of nutrition of Holstein-Friesian bull calves in the prepubertal period on the transcriptome of adipose tissue.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4681-2) contains supplementary material, which is available to authorized users.

Does growth path influence beef lipid deposition and fatty acid composition?

Despite the recent advances in transcriptomics, gene expression studies addressing cattle´s skeletal muscle adaptations in response to compensatory growth are warranted, particularly regarding lipid metabolism due to its impact in meat sensory and nutritional traits. In the present study, in comparison to ad libitum feeding, a period of feed restriction was used in order to understand the changes in bull´s lipid metabolism and gene expression of the adipogenic and lipogenic pathways after re-alimentation. Thus, 40 young Alentejana bulls were either fed ad libitum (CG group) from 9 to 18 months of age or subjected to food restriction from 9 to 15 months of age, and fed ad libitum until 24 months of age (DG group). The intramuscular fat (IMF) and total fatty acids (FA) contents were similar between groups. The major FA (>2%) contents were similar (16:0, 16:1c9, 18:1c9 and 18:2n-6) between treatments with the exception of 18:0 content that was 15% lower in DG than in CG and 20:4n-6 that tended to be greater on DG bulls. Regarding minor FA (<2%), the DG group presented greater proportions (P<0.01) of 17:1c9, 18:1t9, 18:1t10 (, 18:1c11), 18:1c13, 18:3n-6, 22:0, 22:4n-6 and 22:6n-3 and lower (P<0.05) proportions of 20:0, 18:1t16+c14, and branched chain FA (iso-15:0, anteiso-15:0, iso-16:0 and anteiso-17:0) than the CG group. Delta-9 desaturase activity indices were consistently greater (P<0.05) in DG, when compared to the CG group. Regarding microarray analysis, differentially expressed genes between CG and DG bulls were grouped in 5 main biological functions: lipid and nucleic acid metabolisms, small molecule biochemistry, molecular transport and translational modification. Discontinuous growth down-regulated the expression of ACACB (FC (fold-change) = 1.32), FABP3 (FC = 1.45), HADHA (FC = 1.41) and SLC37A4 (FC = 1.40) genes, when compared to the CG system (FDR<0.05). In contrast, in the CG bulls, the expression of ELOVL5 (FC = 1.58) and FASN (FC = 1.71) was down-regulated when compared to DG bulls. These results were confirmed to be significant (P<0.05) in the case of ELOVL5, FASN and SLC37A4, and almost significant for FABP3 by qRT-PCR analysis. The SCD1 and SCD5 gene expressions were not found to be affected by growth path. These results contribute to the still scarce knowledge about the mechanisms involved in fatty acid metabolism during compensatory growth which have decisive role on meat quality produced in Mediterranean areas.