Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid

Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits

BACKGROUND

Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS).

RESULTS

In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits.

CONCLUSIONS

The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.

Candidate genes for longitudinal traits under sequential sampling in beef cattle

Both the measurement age of a longitudinal trait and the common pre-sampling procedures used in beef cattle herds may affect the identification of a functional candidate gene (FCG) that is potentially associated with a trait. To identify the FCG that takes part in the genetic control of body weight at five different ages in a beef cattle population with and without sequential sampling, the animals were weighed at different measurement events, around 330, 385, 440, 495 and 550 days old. Genetic parameters were estimated for body weight at each age using a single trait (STM) and a random regression model (RRM). In addition, two different databases were used to estimate the genetic parameters: the first (DB100) was formed by all animals that were weighed in the five measurement events, and the second (DB70) has records of the same population, considering that 70% of the heaviest animals were selected after each measurement event. For DB100, genome-wide association studies (GWAS) were performed with 21,667 SNP markers to identify genomic windows that explained at least 1% of the genetic variance. Additionally, prioritization analyses were performed and FCGs were selected. We associated seven different FCGs with body weight at different ages. Among them, the gene DUSP10 was suggested as FCG in all five ages evaluated. Genetic parameters estimated for body weight using DB100 were similar when STM and RRM were applied. However, when DB70 was used as phenotypic data, there were differences between the two models. When the STM was applied, there were differences between the genetic parameters estimated for body weight when DB100 or DB70 were used as sources of phenotypes, but not for the estimates obtained with RRM. The importance of each gene for animal growth can change at different ages, and different genes may be more relevant to body weight at each different growth stage for beef cattle. Besides, sequential sampling can affect the GWAS results of a longitudinal trait. The age of the animal when a longitudinal trait is measured and pre-sampling can also contribute to inconsistencies in GWAS results for body weight in beef cattle, depending on the time when that data were collected, and consequently on the identification of FCG between studies, even when models that consider a covariance structure are used.

Muscle transcriptome analysis reveal candidate genes and pathways related to fat and lipid metabolism in Yunling cattle

Yunling cattle (YL) is a recently developed beef breed harboring a quarter of Yunnan ancestral cattle genome, spanning over past 30 years. Compared with Diqing cattle (DQ), a Yunnan native cattle breed, YL presents various advantages, including rapid growth and exquisite meat quality. However, the molecular mechanisms underlying these phenotypic differences are not clearly understood. To further identify the candidate genes responsible for the quality of the meat in the muscle, longissimus dorsi (LD) muscle was used for RNA-Seq analysis. A total of 508 differentially expressed genes (DEGs) were identified in YL (adjusted p-value <0.01 and log2FoldChange >1), of which 243 were up-regulated and 265 were down-regulated. Functional association analysis showed that the identified DEGs mainly enriched the lipid and fat metabolism pathways. Moreover, it was also observed that several fat-related genes were differentially expressed in both cattle breeds, including three up-regulated genes (MOGAT1, ACSM3, PLPP2) and two down-regulated genes (ADIG, GPAT3). In addition, alternative splice analysis was also performed revealing an important 9-11 exon skipping variation of GPAM gene (crucial for beef marbling) in YL, which is three times higher than that in DQ, suggesting that this variation might have played the central role in the 'snow beef' effect in YL. We believe that our results will help in understanding the mechanism of muscle development and promote the further breeding programs in YL cattle.

The Effect of the Feeding System on Fat Deposition in Yak Subcutaneous Fat

Fat deposition is very important to the growth and reproduction of yaks. In this study, the effect of the feeding system on fat deposition in yaks was explored by transcriptomics and lipidomics. The thickness of the subcutaneous fat in yaks under stall (SF) and graze feeding (GF) was evaluated. The transcriptomes and lipidomes of the subcutaneous fat in yaks under different feeding systems were detected by RNA-sequencing (RNA-Seq) and non-targeted lipidomics based on ultrahigh-phase liquid chromatography tandem mass spectrometry (UHPLC-MS), respectively. The differences in lipid metabolism were explored, and the function of differentially expressed genes (DEGs) was evaluated by gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) analysis. Compared with GF yaks, SF yaks possessed stronger fat deposition capacity. The abundance of 12 triglycerides (TGs), 3 phosphatidylethanolamines (PEs), 3 diglycerides (DGs), 2 sphingomyelins (SMs) and 1 phosphatidylcholine (PC) in the subcutaneous fat of SF and GF yaks was significantly different. Under the mediation of the cGMP-PKG signaling pathway, the blood volume of SF and GF yaks may be different, which resulted in the different concentrations of precursors for fat deposition, including non-esterified fatty acid (NEFA), glucose (GLU), TG and cholesterol (CH). The metabolism of C16:0, C16:1, C17:0, C18:0, C18:1, C18:2 and C18:3 in yak subcutaneous fat was mainly realized under the regulation of the INSIG1, ACACA, FASN, ELOVL6 and SCD genes, and TG synthesis was regulated by the AGPAT2 and DGAT2 genes. This study will provide a theoretical basis for yak genetic breeding and healthy feeding.

Nutrigenomics in livestock sector and its human-animal interface-a review

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Nutrigenomics unfolds the link between nutrition and gene expression for productivity.expression profile of intramuscular.

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Nutrigenomics helps scientists discover genes and DNA in each animal's cell or tissue by assisting them in selecting nutrients.

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It brings out the importance of micronutrition for increasing animal production.

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Nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology.

Noncommunicable diseases such as cardiovascular disease, obesity, diabetes, and cancer now outnumber all other health ailments in humans globally due to abrupt changes in lifestyle following the industrial revolution. The industrial revolution has also intensified livestock farming, resulting in an increased demand for productivity and stressed animals. The livestock industry faces significant challenges from a projected sharp increase in global food and high animal protein demand. Nutrition genomics holds great promise for the future as its advances have opened up a whole new world of disease understanding and prevention. Nutrigenomics is the study of the interactions between genes and diet. It investigates molecular relationships between nutrients and genes to identify how even minor modifications could potentially alter animal and human health/performance by using techniques like proteomics, transcriptomics, metabolomics, and lipidomics. Dietary modifications mostly studied in livestock focus mainly on health and production traits through protein, fat, mineral, and vitamin supplementation changes. Nutrigenomics meticulously selects nutrients for fine-tuning the expression of genes that match animal/human genotypes for better health, productivity, and the environment. As a step forward, nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology to better understand the role of food as an epigenetic factor in the occurrence of these diseases. This review aims to provide a comprehensive overview of the fundamental concepts, latest advances, and studies in the field of nutrigenomics, emphasizing the interaction of diet with gene expression, and how it relates to human and animal health along with its human-animal interphase.

Lipidomics and Transcriptome Reveal the Effects of Feeding Systems on Fatty Acids in Yak’s Meat

The differences of fatty acids in yak’s meat under graze feeding (GF) and stall feeding (SF) regimes and the regulation mechanism of the feeding system on the fatty acids content in yak ’s meat was explored in this study. First, the fatty acids in yak’s longissimus dorsi (LD) muscle were detected by gas liquid chromatography (GLC). Compared with GF yaks, the absolute content of ΣSFAs, ΣMUFAs, ΣUFAs, ΣPUFAs and Σn-6PUFAs in SF yak’s LD were higher, whereas Σn-3PUFAs was lower; the relative content of ΣMUFAs, ΣPUFAs, Σn-3PUFAs and ΣUFAs in SF yak’s LD were lower, whereas ΣSFAs was higher. The GF yak’s meat is healthier for consumers. Further, the transcriptomic and lipidomics profiles in yak’s LD were detected by mRNA-Sequencing (mRNA-Seq) and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), respectively. The integrated transcriptomic and lipidomics analysis showed the differences in fatty acids were caused by the metabolism of fatty acids, amino acids, carbohydrates and phospholipids, and were mainly regulated by the FASN, FABP3, PLIN1, SLC16A13, FASD6 and SCD genes in the PPAR signaling pathway. Moreover, the SCD gene was the candidate gene for the high content of ΣMUFA, and FADS6 was the candidate gene for the high content of Σn-3PUFAs and the healthier ratio of Σn-6/Σn-3PUFAs in yak meat. This study provides a guidance to consumers in the choice of yak’s meat, and also established a theoretical basis for improving yak’s meat quality.

Explaining Unsaturated Fatty Acids (UFAs), Especially Polyunsaturated Fatty Acid (PUFA) Content in Subcutaneous Fat of Yaks of Different Sex by Differential Proteome Analysis

Residents on the Tibetan Plateau intake a lot of yak subcutaneous fat by diet. Modern healthy diet ideas demand higher unsaturated fatty acids (UFAs), especially polyunsaturated fatty acid (PUFA) content in meat. Here, the gas chromatography (GC) and tandem mass tag (TMT) proteomic approaches were applied to explore the relationship between the proteomic differences and UFA and PUFA content in the subcutaneous fat of yaks with different sex. Compared with male yaks (MYs), the absolute contents of UFAs, monounsaturated fatty acids (MUFAs) and PUFAs in the subcutaneous fat of female yaks (FYs) were all higher (p < 0.01); the relative content of MUFAs and PUFAs in MY subcutaneous fat was higher, and the value of PUFAs/SFAs was above 0.4, so the MY subcutaneous fat is more healthy for consumers. Further studies showed the transcriptional regulation by peroxisome proliferator-activated receptor delta (PPARD) played a key role in the regulation of UFAs, especially PUFA content in yaks of different sex. In FY subcutaneous fat, the higher abundance of the downstream effector proteins in PPAR signal, including acyl-CoA desaturase (SCD), elongation of very-long-chain fatty acids protein 6 (ELOVL6), lipoprotein lipase (LPL), fatty acid-binding protein (FABP1), very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 (HACD3), long-chain fatty acid CoA ligase 5 (ACSL5) and acyl-CoA-binding protein 2 (ACBP2), promoted the UFAs’ transport and synthesis. The final result was the higher absolute content of c9-C14:1, c9-C18:1, c9,c12-C18:2n-6, c9, c12, c15-C18:3n-3, c5, c8, c11, c14, c17-C20:5n-3, c4, c7, c10, c13, -c16, c19-C22:6n-3, UFAs, MUFAs and PUFAs in FY subcutaneous fat. Further, LPL, FABP1, HACD3, ACSL1 and ACBP2 were the potential biomarkers for PUFA contents in yak subcutaneous fat. This study provides new insights into the molecular mechanisms associated with UFA contents in yak subcutaneous fat.

Integrated analysis of expression profiles with meat quality traits in cattle

MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.

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.

Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle

The aim of this study was to identify mRNA isoforms and small genetic variants that may be affecting marbling and beef color in Nellore cattle. Longissimus thoracis muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate (n = 10) and low (n = 10) groups) and beef color (desirable (n = 10) and undesirable (n = 9) group) traits were used to perform transcriptomic analysis using RNA sequencing. Fourteen and 15 mRNA isoforms were detected as differentially expressed (DE) (P-value ≤ 0.001) between divergent groups for marbling and meat color traits, respectively. Some of those DE mRNA isoforms have shown sites of splicing modified by small structural variants as single nucleotide variant (SNV), insertion, and/or deletion. Enrichment analysis identified metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis, and phenylalanine degradation. The results obtained suggest potential key regulatory genes associated with these economically important traits for the beef industry and for the consumer.

Characterization of novel lncRNA muscle expression profiles associated with meat quality in beef cattle

The aim of this study was to identify novel lncRNA differentially expressed (DE) between divergent animals for beef tenderness and marbling traits in Nellore cattle. Longissimus thoracis muscle samples from the 20 most extreme bulls (of 80 bulls set) for tenderness, tender (n = 10) and tough (n = 10) groups, and marbling trait, high (n = 10) and low (n = 10) groups were used to perform transcriptomic analysis using RNA‐Sequencing. For tenderness, 29 lncRNA were DE (p‐value ≤ 0.01) in tough beef animals in relation to tender beef animals. We observed that genic lncRNAs, for example, lncRNA_595.1, were overlapping exonic part of the PICK gene, while lncRNA_3097.2 and lncRNA_3129.5 overlapped intronic part of the genes GADL1 and PSMD6. The lncRNA associated with PICK1, GADL1, and PMD6 genes were enriched in the pathways associated with the ionotropic glutamate receptor, gamma‐aminobutyric acid synthesis, and the ubiquitin–proteasome pathway. For marbling, 50 lncRNA were DE (p‐value ≤ 0.01) in high marbling group compared with low marbling animals. The genic lncRNAs, such as lncRNA_3191.1, were overlapped exonic part of the ITGAL gene, and the lncRNA_512.1, lncRNA_3721.1, and lncRNA_41.4 overlapped intronic parts of the KRAS and MASP1 genes. The KRAS and ITGAL genes were enriched in pathways associated with integrin signaling, which is involved in intracellular signals in response to the extracellular matrix, including cell form, mobility, and mediates progression through the cell cycle. In addition, the lincRNAs identified to marbling trait were associated with several genes related to calcium binding, muscle hypertrophy, skeletal muscle, lipase, and oxidative stress response pathways that seem to play a role important in the physiological processes related to meat quality. These findings bring new insights to better understand the biology mechanisms involved in the gene regulation of these traits, which will be valuable for a further investigation of the interactions between lncRNA and mRNAs, and of how these interactions may affect meat quality traits.

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

Fatty acids (FA) in ruminants, especially unsaturated FA (USFA) have important impact in meat quality, nutritional value, and flavour quality of meat, and on consumer’s health. Identification of the genetic factors controlling the FA composition and metabolism is pivotal to select sheep that produce higher USFA and lower saturated (SFA) for the benefit of sheep industry and consumers. Therefore, this study was aimed to investigate the transcriptome profiling in the liver tissues collected from sheep with divergent USFA content in longissimus muscle using RNA deep-sequencing. From sheep (n = 100) population, liver tissues with higher (n = 3) and lower (n = 3) USFA content were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample were ranged from 21.28 to 28.51 million with a median of 23.90 million. Approximately, 198 genes were differentially regulated with significance level of p-adjusted value <0.05. Among them, 100 genes were up-regulated, and 98 were down-regulated (p<0.01, FC>1.5) in the higher USFA group. A large proportion of key genes involved in FA biosynthesis, adipogenesis, fat deposition, and lipid metabolism were identified, such as APOA5, SLC25A30, GFPT1, LEPR, TGFBR2, FABP7, GSTCD, and CYP17A. Pathway analysis revealed that glycosaminoglycan biosynthesis- keratan sulfate, adipokine signaling, galactose metabolism, endocrine and other factors-regulating calcium metabolism, mineral metabolism, and PPAR signaling pathway were playing important regulatory roles in FA metabolism. Importantly, polymorphism and association analyses showed that mutation in APOA5, CFHR5, TGFBR2 and LEPR genes could be potential markers for the FA composition in sheep. These polymorphisms and transcriptome networks controlling the FA variation could be used as genetic markers for FA composition-related traits improvement. However, functional validation is required to confirm the effect of these SNPs in other sheep population in order to incorporate them in the sheep breeding program.

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.

Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.

Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle

Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P < 10 - 8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.

Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species

Background

There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses.

Results

In total 120 samples were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified.

Conclusions

These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07667-2.

MicroRNA-mRNA Regulatory Networking Fine-Tunes Polyunsaturated Fatty Acid Synthesis and Metabolism in the Inner Mongolia Cashmere Goat

Fatty acid composition is an important aspect of meat quality in ruminants. Improving the beneficial fatty acid level in cashmere goat meat is important to its economic value. To investigate microRNAs (miRNAs) and mRNAs that regulate or coregulate polyunsaturated fatty acid (PUFA) synthesis and metabolism in the Inner Mongolia cashmere goat, we used longissimus dorsi muscle (WLM) and biceps femoris muscle (WBM) for transcript-level sequencing. RT-qPCR was used to evaluate the expression of mRNAs and miRNAs associated with PUFA synthesis and metabolism. The total PUFA content in the WBM was significantly higher than that in the WLM (P < 0.05). Our study is the first to systematically report miRNAs in cashmere goat meat. At the mRNA level, 20,375 genes were identified. ACSL1, CD36 and TECRL were at the center of a gene regulatory network and contributed significantly to the accumulation and metabolic regulation of fatty acids. At the miRNA level, 426 known miRNAs and 30 novel miRNAs were identified. KEGG analysis revealed that the miRNA target genes were involved mainly in the PPAR signaling pathway. The mRNA-miRNA coregulation analysis showed that ACSL1 was negatively targeted by nine miRNAs: chi-miR-10a-5p, chi-miR-10b-5p, chi-miR-130b-5p, chi-miR-15a-5p_R-1, chi-miR-15b-5p, chi-miR-16a-5p, chi-miR-16b-5p, chi-miR-181c-5p_R+1, and chi-miR-26b-5p. Finally, we speculated that the simultaneous silencing of ACSL1 by one or more of these nine miRNAs through PPAR signaling led to low ACSL1 expression in the WLM and, ultimately to high PUFA content in the WBM. Our study helps elucidate the metabolic regulation of fatty acids in Inner Mongolia cashmere goats.

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.

Genome-wide association study between copy number variation regions and carcass- and meat-quality traits in Nellore cattle

Context Indicine breeds are the main source of beef products in tropical and subtropical regions. However, genetic improvement for carcass- and meat-quality traits in zebu cattle have been limited and genomics studies concerning structural variations that influence these traits are essential. Aim The aim of this study was to perform a genome-wide association study between copy number variation regions (CNVRs) and carcass- and meat quality-traits in Nellore cattle. Methods In total, 3794 animals, males and females included, were genotyped using a 777962 single-nucleotide polymorphism platform of BovineHD BeadChip (777k; Illumina Inc.). Of these, 1751 Nellore bulls were slaughtered at 24 months of age for further carcass beef analysis. The following traits were studied: beef tenderness, marbling, rib-eye area, backfat thickness and meat colour (lightness, redness and yellowness). The CNV detection was conducted through PennCNV software. The association analyses were performed using CNVRuler software. Key results Several identified genomic regions were linked to quantitative trait loci associated with fat deposition (FABP7) and lipid metabolism (PPARA; PLA2 family; BCHE), extracellular matrix (INS; COL10A1), contraction (SLC34A3; TRDN) and muscle development (CAPZP). The gene-enrichment analyses highlighted biological mechanisms directly related to the metabolism and synthesis of lipids and fatty acids. Conclusions The large number of potential candidate genes identified within the CNVRs, as well as the functions and pathways identified, should help better elucidate the genetic mechanisms involved in the expression of beef and carcass traits in Nellore cattle. Several CNVRs harboured genes that might have a functional impact to improve the beef and carcass traits. Implications The results obtained contribute to upgrade the sensorial and organoleptic attributes of Nellore cattle and make feasible the genetic improvement of carcass- and meat-quality traits.

Different expression of lipid metabolism-related genes in Shandong black cattle and Luxi cattle based on transcriptome analysis

To provide new ideas for improving meat quality and generating new breeds of cattle, the important candidate genes affecting fat deposition in two kinds of cattle were identified. Eighteen months Shandong black cattle (n = 3) and Luxi cattle (n = 3) were randomly assigned into two environmental. The longissimus dorsi muscles of Shandong Black Cattle and Luxi Cattle were collected and analyzed by fatty acid determination, high-throughput sequencing transcriptomics, qRT-PCR expression profile and western blot. The ratio of unsaturated fatty acids to saturated fatty acids was 1.37:1 and 1.24:1 in the muscle tissues of Shandong black cattle and Luxi cattle, respectively. The results of RNA-Seq analysis revealed 1320 DEGs between the longissimus dorsi of Shandong black cattle and Luxi cattle. A total of 867 genes were upregulated, and the other 453 genes were downregulated. With GO enrichment analysis, it was found that the identified DEGs were significantly enriched in regulation of the Wnt signaling pathway, negative regulation of the Wnt signaling pathway, cAMP metabolic process, fat cell differentiation and among other functions. We found that regulation of lipolysis in adipocytes was the significant enrichment pathway of upregulated genes and downregulated genes, PPAR signaling pathway and AMPK signaling pathway are highly representative pathways of lipid metabolism in Shandong black cattle. Network analysis showed that PPARGC1A, ADCY4, ANKRD6, COL1A1, FABP4, ADIPOQ, PLIN1, PLIN2, and LIPE genes were correlated with key loci genes in multiple metabolic pathways. Meanwhile we found that FABP4 and ADIPOQ had 7 common regulatory factors in different genes, which were PLIN1, PLIN2, PPARGC1A, RXRA, PCK1, LEPR, LEP. These genes were involved in regulation of lipolysis in adipocytes, adipocytokine signaling pathway, PPAR signaling pathway. FABP4 and ADIPOQ were selected as important candidate marker genes for fat deposition based on the results.

Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle

The Warner-Bratzler shear force (WBSF) and myofibrillar fragmentation index (MFI) are complementary methodologies used to measure beef tenderness. Longissimus thoracis samples from the 20 most extreme bulls (out of 80 bulls set) for WBSF (tender (n = 10) and tough (n = 10)) and MFI (high (n = 10) and low (n = 10)) traits were collected to perform transcriptomic analysis using RNA-Sequencing. All analysis were performed through CLC Genomics Workbench. A total of 39 and 27 transcripts for WBSF and MFI phenotypes were DE, respectively. The possible DE novel mRNA isoforms, for WBSF and MFI traits, are myosin encoders (e.g. MYL1 and MYL6). In addition, we identified potential mRNA isoforms related to genes affecting the speed fibers degradation during the meat aging process. The DE novel transcripts are transcripted by genes with biological functions related to oxidative process, energy production and striated muscle contraction. The results suggest that the identified mRNA isoforms could be used as potential candidate to select animals in order to improve meat tenderness.

An assessment of genomic connectedness measures in Nellore cattle

An important criterion to consider in genetic evaluations is the extent of genetic connectedness across management units (MU), especially if they differ in their genetic mean. Reliable comparisons of genetic values across MU depend on the degree of connectedness: the higher the connectedness, the more reliable the comparison. Traditionally, genetic connectedness was calculated through pedigree-based methods; however, in the era of genomic selection, this can be better estimated utilizing new approaches based on genomics. Most procedures consider only additive genetic effects, which may not accurately reflect the underlying gene action of the evaluated trait, and little is known about the impact of non-additive gene action on connectedness measures. The objective of this study was to investigate the extent of genomic connectedness measures, for the first time, in Brazilian field data by applying additive and non-additive relationship matrices using a fatty acid profile data set from seven farms located in the three regions of Brazil, which are part of the three breeding programs. Myristic acid (C14:0) was used due to its importance for human health and reported presence of non-additive gene action. The pedigree included 427,740 animals and 925 of them were genotyped using the Bovine high-density genotyping chip. Six relationship matrices were constructed, parametrically and non-parametrically capturing additive and non-additive genetic effects from both pedigree and genomic data. We assessed genome-based connectedness across MU using the prediction error variance of difference (PEVD) and the coefficient of determination (CD). PEVD values ranged from 0.540 to 1.707, and CD from 0.146 to 0.456. Genomic information consistently enhanced the measures of connectedness compared to the numerator relationship matrix by at least 63%. Combining additive and non-additive genomic kernel relationship matrices or a non-parametric relationship matrix increased the capture of connectedness. Overall, the Gaussian kernel yielded the largest measure of connectedness. Our findings showed that connectedness metrics can be extended to incorporate genomic information and non-additive genetic variation using field data. We propose that different genomic relationship matrices can be designed to capture additive and non-additive genetic effects, increase the measures of connectedness, and to more accurately estimate the true state of connectedness in herds.

Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig

Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations.

The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.

Transcriptomic changes in bovine skeletal muscle cells after resveratrol treatment

Skeletal muscles constitute a high proportion of the cellular mass that is essential for the growth traits in cattle. Resveratrol (RSV) is a natural polyphenol compound involved in pleiotropic biological activities of muscle. Therefore, the aim of our study was to investigate the transcriptome-level effects of RSV on bovine primary myoblast to reveal differentially expressed genes (DEGs). We treated three replicates of primary myoblasts with 20 μM mother solution containing RSV, whereas three other replicates without RSV were used as control group. Then, we conducted genome-wide transcriptome analysis for the two groups. The results of expression analysis identified 3856 DEGs of which 1805 genes were up-regulated and 2051 genes were down-regulated (adjusted P < 0.05). In addition, qRT-PCR analysis of 19 selected DEGs were consistent with the expression levels observed in the transcriptome data. Gene Ontology (GO) and pathway enrichment analysis showed 72 and 66 significant GO terms and KEGG pathways, respectively (adjusted P < 0.05). The most significant GO term was actin cytoskeleton organization (GO:0030036). The top significant KEGG pathway was focal adhesion (bta04510). Predicted protein-protein interactions (PPIs) showed that CDKN1A encoding cyclindependent kinase inhibitor 1A connects several larger protein complexes. In conclusion, our results found a list of DEGs, significant GO terms and pathways, and provided an improved and expanded understanding of the impact of RSV on cattle muscle cells at the transcriptomic level. The study elucidates the potential of using the genes enriched in pathways mediating resveratrol effects as targets in genomic selection for muscle development and growth in beef cattle.

Differentially expressed genes identified through RNA-seq with extreme values of principal components for beef fatty acid in Nelore cattle

The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.

Proteome alterations associated with the oleic acid and cis-9, trans-11 conjugated linoleic acid content in bovine skeletal muscle

Oleic acid (OA) and cis-9, trans-11 conjugated linoleic acid (c9t11-CLA) are fatty acids found in beef with beneficial effects in human health. This study investigated differentially abundant proteins (DAPs) in skeletal muscle of bovines with extreme values of OA, and c9t11-CLA. For each one of the fatty acids, twenty muscle samples were divided into two groups (N = 10_High; N = 10_Low) and analyzed by high definition mass spectrometry. We identified 103 and 133 DAPs between the groups for each fatty acid. We found 64 and 45 up-regulated and 39 and 68 down-regulated proteins for OA and c9t11-CLA, respectively. Comparative analysis between proteomic and transcriptomic data revealed eight and ten genes with a consistent between mRNA expression levels and protein abundance for OA and c9t11-CLA, respectively. Unconventional myosin-Id (MYO1D), mineralocorticoid receptor (NR3C2), geranylgeranyl transferase type-2 subunit-alpha (RABGGTA), and uveal autoantigen with coiled-coil domains and ankyrin repeats (UACA) were found as putative candidate proteins for OA content. Fatty acid synthase (FASN), tubulin alpha-4A chain (TUBA4A), vinculin (VCL), NADH dehydrogenase 1 alpha subcomplex 5 (NDUFA5), and prefoldin subunit 6 (PFDN6) for c9t11-CLA. Our findings contribute to a deeper understanding of the molecular mechanisms behind the regulation of the OA and c9t11-CLA content in cattle skeletal muscle. SIGNIFICANCE: Questions about the association between meat intake and disease incidence in humans has driven animal scientist to pursue a better understanding of the biological processes associated with differences in the intramuscular fat composition. The beneficial effects of oleic acid and conjugated linoleic acid in human health have been demonstrated by improving the immune system and preventing atherosclerosis, different types of cancers, hypertension, and diabetes. Previous genome-wide association and gene expression studies identified genomic regions and differentially expressed genes associated with the fatty acid profile in skeletal muscle. In this work, differences were evaluated at the protein level. The use of a label-free quantitative proteomic approach, compared with muscle transcriptome results obtained by RNA-sequencing, allowed us to earn new insights into the variability in fatty acid deposition in skeletal muscle of farm animals. This study opens new avenues to explore the effect of the fatty acids in the skeletal muscle of livestock animals, which is associated with nutritional values of the meat, and perhaps to understand the mechanisms correlated with metabolic diseases in other species.

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

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

Comparison between haplotype-based and individual snp-based genomic predictions for beef fatty acid profile in Nelore cattle

The aim of this study was to evaluate the genomic predictions using the single-step genomic best linear unbiased predictor (ssGBLUP) method based on SNPs and haplotype markers associated with beef fatty acids (FAs) profile in Nelore cattle. The data set contained records from 963 Nelore bulls finished in feedlot (±90 days) and slaughtered with approximately 24 months of age. Meat samples from the Longissimus dorsi muscle were taken for FAs profile measurement. FAs were quantified by gas chromatography using a SP-2560 capillary column. Animals were genotyped with the high-density SNP panel (BovineHD BeadChip assay) containing 777,962 markers. SNPs with a minor allele frequency and a call rate lower than 0.05 and 0.90, respectively, monomorphic, located on sex chromosomes, and with unknown position were removed from the data set. After genomic quality control, a total of 469,981 SNPs and 892 samples were available for subsequent analyses. Missing genotypes were imputed and phased using the FImpute software. Haplotype blocks were defined based on linkage disequilibrium using the Haploview software. The model to estimate variance components and genetic parameters and to predict the genomic values included the random genetic additive effects, fixed effects of the contemporary group and the age at slaughter as a linear covariate. Accuracies using the haplotype-based approach ranged from 0.07 to 0.31, and those SNP-based ranged from 0.06 to 0.33. Regression coefficients ranged from 0.07 to 0.74 and from 0.08 to 1.45 using the haplotype- and SNP-based approaches, respectively. Despite the low to moderate accuracies for the genomic values, it is possible to obtain genetic progress trough selection using genomic information based either on SNPs or haplotype markers. The SNP-based approach allows less biased genomic evaluations, and it is more feasible when taking into account the computational and operational cost underlying the haplotypes inference.

Transcriptome profiling of muscle in Nelore cattle phenotypically divergent for the ribeye muscle area

This study aimed to use RNA-Seq to identify differentially expressed genes (DEGs) in muscle of uncastrated Nelore males phenotypically divergent for ribeye muscle area (REA). A total of 80 animals were phenotyped for REA, and 15 animals each with the highest REA and the lowest REA were selected for analyses. DEGs found (N = 288) belonging to families related to muscle cell growth, development, motility and proteolysis, such as actin, myosin, collagen, integrin, solute carrier, ubiquitin and kelch-like. Functional analysis showed that many of the significantly enriched gene ontology terms were closely associated with muscle development, growth, and degradation. Through co-expression network analysis, we predicted three hub genes (PPP3R1, FAM129B and UBE2G1), these genes are involved in muscle growth, proteolysis and immune system. The genes expression levels and its biological process found this study may result in differences in muscle deposition, and therefore, Nelore animals with different REA proportions.

Prediction of hub genes associated with intramuscular fat content in Nelore cattle

BACKGROUND

The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed genes (DEGs) associated with intramuscular fat content.

RESULTS

A total of 30 transcriptomics datasets (RNA-Seq) obtained from longissimus thoracis muscle were selected based on the phenotypic value of divergent intramuscular fat content: 15 with the highest intramuscular fat content (HIF) and 15 with the lowest intramuscular fat content (LIF). The transcriptomics datasets were aligned with a reference genome and 65 differentially expressed genes (DEGs) were identified, including 21 upregulated and 44 downregulated genes in HIF animals. The normalized count data from DEGs was then used for co-expression network construction. From the co-expression network, four modules were identified. The topological properties of the network were analyzed; those genes engaging in the most interactions (maximal clique centrality method) with other DEGs were predicted to be hub genes (PDE4D, KLHL30 and IL1RAP), which consequently may play a role in cellular and/or systemic lipid biology in Nelore cattle. Top modules screened from the gene co-expression network were identify. The two candidate modules had clear associated biological pathways related to fat development, cell adhesion, and muscle differentiation, immune system, among others. The hub genes belonged in top modules and were downregulated in HIF animals. PDE4D and IL1RAP have known effects on lipid metabolism and the immune system through the regulation of cAMP signaling. Given that cAMP is known to play a role in lipid systems, PDE4D and IL1RAP downregulation may contribute to increased levels of intracellular cAMP and thus may have effects on IF content differences in Nelore cattle. KLHL30 may have effects on muscle metabolism. Klhl protein families play a role in protein degradation. However, the downregulation of this gene and its role in lipid metabolism has not yet been clarified.

CONCLUSIONS

The results reported in this study indicate candidate genes and molecular mechanisms involved in IF content difference in Nelore cattle.

NK, S. S, Fairoze MN, Kaur M, Sharma A, Girdhar Y, M. SR, Devatkal SK, Ahlawat S, Vijh RK, S. MS. Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India

This study describes the muscle transcriptome profile of Bandur breed, a consumer favoured, meat type sheep of India. The transcriptome was compared to the less desirable, unregistered local sheep population, in order to understand the molecular factors related to muscle traits in Indian sheep breeds. Bandur sheep have tender muscles and higher backfat thickness than local sheep. The longissimus thoracis transcriptome profiles of Bandur and local sheep were obtained using RNA sequencing (RNA Seq). The animals were male, non-castrated, with uniform age and reared under similar environment, as well as management conditions. We could identify 568 significantly up-regulated and 538 significantly down-regulated genes in Bandur sheep (p≤0.05). Among these, 181 up-regulated and 142 down-regulated genes in Bandur sheep, with a fold change ≥1.5, were considered for further analysis. Significant Gene Ontology terms for the up-regulated dataset in Bandur sheep included transporter activity, substrate specific transmembrane, lipid and fatty acid binding. The down-regulated activities in Bandur sheep were mainly related to RNA degradation, regulation of ERK1 and ERK2 cascades and innate immune response. The MAPK signaling pathway, Adipocytokine signaling pathway and PPAR signaling pathway were enriched for Bandur sheep. The highly connected genes identified by network analysis were CNOT2, CNOT6, HSPB1, HSPA6, MAP3K14 and PPARD, which may be important regulators of energy metabolism, cellular stress and fatty acid metabolism in the skeletal muscles. These key genes affect the CCR4-NOT complex, PPAR and MAPK signaling pathways. The highly connected genes identified in this study, form interesting candidates for further research on muscle traits in Bandur sheep.

Gene expression profiling and identification of hub genes in Nellore cattle with different marbling score levels

The marbling rate evaluation is difficult and expensive, requiring slaughter of the animal or ultrasound measurement. Thus, this trait is generally not included in animal breeding programs. The use of molecular techniques to elucidate intramuscular fat deposition may help improve this trait. In this respect, transcriptome studies and differential gene expression analysis by RNA-Seq can contribute to advances in this area. The objective of this study was to use RNA-Seq to identify differentially expressed genes (DEGs) in muscle tissue (longissimus thoracis) of Nellore cattle divergently ranked on marbling, in order to increase our understanding of genes involved in the expression of this trait. The results revealed 49 DEGs and three hub genes (CISH, UFM1, TSHZ1), all of them involved in insulin and diabetes mellitus metabolism. These results indicating key genes and pathways, which may help to develop strategies designed to select animals with greater marbling.

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson’s r  > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.

Genomic, Transcriptomic, and Epigenomic Features Differentiate Genes That Are Relevant for Muscular Polyunsaturated Fatty Acids in the Common Carp

Polyunsaturated fatty acids (PUFAs) are a set of important nutrients that mainly include arachidonic acid (ARA4), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and α-linolenic acid (ALA). Recently, fish-derived PUFAs have been associated with cardiovascular health, fetal development, and improvement of brain functions. Studies have shown that fish muscular tissues are rich in PUFAs, which are influenced by various factors, including genetic variations, regulatory profiles, and methylation status of desaturase genes during fatty acid desaturation and elongation processes. However, the genetic mechanism and the pathways involved in fatty acid metabolism in fishes remain unclear. The overall aim of this study was to assess differences in gene expression responses among fishes with different fatty acid levels. To achieve this goal, we conducted genome-wide association analysis (GWAS) using a 250K SNP array in a population of 203 samples of common carp (Cyprinus carpio) and identified nine SNPs and 15 genes associated with muscular PUFA content. Then, RNA-Seq and whole genome bisulfite sequencing (WGBS) of different groups with high and low EPA, DHA, ARA4, and ALA contents in muscle, liver and brain tissues were conducted, resulting in 6,750 differentially expressed genes and 5,631 genes with differentially methylated promoters. Gene ontology and KEGG pathway enrichment analyses of RNA-Seq and WGBS results identified enriched pathways for fatty acid metabolism, which included the adipocytokine signaling pathway, ARA4 and linoleic acid metabolism pathway, and insulin signaling pathway. Integrated analysis indicated significant correlations between gene expression and methylation status among groups with high and low PUFA contents in muscular tissues. Taken together, these multi-level results uncovered candidate genes and pathways that are associated with fatty acid metabolism and paved the way for further genomic selection and carp breeding for PUFA traits.

Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle

Background

Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the genetic mechanism underpinning these traits and promote the improvement of fatty acid profiles. In this study, we performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle.

Results

In total, we detected 15 and 8 significant genome-wide SNPs for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, respectively. Also, we identified nine candidate genes based on 100 kb regions around associated SNPs. Four SNPs significantly associated with C14:1 cis-9 were embedded with stearoyl-CoA desaturase (SCD), while three SNPs in total were identified for C22:6 n-3 within Phospholipid scramblase family member 5 (PLSCR5), Cytoplasmic linker associated protein 1 (CLASP1), and Chymosin (CYM). Notably, we found the top candidate SNP within SCD can explain ~ 7.37% of phenotypic variance for C14:1 cis-9. Moreover, we detected several blocks with high LD in the 100 kb region around SCD. In addition, we found three significant SNPs within a 100 kb region showing pleiotropic effects related to multiple FA groups (PUFA, n-6, and PUFA/SFA), which contains BAI1 associated protein 2 like 2 (BAIAP2L2), MAF bZIP transcription factor F (MAFF), and transmembrane protein 184B (TMEM184B).

Conclusions

Our study identified several significant SNPs and candidate genes for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, and these findings will further assist the design of breeding programs for meat quality in cattle.

Review: Nutrigenomics of marbling and fatty acid profile in ruminant meat

The present review will present the recent published results and discuss the main effects of nutrients, mainly fatty acids, on the expression of genes involved in lipid metabolism. In this sense, the review focuses in two phases: prenatal life and finishing phase, showing how nutrients can modulate gene expression affecting marbling and fatty acid profile in meat from ruminants. Adiposity in ruminants starts to be affected by nutrients during prenatal life when maternal nutrition affects the differentiation and proliferation of adipose cells enhancing the marbling potential. Therefore, several fetal programming studies were carried out in the last two decades in order to better understand how nutrients affect long-term expression of genes involved in adipogenesis and lipogenesis. In addition, during the finishing phase, marbling becomes largely dependent on starch digestion and glucose metabolism, being important to create alternatives to increase these metabolic processes, and modulates gene expression. Different lipid sources and their fatty acids may also influence the expression of genes responsible to encode enzymes involved in fat tissue deposition, influencing meat quality. In conclusion, the knowledge shows that gene expression is a metabolic factor affecting marbling and fatty acid profile in ruminant meat and diets and their nutrients have direct effect on how these genes are expressed.

Transcriptome signature of liver tissue with divergent mutton odour and flavour using RNA deep sequencing

Mutton consumption is less popular in many Asian countries including Indonesia, whose consumers often complain about the unpleasant flavour and odour of the meat. The main causes of mutton odour are the two compounds of branched chain fatty acid (BCFA): methylnonanoic (MNA), phenol, 3-methyl (MP), 4-methylnonanoic (MNA) and 4-ethyloctanoic (EOA) present in all the adipose tissue; and the 3-methylindole (MI) or skatole and indole, which are originated from pastoral diets. It is crucial to understand the genetic mechanism of mutton odour and flavour (MOF) to select sheep for lower BCFA and indole thus reduce the unpleasant flavour of meat. The aim of the present study was to investigate transcriptome profiling in liver tissue with divergent MOF using RNA deep sequencing. Liver tissues from higher (n = 3) and lower (n = 3) MOF sheep were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample ranged from 21.37 to 25.37 million. Approximately 103 genes were differentially expressed (DEGs) with significance level of p-adjusted value <0.05. Among them, 60 genes were up-regulated, and 43 were down-regulated (p < 0.01, FC > 1.5) in higher MOF group. Differentially regulated genes in high MOF liver samples were enriched in biological processes such as cellular response to chemical stimulus and endogenous stimulus; cellular components such as such as basement membrane and extracellular matrix; and molecular functions such as haeme binding and oxidoreductase activity. Among the DEGs, metabolic phase I related genes belonging to the cytochrome P450 CYP2A6 were dominantly expressed. Additionally, phase II conjugation genes including UDP glucuronosyltransferases UGT2B18, sulfotransferase SULT1C1, and glutathione S-transferase GSTM1 were identified. The dominant candidate genes for SOF could be cytochrome P450, sodium-channel protein, transmembrane protein, glutathione transferase, UDP glucuronosyltransferases and sulfotransferase. Pathway analysis identified steroid hormone biosynthesis and chemical carcinogenesis by cytochrome P450 pathways which may play important roles in MOF-related molecules metabolism. This work highlighted potential genes and gene-networks that may affect meat off flavour and odour in sheep.

Skeletal muscle and liver gene expression profiles in finishing steers supplemented with Amaize

Our main objective was to evaluate the effects of feeding α-amylase (Amaize, Alltech Inc., Nicholasville, KY, USA) for 140 days on skeletal muscle and liver gene transcription in beef steers. Steers fed Amaize had lower average daily gain (p = .03) and gain:feed ratio (p = .05). No differences (p > .10) in serum metabolites or carcass traits were detected between the two groups but Amaize steers tended (p < .15) to have increased 12th rib fat depth. Microarray analysis of skeletal muscle revealed 21 differentially expressed genes (DEG), where 14 were up-regulated and seven were down-regulated in Amaize-fed steers. The bioinformatics analysis indicated that metabolic pathways involved in fat formation and deposition, stress response, and muscle function were activated, while myogenesis was inhibited in Amaize-fed steers. The quantitative PCR results for liver revealed a decrease (p < .01) in expression of fatty acid binding protein 1 (FABP1) and 3-hydroxybutyrate dehydrogenase 1 (BDH1) with Amaize. Because these genes are key for intracellular fatty acid transport, oxidation and ketone body production, data suggest a reduction in hepatic lipid catabolism. Future work to investigate potential positive effects of Amaize on cellular stress response, muscle function, and liver function in beef cattle appears warranted.

Deciphering signature of selection affecting beef quality traits in Angus cattle

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.