Traits In Beef Cattle Research Articles

Mutations in the GDF8 Gene in Double-Muscled Cattle: Mechanisms of Action and Relevance for Livestock Production

Myostatin (MSTN) has the function of limiting muscle growth, keeping satellite cells quiescent and acting on cell development, proliferation, differentiation, adhesion, migration and apoptosis. The mutation in the GDF8 gene proved to be advantageous as it presents some important attributes for the production of beef cattle, such as: gains in feed conversion and meat quality, making the meat leaner and more tender, resulting in intense selection for use in crossing programs in Brazil and around the world. We carried out a literature review on the mutation in the GDF8 gene in different breeds of Double Muscled cattle. We evaluated the frequency of polymorphisms present in research and observed that Indel c. 818 and MSTN-F94L were the markers most used in research. The MSTN-F94L polymorphism influenced musculature in the Jersey-Limousin backcross population. Furthermore, the polymorphism is strongly associated with the additive effect on birth weight, weaning weight and yearling weight, in addition to increasing the ease of direct birth in pure or mixed breeds. GDF8 gene polymorphisms can be used to improve performance traits in beef cattle. However, the influence of these markers needs to be determined in each herd.

Genetic parameters of behavior traits of beef cattle classified using wearable devices.

With the development of wearable devices, it is now possible to monitor livestock behavior 24 h a day. In this study, we estimated the genetic parameters of the daily duration of six behaviors (feeding, moving, lying, standing, ruminating while lying, and ruminating while standing) in beef cattle, automatically classified using wearable devices. The devices were attached to 332 Japanese beef cattle at two stations for approximately 5months. We compared repeatability, Poisson regression, and random regression models using the deviance information criterion. Poisson regression models were selected for all traits at each station, probably because of the non-normal distribution of the phenotypes. The heritability estimates by the Poisson regression models were moderate at each station: 0.67 and 0.68 for feeding, 0.68 and 0.53 for moving, 0.47 and 0.55 for lying, 0.45 and 0.40 for standing, 0.51 and 0.59 for ruminating while lying, and 0.37 and 0.45 for ruminating while standing. The genetic correlations between these traits were all negative at both stations, whereas the residual correlations showed different directions depending on the station. Although validation studies with larger populations are needed to confirm these findings, this study provides fundamental knowledge of the genetic basis of daily behavior in beef cattle.

Study of the beef cattle genetic potential realization indicators for digitalization of the animals breeding qualities assessment

In the course of the study, the indicators of the realization of the genetic potential of economically useful traits of beef cattle were considered, allowing to expand the completeness of the assessment of the breeding qualities of animals: exterior criteria (height at the withers, chest depth, trunk width, chest girth, etc.) related to productivity (average daily weight gain, removable live weight, etc.). Factors of selection were studied - genetic and phenotypic features. Particular attention was paid to the phenotypic indicators of the realization of the genetic potential of beef cattle, reflecting the important contribution of genotype and environmental factors. The high level of their variability contributes to the efficiency of selection. At the same time, a significant proportion of variability is due to the action of non-genetic factors, primarily the influence of changeable and unchangeable environmental factors. The accuracy of the assessment of breeding qualities of animals directly depends on the methods of their identification, registration and control of their productivity. The purpose of the study is to study a number of indicators of the best expression of signs of the realization of the genetic potential of animals for the digitalization of the evaluation of breeding qualities of beef cattle. An assessment of breeding animals is proposed, which will allow obtaining an instrument of expanded boundaries of genetic variability in the formation of the desired type of beef cattle. The development of the direction of digitalization of signs of qualitative genetics, in particular, signs of the exterior of an animal related to productivity and their inclusion in programs and plans to increase the genetic potential of animals, will be one of the effective methods of increasing it in cattle herds. Digitalization of the assessment of breeding qualities of beef cattle allows you to realize hidden reserves to increase the genetic potential of signs of meat productivity and covers the use of indicators that were previously not used due to the use of significant resources and the complexity of existing methods of collecting a large amount of data on animals. The proposed assessment of breeding animals will allow us to obtain an instrument of expanded boundaries of genetic variability in the formation of the desired type of beef cattle and will serve as an addition to the zootechnical rules and in the development of an automated system for managing breeding work in beef cattle breeding.

Genomic analysis of feed efficiency traits in beef cattle using random regression models.

Feed efficiency plays a major role in the overall profitability and sustainability of the beef cattle industry, as it is directly related to the reduction of the animal demand for input and methane emissions. Traditionally, the average daily feed intake and weight gain are used to calculate feed efficiency traits. However, feed efficiency traits can be analysed longitudinally using random regression models (RRMs), which allow fitting random genetic and environmental effects over time by considering the covariance pattern between the daily records. Therefore, the objectives of this study were to: (1) propose genomic evaluations for dry matter intake (DMI), body weight gain (BWG), residual feed intake (RFI) and residual weight gain (RWG) data collected during an 84-day feedlot test period via RRMs; (2) compare the goodness-of-fit of RRM using Legendre polynomials (LP) and B-spline functions; (3) evaluate the genetic parameters behaviour for feed efficiency traits and their implication for new selection strategies. The datasets were provided by the EMBRAPA-GENEPLUS beef cattle breeding program and included 2920 records for DMI, 2696 records for BWG and 4675 genotyped animals. Genetic parameters and genomic breeding values (GEBVs) were estimated by RRMs under ssGBLUP for Nellore cattle using orthogonal LPs and B-spline. Models were compared based on the deviance information criterion (DIC). The ranking of the average GEBV of each test week and the overall GEBV average were compared by the percentage of individuals in common and the Spearman correlation coefficient (top 1%, 5%, 10% and 100%). The highest goodness-of-fit was obtained with linear B-Spline function considering heterogeneous residual variance. The heritability estimates across the test period for DMI, BWG, RFI and RWG ranged from 0.06 to 0.21, 0.11 to 0.30, 0.03 to 0.26 and 0.07 to 0.27, respectively. DMI and RFI presented within-trait genetic correlations ranging from low to high magnitude across different performance test-day. In contrast, BWG and RWG presented negative genetic correlations between the first 3 weeks and the other days of performance tests. DMI and RFI presented a high-ranking similarity between the GEBV average of week eight and the overall GEBV average, with Spearman correlations and percentages of individuals selected in common ranging from 0.95 to 1.00 and 93 to 100, respectively. Week 11 presented the highest Spearman correlations (ranging from 0.94 to 0.98) and percentages of individuals selected in common (ranging from 85 to 94) of BWG and RWG with the average GEBV of the entire period of the test. In conclusion, the RRM using linear B-splines is a feasible alternative for the genomic evaluation of feed efficiency. Heritability estimates of DMI, RFI, BWG and RWG indicate enough additive genetic variance to achieve a moderate response to selection. A new selection strategy can be adopted by reducing the performance test to 56 days for DMI and RFI selection and 77 days for BWG and RWG selection.

Genome-wide scans identify biological and metabolic pathways regulating carcass and meat quality traits in beef cattle

Genome association studies (GWAS) provides knowledge about the genetic architecture of beef-related traits that allow linking the target phenotype to genomic information aiding breeding decision. Thus, the present study aims to uncover the genetic mechanism involved in carcass (REA: rib eye area, BF: backfat thickness, and HCW: hot carcass weight) and meat quality traits (SF: shear-force, MARB: marbling score, and IMF: intramuscular fat content) in Nellore cattle. For this, 6910 young bulls with phenotypic information and 23,859 animals genotyped with 435 k markers were used to perform the weighted single-step GBLUP (WssGBLUP) approach, considering two iterations. The top 10 genomic regions explained 8.13, 11.81, and 9.58% of the additive genetic variance, harboring a total of 119, 143, and 95 positional candidate genes for REA, BF, and HCW, respectively. For meat quality traits, the top 10 windows explained a large proportion of the total genetic variance for SF (14.95%), MARB (17.56%), and IMF (21.41%) surrounding 92, 155, and 111 candidate genes, respectively. Relevant candidate genes (CAST, PLAG1, XKR4, PLAGL2, AQP3/AQP7, MYLK2, WWOX, CARTPT, and PLA2G16) are related to physiological aspects affecting growth, carcass, meat quality, feed intake, and reproductive traits by signaling pathways controlling muscle control, key signal metabolic molecules INS / IGF-1 pathway, lipid metabolism, and adipose tissue development. The GWAS results provided insights into the genetic control of the traits studied and the genes found are potential candidates to be used in the improvement of carcass and meat quality traits.

Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves

BackgroundBeef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.ResultsUsing a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.ConclusionsWithin the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.

Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle.

For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.

Influence of targeted protein-vitamin-mineral concentrates on the beef traits of steers of different breeds

Currently, research is relevant to the development and testing of recipes for proteinvitamin- mineral concentrates (PVMC) based on extruded soybeans and synthetic nitrogen-containing substances, which allows optimizing the protein and mineral nutrition of animals. The purpose of the research was to study the infl uence of targeted PVMC on meat productivity and beef quality of steers of diff erent breeds in the Kurgan region. The eff ect of PVMC on meat productivity was studied on steers of Black-and-White and Aberdeen-Angus breeds. For this purpose, three groups were formed in each breed, which included 15 heads of steers aged 12 months. The steers of the control group were fed PVMC -65, the steers of the 1st experimental group were fed the experimental PVMC-65K, and the 2nd experimental group were fed PVMC-65KB at 200 g per 100 kg of live weight. Feeding targeted PVMC-65KB had a positive eff ect on the meat productivity of steers. Over 150 days of fattening, the live weight of steers of Black-and-White breed was 8,9 % higher, and steers of Aberdeen-Angus breed was 6,1 % higher compared to the control herdmates. The slaughter yield for steers of the experimental groups received PVMC-65KB was 53,7 % for steers of Black-and-White breed and 57,3 % for steers of Aberdeen-Angus breed, which was 1,62 and 1,56 abs.% more than their herdmates from control groups. The proportion of muscle tissue in the experimental groups of steers received PVMC-65KB was higher by 1,73 abs.% in Black-and-White and by 2,37 abs.% in Aberdeen-Angus compared to control herdmates. It was found that optimization of feeding of steers stimulated muscle raising in animals of the experimental groups, in the same time in the control group at this age the deposition of adipose tissue had already begun.

PSIII-20 Transcriptional and Functional Analyses of Intramuscular, Subcutaneous, and Visceral Adipose Tissue in Finished Beef Cattle

Abstract Intramuscular adipose tissue (IMAT; marbling) deposition is a highly desired trait in beef cattle. Unlike excessive subcutaneous (SCAT) and visceral (VIAT) adipose tissue, which have relatively low value, increased marbling is associated with meat sensory traits and is a primary factor influencing beef quality grading in the U.S. However, this trait is difficult to achieve. Our objective was to assess depot-specific characteristics and gene profile of IMAT, SCAT, and VIAT in beef cattle. IMAT and SCAT samples from the longissimus muscle (9-11th ribs), and VIAT from the greater omentum were collected from four beef animals at harvest. Adipose tissue (AT) samples were flash frozen in liquid nitrogen, followed by RNA extraction (Trizol reagent) and RNA sequencing analysis on an Illumina Novaseq 6000 platform to generate 150 bp paired-end reads. DESeq2 R package was used for differential gene expression analysis (DEG) and DEG (P ≤ 0.05, log2FC ≥ 1) were evaluated for KEGG enrichment pathways. Remainder tissue samples were assessed for viscoelasticity (rheometer), collagen fibrillogenesis (kinetics), and adipocyte size (K2 Cellometer). Transcriptome analysis revealed over 4,000 DEG between IMAT and SCAT, over 3,000 DEG between VIAT and IMAT, and 1,018 DEG between VIAT and SCAT, thus indicating substantial transcriptional diversity among AT depots (Figure 1). Top upregulated genes in SCAT vs. IMAT were associated with increased lipid accumulation and regulation such as LIPE, LEP, ADIPOQ, PPARG, and extracellular matrix (ECM) remodeling, including collagens, MMP14, and TIMP4. Accordingly, enrichment analysis revealed an activation of PPARG signaling pathways and fatty acid metabolism in SCAT vs. IMAT, which are key for lipogenesis and adipogenesis (Figure 2). IMAT showed activation of pathways for thermogenesis and oxidative phosphorylation compared with both SCAT and VIAT, indicating that IMAT utilization may be more directed towards muscle function and development (Figure 2 and 3). Top VIAT DEG were primarily associated with immune cell adhesion, and immune response (CDHR1, TENM2, and TNFRSF9), suggesting a pro-inflammatory profile of visceral adiposity. Notably, enrichment analysis showed an activation of the immune function in VIAT compared with IMAT and SCAT (Figures 3 and 4). In agreement with transcriptome analysis, adipocyte size was increased in SCAT vs. IMAT and VIAT, implying higher lipid accumulation (Figure 5). SCAT was also stiffer and had increased collagen fibrillogenesis compared with IMAT, suggesting a key role for ECM in mechanisms of AT adipogenesis and lipogenesis (Figure 5). In summary, these results indicate that AT anatomical location impacts AT transcriptome, which may translate into functional differences in adipogenesis and ECM remodeling. Understanding transcriptional and functional differences among IMAT, SCAT and VIAT can help on the identification of target genes to modulate AT deposition in distinct areas of the body, therefore, improving quality of beef carcasses and industry profitability.

Sequence-based GWAS meta-analyses for beef production traits

BackgroundCombining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. As part of the H2020 BovReg project, we performed sequence-level MA for beef production traits. Five partners from France, Switzerland, Germany, and Canada contributed summary statistics from sequence-based GWAS conducted with 54,782 animals from 15 purebred or crossbred populations. We combined the summary statistics for four growth, nine morphology, and 15 carcass traits into 16 MA, using both fixed effects and z-score methods.ResultsThe fixed-effects method was generally more informative to provide indication on potentially causal variants, although we combined substantially different traits in each MA. In comparison with within-population GWAS, this approach highlighted (i) a larger number of quantitative trait loci (QTL), (ii) QTL more frequently located in genomic regions known for their effects on growth and meat/carcass traits, (iii) a smaller number of genomic variants within the QTL, and (iv) candidate variants that were more frequently located in genes. MA pinpointed variants in genes, including MSTN, LCORL, and PLAG1 that have been previously associated with morphology and carcass traits. We also identified dozens of other variants located in genes associated with growth and carcass traits, or with a function that may be related to meat production (e.g., HS6ST1, HERC2, WDR75, COL3A1, SLIT2, MED28, and ANKAR). Some of these variants overlapped with expression or splicing QTL reported in the cattle Genotype-Tissue Expression atlas (CattleGTEx) and could therefore regulate gene expression.ConclusionsBy identifying candidate genes and potential causal variants associated with beef production traits in cattle, MA demonstrates great potential for investigating the biological mechanisms underlying these traits. As a complement to within-population GWAS, this approach can provide deeper insights into the genetic architecture of complex traits in beef cattle.

Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle.

Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.

Multi‐trait genomic predictions using GBLUP and Bayesian mixture prior model in beef cattle

AbstractMultiple trait genomic selection incorporating correlated traits can improve the predictive ability of low‐heritability traits. In this study, we evaluated genomic prediction accuracy using multi‐trait BayesCπ method (MT‐BayesCπ), which allows for a broader range of mixture priors for important traits in beef cattle. We compared the prediction performance of MT‐BayesCπ with single‐trait genomic best linear unbiased prediction (ST‐GBLUP), multi‐trait GBLUP (MT‐GBLUP), and single‐trait BayeCπ (ST‐BayesCπ) methods. We found that ribeye area (REA) and ribeye weight (REWT) showed high heritability, while slaughter weight (SWT) and carcass weight (CWT) displayed medium heritability, and slaughter rate (SR) and feedlot average daily gain (FDG) showed low heritability. Highly positive genetic correlations were observed between CWT and SWT (0.981) and SR and REWT (0.921). Notably, the MT‐BayesCπ method showed superior predictive abilities compared to other models. Using MT‐BayesCπ method, the accuracy increased from 0.272 to 0.694 for CWT compared to ST‐GBLUP and ST‐BayesCπ. MT‐GBLUP and ST‐BayesCπ showed similar prediction accuracies, while MT‐BayesCπ showed the least biased evaluations. Additionally, our results suggested that prediction accuracy of low‐heritability traits significantly increased when they were combined with traits with high genetic correlation in a multi‐trait prediction. Our study suggests that multi‐trait genomic predictions using GBLUP and Bayesian mixture prior models is feasible for genomic selection in beef cattle. Our findings indicate that MT‐BayesCπ outperforms other models (ST‐GBLUP, MT‐GBLUP and ST‐BayesCπ), especially for low‐heritability traits.

Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions.

The prenatal environment is recognized as crucial for the postnatal performance in cattle. In tropical regions, pregnant beef cows commonly experience nutritional restriction during the second half of the gestation period. Thus, the present study was designed to analyze the genotype by prenatal environment interaction (G × Epn) and to identify genomic regions associated with the level and response in growth and reproduction-related traits of beef cattle to changes in the prenatal environment. A reaction norm model was applied to data from two Nelore herds using the solutions of contemporary groups for birth weight as a descriptor variable of the gestational environment quality. A better gestational environment favored weights until weaning, scrotal circumference at yearling, and days to first calving of the offspring. The G × Epn was strong enough to result in heterogeneity of variance components and genetic parameters in addition to reranking of estimated breeding values and SNPs effects. Several genomic regions associated with the level of performance and specific responses of the animals to variations in the gestational environment were revealed, which harbor QTLs and can be exploited for selection purposes. Therefore, genetic evaluation models considering G × Epn and special management and nutrition care for pregnant cows are recommended.

Genome-wide signature of positive selection in Ethiopian indigenous and European beef cattle breeds

BackgroundDespite the availability of genome-wide SNPs to uncover the origin and divergence of Ethiopian cattle population, knowledge regarding their genetic adaptability and divergence remain limited. To investigate signature of selection, three Ethiopian cattle breeds were genotyped with 80 K SNP array and three European beef cattle breeds were also used for comparison purposes. ResultsAcross Ethiopian cattle populations, the mean observed and expected heterozygosity were 0.403 and 0.400, respectively, and for European beef cattle breeds observed and expected heterozygosity were 0.25 and 0.26 respectively. PCA and NJ-tree grouped the study cattle according to their breed group with close clustering of Ethiopian cattle breeds. The top 1% values were considered to delimit genomic regions under positive selection. Some of the candidate genes involved in biological processes and pathways linked to meat quality attributes. Furthermore, some of the candidate genes associated with tropical adaptation like heat tolerance and resistance to disease. ConclusionThe genetic divergence of Ethiopian breeds from European beef breeds coincides with existing knowledge that European cattle breeds considered in this study are artificially selected for beef traits, while Ethiopian indigenous breeds are naturally selected.

Long Non-Coding RNA BNIP3 Inhibited the Proliferation of Bovine Intramuscular Preadipocytes via Cell Cycle.

The intramuscular fat (or marbling fat) content is an essential economic trait of beef cattle and improves the flavor and palatability of meat. Several studies have highlighted the correlation between long non-coding RNAs (lncRNAs) and intramuscular fat development; however, the precise molecular mechanism remains unknown. Previously, through a high-throughput sequencing analysis, we found a lncRNA and named it a long non-coding RNA BNIP3 (lncBNIP3). The 5' RACE and 3' RACE explored 1945 bp total length of lncBNIP3, including 1621 bp of 5'RACE, and 464 bp of 3'RACE. The nucleoplasmic separation and FISH results explored the nuclear localization of lncBNIP3. Moreover, the tissue expression of lncBNIP3 was higher in the longissimus dorsi muscle, followed by intramuscular fat. Furthermore, down-regulation of lncBNIP3 increased the 5-Ethynyl-2'- deoxyuridine (EdU)-EdU-positive cells. The flow cytometry results showed that the number of cells in the S phase was significantly higher in preadipocytes transfected with si-lncBNIP3 than in the control group (si-NC). Similarly, CCK8 results showed that the number of cells after transfection of si-lncBNIP3 was significantly higher than in the control group. In addition, the mRNA expressions of proliferative marker genes CyclinB1 (CCNB1) and Proliferating Cell Nuclear Antigen (PCNA) in the si-lncBNIP3 group were significantly higher than in the control group. The Western Blot (WB) results also showed that the protein expression level of PCNA transfection of si-lncBNIP3 was significantly higher than in the control group. Similarly, the enrichment of lncBNIP3 significantly decreased the EdU-positive cells in the bovine preadipocytes. The results of flow cytometry and CCK8 assay also showed that overexpression of lncBNIP3 inhibited the proliferation of bovine preadipocytes. In addition, the overexpression of lncBNIP3 significantly inhibited the mRNA expressions of CCNB1 and PCNA. The WB results showed that the overexpression of lncBNIP3 significantly inhibited the expression of the CCNB1 protein level. To further explore the mechanism of lncBNIP3 on the proliferation of intramuscular preadipocytes, RNA-seq was performed after interference with si-lncBNIP3, and 660 differentially expressed genes (DEGs) were found, including 417 up-regulated DEGs and 243 down-regulated DEGs. The KEGG pathway analysis showed that the cell cycle was the most significant pathway for the functional enrichment of DEGs, followed by the DNA replication pathway. The RT-qPCR quantified the expression of twenty DEGs in the cell cycle. Therefore, we speculated that lncBNIP3 regulated intramuscular preadipocyte proliferation through the cell cycle and DNA replication pathways. To further confirm this hypothesis, the cell cycle inhibitor Ara-C was used to inhibit DNA replication of the S phase in intramuscular preadipocytes. Herein, Ara-C and si-lncBNIP3 were simultaneously added to the preadipocytes, and the CCK8, flow cytometry, and EdU assays were performed. The results showed that the si-lncBNIP3 could rescue the inhibitory effect of Ara-C in the bovine preadipocyte proliferation. In addition, lncBNIP3 could bind to the promoter of cell division control protein 6 (CDC6), and down-regulation of lncBNIP3 promoted the transcription activity and the expression of CDC6. Therefore, the inhibitory effect of lncBNIP3 on cell proliferation might be understood through the cell cycle pathway and CDC6 expression. This study provided a valuable lncRNA with functional roles in intramuscular fat accumulation and revealed new strategies for improving beef quality.

Effects of the CDC10 (Septin 7) Gene on the Proliferation and Differentiation of Bovine Intramuscular Preadipocyte and 3T3-L1 Cells.

Intramuscular fat content and marbling affecting meat quality are important economic traits in beef cattle. CDC10 (cell division cycle 10 or Septin 7), a member of the septin family involved in cellular proliferation, was considered as a functional and positional candidate gene for beef marbling. In a previous study, we revealed that the expression levels of CDC10 were also positively correlated with marbling scores in Japanese Black cattle. However, the regulatory mechanism of the CDC10 gene on IMF deposition in cattle remains unclear. In the present study, flow cytometry, EdU proliferation assays, and Oil Red O staining results showed that overexpression of CDC10 could promote the differentiation of bovine intramuscular preadipocyte (BIMP) and 3T3-L1 cells, whereas knockdown of CDC10 resulted in the opposite consequences. Furthermore, quantitative PCR and Western blotting results showed that overexpression of CDC10 could promote the expression levels of adipogenic marker genes PPARγ and C/EBPα at both mRNA and protein levels in BIMP and 3T3-L1 cells, whereas knockdown of CDC10 resulted in the opposite consequences. Our results provide new insights into the regulatory roles of CDC10 in adipocytes in animals.

Indicators of beef productivity when feeding targeted PVMC to fattening steers

Targeted protein-vitamin-mineral concentrates (PVMC) based on domestic raw materials have been developed. The composition of protein-vitamin-mineral concentrates includes full-fat extruded soy, sunfl ower cake, feed tricalcium phosphate and vitamin-mineral complex. The purpose of the research was to study the indicators of meat productivity when feeding targeted PVMC to fattening steers. Amidoconcentrate additive and bentonite were introduced into experimental protein-vitaminmineral concentrates. After analyzing the chemical composition and nutritional value of the ration in the experimental PVMC-65K and PVMC-65KB, the content of a number of minerals was changed: iron, manganese, cobalt, etc. This made it possible to optimize the ration for these trace elements: reduce the excess of iron and manganese, as well as increase the content of copper and cobalt. During 5 months of fattening, the live weight of the steers of the control group increased by 136,4 kg, the 1st experimental group by 144,9 kg, and in the 2nd experimental group by 148,5 kg, which was more by 6,23 and 8,87 %, respectively. Feeding targeted PVMC-65K allowed to ensure the formation of good beef traits in animals. So, the steers of the 2nd experimental group compared with the herdmates of the control group had a greater pre–slaughter weight by 1,96 %, the carcass weight by 4,8, the internal fat mass by 12,59, and the carcass yield by 1,42 abs.%. The slaughter yield of the steers of the 1st experimental group was 53,23 %, and the 2nd it was 53,70 %, which was respectively 1,15 and 1,62 abs.% more than in the control group. The level of profi tability of beef production in the control group was 21,28 %, in the 1st experimental group it was higher by 9,06 abs.%, and in the 2nd by 14,36 abs.%.

Variance component estimates for growth traits in beef cattle using selected variants from imputed low-pass sequence data.

A beef cattle population (n = 2,343) was used to assess the impact of variants identified from the imputed low-pass sequence (LPS) on the estimation of variance components and genetic parameters of birth weight (BWT) and post-weaning gain (PWG). Variants were selected based on functional impact and were partitioned into four groups (low, modifier, moderate, high) based on predicted functional impact and re-partitioned based on the consequence of mutation, such as missense and untranslated region variants, into six groups (G1-G6). Each subset was used to construct a genomic relationship matrix (GRM) for univariate animal models. Multiple analyses were conducted to compare the proportion of additive genetic variation explained by the different subsets individually and collectively, and these estimates were benchmarked against all LPS variants in a single GRM and array (e.g., GeneSeek Genomic Profiler 100K) genotypes. When all variants were included in a single GRM, heritability estimates for BWT and PWG were 0.43 ± 0.05 and 0.38 ± 0.05, respectively. Heritability estimates for BWT ranged from 0.10 to 0.42 dependent on which variant subsets were included. Similarly, estimates for PWG ranged from 0.05 to 0.38. Results showed that variants in the subsets modifier and G1 (untranslated region) yielded the highest heritability estimates and were similar to the inclusion of all variants, while estimates from GRM containing only variants in the categories High, G4 (non-coding transcript exon), and G6 (start and stop loss/gain) were the lowest. All variants combined provided similar heritability estimates to chip genotypes and provided minimal to no additional information when combined with chip data. This suggests that the chip single nucleotide polymorphisms and the variants from LPS predicted to be less consequential are in relatively high linkage disequilibrium with the underlying causal variants as a whole and sufficiently spread throughout the genome to capture larger proportions of additive genetic variation.

An investigation into potential genetic predictors of birth weight in tropically adapted beef cattle in northern Australia

Context Birth weight can be an important trait in beef cattle through its association with dystocia and increased likelihood of calf and cow mortality. Recording large numbers of birth weights in beef cattle to obtain a suitable genetic evaluation has often been hard to achieve. Aims We assess if coronet circumference measurements taken at birth and weights and coronet circumference measured post-birth are suitable predictors of birth weight for use in genetic evaluation in northern Australian tropically adapted beef breeds. Methods Animals were recorded at birth for weight (N = 5352) and coronet circumference (N = 2552), at 3 months of age for the liveweight (N = 2848) and coronet circumference (N = 2855) and liveweight at 6 months (N = 4929). Data were from three tropically adapted beef cattle breeds (viz. Brahman, Droughtmaster and Santa Gertrudis) recorded in two northern Australia herds. Genetic parameters were estimated from a pooled dataset containing all three breeds. Results Birth weight had an estimated direct and maternal heritability of 0.51 (0.04) and 0.14 (0.02) respectively. Coronet circumference also had high heritabilities, with estimates at birth and 3 months of 0.50 (0.07) and 0.55 (0.06) respectively. The estimated genetic correlation between birth weight and coronet circumference measured at birth was 0.86 (0.03). Birth weight genetic correlations were 0.75 (0.05) with 3-month weight, 0.69 (0.05) with weaning weight and 0.62 (0.05) with coronet circumference at 3 months. Conclusions Coronet measurements could be used in genetic evaluation as a proxy for birth weight. However, the most useful coronet measure was when it was recorded at birth. This would still require catching the calf at birth, thus greatly reducing the benefit of having an alternative measure. Coronet circumference recorded in the branding cradle at 3 months of age was also a useful predictor of birth weight but added little if post-birth weights were available. Importantly, all post-birth indirect measures of birth weight require adjustment for animal age and, therefore, would need recording of the individual calf’s date of birth. Implications Coronet circumference recorded at birth and 3 months of age does not appear to be a suitable proxy for genetic evaluation of birth weight.

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.