Bioinformatics and genetic variants analysis of FGF10 gene promoter with their association at carcass quality and body measurement traits in Qinchuan beef cattle.

The fibroblast growth factor 10 (FGF10) gene regulates adipogenesis and myogensis. In this study, sequencing of FGF10 prompter region identified three SNPs at loci g.78G > A, g.116C > T and g.201A > T. Each SNP yields three genotypes as GG, GA and AA at loci g.78G > A, CC, CT and TT at loci g.116C > T and AA, AT and TT at loci g.201A > T. Allelic and genotypic frequencies of all three SNPs deviated from the Hardy-Weinberg equilibrium (HWE) (P < 0.05) and were found highly polymorphic as PIC (0.25 < PIC < 0.50). Moreover, we found highest LD (D'/γ2) between SNP2 and SNP3 (0.989/0.909), followed by SNP1 and SNP3 (0.944/0.796). Moreover, three variants of FGF10 gene promoter exhibited significant (P < 0.05) association with body measurement and carcass quality traits in Qinchuan beef cattle. At loci g.78G > A, the genotype GG showed significantly (P < 0.01) larger body length (BL), rump length (RL), chest depth (CD), chest circumference (CC) and ultrasound loin area (ULA). The genotype TC at loci g.116C > T showed significantly (P < 0.01 and 0.05) larger body measurement and intramuscular fat, and ultrasound loin area (ULA). In addition to that, at loci g.201A > T, genotype TT showed significantly (P < 0.01 and P < 0.05) larger body length (BL), rump length (RL), hip width (HW), chest circumference (CC) and ultrasound loin area (ULA). Additionally, screening of promoter sequence of FGF10 gene explored loss of four TFs binding sites (KLF3, ZNF37α, GLIS2 and BCL11A) at g.116C > T because of SNP2. However, a single TF binding site was lost at g.202A > T due to SNP3. Interestingly, none of TF binding site was lost at g.78G > A in SNP1; however, one new TF binding site was gained at this location due to SNP1. These findings conclude that genotype GG, TC and TT could be used as genetic markers of FGF10 gene for body measurement and carcass quality traits in Qinchuan beef cattle.

Tissue Expression Analysis, Cloning, and Characterization of the 5'-Regulatory Region of the Bovine LATS1 Gene.

As a member of the large tumor suppressor (LATS) gene family, LATS1 plays an important role in regulating muscle growth and development. In this study, we determined the distinct exhibit patterns of tissue expression of bovine LATS1. Further, we determined the functional proximal minimal promoter of bovine LATS1 and identified the key transcription factors in the core promoter region to elucidate its molecular regulation mechanism. The results showed that bovine LATS1 was highly expressed in the longissimus thoracis and upregulation in infancy muscle. An electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assay in combination with site-directed mutation and small interfering RNA (siRNA) interference demonstrated that myogenic differentiation 1 (Myod1) and myocyte enhancer factor 2A (MEF2A) binding in the core promoter region (-298/-123 bp) play important roles in the transcriptional regulation of the bovine LATS1 promoter. Taken together, these interactions provide insight into the regulatory mechanisms of LATS1 transcription in mediating skeletal muscle growth in cattle.

RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation.

Intramuscular fat is a real challenge for the experts of animal science to improve meat quality traits. Research on the mechanism of adipogenesis provides invaluable information for the improvement of meat quality traits. This study investigated the effect of bta-miR-149-5p and its underlying mechanism on lipid metabolism in bovine adipocytes. Bovine adipocytes were differentiated and transfected with bta-miR-149-5p mimics or its negative control (NC). A total of 115 DEGs including 72 upregulated and 43 downregulated genes were identified in bovine adipocytes. The unigenes and GO term biological processes were the most annotated unigene contributor parts at 80.08%, followed by cellular component at 13.4% and molecular function at 6.7%. The KEGG pathways regulated by the DEGs were PI3K-Akt signaling pathway, calcium signaling pathway, pathways in cancer, MAPK signaling pathway, lipid metabolism/metabolic pathway, PPAR signaling pathway, AMPK signaling pathway, TGF-beta signaling pathway, cAMP signaling pathway, cholesterol metabolism, Wnt signaling pathway, and FoxO signaling pathway. In addition to this, the most important reactome enrichment pathways were R-BTA-373813 receptor CXCR2 binding ligands CXCL1 to 7, R-BTA-373791 receptor CXCR1 binding CXCL6 and CXCL8 ligands, R-BTA-210991 basigin interactions, R-BTA-380108 chemokine receptors binding chemokines, R-BTA-445704 calcium binding caldesmon, and R-BTA-5669034 TNFs binding their physiological receptors. Furthermore, the expression trend of the DEGs in these pathways were also exploited. Moreover, the bta-miR-149-5p significantly (p < 0.01) downregulated the mRNA levels of adipogenic marker genes such as CCND2, KLF6, ACSL1, Cdk2, SCD, SIK2, and ZEB1 in bovine adipocytes. In conclusion, our results suggest that bta-miR-149-5p regulates lipid metabolism in bovine adipocytes. The results of this study provide a basis for studying the function and molecular mechanism of the bta-miR-149-5p in regulating bovine adipogenesis.

Association between Single Nucleotide Polymorphisms in SIRT1 and SIRT2 Loci and Growth in Tibetan Sheep.

Silent information regulator 1 and 2 (SIRT1, 2) were NAD+-dependent histone or non-histone deacetylase, which emerged as key metabolic sensors in several tissues of mammals. In the present study, the search for polymorphisms within the ovine SIRT1 and SIRT2 loci as well as association analyses between SNPs and growth-related traits were performed in Tibetan sheep. To determine the expression pattern of SIRT1 and SIRT2 genes in Tibetan sheep, the quantitative real-time polymerase chain reaction (qPCR) analysis revealed that those two genes were widely expressed in diverse tissues. Expression of SIRT1 was less in abomasum of lamb, whereas it was greater in duodenum within adult stage. In the case of SIRT2, the greatest expression was observed in reticulum (lamb) and in muscle (adult), whereas the least expression was in liver for lamb and in kidney for adult animals. The association analysis demonstrated that g.3148 C > T polymorphism of SIRT1 affected heart girth (p = 0.002). The g.8074 T > A SNP of SIRT2 had a significant correlation with body weight (p = 0.011) and body length (p = 0.008). These findings suggested that the SIRT1 and SIRT2 polymorphism was involved in growth-related traits in Tibetan sheep, which may be considered to be genetic markers for improving the growth traits of Tibetan sheep.

Association of hormone-sensitive lipase (HSL) gene polymorphisms with the intramuscular fat content in two Chinese beef cattle breeds.

Hormone-sensitive lipase (HSL) was considered as an essential enzyme in glucolipid metabolism. It has been proposed to be a lead candidate gene for genetic markers of lipid deposition in livestock. The aim of this study was to identify sequence variants (SVs) of the bovine HSL gene and evaluate the relations to intramuscular fat in two indigenous Chinese beef cattle breeds. Expression analysis by quantitative real-time polymerase chain reactions (qPCR) indicated that expression levels of bovine HSL gene were highest in the perirenal fat and heart within two different age stage (adult and calf), respectively. Five SVs were identified by direct DNA sequencing, which included four missense mutations (g.16563C>T, g.16734G>A, g.16896A>G, g.17388G>T) in exon 8 and a synonymous mutation (g.17402C>T) in exon 9. Population genetic analysis showed that except for g.16563C>T and g.17402C>T, all the other detected SVs strongly affected the bovine intramuscular fat content (P < 0.01 or P < 0.05). The individuals with Hap5/5 diplotypes (CC-GG-GG-GG-CC) was highly significantly associated with intramuscular fat content than the other diplotypes (P < 0.01). The above results suggested that the HSL gene can used as potential candidate markers gene for the beef breed improvement through marker assisted selection in Chinese cattle breeds.

Polymorphism of the PLIN1 gene and its association with body measures and ultrasound carcass traits in Qinchuan beef cattle.

The PLIN1 gene produces a phosphorylated protein wrapped in lipid droplets in adipocytes. This phosphorylation assists the mobilization of fat into adipose tissue. The purpose of the experiment was to study the polymorphism of the PLIN1 gene and its relationship with the body and carcass characteristics of Qinchuan cattle to find molecular genetic markers that can be used for breeding. The expression level of the PLIN1 gene was determined in various tissues by qRT-PCR. The results showed that the highest level of PLN1 expression was found in subcutaneous fat, followed by the heart and longissimus muscle, and the lowest level was found in the kidney. Five SNP loci of the PLIN1 gene were identified in 510 Qinchuan cattle, including g.3580T>C (SNP1), g.3898G>A (SNP2), g.8333G>A (SNP3), g.10517T>C (SNP4), and g.10538G>T (SNP5). The results show that SNP1, SNP2, SNP3, and SNP4 were moderately polymorphic (0.25 < PIC < 0.5), while SNP5 was minimally polymorphic (PIC < 0.25). SNP2, SNP3, and SNP5 were within Hardy-Weinberg equilibrium (P > 0.05), but SNP1 and SNP4 were not (P < 0.05). Correlation analysis showed that the five SNPs of the PLIN1 gene were correlated with back-fat depth, intramuscular fat, and chest depth of Qinchuan cattle. The double haplotype H2H4 in Qinchuan beef was associated with body and carcass traits. We conclude that variants mapped within PLIN1 can be used in marker-assisted selection for carcass quality and body traits in breed improvement programs for Qinchuan cattle.

Genetic variants in the TORC2 gene promoter and their association with body measurement and carcass quality traits in Qinchuan cattle.

The TORC2 gene is responsible for nutrient metabolism, gluconeogenesis, myogenesis and adipogenesis through the PI3K-Akt, AMPK, glucagon and insulin resistance signaling pathways. Sequencing of PCR amplicons explored three novel SNPs at loci g.16534694G>A, g.16535011C>T, and g.16535044A>T in the promoter region of the TORC2 gene in the Qinchuan breed of cattle. Allelic and genotypic frequencies of these SNPs deviated from Hardy-Weinberg equilibrium (HWE) (P < 0.05). SNP1 genotype GG, SNP2 genotype CT and SNP3 genotype AT showed significantly (P <0.05) larger body measurement and improved carcass quality traits. Haplotype H1 (GCA) showed significantly (p<0.01) higher transcriptional activity (51.44%) followed by H4 (ATT) (34.13%) in bovine preadipocytes. The diplotypes HI-H3 (GG-CC-AT), H1-H2 (GG-CT-AT) and H3-H4 (GA-CT-TT) showed significant (P<0.01) associations with body measurement and improved carcass quality traits. Analysis of the relative mRNA expression level of the TORC2 gene in different tissues within two different age groups revealed a significant increase (P<0.01) in liver, small intestine, muscle and fat tissues with growth from calf stage to adult stage. We can conclude that variants mapped within TORC2 can be used in marker-assisted selection for carcass quality and body measurement traits in breed improvement programs of Qinchuan cattle.

Flavonoid bioactive compounds of hawthorn extract can promote growth, regulate electrocardiogram waves, and improve cardiac parameters of pulmonary hypertensive chickens.

The effect of orally administered hawthorn flavonoid extract (HFE) on growth, electrocardiographic waves, and cardiac parameters of pulmonary hypertensive chickens reared at high altitude (2,100 m above sea level) was examined. A total of 225 one-day-old, mixed broiler chicks (3 treatments with 5 replicates and 15 chicks per each, totally 75 birds/treatment) were assigned to 3 experimental groups: 0, 0.1, and 0.2 ml of HFE per 1 L of drinking water. Birds were administered the drinking water HFE treatments for 42 D. At an age of 28 and 42 D, electrocardiograms were undertaken and cardiac parameters such as the RV:TV, RV:BW, and TV:BW, and indicators of PHS on selected birds were measured. The final BW of chickens receiving the HFE at 0.2 ml/L was greater (2,579 ± 64 g) than that of birds receiving 0.1 ml/L (2,497 ± 62 g) and 0 ml/L (2,323 ± 57 g). Therefore, no supplemented group had a lower final BW than others (P < 0.05). Amplitudes of S and T waves in 0.1- and 0.2-ml/L HFE consumed groups at 28 and 42 D of age decreased compared with that in the control group (P < 0.05). The HFE reduced the heart weight and RV:TV, RV:BW, and TV:BW ratios when supplemented in drinking water at 0.1 and 0.2 mL/L compared with 0 mL/L (P < 0.05). In conclusion, supplementation of HFE in drinking water can reduce the PHS and incidence of cardiac disorders. Owing to the positive effect of HFE on cardiac parameters that mediated through flavonoids bioactive compounds, this product can be used to prevent complications of pulmonary hypertension and disarray of electrocardiographic waves in broiler chickens reared at high altitude.