Selection signatures of Qinchuan cattle based on whole-genome sequences.

Qinchuan cattle has gradually improved in body shape and growth rate in the long-term breeding process from the draft cattle to beef cattle. As the head of the five local yellow cattle in China, the Qinchuan cattle has been designated as a specialized beef cattle breed. We investigated the selection signatures using whole genome sequencing data in Qinchuan cattle. Based on Fst, we detected hundreds of candidate genes under selection across Qinchuan, Red Angus, and Japanese Black cattle. Through protein-protein interaction analysis and functional annotation of candidate genes, the results revealed that KMT2E, LTBP1 and NIPBL were related to brain size, body characteristics, and limb development, respectively, suggesting that these potential genes may affect the growth and development traits in Qinchuan cattle. ARIH2, DACT1 and DNM2, et al. are related to meat quality. Meanwhile, TBXA2R can be used as a gene associated with reproductive function, and USH2A affect coat color. This provided a glimpse into the formation of breeds and molecular genetic breeding. Our findings will promote genome-assisted breeding to improve animal production and health.

Genetic variants of TORC1 gene promoter and their association with carcass quality and body measurement traits in Qinchuan beef cattle.

In the present study, sequencing of TORC1 prompter region explored three SNPs at loci g.80G>T, g.93A>T, and g.1253G>A. The SNP1 produced GG, GT and TT, SNP2 AA, AT and TT, and SNP3 produced GG, GA and AA genotypes. Allelic and genotypic frequencies analysis exhibited that SNP1 is within Hardy-Weinberg equilibrium (HWE). All three SNPs were found highly polymorphic as PIC value (0.25 < PIC < 0.50). At loci g.80G>T the cattle with genotype GG showed significantly (P <0.01) larger body length (BL), Wither height (WH), Hip height (HH), Rump length (RL), Hip width (HW), Chest depth (CD), and Chest circumference (CC). The genotype AA at g.93A>T showed significantly (P< 0.01 and 0.05) Larger body length (BL), Wither height (WH), Hip height, Rump length (RL), Hip width (HW), Chest depth (CD), and Chest circumference (CC). Interestingly, the carcass quality parameters such as Ultrasound loin area (ULA) and Intramuscular fat percentage (IF%) was highest in genotype GG at loci g.1253G>A. These findings conclude that genotype GG at loci g.80 G>T and AA at loci g.93A>T could be used as genetic markers for body measurement and genotype GG at loci g.1253G>A for carcass quality traits of TORC1 gene in Qinchuan beef cattle.

Identification of the hub genes related to adipose tissue metabolism of bovine.

Due to the demand for high-quality animal protein, there has been consistent interest in how to obtain more high-quality beef. As well-known, the adipose content of beef has a close connection with the taste and quality of beef, and cattle with different energy or protein diet have corresponding effects on the lipid metabolism of beef. Thus, we performed weighted gene co-expression network analysis (WGCNA) with subcutaneous adipose genes from Norwegian red heifers fed different diets to identify hub genes regulating bovine lipid metabolism. For this purpose, the RNA sequencing data of subcutaneous adipose tissue of 12-month-old Norwegian red heifers (n = 48) with different energy or protein levels were selected from the GEO database, and 7,630 genes with the largest variation were selected for WGCNA analysis. Then, three modules were selected as hub genes candidate modules according to the correlation between modules and phenotypes, including pink, magenta and grey60 modules. GO and KEGG enrichment analysis showed that genes were related to metabolism, and participated in Rap, MAPK, AMPK, VEGF signaling pathways, and so forth. Combined gene interaction network analysis using Cytoscape software, eight hub genes of lipid metabolism were identified, including TIA1, LOC516108, SNAPC4, CPSF2, ZNF574, CLASRP, MED15 and U2AF2. Further, the expression levels of hub genes in the cattle tissue were also measured to verify the results, and we found hub genes in higher expression in muscle and adipose tissue in adult cattle. In summary, we predicted the key genes of lipid metabolism in the subcutaneous adipose tissue that were affected by the intake of various energy diets to find the hub genes that coordinate lipid metabolism, which provide a theoretical basis for regulating beef quality.

Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo.

Background: Buffalo meat is increasingly widely accepted for consumption as it shares several quality attributes with cattle meat (beef). Hence, there is a huge opportunity for growth in the buffalo meat industry. However, buffalo meat has relatively low intramuscular fat (IMF) content, affecting its flavor, tenderness and juiciness. As there is a dearth of information on factors that control fat deposition, this study was undertaken to provide new candidate factor associated with buffalo fat deposition. Circular RNA (circRNA) is a novel class of non-coding RNA with a closed-loop structure, and play an important role in fat deposition. Methods: In this study, weighted gene co-expression network analysis (WGCNA) was used to construct a circRNA co-expression network and revealed a candidate circRNA that may affect the IMF deposition of buffalo as determined by RT-qPCR, semiquantitative PCR and gain-of-function experiments. Results: Herein, WGCNA determined that one module (turquoise module) is significantly associated with the growth and development stages of buffalo. Further analysis revealed a total of 191 overlapping circRNAs among differentially expressed (DE) circRNAs and the co-expression module. A candidate circRNA was found, 21:6969877|69753491 (circRNA_ID), with a reported involvement in lipid metabolism. This circRNA is stably expressed and originates from the MARK3 gene, hence the name circMARK3. circMARK3 is highly expressed in adipose tissue and mature adipocytes and is located in the cytoplasm. Gain-of-function experiments demonstrated that circMARK3 promoted adipogenic differentiation of buffalo adipocytes and 3T3-L1 cells by up-regulating the expression levels of adipogenic marker genes PPARG, C/EBPα and FABP4. Conclusion: These results indicate that circMARK3 is a potential factor that promotes fat deposition by regulating adipocyte differentiation and adipogenesis in buffalo.

Lytic Bacteriophage PZL-Ah152 as Biocontrol Measures Against Lethal Aeromonas hydrophila Without Distorting Gut Microbiota.

Phage therapy is an alternative approach to overcome the problem of multidrug resistance in bacteria. In this study, a bacteriophage named PZL-Ah152, which infects Aeromonas hydrophila, was isolated from sewage, and its biological characteristics and genome were studied. The genome contained 54 putative coding sequences and lacked known putative virulence factors, so it could be applied to phage therapy. Therefore, we performed a study to (i) investigate the efficacy of PZL-Ah152 in reducing the abundance of pathogenic A. hydrophila strain 152 in experimentally infected crucian carps, (ii) evaluate the safety of 12 consecutive days of intraperitoneal phage injection in crucian carps, and (iii) determine how bacteriophages impact the normal gut microbiota. The in vivo and in vitro results indicated that the phage could effectively eliminate A. hydrophila. Administering PZL-Ah152 (2 × 109 PFU) could effectively protect the fish (2 × 108 CFU/carp). Furthermore, a 12-day consecutive injection of PZL-Ah152 did not cause significant adverse effects in the main organs of the treated animals. We also found that members of the genus Aeromonas could enter and colonize the gut. The phage PZL-Ah152 reduced the number of colonies of the genus Aeromonas. However, no significant changes were observed in α-diversity and ß-diversity parameters, which suggested that the consumed phage had little effect on the gut microbiota. All the results illustrated that PZL-Ah152 could be a new therapeutic method for infections caused by A. hydrophila.

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.

Genetic variants in the serum amyloid A2 (SAA2) gene as a potential marker for milk production traits in Chinese Holstein cows.

BACKGROUND: This study was conducted to detect potential polymorphisms of the serum amyloid A2 (SAA2) gene and explore their relationships with milk production traits in Chinese Holstein cows. OBJECTIVES: THIS STUDY USED: sequencing technology conducted in 532 Chinese Holstein cows. METHODS: Three single nucleotide polymorphisms (SNPs) were identified within intron 1, named g.14061A>G, g.14072G>C and g.14819C>T. Eight estimated haplotypes were identified, of which three major haplotypes had a frequency of Hap3 (-ACC-), Hap5 (-GCC-) and Hap2 (-AGT-), with 17.9%, 12.30% and 8.10%, respectively. RESULTS: The association analysis of single markers (g.14061A>G and g.14819C>T) and combined genotypes (Hap1/5) revealed prominent effects on milk production traits in Chinese Holstein cows (p < 0.05). CONCLUSIONS: Our results suggest that the SAA2 gene is associated with economic traits in Chinese Holstein cows and may be used as candidate gene for marker-assisted selection and management in breeding programs.

Molecular dynamics simulation analysis of alpha-cobra toxin docked with phytochemical compounds.

It is of interest to document data on the molecular dynamics simulation analysis of alpha-cobratoxin docked with phytochemical compounds. This can be used as effective drug candidates against the snake and scorpion venom. It should be noted experimental verification is needed to further validate the current data.