Uncovering the genetic diversity and adaptability of Butuo Black Sheep through whole-genome re-sequencing.

The Butuo Black Sheep (BBS) is well-known for its ability to thrive at high altitudes, resist diseases, and produce premium-quality meat. Nonetheless, there is insufficient data regarding its genetic diversity and population-specific Single nucleotide polymorphisms (SNPs). This paper centers on the genetic diversity of (BBS). The investigation conducted a whole-genome resequencing of 33 BBS individuals to recognize distinct SNPs exclusive to BBS. The inquiry utilized bioinformatic analysis to identify and explain SNPs and pinpoint crucial mutation sites. The findings reveal that reproductive-related genes (GHR, FSHR, PGR, BMPR1B, FST, ESR1), lipid-related genes (PPARGC1A, STAT6, DGAT1, ACACA, LPL), and protein-related genes (CSN2, LALBA, CSN1S1, CSN1S2) were identified as hub genes. Functional enrichment analysis showed that genes associated with reproduction, immunity, inflammation, hypoxia, PI3K-Akt, and AMPK signaling pathways were present. This research suggests that the unique ability of BBS to adapt to low oxygen levels in the plateau environment may be owing to mutations in a variety of genes. This study provides valuable insights into the genetic makeup of BBS and its potential implications for breeding and conservation efforts. The genes and SPNs identified in this study could serve as molecular markers for BBS.

Functional prediction of AMP deaminase 1 in Jingyuan chicken and evaluation of the biological activities of its expression vectors.

This study investigated the function of AMP deaminase 1 (AMPD1) in Jingyuan chicken and the biological activity of its expression vector. AMPD1 was cloned and sequenced from chicken breast muscle tissue by RT-PCR and further analyzed using Cluster, DNASTAR, and online bioinformatics software, as well as vector construction, qPCR, Western blotting, enzymatic digestion, and sequencing. The coding sequence was 2162 bp, encoding 683 amino acids and producing a protein of approximately 78.95 kDa. After verification, the overexpression plasmids pEGFP-AMPD1, Cas9/sgRNA2, and Cas9/sgRNA3 were found to have biological activity in chicken muscle cells and individual chickens, and two sgRNAs (sgRNA2, sgRNA3) were identified that could edit AMPD1. The qPCR and Western blotting result showed that the pEGFP-AMPD1 plasmid significantly increased both mRNA and protein expression of AMPD1. T7EI digestion showed editing efficiencies of approximately 35 %, 37 %, and 33 % for sgRNA2, sgRNA3, and sgRNA2 + sgRNA3 of AMPD1 in chicken muscle cells. In comparison, TA cloning sequencing showed editing efficiencies of approximately 36.7 %, 86.7 %, and 26.7 % and editing efficiencies in chicken individuals of approximately 71 %, 45 %, and 76.7 %, respectively. These results provide a theoretical basis and support for further investigation into the function of the AMPD1 gene.

Integrating proteomics and metabolomics to elucidate the molecular network regulating of inosine monophosphate-specific deposition in Jingyuan chicken.

Inosine monophosphate (IMP) plays a significant role in meat taste, yet the molecular mechanisms controlling IMP deposition in muscle tissues still require elucidation. The present study systematically and comprehensively explores the molecular network governing IMP deposition in different regions of Jingyuan chicken muscle. Two muscle groups, the breast and leg, were examined as test materials. Using nontargeted metabolomic sequencing, we screened and identified 20 metabolites that regulate IMP-specific deposition. We maintained regular author and institution formatting, used clear, objective, and value-neutral language, and avoided biased or emotional language. We followed a consistent footnote style and formatting features and used precise word choice with technical terms where appropriate. Out of these, 5 were identified as significant contributors to the regulation of IMP deposition. We explained technical term abbreviations when first used and ensured a logical flow of information with causal connections between statements. The results indicate that PGM1, a key enzyme involved in synthesis, is higher in the breast muscle compared to the leg muscle, which may provide an explanation for the increased deposition of IMP in the breast muscle. We aimed for a clear structure with logical progression, avoided filler words, and ensured grammatical correctness. The activity of key enzymes (PKM2, AK1, AMPD1) involved in this process was higher in the breast muscle than in the leg muscle. In the case of IMP degradation metabolism, the activity of its participating enzyme (PurH) was lower in the breast muscle than in the leg muscle. These findings suggest that the increased deposition of IMP in Jingyuan chickens' breast muscle may result from elevated metabolism and reduced catabolism of key metabolites. In summary, a metaomic strategy was utilized to assess the molecular network regulation mechanism of IMP-specific deposition in various segments of Jingyuan chicken. These findings provide insight into genetic improvement and molecular breeding of meat quality traits for top-notch broilers.

Characterization of feed efficiency-related key signatures molecular in different cattle breeds.

Feed efficiency is a major constraint in the beef industry and has a significant negative correlation with residual feed intake (RFI). RFI is widely used as a measure of feed efficiency in beef cattle and is independent of economic traits such as body weight and average daily gain. However, key traits with commonality or specificity among beef cattle breeds at the same level of RFI have not been reported. Accordingly, the present study hypothesized that signatures associated with feed efficiency would have commonality or specificity in the liver of cattle breeds at the same RFI level. By comparing and integrating liver transcriptome data, we investigated the critical signatures closely associated with RFI in beef cattle using weighted co-expression network analysis, consensus module analysis, functional enrichment analysis and protein network interaction analysis. The results showed that the consensus modules in Angus and Charolais cattle were negatively correlated, and four (turquoise, red, tan, yellow) were significantly positively correlated in Angus liver, while (turquoise, red) were significantly negatively correlated in Charolais liver. These consensus modules were found to be primarily involved in biological processes such as substance metabolism, energy metabolism and gene transcription, which may be one of the possible explanations for the difference in feed efficiency between the two beef breeds. This research also identified five key candidate genes, PLA2G12B, LCAT, MTTP, LCAT, ABCA1 and FADS1, which are closely associated with hepatic lipid metabolism. The present study has identified some modules, genes and pathways that may be the major contributors to the variation in feed efficiency among different cattle breeds, providing a new perspective on the molecular mechanisms of feed efficiency in beef cattle and a research basis for investigating molecular markers associated with feed efficiency in beef cattle.

Technology characteristics and flavor changes of traditional green wheat product nian zhuan in Northern China.

Nian zhuan has its aroma as one of the perceived principal characteristics. The current study was aimed mainly to investigate the potential to include the aroma of nian zhuan as a new target criterion into the green wheat product chain. By improving the conditions for the traditional processing of nian zhuan, the optimal processing conditions were determined as green wheat (GW) 14 d, steaming the green wheat with the skin (SGWS) 26 min and cooked green wheat peeled (CGWP) 280 min, to evaluate the feasibility of using electronic nose (E-nose) and gas chromatography mass spectrometry (GC-MS) to discriminate nian zhuan in different stages. E-nose was used to recognize nian zhuan odors in different processing stages, and GC-MS to identify the individual volatile compounds. A total of 139 volatile compounds were detected by GC-MS, of which 71 key were screened by t-test (P < 0.01). The W1W, W1S, W2W and W2S sensors of E-nose gave higher responses to all samples, and effectively discriminated the samples. The most volatile compounds were produced in the millstone milling (MSM) stage of nian zhuan, and millstone could promote the release of volatile compounds from cooked green wheat by milling.

Analysis of the molecular mechanism of inosine monophosphate deposition in Jingyuan chicken muscles using a proteomic approach.

Inosine monophosphate (IMP) is an indicator of meat taste, and the molecular mechanism underlying IMP deposition in muscle tissues is important to developing superior poultry breeds. The aim of this study was to identify the key proteins regulating IMP deposition in different muscle groups of 180-day-old Jingyuan chickens (Hen) using a proteomics-based approach. We identified 1,300 proteins in the muscle tissues of Jingyuan chickens, of which 322 were differentially expressed between the breast and leg muscles (129 proteins were highly expressed in breast muscles and 193 proteins were highly expressed in leg muscles). PGM1, PKM2, AK1, AMPD1, and PurH/ATIC were among the differentially expressed proteins (DEPs) involved in the purine metabolism pathway, of which purH was highly expressed in leg muscles, while the others were highly expressed in breast muscles. The proteomics screening results were verified by PRM, qPCR, and western blotting, showing consistency with the proteomics results. Our findings are not only significant in terms of protecting the Jingyuan chicken germplasm resources, but also provide the molecular basis for generating high-quality broiler chicken breeds.

Research progress on inosine monophosphate deposition mechanism in chicken muscle.

With the continuous improvements in human diet, there is an ever-increasing demand for high-quality chicken, so it is particularly important for poultry breeders to carry out the breeding of high-quality broilers in a timely fashion. Inosine monophosphate (IMP) is a flavor-enhancing substance, which plays a critical role in the umami taste of the muscle, making the content of IMP an important umami taste indicator. Currently, research on the deposition mechanism of IMP in chicken is not only necessary for chicken breeders to promote the production of high-quality meat and poultry but also to meet the human demand for chicken meat. In this paper, the research history of IMP, its structure and taste mechanisms, the pathway and influencing factors of de novo IMP synthesis, and the key genes regulating IMP synthesis and metabolism are briefly summarized. Our aim was to lay a theoretical foundation and provide scientific background and research directions for further research on high-quality broiler breeding.

Identifying the key genes and functional enrichment pathways associated with feed efficiency in cattle.

Residual feed intake (RFI) is a measurement of feed efficiency, and is inversely correlated with feed efficiency. The differentially expressed genes (DEGs) associated with RFI vary substantially among studies, posing great challenges in finding the RFI-related marker genes. This study attempted to resolve this issue by integrating and comparing the multiple transcriptome sequencing data associated with RFI in the cattle liver, using differential, functional enrichment, protein-protein interaction (PPI) network, weighted co-expression network (WGCNA), and gene set enrichment analyses (GSEA) to identify the candidate genes and functional enrichment pathways that are closely associated with RFI. Four candidate genes namely SHC1, GPX4, ACADL, and IGF1 were identified and validated as the marker genes for RFI. Four functional enrichment pathways, namely the fatty acid metabolism, sugar metabolism, energy metabolism, and protein ubiquitination were also found to be closely related to RFI. This study identified several genes and signaling pathways with shared characteristics, which will provide new insights into the molecular mechanisms related to the regulation of feed efficiency, and provide basis for molecular markers related to feed efficiency in beef cattle.

Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq.

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = -0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.

Correlation Analysis between AK1 mRNA Expression and Inosine Monophosphate Deposition in Jingyuan Chickens.

In this study, we examined correlations between the deposition of inosine monophosphate (IMP) and mRNA expression of the adenylate kinase 1 (AK1) gene in Jingyuan chicken. The IMP content was determined by high-performance liquid chromatography. Transcriptome sequencing was used to screen the differentially expressed gene AK1 and real-time quantitative polymerase chain reaction (PCR) to determine the expression level of AK1 mRNA associated with IMP synthesis. IMP and inosine content in the breast muscles of both Jingyuan cocks and hens was found to be significantly higher than that in the leg muscles. Similarly, the expression of AK1 mRNA in the breast muscles of cocks and hens was significantly higher than that in the leg muscles. Moreover, AK1 mRNA expression in cock breast muscles was negatively correlated with IMP content, whereas its expression in cock leg muscles was positively correlated with IMP content. In contrast, the expression of AK1 mRNA in hen breast and leg muscles was significantly positively correlated with IMP content. These findings provide a scientific basis for enhancing the meat flavor of Jingyuan chicken and promoting the development and utilization of local variety resources, as well as constituting a basis for screening IMP-regulated genes. Our study will advance our current understanding of AK1 function.

Cloning expression and immunogenicity analysis of inhibin gene in Ye Mule Aries sheep.

BACKGROUND: Ye Mule Aries sheep is one of the most important sheep breeds in Xinjiang, China. This breed is well adapted to harsh environmental conditions and displays strong disease resistance, fast growth, and high cold tolerance. To analyze the clonal expression and immunogenicity of the Ye Mule Aries sheep inhibin gene, total RNA was extracted from sheep ovarian tissue and used as a template to generate a eukaryotic expression vector and study inhibin immunogenicity. METHODS: Primers were designed to amplify the inhibin A gene via polymerase chain reaction and the amplified product was cloned between the ScalI and EcoRI restriction sites of the expression vector pEGFP-N1 to construct a recombinant plasmid, pEGFP-INHα. Following the validation of successful cloning, the pEGFP-INHα plasmid was transfected into BHK cells to verify expression in eukaryotes and subsequently utilized as an antigen in rabbits. Rabbits were tested for anti-inhibin antibodies and serum follicle-stimulating hormone (FSH) concentrations. RESULTS: The analysis of the INHα gene sequence revealed that INHα is 1109 bp long and is translated to an approximately 40 KDa protein. Bioinformatics approach indicated that the INHα gene is highly conserved between organisms. Immunization with the eukaryotic expression vector, pEGFP-INHα, which expresses the INHα gene elicited immune response and generatigeneration on of anti-INHα antibody. The antibody had a significant regulatory effect on the serum concentration of FSH in rabbits and led to higher levels of FSH, indicating increased ovary function. CONCLUSIONS: The present work resulted in a successful construction of eukaryotic expression plasmid pEGFP-INHα and verified the immunogenicity of this highly conserved protein. Further, the expression of pEGFP-INHα was shown to have a significant impact on the secretion of FSH, indicating a potential regulatory role in ovarian function. In conclusion, our current findings can serve as a working model for studying the effect of INHα on the breeding performance of Ye Mule Aries sheep, providing a novel strategy to improve their reproduction rates.