The role of lncFABP4 in modulating adipogenic differentiation in buffalo intramuscular preadipocytes.

Intramuscular fat (IMF) is a crucial determinant of meat quality and is influenced by various regulatory factors. Despite the growing recognition of the important role of long noncoding RNAs (lncRNAs) in IMF deposition, the mechanisms underlying buffalo IMF deposition remain poorly understood. In this study, we identified and characterized a lncRNA, lncFABP4, which is transcribed from the antisense strand of fatty acid-binding protein 4 (FABP4). lncFABP4 inhibited cell proliferation in buffalo intramuscular preadipocytes. Moreover, lncFABP4 significantly increased intramuscular preadipocyte differentiation, as indicated by an increase in the expression of the adipogenic markers peroxisome proliferator-activated receptor gamma (PPARG), CCAAT enhancer binding protein alpha (C/EBPα), and FABP4. Mechanistically, lncFABP4 was found to have the potential to regulate downstream gene expression by participating in protein-protein interaction pathways. These findings contribute to further understanding of the intricate mechanisms through which lncRNAs modulate intramuscular adipogenesis in buffaloes.

Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses.

In the Suidae family, warthogs show significant survival adaptability and trait specificity. This study offers a comparative genomic analysis between the warthog and other Suidae species, including the Luchuan pig, Duroc pig, and Red River hog. By integrating the four genomes with sequences from the other four species, we identified 8868 single-copy orthologous genes. Based on 8868 orthologous protein sequences, phylogenetic assessments highlighted divergence timelines and unique evolutionary branches within suid species. Warthogs exist on different evolutionary branches compared to DRCs and LCs, with a divergence time preceding that of DRC and LC. Contraction and expansion analyses of warthog gene families have been conducted to elucidate the mechanisms of their evolutionary adaptations. Using GO, KEGG, and MGI databases, warthogs showed a preference for expansion in sensory genes and contraction in metabolic genes, underscoring phenotypic diversity and adaptive evolution direction. Associating genes with the QTLdb-pigSS11 database revealed links between gene families and immunity traits. The overlap of olfactory genes in immune-related QTL regions highlighted their importance in evolutionary adaptations. This work highlights the unique evolutionary strategies and adaptive mechanisms of warthogs, guiding future research into the distinct adaptability and disease resistance in pigs, particularly focusing on traits such as resistance to African Swine Fever Virus.

Isolation methods, proliferation, and adipogenic differentiation of adipose-derived stem cells from different fat depots in bovines.

The adipose-derived stem cells (ASCs) are a valuable resource for regenerative medicine and essential materials for research in fat deposition. However, the isolation procedure of ASCs has not been standardized and needs to be harmonized; differences in proliferation and adipogenic differentiation of ASCs obtained from different fat depots have not been well characterized. In the present study, we compared the efficiency of ASCs isolation by enzymatic treatment and explant culture methods and the proliferation ability and adipogenic differentiation potential of ASCs isolated from subcutaneous and visceral fat depots. The explant culture method was simple and with no need for expensive enzymes while the enzymatic treatment method was complex, time consuming and costly. By the explant culture method, a larger number of ASCs were isolated from subcutaneous and visceral fat depots. By contrast, fewer ASCs were obtained by the enzymatic treatment method, especially from visceral adipose. ASCs isolated by the explant culture method performed well in cell proliferation and adipogenic differentiation, though they were slightly lower than those by the enzymatic treatment method. ASCs isolated from visceral depot demonstrated higher proliferation ability and adipogenic differentiation potential. In total, the explant culture method is simpler, more efficient, and lower cost than the enzymatic treatment method for ASCs isolation; compared with visceral adipose, subcutaneous adipose is easier to isolate ASCs; however, the visceral ASCs are superior to subcutaneous ASCs in proliferation and adipogenic differentiation.

Functionally conserved PPARG exonic circRNAs enhance intramuscular fat deposition by regulating PPARG and HSL.

Circular RNAs (circRNA) are a kind of endogenous biological macromolecules that play significant roles in many biological processes, including adipogenesis, a precisely orchestrated process that is mediated by a large number of factors. Among them, peroxisome proliferator-activated receptor gamma (PPARG), is undoubtedly the most important regulator of adipocyte development in all types of adipose tissue. The formation of intramuscular fat (IMF), is a key factor that influences the meat quality in livestock animals. PPARG has been demonstrated to show a positive correlation with IMF deposition although the regulatory mechanism involved is not known. This study demonstrates that PPARG mediates IMF deposition by producing multiple exonic circRNAs (circPPARGs). Three circPPARGs promote adipogenic differentiation and inhibit the proliferation of intramuscular preadipocytes and these effects are conserved across several species including buffaloes, cattle and mice. Notably, circPPARG1 interacts with PPARG protein to inhibit the transcription of hormone sensitive lipase (HSL) involved in lipolysis. In addition, the positive effects of circPPARG1 on IMF deposition were identified in mice in vivo. Thus, PPARG drives IMF deposition, not only through the common transcription factor pathway, but also by producing circRNAs. This study provides new insights into our understanding of the regulatory mechanisms of PPARG in IMF deposition.

A Circular RNA Generated from Nebulin (NEB) Gene Splicing Promotes Skeletal Muscle Myogenesis in Cattle as Detected by a Multi-Omics Approach.

Cattle and the draught force provided by its skeletal muscle have been integral to agro-ecosystems of agricultural civilization for millennia. However, relatively little is known about the cattle muscle functional genomics (including protein coding genes, non-coding RNA, etc.). Circular RNAs (circRNAs), as a new class of non-coding RNAs, can be effectively translated into detectable peptides, which enlightened us on the importance of circRNAs in cattle muscle physiology function. Here, RNA-seq, Ribosome profiling (Ribo-seq), and peptidome data are integrated from cattle skeletal muscle, and detected five encoded peptides from circRNAs. It is further identified and functionally characterize a 907-amino acids muscle-specific peptide that is named circNEB-peptide because derived by the splicing of Nebulin (NEB) gene. This peptide localizes to the nucleus and cytoplasm and directly interacts with SKP1 and TPM1, key factors regulating physiological activities of myoblasts, via ubiquitination and myoblast fusion, respectively. The circNEB-peptide is found to promote myoblasts proliferation and differentiation in vitro, and induce muscle regeneration in vivo. These findings suggest circNEB-peptide is an important regulator of skeletal muscle regeneration and underscore the possibility that more encoding polypeptides derived by RNAs currently annotated as non-coding exist.

A preliminary composite of blood-based biomarkers to distinguish major depressive disorder and bipolar disorder in adolescents and adults.

BACKGROUND: Since diagnosis of mood disorder heavily depends on signs and symptoms, emerging researches have been studying biomarkers with the attempt to improve diagnostic accuracy, but none of the findings have been broadly accepted. The purpose of the present study was to construct a preliminary diagnostic model to distinguish major depressive disorder (MDD) and bipolar disorder (BD) using potential commonly tested blood biomarkers. METHODS: Information of 721 inpatients with an ICD-10 diagnosis of MDD or BD were collected from the electronic medical record system. Variables in the nomogram were selected by best subset selection method after a prior univariable screening, and then constructed using logistic regression with inclusion of the psychotropic medication use. The discrimination, calibration and internal validation of the nomogram were evaluated by the receiver operating characteristic curve (ROC), the calibration curve, cross validation and subset validation method. RESULTS: The nomogram consisted of five variables, including age, eosinophil count, plasma concentrations of prolactin, total cholesterol, and low-density lipoprotein cholesterol. The model could discriminate between MDD and BD with an area under the ROC curve (AUC) of 0.858, with a sensitivity of 0.716 and a specificity of 0.890. CONCLUSION: The comprehensive nomogram constructed by the present study can be convenient to distinguish MDD and BD since the incorporating variables were common indicators in clinical practice. It could help avoid misdiagnoses and improve prognosis of the patients.

Effects of Dietary Inclusion of Asiaticoside on Growth Performance, Lipid Metabolism, and Gut Microbiota in Yellow-Feathered Chickens.

Excessive abdominal fat deposition in chickens is a major concern in the poultry industry. Nutritional interventions are a potential solution, but current options are limited. Asiaticoside (Asi), a herbal extract, has shown positive effects in animals, but its impact on poultry lipid metabolism is still unknown. In this study, the effects of dietary Asi on yellow-feathered chicken lipid metabolism and its potential mechanisms were investigated. A total of 120 chickens were randomly divided into three groups, with five replicates per group and 8 chickens per replicate. The chickens were fed a basal diet supplemented with 0, 0.01, or 0.05% Asi for 6 wk. The results showed that Asi down-regulated lipogenic gene expression and up-regulated lipid-breakdown-related genes in both the liver and fat tissues of the chickens, which resulted in a half reduction in abdominal fat while not affecting meat yield. Mechanistically, the hepatic and adipose PI3K/AKT pathway may be involved in Asi-induced fat loss in chickens as revealed by computer-aided reverse drug target prediction and gene expression analysis. Moreover, Asi ingestion also significantly modified the cecal microbiota of the chickens, resulting in a reduced Firmicutes to Bacteroidetes ratio and decreased abundance of bacteria positively correlated with abdominal fat deposition such as Ruminococcus, while increasing the abundance of bacteria inversely correlated with abdominal fat deposition such as Lactobacillus, Bacteroides, and Blautia. Collectively, these data suggest that Asi could ameliorate the abdominal fat deposition in yellow-feathered chickens, probably through modulating the PI3K/AKT pathway and gut microbiota function.

Diversity in Cell Morphology, Composition, and Function among Adipose Depots in River Buffaloes.

Fat deposition is a significant economic trait in livestock animals. Adipose tissues (ATs) developed in subcutaneous and visceral depots are considered waste whereas those within muscle are highly valued. In river buffaloes, lipogenesis is highly active in subcutaneous (especially in the sternum subcutaneous) and visceral depots but not in muscle tissue. Revealing the features and functions of ATs in different depots is significant for the regulation of their development. Here, we characterize the cell size, composition, and function of six AT depots in river buffaloes. Our data support that the subcutaneous AT depots have a larger cell size than visceral AT depots, and the subcutaneous AT depots, especially the sternum subcutaneous AT, are mainly associated with the extracellular matrix whereas the visceral AT depots are mainly associated with immunity. We found that sternum subcutaneous AT is significantly different from ATs in other depots, due to the high unsaturated fatty acid content and the significant association with metabolic protection. The perirenal AT is more active in FA oxidation for energy supply. In addition, the expression of HOX paralogs supports the variable origins of ATs in different depots, indicating that the development of ATs in different depots is mediated by their progenitor cells. The present study enhances our understanding of the cellular and molecular features, metabolism, and origin of AT depots in buffaloes, which is significant for the regulation of fat deposition and provides new insights into the features of AT depots in multiple discrete locations.

Mitophagy-related gene signature predicts prognosis, immune infiltration and chemotherapy sensitivity in colorectal cancer.

BACKGROUND: Mitophagy plays essential role in the development and progression of colorectal cancer (CRC). However, the effect of mitophagy-related genes in CRC remains largely unknown. AIM: To develop a mitophagy-related gene signature to predict the survival, immune infiltration and chemotherapy response of CRC patients. METHODS: Non-negative matrix factorization was used to cluster CRC patients from Gene Expression Omnibus database (GSE39582, GSE17536, and GSE37892) based on mitophagy-related gene expression. The CIBERSORT method was applied for the evaluation of the relative infiltration levels of immune cell types. The performance signature in predicting chemotherapeutic sensitivity was generated using data from the Genomics of Drug Sensitivity in Cancer database. RESULTS: Three clusters with different clinicopathological features and prognosis were identified. Higher enrichment of activated B cells and CD4+ T cells were observed in cluster III patients with the most favorable prognosis. Next, a risk model based on mitophagy-related genes was developed. Patients in training and validation sets were categorized into low-risk and high-risk subgroups. Low risk patients showed significantly better prognosis, higher enrichment of immune activating cells and greater response to chemotherapy (oxaliplatin, irinotecan, and 5-fluorouracil) compared to high-risk patients. Further experiments identified CXCL3 as novel regulator of cell proliferation and mitophagy. CONCLUSION: We revealed the biological roles of mitophagy-related genes in the immune infiltration, and its ability to predict patients' prognosis and response to chemotherapy in CRC. These interesting findings would provide new insight into the therapeutic management of CRC patients.

Association between serum creatinine and type 2 diabetes in the Chinese population: a retrospective cohort study.

The relationship between serum creatinine and type 2 diabetes is limited. We aimed to investigate the association of baseline serum creatinine and new-onset type 2 diabetes in Chinese population. This retrospective cohort study was conducted using data from the health screening program in China. The population were divided into four groups based on serum creatinine levels, and the outcome of interest was the occurrence of a diabetic event. Cox proportional risk model was used to assess the independent effect of baseline serum creatinine level on future diabetes risk. Sensitivity and subgroup analysis were used to verify the reliability of the results. After an average follow-up of 3.12 years, among 201,298 individuals aged ≥ 20 years, 3389 patients developed diabetes. Compared with participants in quartile 2-4 (> 51.6umol/L for female, > 71.8umol/L for male,), a significantly higher risk of new-onset Type 2 Diabetes (OR, 1.15; 95%CI: 1.07-1.23) was found in those in quartile 1 (< 51.6umol/L for female, < 71.8umol/L for male). Moreover, Similar results were found in various subgroups stratified by age, BMI, TG, TC, FPG and family history group. Low serum creatinine is independently associated with increased risk of type 2 diabetes in Chinese adults. It was also stable in various subgroups stratified.

A long non-coding RNA lnc210 promotes adipogenic differentiation of buffalo intramuscular adipocytes.

Intramuscular fat (IMF) content is one of the most significant factors influencing beef quality in terms of tenderness, flavor, and juiciness. Thus, internal factors affecting IMF deposition have received considerable attention for decades. In this study, we demonstrated a long non-coding RNA, lnc210, promoted adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was rich in adipose tissue and showed increased expression with the adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was mainly expressed in the nucleus of adipocytes. Full-length lnc210 was obtained by rapid amplification of cDNA ends technology. lnc210 overexpression promoted lipid accumulation by upregulating the mRNA expression of peroxisome proliferator-activated receptor gamma (PPARG) and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo intramuscular adipocytes. These results provide a basis for an in-depth analysis of the role of lnc210 in accelerating IMF deposition in buffaloes.

TRPV3 inhibits colorectal cancer cell proliferation and migration by regulating the MAPK signaling pathway.

Background: The aim of this study was to investigate the inhibiting effect of transient receptor potential vanilloid 3 (TRPV3) on the proliferation and migration of colorectal cancer (CRC) cells and to explore the underlying mechanism. Methods: A microarray dataset from the publicly available Gene Expression Omnibus (GEO) database was used to investigate the prognostic value of TRPV3 in CRC. In addition, 100 CRC tissue samples were collected at our center to further validate its prognostic value at the protein level. Cell proliferation ability was detected by Cell Counting Kit-8 (CCK-8) assay, and cell migration ability was detected by transwell assay. Gene set variation analysis (GSVA) was performed to identify the potential pathways regulated by TRPV3. Results: Based on the largest microarray dataset (GSE39582), low expression of TRPV3 was found to be significantly associated with poor prognosis in CRC patients, and this result was successfully validated at our cancer center. Functional experiments showed that knockdown of TRPV3 enhanced cell proliferation and migration, while enforced TRPV3 expression exhibited the opposite effect. GSEA based on public microarray data revealed that the mitogen-activated protein kinase (MAPK) signaling pathway was notably activated in patients with low expression of TRPV3. Further experiments in vivo confirmed that TRPV3 silencing promoted cell proliferation and migration by activating the MAPK signaling pathway. Conclusions: Low expression of TRPV3, which stimulates cell proliferation and migration by provoking the MAPK signaling pathway, indicated poor prognosis in CRC patients.

FATP1 Exerts Variable Effects on Adipogenic Differentiation and Proliferation in Cells Derived From Muscle and Adipose Tissue.

In livestock, intramuscular adipose tissue is highly valued whereas adipose tissue in other depots is considered as waste. Thus, genetic factors that favor fat deposition in intramuscular compartments over that in other adipose depots are highly desirable in meat-producing animals. Fatty acid transport 1 (FATP1) has been demonstrated to promote cellular fatty acid uptake and metabolism; however, whether it also influences cellular lipid accumulation remains unclear. In the present study, we investigated the effects of FATP1 on the differentiation and proliferation of adipocytes in five types of cells derived from muscle and adipose tissue and estimated the effects of FATP1 on intramuscular fat (IMF) deposition. We showed that FATP1 is mainly expressed in heart and muscle tissue in buffaloes as well as cells undergoing adipogenic differentiation. Importantly, we found that FATP1 promoted the adipogenic differentiation of muscle-derived cells (buffalo myocytes and intramuscular preadipocytes and mouse C2C12 cells) but did not affect, or even inhibited, that of adipose-derived cells (buffalo subcutaneous preadipocytes and mouse 3T3-L1 cells, respectively). Correspondingly, our results further indicated that FATP1 promotes IMF deposition in mice in vivo. Meanwhile, FATP1 was found to enhance the proliferative activity of all the assessed cells, except murine 3T3-L1 cells. These results provide new insights into the potential effects of FATP1 on IMF deposition, especially regarding its positive effects on meat quality in buffaloes and other livestock.

Clinical characteristics of fever clinic visits during the coronavirus disease 2019 pandemic: a retrospective case-control study.

Background: Little is known about the change in characteristics of fever-clinic visits during the coronavirus disease 2019 (COVID-19) pandemic. We sought to examine the changes in the volume, characteristics, and outcomes of patients presenting at a fever clinic duringclinic during the first-level response to COVID-19. Methods: We conducted a single tertiary-center retrospective case-control study. We included consecutive patients aged 14 years or older who visited the fever clinic of a tertiary hospital during the period of the first-level response to the COVID-19 pandemic in Fuzhou, China (from 24 January to 26 February 2020). We also analyzed the data of patients in the same period of 2019 as a control. We compared a number of outcome measures, including the fever clinic volumes, consultation length, proportion of patients with pneumonia, hospital admission rate, and in-hospital mortality, using the fever-clinic visit data during the two periods. Results: We included 1,013 participants [median age: 35; interquartile range (IQR): 27-50, 48.7% male] in this retrospective study, including 707 in 2020 and 306 in 2019. The median daily number of participants who presented at the fever clinic in 2020 was significantly higher than that in 2019 [18 (IQR: 15-22) vs. 13 (IQR: 8-17), P=0.001]. Participants in 2020 had a longer consultation length than those in 2019 [127 (IQR: 51-204) vs. 20 (IQR: 1-60) min, P<0.001]. Participants in 2020 were also more likely to be diagnosed with acute pneumonia than those in 2019 [168 (23.8%) vs. 40 (13.1%), P<0.001]. The hospital admission rate in 2020 was higher than in 2019 [73 (10.3%) vs. 13 (4.2%), P=0.001]. No significant difference was found in terms of the in-hospital mortality of participants in 2020 and 2019 [8 (1.1%) vs. 0, P=0.114]. Conclusions: Our findings suggest a higher visits volume, proportion of acute pneumonia, and hospital admission rate among patients presenting at fever clinic during the COVID-19 pandemic. Improved measures need to be implemented.

Impact of the Moderating Effect of National Culture on Adoption Intention in Wearable Health Care Devices: Meta-analysis.

BACKGROUND: Wearable health care devices have not yet been commercialized on a large scale. Additionally, people in different countries have different utilization rates. Therefore, more in-depth studies on the moderating effect of national culture on adoption intention in wearable health care devices are necessary. OBJECTIVE: This study aims to explore the summary results of the relationships between perceived usefulness and perceived ease of use with adoption intention in wearable health care devices and the impact of the moderating effect of national culture on these two relationships. METHODS: We searched for studies published before September 2021 in the Web of Science, EBSCO, Engineering Village, China National Knowledge Infrastructure, IEEE Xplore, and Wiley Online Library databases. CMA (version 2.0, Biostat Inc) software was used to perform the meta-analysis. We conducted publication bias and heterogeneity tests on the data. The random-effects model was used to estimate the main effect size, and a sensitivity analysis was conducted. A meta-regression analysis was used to test the moderating effect of national culture. RESULTS: This meta-analysis included 20 publications with a total of 6128 participants. Perceived usefulness (r=0.612, P<.001) and perceived ease of use (r=0.462, P<.001) positively affect adoption intention. The relationship between perceived usefulness and adoption intention is positively moderated by individualism/collectivism (ß=.003, P<.001), masculinity/femininity (ß=.008, P<.001) and indulgence/restraint (ß=.005, P<.001), and negatively moderated by uncertainty avoidance (ß=-.005, P<.001). The relationship between perceived ease of use and adoption intention is positively moderated by individualism/collectivism (ß=.003, P<.001), masculinity/femininity (ß=.006, P<.001) and indulgence/restraint (ß=.009, P<.001), and negatively moderated by uncertainty avoidance (ß=-.004, P<.001). CONCLUSIONS: This meta-analysis provided comprehensive evidence on the positive relationship between perceived usefulness and perceived ease of use with adoption intention and the moderating effect of national culture on these two relationships. Regarding the moderating effect, perceived usefulness and perceived ease of use have a greater impact on adoption intention for people in individualistic, masculine, low uncertainty avoidance, and indulgence cultures, respectively.

A LASSO-derived clinical score to predict severe acute kidney injury in the cardiac surgery recovery unit: a large retrospective cohort study using the MIMIC database.

OBJECTIVES: We aimed to develop an effective tool for predicting severe acute kidney injury (AKI) in patients admitted to the cardiac surgery recovery unit (CSRU). DESIGN: A retrospective cohort study. SETTING: Data were extracted from the Medical Information Mart for Intensive Care (MIMIC)-III database, consisting of critically ill participants between 2001 and 2012 in the USA. PARTICIPANTS: A total of 6271 patients admitted to the CSRU were enrolled from the MIMIC-III database. PRIMARY AND SECONDARY OUTCOME: Stages 2-3 AKI. RESULT: As identified by least absolute shrinkage and selection operator (LASSO) and logistic regression, risk factors for AKI included age, sex, weight, respiratory rate, systolic blood pressure, diastolic blood pressure, central venous pressure, urine output, partial pressure of oxygen, sedative use, furosemide use, atrial fibrillation, congestive heart failure and left heart catheterisation, all of which were used to establish a clinical score. The areas under the receiver operating characteristic curve of the model were 0.779 (95% CI: 0.766 to 0.793) for the primary cohort and 0.778 (95% CI: 0.757 to 0.799) for the validation cohort. The calibration curves showed good agreement between the predictions and observations. Decision curve analysis demonstrated that the model could achieve a net benefit. CONCLUSION: A clinical score built by using LASSO regression and logistic regression to screen multiple clinical risk factors was established to estimate the probability of severe AKI in CSRU patients. This may be an intuitive and practical tool for severe AKI prediction in the CSRU.

Knowledge domain and emerging trends of climate-smart agriculture: a bibliometric study.

Climate-smart agriculture (CSA) is a new agricultural development pattern to address future food crises. Since CSA was proposed in 2010, it has attracted the attention of scholars from all over the world. It is of great significance to scientifically summarize the overview and emerging trends of CSA research, providing ideas for scholars concerned about CSA to engage in research in this field. Based on bibliometrics and CSA-related literature data in the WOS database, this paper used CiteSpace software to draw knowledge maps to scientifically analyze publications in the field of CSA. Our study found that (1) CSA research is showing a rapid upward trend, focusing on the environmental sciences and agricultural economic management; (2) international organizations such as the FAO, World Bank, and the international agricultural research institute have made significant contributions to CSA research; (3) among the nine clusters in the CSA literature, CSA practice, conservation agriculture, smallholder farmers, and sub-Saharan Africa have been consistently given high attention; (4) CSA research can be divided into three phases, and the research hotspots have transferred from essential elements of CSA to household and carbon emissions. We believe that in future research, more attention should be paid to the trade-off and synergy of the three pillars of CSA, as well as the investment, finance, and evaluation criteria of CSA. Such strengthening is of great significance to the sustainable promotion of CSA.

Identification of key genes and functional enrichment pathways involved in fat deposition in Xinyang buffalo by WGCNA.

The Xinyang buffalo is a valuable and endangered domestic heritage resource in the Dabie Mountain region in China. With the increasing mechanization of agriculture, the Xinyang buffalo, mainly used for labor, faces unprecedented challenges. One of the feasible approaches to conserve and expand the species is to transfer Xinyang buffalo from service-use to meat-use, but the main hindrance to this transformation is the inferior meat quality of Xinyang buffalo, which is not popular with consumers. Based on the above, this study was conducted to evaluate the growth performance (n = 120) and slaughter performance (n = 3) of Xinyang buffalo and to measure the amino acid levels of the eye muscle (EM), and assess the meat quality. Later, transcriptome sequencing was performed on the subcutaneous fat of the back at six (n = 3) and 30 months of age (n = 3), together with the excavation of candidate genes associated with fat deposition using the weighted co-expression network analysis (WGCNA) method. The results showed that the slaughter rate of Xinyang buffalo was 43.09%, net meat percentage was 33.04%, the ocular area was 59.16 ± 7.58, the backfat thickness was 1.03 ± 0.16, and meat bone ratio was 3.29. The total amino acid contents were 0.63 g per gram of beef, which contained 0.05 g of essential amino acids, and the three most abundant amino acids were Ser (447.17 mg/g), Asp (29.8 mg/g), and Pro (27.24 mg/g). The WGCNA results showed that six phenotypes measured were significantly correlated with the turquoise module (r > 0.97, P < 0.001), and the genes in these modules were significantly enriched in the pathways related to substance metabolism and energy metabolisms, such as metabolic pathways, citrate cycle, and fatty acid metabolism. Meanwhile, six key candidate genes (FH, MECR, GPI, PANK3, ATP6V1A, PHYH) were identified, which were associated with growth and development, fat deposition, and intra-muscular amino acid levels (P < 0.05). In short, this study provides another feasible way to preserve buffalo and enriches the theory of its molecular genetic breeding.

Chromosome-level genome and recombination map of the male buffalo.

BACKGROUND: The swamp buffalo (Bubalus bubalis carabanesis) is an economically important livestock supplying milk, meat, leather, and draft power. Several female buffalo genomes have been available, but the lack of high-quality male genomes hinders studies on chromosome evolution, especially Y, as well as meiotic recombination. RESULTS: Here, a chromosome-level genome with a contig N50 of 72.2 Mb and a fine-scale recombination map of male buffalo were reported. We found that transposable elements (TEs) and structural variants (SVs) may contribute to buffalo evolution by influencing adjacent gene expression. We further found that the pseudoautosomal region (PAR) of the Y chromosome is subject to stronger purification selection. The meiotic recombination map showed that there were 2 obvious recombination hotspots on chromosome 8, and the genes around them were mainly related to tooth development, which may have helped to enhance the adaption of buffalo to inferior feed. Among several genomic features, TE density has the strongest correlation with recombination rates. Moreover, the TE subfamily, SINE/tRNA, is likely to play a role in driving recombination into SVs. CONCLUSIONS: The male genome and sperm sequencing will facilitate the understanding of the buffalo genomic evolution and functional research.

Selection and validation of reference genes for RT-qPCR in adipose and longissimus dorsi muscle tissues of buffalo.

Real-time quantitative PCR (RT-qPCR) is widely used to measure and evaluate gene expression. The precision and reliability of RT-qPCR are critically dependent on the selection of suitable reference genes (RGs). In this study, an effort was made to identify the optimal RGs for RT-qPCR analysis of adipose and the longissimus dorsi muscle (LM) in buffaloes. RNA sequencing data were firstly analyzed to obtain 10 candidate genes (FKBP1A, C25H16orf72, PNRC2, IQGAP1, ATP5PD, RPL6, NDUFB4, TRA2A, CAPRIN1, and METAP2) that with high and stable expression across adipose tissues. Four other identified RGs (GAPDH, ACTB, TOP2B, and UXT) were selected as well. The expression stability of the candidate RGs was evaluated by three algorithms (geNorm, NormFinder, and BestKeeper) and then further validated by adipocyte and myocyte markers. Our results showed that UXT and TOP2B were the optimal RGs for RT-qPCR analysis across adipose tissues in buffaloes; three RGs, RPL6, UXT, and TOP2B, were the optimal RGs for RT-qPCR analysis across adipose and the LM tissues in buffaloes. This study provides significant information for improving the accuracy of gene expression in research on intramuscular fat deposition in buffaloes.