RESUMO
Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.
Assuntos
Búfalos , Variações do Número de Cópias de DNA , Leite , Animais , Búfalos/genética , Leite/metabolismo , Feminino , Genoma , Cruzamento , Lactação/genéticaRESUMO
Identifying key causal genes is critical for unraveling the genetic basis of complex economic traits, yet it remains a formidable challenge. The advent of large-scale sequencing data and computational algorithms, such as transcriptome-wide association studies (TWASs), offers a promising avenue for identifying potential causal genes. In this study, we harnessed the power of TWAS to identify genes potentially responsible for milk production traits, including daily milk yield (MY), fat percentage (FP), and protein percentage (PP), within a cohort of 100 buffaloes. Our approach began by generating the genotype and expression profiles for these 100 buffaloes through whole-genome resequencing and RNA sequencing, respectively. Through comprehensive genome-wide association studies (GWAS), we pinpointed a total of seven and four single nucleotide polymorphisms (SNPs) significantly associated with MY and FP traits, respectively. By using TWAS, we identified 55, 71, and 101 genes as significant signals for MY, FP, and PP traits, respectively. To delve deeper, we conducted protein-protein interaction (PPI) analysis, revealing the categorization of these genes into distinct PPI networks. Interestingly, several TWAS-identified genes within the PPI network played a vital role in milk performance. These findings open new avenues for identifying potentially causal genes underlying important traits, thereby offering invaluable insights for genomics and breeding in buffalo populations.
Assuntos
Búfalos , Leite , Humanos , Animais , Leite/metabolismo , Estudo de Associação Genômica Ampla , Transcriptoma , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo ÚnicoRESUMO
As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating FST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.
Assuntos
Bison , Búfalos , Variações do Número de Cópias de DNA , Animais , Bovinos , Bison/genética , Búfalos/genética , Genoma , FenótipoRESUMO
The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
Assuntos
Endogamia , Polimorfismo de Nucleotídeo Único , Bovinos/genética , Animais , Paquistão , Polimorfismo de Nucleotídeo Único/genética , Homozigoto , Genoma/genética , GenótipoRESUMO
The sterol regulatory element-binding factor (SREBF) genes are a vital group of proteins binding to the sterol regulatory element 1 (SRE-1) regulating the synthesis of fatty acid. Two potential candidate genes (SREBF1 and SREBF2) have been identified as affecting milk traits. This study aims to identify the SREBF family of genes and find candidate markers or SREBF genes influencing lactation production in buffalo. A genome-wide study was performed and identified seven SREBF genes randomly distributed on 7 chromosomes and 24 protein isoforms in buffalos. The SREBF family of genes were also characterized in cattle, goat, sheep and horse, and using these all-protein sequences, a phylogenetic tree was built. The SREBF family genes were homologous between each other in the five livestock. Eight single nucleotide polymorphisms (SNPs) within or near the SREBF genes in the buffalo genome were identified and at least one milk production trait was associated with three of the SNP. The expression of SREBF genes at different lactation stages in buffalo and cattle from published data were compared and the SREBF genes retained a high expression throughout lactation with the trend being the same for buffalo and cattle. These results provide valuable information for clarifying the evolutionary relationship of the SREBF family genes and determining the role of SREBF genes in the regulation of milk production in buffalo.
Assuntos
Estudo de Associação Genômica Ampla , Leite , Feminino , Bovinos/genética , Animais , Cavalos/genética , Ovinos/genética , Leite/química , Estudo de Associação Genômica Ampla/veterinária , Filogenia , Lactação/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Búfalos/genéticaRESUMO
Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted for approximately 72.29% of all ROH. In contrast, the larger ROH (>8 Mb) class accounted for only 7.97% of all ROH segments. Estimated inbreeding coefficients from ROH (FROH) ranged from 0.0201 to 0.0371. Pearson correlations between FROH and genomic relationship matrix increased with the increase of ROH length. We identified ROH hotspots in 12 genomic regions, located on chromosomes 1, 2, 3, 5, 17, and 19, harboring a total of 122 genes. Protein-protein interaction (PPI) analysis revealed the clustering of these genes into 7 PPI networks. Many genes located in these regions were associated with different production traits. In addition, 5 ROH islands overlapped with cattle quantitative trait loci that were mainly associated with milk traits. These findings revealed the genome-wide autozygosity patterns and inbreeding levels in Mediterranean buffalo. Our study identified many candidate genes related to production traits that could be used to assist in selective breeding for genetic improvement of buffalo.
Assuntos
Búfalos , Polimorfismo de Nucleotídeo Único , Animais , Búfalos/genética , Bovinos , Diarreia/veterinária , Genótipo , Homozigoto , Endogamia , Itália , Locos de Características QuantitativasRESUMO
Protein disulfide isomerase family A member 3 (PDIA3) is a multifunctional protein, and it plays a vital role in modulating various cell biological functions under physiological and pathological conditions. Our previous study on Mediterranean buffalo demonstrated that PDIA3 is a potential candidate gene associated with milk yield based on genome-wide association study analysis. However, the genetic effects of the PDIA3 gene on milk performance in dairy cattle and the corresponding mechanism have not been documented. This study aims to explore the genetic effects of PDIA3 polymorphisms on milk production traits in 362 Chinese Holstein cattle. The results showed that 4 SNPs were identiï¬ed from the 5' untranslated region of the PDIA3 gene in the studied population, of which 2 SNPs (g.-1713 C>T and g.-934 G>A) were confirmed to be significantly associated with milk protein percentage, whereas g.-434 C>T was significantly associated with milk fat percentage. Notably, linkage disequilibrium analysis indicated that 3 SNPs (g.-1713 C>T, g.-934 G>A, and g.-695 A>C) formed one haplotype block, which was found to be significantly associated with milk protein percentage. The luciferase assay demonstrated that allele C of g.-434 C>T exhibited a higher promotor activity compared with allele T, suggesting that g.-434 C>T might be a potential functional mutation affecting PDIA3 expression. Furthermore, overexpression of the PDIA3 gene was found to induce higher levels of triglyceride and BODIPY fluorescence intensity. In addition, PDIA3 overexpression was also found to positively regulate the synthesis and secretion of α-casein, ß-casein, and κ-casein, whereas knockdown of this gene showed the opposite effects. In summary, our findings revealed significant genetic effects of PDIA3 on milk composition traits, and the identified SNP and the haplotype block might be used as genetic markers for dairy cow selected breeding.
Assuntos
Estudo de Associação Genômica Ampla , Leite , Animais , Bovinos/genética , China , Feminino , Estudo de Associação Genômica Ampla/veterinária , Leite/metabolismo , Proteínas do Leite/metabolismo , Mutação , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Acylglycerophosphate acyltransferases (AGPATs) are the rate-limiting enzymes for the de novo pathway of triacylglycerols (TAG) synthesis. Although AGPATs have been extensively explored by evolution, expression and functional studies, little is known on functional characterization of how many members of the AGPAT family are involved in TAG synthesis and their impact on the cell proliferation and apoptosis. Here, 13 AGPAT genes in buffalo were identified, of which 12 AGPAT gene pairs were orthologous between buffalo and cattle. Comparative transcriptomic analysis and real-time quantitative reverse transcription PCR (qRT-PCR) further showed that both AGPAT1 and AGPAT6 were highly expressed in milk samples of buffalo and cattle during lactation. Knockdown of AGPAT1 or AGPAT6 significantly decreased the TAG content of buffalo mammary epithelial cells (BuMECs) and bovine mammary epithelial cells (BoMECs) by regulating lipogenic gene expression (p < 0.05). Knockdown of AGPAT1 or AGPAT6 inhibited proliferation and apoptosis of BuMECs through the expression of marker genes associated with the proliferation and apoptosis (p < 0.05). Our data confirmed that both AGPAT1 and AGPAT6 could regulate TAG synthesis and growth of mammary epithelial cells in buffalo. These findings will have important implications for understanding the role of the AGPAT gene in buffalo milk performance.
Assuntos
Aciltransferases , Búfalos , Animais , Bovinos , Feminino , Aciltransferases/genética , Aciltransferases/metabolismo , Búfalos/genética , Búfalos/metabolismo , Células Epiteliais/metabolismo , Lactação/genética , Glândulas Mamárias Animais/metabolismo , Leite/metabolismo , Triglicerídeos/metabolismoRESUMO
Fatty acid synthase (FASN) is a multifunctional protein that catalyzes the synthesis of long-chain saturated fatty acid. In this study, we identified the single nucleotide polymorphisms (SNPs), and their association with milk traits in Mediterranean buffalo, and the expression of FASN gene in different tissues was measured. Nine SNPs (g.-1640G > A, g.-1099C > T, g.1095C > A, g.3221G > A, g.4762G > A, g.5299G > A, g.7164G > A, g.7272 T > C, and g.8927 T > C) were identified by DNA pooled sequencing and then genotyped. Seven identified SNPs except g.3221G > A and g.8927 T > C were found significantly associated with both fat and protein percentage, and also the g.7164G > A and g.8927 T > C had significant association with peak milk yield and protein percentage, respectively. One haplotype block was successfully constructed by linkage disequilibrium (LD) analysis and it showed a significant association with both fat percentage and protein percentage. Expression of FASN gene was found in almost all the buffalo tissues including mammary gland, heart, liver, spleen, lung, kidney, uterus, and ovary, and to be highest in lung and mammary gland. Our findings suggest that polymorphisms in the buffalo FASN gene are associated with milk production traits and can be used as a candidate gene for milk traits and marker-assisted selection in buffalo breeding program.
Assuntos
Búfalos , Leite , Animais , Búfalos/genética , Ácido Graxo Sintases/genética , Feminino , Genótipo , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Maternal-effect genes are especially critical for early embryonic development after fertilization and until massive activation of the embryonic genome occurs. By applying a tandem mass tag (TMT)-labeled quantitative proteomics combined with RNA sequencing approach, the proteome of the buffalo was quantitatively analyzed during parthenogenesis of mature oocytes and the two-cell stage embryo. Of 1908 quantified proteins, 123 differed significantly. The transcriptome was analyzed eight stages (GV, MII, 2-cell, 4-cell, 8-cell, 16-cell, morula, blastocyst) of Buffalo using the RNA sequencing approach, and a total of 3567 unique genes were identified to be differently expressed between all consecutive stages of pre-implantation development. Validation of proteomics results (TUBB3, CTNNA1, CDH3, MAP2K1), which are involved in tight junction and gap junction, revealing that the maternal expression of the proteins possibly plays a role in the formation of cellular junctions firstly after parthenogenetic activation. Correlation and hierarchical analyses of transcriptional profiles and the expression of NPM2 and NLRP5 mRNA of buffalo in vitro developed oocytes and parthenogenetic embryos indicated that the "maternal-to-zygotic transition" (MZT) process might exist in the model of parthenogenesis, which is similar to a normally fertilized embryo, and may occur between the 8-cell to 16-cell stage. These data provide a rich resource for further studies on maternal proteins and genes and are conducive to improving nuclear transfer technology.
Assuntos
Búfalos/genética , Búfalos/metabolismo , Perfilação da Expressão Gênica , Oócitos/metabolismo , Partenogênese/genética , Proteoma/metabolismo , Proteômica/métodos , Animais , Embrião de Mamíferos/metabolismo , Feminino , Junções Comunicantes/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Ontologia Genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reprodutibilidade dos Testes , Junções Íntimas/metabolismo , Regulação para CimaRESUMO
Maternal mRNAs deposited in the egg during oogenesis are critical during the development of early embryo, before the activation of the embryonic genome. However, there is little known about the dynamic expression of maternally expressed genes in mammals. In this study, we made buffalo parthenogenesis as our research model to analyse maternal transcription profiles of pre-implantation embryo in buffalo using RNA sequencing. In total, 3,567 unique genes were detected to be differentially expressed among all constant stages during early embryo development (FPKM > 0). Interestingly, a total of 10,442 new genes were discovered in this study, and gene ontology analysis of the new differentially expressed genes indicated that the new genes have a wide cellular localization and are involved in many molecular functions and biological processes. Moreover, we identified eight clusters that were only highly expressed in a particular developmental stage and enriched a number of GO terms and KEGG pathways that were related to specific stage. Furthermore, we identified 1,530 hub genes (or key members) from the maternally expressed gene networks, and these hub genes were involved in 11 stage-specific modules. After visualization using Cytoscape 3.2.1 software, we obtained complex interaction network of hub genes, indicating the highly efficient cooperation between genes during the development in buffalo embryos. Further research of these genes will greatly deepen our understanding of embryo development in buffalo. Collectively, this research lays the foundation for future studies on the maternal genome function, buffalo nuclear transfer and parthenogenetic embryonic stem cells.
Assuntos
Búfalos/embriologia , Búfalos/genética , Perfilação da Expressão Gênica , Animais , Búfalos/metabolismo , Embrião de Mamíferos/metabolismo , Desenvolvimento Embrionário/genética , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Técnicas de Maturação in Vitro de Oócitos/veterinária , Partenogênese/genética , Análise de Sequência de RNARESUMO
The study reported in this Research Communication was conducted to investigate the molecular characterisation of buffalo SCAP gene, expression analysis, and the association between single nucleotide polymorphisms and milk production traits in 384 buffaloes. Sequence analysis revealed the SCAP gene had an open reading frame of 3837 bp encoding 1279 amino acids. A ubiquitous expression profile of SCAP gene was detected in various tissues with extreme predominance in the mammary gland during early lactation. Moreover, eleven SNPs in buffalo SCAP gene were identified, six of them (g.1717600A>G, g.1757922C>T, g.1758953G>A, g.1759142C>T, g.1760740G>A, and g.1766036T>C) were found to be significantly associated with 305-day milk yield. Thus, buffalo SCAP could sever as a candidate gene affecting milk production traits in buffalo and the identified SNPs might potentially be genetic markers.
Assuntos
Búfalos/genética , Peptídeos e Proteínas de Sinalização Intracelular/genética , Lactação/genética , Proteínas de Membrana/genética , Animais , Cruzamento/métodos , China , Feminino , Expressão Gênica , Marcadores Genéticos , Genótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Análise de Sequência de DNARESUMO
Insulin-induced genes (INSIGs), including INSIG1 and INSIG2, are important mediators that play a pivotal role in the lipid metabolism and could cause the retention of the SCAP/SREBP complex. Therefore, the objective of this study is to detect the single nucleotide polymorphisms (SNPs) of buffalo INSIG2 gene and evaluate their associations with milk production traits in Chinese buffaloes. A total of four SNPs (g.621272A > G, g.621364A > C, g.632543G > A, and g.632684C > T) were identified using DNA pooled sequencing, and the SNP genotyping for the identified SNPs was performed by using Matrix-assisted laser desorption/ionization time of flight mass spectrometry method from 264 individuals. The results showed that four SNPs were significantly associated with 305-day milk yield or protein percentage in Murrah and crossbred breeds (P < 0.05), but they had no significant effect on milk production traits in Nili-Ravi buffaloes (P > 0.05). Linkage disequilibrium (LD) analysis revealed that one haplotype block was successfully constructed, of which the diplotype H1H1 showed significant association with 305-day milk yield in Murrah buffaloes (P < 0.05). Our findings provide evidence that polymorphisms in buffalo INSIG2 gene are associated with milk production traits, and could be used as a candidate gene for marker-assisted selection in buffalo breeding program.
Assuntos
Búfalos/genética , Estudos de Associação Genética , Proteínas de Membrana/genética , Leite/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Característica Quantitativa Herdável , Alelos , Animais , Cruzamento , Frequência do Gene , Técnicas de Genotipagem , Haplótipos/genética , Desequilíbrio de Ligação/genéticaRESUMO
Signal transducer and activator of transcription 1 (STAT1) is a critical component of the transcription factor complex in the interferon (IFN) signaling pathways. Of the seven STAT isoforms, STAT1 is a key mediator of type I and type III IFN signaling, but limited information is available for the STAT genes in the water buffalo. Here, we amplified and identified the complete coding sequence (CDS) of the buffalo STAT1 gene by using reverse transcription polymerase chain reaction (RT-PCR). Sequence analysis indicated that the buffalo STAT1 gene length size was 3437 bp, containing an open reading frame (ORF) of 2244 bp that encoded 747 amino acids for the first time. The buffalo STAT1 CDS showed 99, 98, 89, 93, 86, 85, and 87% identity with that of Bos taurus, Ovis aries, Homo sapiens, Sus scrofa, Rattus norvegicus, Mus musculus, and Capra hircus. The phylogenetic analyses revealed that the nearest relationship existed between the water buffalo and B. taurus. The STAT1 gene was ubiquitously expressed in 11 buffalo tissues by real-time PCR, whereas STAT1 was expressed at higher levels in the lymph. The STAT1 gene contained five targeted microRNA sequences compared with the B. taurus by the miRBase software that provide a fundamental for identifying the STAT1 gene function.
Assuntos
Búfalos/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Fator de Transcrição STAT1/metabolismo , Sequência de Aminoácidos , Animais , Bovinos , Clonagem Molecular , Cabras , Humanos , Camundongos , MicroRNAs/genética , MicroRNAs/metabolismo , Dados de Sequência Molecular , Fases de Leitura Aberta , Filogenia , Estrutura Terciária de Proteína , Ratos , Reação em Cadeia da Polimerase em Tempo Real , Fator de Transcrição STAT1/genética , Ovinos , Especificidade da Espécie , Suínos , Distribuição TecidualRESUMO
Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.
Assuntos
Doenças dos Bovinos , Diarreia , Farmacorresistência Bacteriana , Infecções por Escherichia coli , Escherichia coli , Microbioma Gastrointestinal , Fatores de Virulência , Bovinos , Animais , Fatores de Virulência/genética , Diarreia/veterinária , Diarreia/microbiologia , Diarreia/genética , Escherichia coli/genética , Escherichia coli/patogenicidade , Escherichia coli/efeitos dos fármacos , Infecções por Escherichia coli/veterinária , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/genética , Infecções por Escherichia coli/tratamento farmacológico , Doenças dos Bovinos/microbiologia , Doenças dos Bovinos/genética , Microbioma Gastrointestinal/efeitos dos fármacos , Microbioma Gastrointestinal/genética , Farmacorresistência Bacteriana/genética , Antibacterianos/farmacologia , Metabolômica , MultiômicaRESUMO
Fibroblast growth factors (FGFs) are important polypeptide growth factors that play a critical role in many developmental processes, including differentiation, cell proliferation, and migration in mammals. This study employs in silico analyses to characterize the FGF gene family in buffalo, investigating their genome-wide identification, physicochemical properties, and evolutionary patterns. For this purpose, genomic and proteomic sequences of buffalo, cattle, goat, and sheep were retrieved from NCBI database. We identified a total of 22 FGF genes in buffalo. Physicochemical properties observed through ProtParam tool showed notable features of these proteins including in-vitro instability, thermostability, hydrophilicity, and basic nature. Phylogenetic analysis grouped 22 identified genes into nine sub-families based on evolutionary relationships. Additionally, analysis of gene structure, motif patterns, and conserved domains using TBtools revealed the remarkable conservation of this gene family across selected species throughout the course of evolution. Comparative amino acid analysis performed through ClustalW demonstrated significant conservation between buffalo and cattle FGF proteins. Mutational analysis showed three non-synonymous mutations at positions R103 > G, P7 > L, and E98 > Q in FGF4, FGF6, and FGF19, respectively in buffalo. Duplication events revealed only one segmental duplication (FGF10/FGF22) in buffalo and two in cattle (FGF10/FGF22 and FGF13/FGF13-like) with Ka/Ks values <1 indicating purifying selection pressure for these duplications. Comparison of protein structures of buffalo, goat, and sheep exhibited more similarities in respective structures. In conclusion, our study highlights the conservation of the FGF gene family in buffalo during evolution. Furthermore, the identified non-synonymous mutations may have implications for the selection of animals with better performance.Communicated by Ramaswamy H. Sarma.
RESUMO
IMPORTANCE: Calf diarrhea is of great concern to the global dairy industry as it results in significant economic losses due to lower conception rates, reduced milk production, and early culling. Although there is evidence of an association between altered gut microbiota and diarrhea, remarkably little is known about the microbial and metabolic mechanisms underlying the link between gut microbiota dysbiosis and the occurrence of calf diarrhea. Here, we used fecal metagenomic and metabolomic analyses to demonstrate that gut microbiota-driven metabolic disorders of purine or arachidonic acid were associated with calf diarrhea. These altered gut microbiotas play vital roles in diarrhea pathogenesis and indicate that gut microbiota-targeted therapies could be useful for both prevention and treatment of diarrhea.
Assuntos
Microbioma Gastrointestinal , Animais , Bovinos , Microbioma Gastrointestinal/genética , Diarreia/veterinária , Fezes , Metagenoma , MetabolômicaRESUMO
Knowledge of RNA molecules regulating testicular development and spermatogenesis in bulls is essential for elite bull selection and an ideal breeding program. Herein, we performed direct RNA sequencing (DRS) to explore the functional characterization of RNA molecules produced in the testicles of 9 healthy Simmental bulls at three testicular development stages (prepuberty, puberty, and postpuberty). We identified 5,043 differentially expressed genes associated with testicular weight. These genes exhibited more alternative splicing at sexual maturity, particularly alternative 3' (A3) and 5' (A5) splice sites usage and exon skipping (SE). The expression of hub genes in testicular developmental stages was also affected by both m6A and m5C RNA modifications. We found m5C-mediated splicing events significantly (p < 0.05) increased MAEL gene expression at the isoform level, likely promoting spermatogenesis. Our findings highlight the complexity of RNA processing and expression as well as the regulation of transcripts involved in testicular development and spermatogenesis.
RESUMO
Cattle and buffalo served as the first and second largest dairy animals, respectively, providing 96% milk products worldwide. Understanding the mechanisms underlying milk synthesis is critical to develop the technique to improve milk production. Thiolases, also known as acetyl-coenzyme A acetyltransferases (ACAT), are an enzyme family that plays vital roles in lipid metabolism, including ACAT1, ACAT2, ACAA1, ACAA2, and HADHB. Our present study showed that these five members were orthologous in six livestock species including buffalo and cattle. Transcriptomic data analyses derived from different lactations stages showed that ACAA1 displayed different expression patterns between buffalo and cattle. Immunohistochemistry staining revealed that ACAA1 were dominantly located in the mammary epithelial cells of these two dairy animals. Knockdown of ACAA1 inhibited mammary epithelial cell proliferation and triglyceride and ß-casein secretion by regulating related gene expressions in cattle and buffalo. In contrast, ACAA1 overexpression promoted cell proliferation and triglyceride secretion. Finally, three novel SNPs (g.-681A>T, g.-23117C>T, and g.-24348G>T) were detected and showed significant association with milk production traits of Mediterranean buffaloes. In addition, g.-681A>T mutation located in the promoter region changed transcriptional activity significantly. Our findings suggested that ACAA1 play a key role in regulating buffalo and cattle milk synthesis and provided basic information to further understand the dairy animal lactation physiology.