RESUMO
BARKGROUND: Circular RNAs (circRNAs) play important regulatory roles in a variety of biological processes in mammals. Multiple birth-traits in goats are affected by several factors, but the expression and function of circRNAs in follicular development of goats are not clear. In this study, we aimed to investigate the possible regulatory mechanisms of circRNA and collected five groups of large follicles (Follicle diameter > 6 mm) and small follicles (1 mm < Follicle diameter < 3 mm) from Leizhou goats in estrus for RNA sequencing. RESULTS: RNA sequencing showed that 152 circRNAs were differentially expressed in small and large follicles. Among them, 101 circRNAs were up-regulated in large follicles and 51 circRNAs were up-regulated in small follicles. GO and KEGG enrichment analyses showed that parental genes of the differential circRNAs were significantly enriched in important pathways, such as ovarian steroidogenesis, GnRH signaling pathway, animal autophagy and oxytocin signalling pathway. BioSignal analysis revealed that 152 differentially expressed circRNAs could target 91 differential miRNAs including miR-101 family (chi-miR-101-3p, chi-miR-101-5p), miR-202 family (chi-miR-202-5p, chi-miR-202-3p),60 circRNAs with translation potential. Based on the predicted sequencing results, the ceRNA networks chicirc_008762/chi-miR-338-3p/ARHGAP18 and chicirc_040444/chi-miR-338-3p/STAR were constructed in this study. Importantly, the new gene circCFAP20DC was first discovered in goats. The EDU assay and flow cytometry results indicated that circCFAP20DC enhanced the proliferation of follicular granulosa cells(GCs). Real-time quantitative PCR and western blotting assays showed that circCFAP20DC activated the Retinoblastoma(RB) pathway and promoted the progression of granulosa cells from G1 to S phase. CONCLUSION: Differential circRNAs in goat size follicles may have important biological functions for follicular development. The novel gene circCFAP20DC activates the RB pathway, promoting the progression of GCs from G1 to S phase. This, in turn, enhances the proliferation of follicular GCs in goats.
Assuntos
Cabras , Folículo Ovariano , RNA Circular , Animais , Cabras/genética , Feminino , RNA Circular/genética , Folículo Ovariano/metabolismo , Folículo Ovariano/crescimento & desenvolvimento , MicroRNAs/genética , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Análise de Sequência de RNARESUMO
Litter size is a crucial quantitative trait in animals, closely linked to follicular development. Circular RNA (circRNA), a type of single-stranded closed-loop endogenous RNA with stable expression, plays pivotal roles in various biological processes, yet its function in goat follicular development remains unclear. In this study, we collected large (follicle diameter > 3 mm) and small (1 mm < follicle diameter < 3 mm) follicles from black goats in the Chuanzhong region for circRNA sequencing, with the aim of elucidating the functional circRNAs that influence follicle development in goats. Differential analysis revealed that 17 circRNAs were upregulated in large follicles, and 28 circRNAs were upregulated in small follicles. Functional enrichment analysis revealed significant enrichment of pathways related to reproduction, including cellular response to follicle-stimulating hormone stimulus, the PI3K-Akt signaling pathway, the MAPK signaling pathway, and the Notch signaling pathway. Based on the ceRNA mechanism, 45 differentially expressed circRNAs were found to target and bind a total of 418 miRNAs, and an intercalation network including miR-324-3p (circRNA2497, circRNA5650), miR-202-5p (circRNA3333, circRNA5501), and miR-493-3p (circRNA4995, circRNA5508) was constructed. In addition, conservation analysis revealed that 2,239 circRNAs were conserved between goats and humans. Prediction of translation potential revealed that 154 circRNAs may potentially utilize both N6-methyladenosine (m6A) and internal ribosome entry site (IRES) translation mechanisms. Furthermore, the differential expression and circularization cleavage sites of five circRNAs were validated through RT-qPCR and DNA sequencing. Our study constructed a circRNA map in goat follicle development, offering a theoretical foundation for enhancing goat reproductive performance.
Assuntos
Cabras , Folículo Ovariano , RNA Circular , Animais , Cabras/genética , RNA Circular/genética , RNA Circular/metabolismo , Feminino , Folículo Ovariano/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Perfilação da Expressão Gênica , Transdução de Sinais , Redes Reguladoras de GenesRESUMO
The objectives of this investigation were to identify differentially expressed circular RNAs (circRNAs) in the hypothalamus of goats with high and low prolificacy and construct a circRNA-mRNA regulatory network to uncover key potential circRNAs that influence goat prolificacy. Transcriptome analysis was performed on hypothalamus samples from low-prolificacy (n = 5) and high-prolificacy (n = 6) Chuanzhong black goats to identify circRNAs that influence prolificacy in these goats. Differential expression analysis identified a total of 205 differentially expressed circRNAs, comprising 100 upregulated and 105 downregulated circRNAs in the high-prolificacy group compared with the low-prolificacy group. Enrichment analysis of these differentially expressed circRNAs indicated significant enrichment in Gene Ontology terms associated with mammalian oogenesis, negative regulation of neurotransmitter secretion, reproductive developmental processes, hormone-mediated signaling pathways, and negative regulation of hormone secretion. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted significant enrichment in the oxytocin signaling pathway, GnRH signaling pathway, and hormone-mediated oocyte maturation. The hypothalamus of low- and high-prolificacy goats contains circular RNAs (circRNAs), including chicirc_063269, chicirc_097731, chicirc_017440, chicirc_049641, chicirc_008429, chicirc_145057, chicirc_030156, chicirc_109497, chicirc_030156, chicirc_176754, and chicirc_193363. Chuanzhong black goats have the potential to influence prolificacy by modulating the release of serum hormones from the hypothalamus. A circRNA-miRNA regulatory network was constructed, which determined that miR-135a, miR-188-3p, miR-101-3p, and miR-128-3p may interact with differentially expressed circRNAs, thereby regulating reproductive capacity through the hypothalamic-pituitary-gonadal axis. The results of this study enhance our knowledge of the molecular mechanisms that regulate prolificacy in Chuanzhong black goats at the hypothalamic level.
Assuntos
Redes Reguladoras de Genes , Cabras , Hipotálamo , RNA Circular , Reprodução , Animais , Cabras/genética , RNA Circular/genética , Hipotálamo/metabolismo , Feminino , Reprodução/genética , Perfilação da Expressão Gênica , Ontologia Genética , Transcriptoma , Regulação da Expressão GênicaRESUMO
The proliferation and apoptosis of granulosa cells (GCs) affect follicle development and reproductive disorders, with microRNAs playing a crucial regulatory role. Previous studies have shown the differential expression of miR-128-3p at different stages of goat follicle development, which suggests its potential regulatory role in follicle development. In this study, through the Cell Counting Kit-8 assay, the EDU assay, flow cytometry, quantitative real-time polymerase chain reaction, Western blot, and the dual-luciferase reporter assay, we used immortal human ovarian granulosa tumor cell line (KGN) cells as materials to investigate the effects of miR-128-3p and its predicted target gene growth hormone secretagogue receptor (GHSR) on GC proliferation and apoptosis. The results show that overexpression of miR-128-3p inhibited the proliferation of KGN cells, promoted cell apoptosis, and suppressed the expression of proliferating cell nuclear antigen (PCNA) and B-cell lymphoma-2 (BCL2) while promoting that of Bcl-2 associated X protein (BAX). The dual-luciferase reporter assay revealed that miR-128-3p bound to the 3' untranslated region sequence of GHSR, which resulted in the inhibited expression of GHSR protein. Investigation of the effects of GHSR on GC proliferation and apoptosis revealed that GHSR overexpression promoted the expression of PCNA and BCL2, enhanced GC proliferation, and inhibited cell apoptosis, whereas the opposite effects were observed when GHSR expression was inhibited. In addition, miR-128-3p and GHSR can influence the expression of extracellular signal-regulated kinase 1/2 protein. In conclusion, miR-128-3p inhibits KGN cell proliferation and promotes cell apoptosis by downregulating the expression of the GHSR gene.
Assuntos
MicroRNAs , Receptores de Grelina , Feminino , Humanos , Antígeno Nuclear de Célula em Proliferação , MicroRNAs/genética , Apoptose/genética , Proliferação de Células/genética , Luciferases , Linhagem Celular TumoralRESUMO
This paper aims to explore the role of circRNA expression profiles and circRNA-associated ceRNA networks in the regulation of myogenesis in the longissimus dorsi of cattle breeds surviving under subtropical conditions in southern China by RNA sequencing and bioinformatics analysis. It also aims to provide comprehensive understanding of the differences in muscle fibers in subtropical cattle breeds and to expand the knowledge of the molecular networks that regulate myogenesis. With regard to meat quality indicators, results showed that the longissimus dorsi of LQC had lower pH (P < 0.0001), lower redness (P < 0.01), lower shear force (P < 0.05), and higher brightness (P < 0.05) than the longissimus dorsi of LFC. With regard to muscle fiber characteristics, the longissimus dorsi of LQC had a smaller diameter (P < 0.0001) and higher density of muscle fibers (P < 0.05). The analysis results show that the function of many circRNA-targeted mRNAs was related to myogenesis and metabolic regulation. Furthermore, in the analysis of the function of circRNA source genes, we hypothesized that btacirc_00497 and btacirc_034497 may regulate the function and type of myofibrils by affecting the expression of MYH6, MYH7, and NEB through competitive linear splicing.
Assuntos
Biologia Computacional , RNA Circular , Animais , Bovinos/genética , China , Carne , Músculos ParaespinaisRESUMO
Endometrial receptivity is one of the main factors underlying a successful pregnancy, with reports substantiating the fact that suboptimal endometrial receptivity accounts for two-thirds of early implantation event failures. The association between circRNAs and endometrial receptivity in the goat remains unclear. This study aims to identify potential circRNAs and regulatory mechanisms related to goat endometrial receptivity. Therefore, the endometrial samples on day 16 of pregnancy and day 16 of the estrous cycle were analyzed using high-throughput RNA-seq and bioinformatics. The results show that 4666 circRNAs were identified, including 7 downregulated and 11 upregulated differentially expressed circRNAs (DE-circRNAs). Back-splicing and RNase R resistance verified the identified circRNAs. We predicted the competing endogenous RNA (ceRNA) regulatory mechanism and potential target genes of DE-circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these predicted target genes suggest that DE-circRNAs were significantly involved in establishing endometrial receptivity. Furthermore, Sanger sequencing, qPCR, correlation analysis and Fluorescence in Situ Hybridization (FISH) show that circ_MYRF derived from the host gene myelin regulatory factor (MYRF) might regulate the expression of interferon stimulating gene 15 (ISG15), thereby promoting the formation of endometrial receptivity. These novel findings may contribute to a better understanding of the molecular mechanisms regulating endometrial receptivity and promoting the maternal recognition of pregnancy (MRP).
Assuntos
MicroRNAs , RNA Circular , Gravidez , Feminino , Animais , RNA Circular/genética , Cabras/genética , Cabras/metabolismo , Hibridização in Situ Fluorescente , RNA/metabolismo , Fatores de Transcrição/genética , MicroRNAs/genéticaRESUMO
Identification and utilization of sheep major fecundity genes offer opportunities for the increase in litter size, as well as the improvement of production efficiency in livestock industry. BMPR-IB gene belongs to the TGF-ß superfamily, and is also considered as a regulator for sheep reproductive performance due to its involvement in the mammalian gametogenesis pathway. This study aimed to detect the variations of BMPR-IB gene in Hu sheep (N = 934) and to evaluate their effects on the litter size trait. qRT-PCR results showed that the mRNA expression level of BMPR-IB in kidney was the highest. And in the tissues of ovary and pituitary, the expression levels of prolific group were significantly higher than that of non-prolific group (p < 0.05). Through DNA sequencing and PCR-RFLP, three SNPs were identified in the genomic region of BMPR-IB gene; the individuals with CC in g.29362047T > C, AA in g.29427689G > A and GG in FecB had better fecundity characterization. Additionally, association analysis indicated that two diplotypes of Hap2/2 and Hap2/4 showed larger litter size. Overall, our results verified several useful markers which would contribute to further development of sheep breeding strategies.
Assuntos
Receptores de Proteínas Morfogenéticas Ósseas Tipo I , Polimorfismo de Nucleotídeo Único , Animais , Receptores de Proteínas Morfogenéticas Ósseas Tipo I/genética , China , Feminino , Genótipo , Tamanho da Ninhada de Vivíparos/genética , Mamíferos , Polimorfismo de Nucleotídeo Único/genética , Gravidez , Ovinos/genéticaRESUMO
Follicle maturation is a complex biological process governed by numerous factors, and researchers have observed follicle development by studying the proliferation and apoptosis of follicular granulosa cells (GCs). However, the regulatory mechanisms of GCs proliferation and death during follicle development are largely unknown. To investigate the regulatory mechanisms of lncRNAs, mRNAs, and microRNAs, RNA sequencing (RNA-seq) and small RNA-seq were performed on large (>10 mm) and small follicles (<3 mm) of Leizhou black goat during estrus. We discovered two microRNAs, miR-450-5p and miR-202-5p, which can target GCs in goats and may be involved in follicle maturation, and the effects of miR-450-5p and miR-202-5p on ovarian granulosa cell lines were investigated (KGN). Using cell counting kit-8 (CCK-8) assays, 5-Ethynyl-2'-deoxyuridine (EdU) assay and flow cytometry, miR-202-5p overexpression could suppress the proliferation and induce apoptosis of GCs, whereas miR-450-5p overexpression induced the opposite effects. The dual-luciferase reporter assay confirmed that miR-450-5p could directly target the BMF gene (a BCL2 modifying factor), and miR-202-5p targeted the BCL2 gene. A considerable rise in phosphorylated Akt (p-AKT) protein was observed following the downregulation of BMF by miR-450-5p mimics. After BMF gene RNAi therapy, a notable elevation in p-AKT was detected. Mimics of miR-202-5p inhibited BCL2 protein expression, significantly decreasing p-AMPK protein expression. These results imply that during the follicular development in black goats, the miR-450-5p-BMF axis favored GC proliferation on a wide scale, while the miR-202-5p-BCL2 axis triggered GC apoptosis.
Assuntos
MicroRNAs , Folículo Ovariano , Animais , Feminino , Apoptose/genética , Proliferação de Células/genética , Cabras/genética , Cabras/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Proteínas Proto-Oncogênicas c-akt , Proteínas Proto-Oncogênicas c-bcl-2 , Folículo Ovariano/crescimento & desenvolvimentoRESUMO
With the rapid development of dairy industry, the breeding process of dairy cows has been accelerated. In previous genome-wide association studies (GWAS), a large number of genetic markers have been reported which may contribute to the selection of Holstein populations with superior milk-producing traits, but they remain to be further verified before practical application. In this study, 90 single nucleotide polymorphisms (SNPs) were selected, which were reported to be significantly associated with five milk production traits, including 305-day milk yield (305MY), 305-day milk fat percent (305FC), 305-day milk protein percent (305PC), 305-day milk fat yield (305FY) and 305-day milk protein yield (305PY). Effective 305-day data and fresh DNA samples were obtained from 295 healthy cows with gestational age of 1-4. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) was used to perform precise genotyping of these loci, followed by site association and haplotype analysis. Results showed that 36 out of 90 loci were supported to be used as genetic markers. In particular, several novel and effective haplotypes were also presented. Overall, our results verified tens of useful markers and provided a basis for further development of breeding strategies.
Assuntos
Bovinos/genética , Marcadores Genéticos/genética , Leite , Polimorfismo de Nucleotídeo Único/genética , Animais , China , Indústria de Laticínios , Feminino , Estudo de Associação Genômica Ampla , Lactação/genéticaRESUMO
BACKGROUND: Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play critical roles in ovarian biological processes, the interaction between mRNAs and miRNAs in follicular development is not yet completely understood. In addition, less attention has been given to the study of single follicle (dominant or atretic follicle) in goats. This study aimed to identify mRNAs, miRNAs, and signaling pathways as well as their interaction networks in the ovarian follicles (large follicles and small follicles) of uniparous and multiple Chuanzhong black goats at estrus phase using RNA-sequencing (RNA-seq) technique. RESULTS: The results showed that there was a significant difference in the number of large follicles between uniparous and multiple goats (P < 0.05), but no difference in the number of small follicles was observed (P > 0.05). For the small follicles of uniparous and multiple goats at estrus phase, 289 differentially expressed mRNAs (DEmRNAs) and 16 DEmiRNAs were identified; and for the large follicles, 195 DEmRNAs and 7 DEmiRNAs were identified. The functional enrichment analysis showed that DE genes in small follicles were significantly enriched in ovarian steroidogenesis and steroid hormone biosynthesis, while in large follicles were significantly enriched in ABC transporters and steroid hormone biosynthesis. The results of quantitative real-time polymerase chain reaction were consistent with those of RNA-seq. Analysis of the mRNA-miRNA interaction network suggested that CD36 (miR-122, miR-200a, miR-141), TNFAIP6 (miR-141, miR-200a, miR-182), CYP11A1 (miR-122), SERPINA5 (miR-1, miR-206, miR-133a-3p, miR-133b), and PTGFR (miR-182, miR-122) might be related to fertility, but requires further research on follicular somatic cells. CONCLUSIONS: This study was used for the first time to reveal the DEmRNAs and DEmiRNAs as well as their interaction in the follicles of uniparous and multiple goats at estrus phase using RNA-seq technology. Our findings provide new clues to uncover the molecular mechanisms and signaling networks of goat reproduction that could be potentially used to increase ovulation rate and kidding rate in goat.
Assuntos
Estro/fisiologia , MicroRNAs/metabolismo , Folículo Ovariano/metabolismo , RNA Mensageiro/metabolismo , Animais , Estro/genética , Feminino , Perfilação da Expressão Gênica , Cabras , MicroRNAs/genética , RNA Mensageiro/genética , RNA-Seq , Reação em Cadeia da Polimerase em Tempo RealRESUMO
Fecundity improvement is one of the most important objectives for goat breeders as it can considerably greatly increase production efficiency. The molecular mechanisms underlying fecundity in goats remain largely unknown. To explore the molecular and genetic mechanisms related to the fecundities and prolificacies in Chuanzhong black goats, we performed high-throughput RNA sequencing to identify differentially expressed long non-coding RNAs (lncRNAs) and mRNAs (DElncRNAs and DEmRNAs, respectively) the ovaries of high-fecundity and low-fecundity goats; furthermore, we conducted functional annotation analyses to identify pathways of interest. Overall, 1,353 DEmRNAs and 168 DElncRNAs were identified. Quantitative real-time PCR (qRT-PCR) was performed to validate some randomly selected DElncRNAs and DEmRNAs. We found that two DElncRNAs ENSCHIT00000005909 and ENSCHIT00000005910 might positively influence the expression of the corresponding gene IL1R2 (upregulated in high-fecundity group), exerting co-regulative effects on the ovarian function, through which litter size might show variations. KEGG pathway analysis indicated that the DEmRNAs SRD5A2, LOC102191297 and LOC102171967 were significantly enriched in steroid hormone biosynthesis-this pathway was related to animal reproduction. To summarize, our findings expand the understanding pertaining to the biological functions of lncRNAs and contribute to the annotation of the goat genome; moreover, they should be helpful for further studying the role of lncRNAs in ovulation and lambing.
Assuntos
Perfilação da Expressão Gênica , Cabras/genética , Tamanho da Ninhada de Vivíparos/genética , RNA Longo não Codificante , RNA Mensageiro , Animais , Cruzamento , Feminino , Fertilidade/genética , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Ovário/metabolismo , Reação em Cadeia da Polimerase em Tempo Real/veterináriaRESUMO
A new strain of Qinchuan cattle (QNS) has been obtained after more than forty years of selective breeding, and it shows good performance and production traits. To characterize the genetic changes that have resulted from breeding, we sequenced 10 QNS and 10 of the original breed Qinchuan cattle (QCC) for the first time, with average of 12.5-fold depth. A total of 31,242,284 and 29,612,517 SNPs were identified in the QCC and QNS genomes, 47.81% and 44.36% of which were found to be novel, respectively. Furthermore, population structure analysis revealed the selection that these cattle had experienced. Then, 332 and 571 potential selected genes were obtained, associated with enhanced immunity and acclimatization in QCC (CD5, SMARCA2, CATHL2, etc.) and production or meat quality traits in QNS (PLCD3, MB, PPARGC1A, etc.). These results revealed the efforts of selective breeding for Chinese Qinchuan cattle, and will be helpful for future cattle breeding.
Assuntos
Bovinos/genética , Carne , Animais , Cruzamento , Variação Genética , Mutação INDEL , Anotação de Sequência Molecular , Fenótipo , Polimorfismo de Nucleotídeo Único , Sequenciamento Completo do GenomaRESUMO
This study investigated the effects of lycopene on the gene expression profile and expression of genes related to fat metabolism of Xinghua breeding hens. Seven hundred and twenty healthy breeding hens were randomly assigned to four treatments; each treatment was replicated six times with 30 hens each. Broken rice and soybean meal were adopted for the basal diet and added with 0 (control group), 20, 40 and 80 mg/kg lycopene respectively. Gene expression profile of the liver induced by lycopene and expression of genes related to fat metabolism in hens liver and intestine were analysed after 42-day feeding trial including 7-day pre-feeding period and 35-day formal period. The genes involved in fat metabolism were analysed, and we found that lycopene significantly increased the expression of PGC1α, PPARα, RXRα and RARα in the liver, PPARγ, RXRα and RXRγ in the jejunum, and RARα in the duodenum (p < .05); reduced the expression of FABP1 and FABP10 in the liver, and FATP4 in the jejunum (p < .05). By analysing gene expression profile, 158 differentially expressed genes (DEGs) including 69 up-regulated genes and 89 down-regulated genes were obtained between control group and 40 mg/kg group. KEGG pathway analysis was performed on all DEGs, and 5 pathways were obtained. In conclusion, lycopene can affect the expression of related genes, and this may be one of the reasons that lycopene can regulate fat metabolism.
Assuntos
Ração Animal/análise , Galinhas/fisiologia , Dieta/veterinária , Gorduras na Dieta/metabolismo , Licopeno/farmacologia , Fenômenos Fisiológicos da Nutrição Animal , Animais , Suplementos Nutricionais , Feminino , Regulação da Expressão Gênica/efeitos dos fármacos , Licopeno/administração & dosagem , Oviposição/fisiologia , TranscriptomaRESUMO
Pili have been demonstrated to contribute to the pathogenicity of many bacterial pathogens. Flp pilus encoded by the tad locus belongs to the type IVb pilus. Our previous study has revealed that the intact tad locus is essential for Flp pilus formation in Actinobacillus pleuropneumoniae, a very important porcine respiratory pathogen. To further investigate the functions of Flp pilus in A. pleuropneumoniae pathogenesis, the flp1 and tadD single deletion mutants were constructed by homologous recombination. Both of the mutant strains lost pilus on their cell surfaces. The abilities of biofilm formation, cell adhesion, resistance to phagocytosis, survival in swine whole blood, and in vivo colonization of the two mutants were significantly reduced compared with those of the parental strain. The corresponding complemented strains recovered the phenotypes. These results demonstrated that flp1 and tadD were essential for the biosynthesis of Flp pilus and that the pilus played important roles during infection of A. pleuropneumoniae.
Assuntos
Infecções por Actinobacillus/microbiologia , Actinobacillus pleuropneumoniae/metabolismo , Actinobacillus pleuropneumoniae/patogenicidade , Proteínas de Bactérias/metabolismo , Proteínas de Fímbrias/metabolismo , Fímbrias Bacterianas/metabolismo , Infecções por Actinobacillus/sangue , Actinobacillus pleuropneumoniae/crescimento & desenvolvimento , Animais , Aderência Bacteriana/genética , Proteínas de Bactérias/genética , Biofilmes/crescimento & desenvolvimento , Linhagem Celular , Modelos Animais de Doenças , Feminino , Proteínas de Fímbrias/genética , Fímbrias Bacterianas/genética , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos , Recombinação Homóloga , Camundongos Endogâmicos BALB C , Viabilidade Microbiana , Fagocitose , Fenótipo , Deleção de Sequência , VirulênciaRESUMO
Crossbreeding can provide productive gains through heterosis, however, surveys about the effects of crossbreeding through global transcriptomic sequencing are few. This study revealed that Angus × Qinchuan cattle (AQF) have improved performance characteristics compared to Qinchuan cattle (QCF). We performed RNA-seq on the subcutaneous fat tissue of QCF and AQF. More than 42.2 million clean reads were obtained in each sample. We detected 40 and 21 breed-specific highly expressed genes (FPKM > 500) in QCF and AQF, respectively. Furthermore, a total of 353 differentially expressed genes (DEGs, |log2 ratio| ≥ 1 and Probability ≥ 0.8) were found between these two groups, of which 227 genes were upregulated in AQF and 126 genes were upregulated in QCF. Functional enrichment analyses showed that breed-specific highly expressed genes and DEGs were closely related to terms such as development in AQF, and adaption or immune in QCF. In addition, we also identified the novel transcript units, alternative splicing events, single-nucleotide polymorphisms and Indels. Our results revealed differences in inherent characteristics and genetic differences when comparing QCF with AQF.
Assuntos
Bovinos/genética , Regulação da Expressão Gênica/genética , Transcriptoma , Processamento Alternativo , Animais , Bovinos/crescimento & desenvolvimento , Quimera , Feminino , Hibridização Genética , Mutação INDEL , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de RNA/veterinária , Gordura SubcutâneaRESUMO
A 30-day experiment was performed to determine the effect of pigeon pea leaves (PPL) on growth performance, carcass trait, meat quality, nutrient digestibility, antioxidant capacity and biochemical parameters of growing rabbits. In a completely randomized design, PPL replaced alfalfa meal at the level of 0%, 10%, 20% and 30%, which were named PPL0 (control), PPL10, PPL20 and PML30 respectively. Two hundred New Zealand white rabbits at 6 weeks with similar weight (870.23 ± 15.98 g) were allocated to four dietary groups with five replicates containing 10 rabbits/per replicate (male). The results showed that: (a) PPL powder contained 24.26% crude protein, 4.34% crude fat, 17.86% crude fibre, 7.05% ash, 1.35% calcium, 0.28% phosphorus, 1.09% lysine and 0.20% methionine, and the chemical compositions are on DM basis; (b) the ratio of feed to gain of rabbits fed diet PPL10 was significantly better (p < 0.05) than those fed other three diets; (c) the content of longissimus dorsi (LD) moisture in the rabbits fed diets without PPL (control group) was 12% lower than that in the PPL30 diets (60.1 vs. 72.1; p < 0.05). In PPL10, PPL20 and PPL30 diets, the leg muscle (LM) b*(yellowness) value was 33%, 30% and 22.6% higher than the control group respectively. The rabbits fed diets PPL0 had lower (p < 0.05) LM crude protein and ash and higher (p < 0.05) crude fat of LD and LM as compared with those fed other diets; (d) crude protein and energy digestibility of PPL0 and PPL10 diets were significantly higher (p < 0.05) than PPL30 diets; and (e) serum glutathione peroxidase (GSH-Px) activity of the rabbits fed PPL10 and PPL30 diets was significantly higher (p < 0.05) than that fed PPL20 diets. Liver total antioxidant capacity (T-AOC) activity of the PPL30 groups was 1.3% higher (p < 0.05) than the PPL10 group. Additionally, the control group (PPL0) had the highest (p < 0.05) blood urea nitrogen (BUN), total cholesterol (TCHO) and low-density lipoprotein cholesterol (LDLC) content compared with the groups supplemented with PPL. The PPL30 group had the highest (p < 0.05) triiodothyronine (T3 ) and tetraiodothyroxine (T4 ) value among the dietary groups.
Assuntos
Ração Animal/análise , Cajanus , Medicago sativa , Folhas de Planta , Coelhos/fisiologia , Fenômenos Fisiológicos da Nutrição Animal , Animais , Antioxidantes/metabolismo , Composição Corporal , Dieta/veterinária , DigestãoRESUMO
BACKGROUND: Striped bass (Morone saxatilis) spermatozoa are used to fertilize in vitro the eggs of white bass (M. chrysops) to produce the preferred hybrid for the striped bass aquaculture industry. Currently, only one source of domestic striped bass juveniles is available to growers that is not obtained from wild-caught parents and is thus devoid of any genetic improvement in phenotypic traits of importance to aquaculture. Sperm epigenetic modification has been predicted to be associated with fertility, which could switch genes on and off without changing the DNA sequence itself. DNA methylation is one of the most common epigenetic modification types and changes in sperm epigenetics can be correlated to sub-fertility or infertility in male striped bass. The objective of this study was to find the differentially methylated regions (DMRs) between high-fertility and sub-fertility male striped bass, which could potentially regulate the fertility performance. RESULTS: In our present study, we performed DNA methylation analysis of high-fertility and sub-fertility striped bass spermatozoa through MBD-Seq methods. A total of 171 DMRs were discovered in striped bass sperm correlated to fertility. Based on the annotation of these DMRs, we conducted a functional classification analysis and two important groups of genes including the WDR3/UTP12 and GPCR families, were discovered to be related to fertility performance of striped bass. Proteins from the WDR3/UTP12 family are involved in forming the sperm flagella apparatus in vertebrates and GPCRs are involved in hormonal signaling and regulation of tissue development, proliferation and differentiation. CONCLUSIONS: Our results contribute insights into understanding the mechanism of fertility in striped bass, which will provide powerful tools to maximize reproductive efficiencies and to identify those males with superior gametes for this important aquaculture species.
Assuntos
Bass/genética , Metilação de DNA , Fertilidade/genética , Espermatozoides/fisiologia , Animais , Bass/fisiologia , Ontologia Genética , Masculino , Análise de Sequência de DNARESUMO
Marek's Disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. Chicken Lines 63 and 72, as well as their recombinant congenic strains (RCS) with varied susceptibility to MD, are ideal models to study the complex mechanisms of genetic resistance to MD. In this study, we investigated copy number variation (CNV) in these inbred chicken lines using the Affymetrix Axiom HD 600 K SNP genotyping array. We detected 393 CNV segments across all ten chicken lines, of which 12 CNVs were specifically identified in Line 72. We then assessed genetic structure based on CNV and observed markedly different patterns. Finally, we validated two deletion events in Line 72 and correlated them with genes expression using qPCR and RNA-seq, respectively. Our combined results indicated that these two CNV deletions were likely to contribute to MD susceptibility.
Assuntos
Galinhas/genética , Variações do Número de Cópias de DNA , Doença de Marek/genética , Animais , Deleção de GenesRESUMO
The BMP Binding Endothelial Regulator (BMPER) is an inhibitor of bone morphogenetic proteins (BMPs), which play fundamental roles in adipocyte differentiation, fat development and energy balance. The objectives of this study were to detect polymorphisms of BMPER gene in four indigenous Chinese cattle populations and to investigate their effects on body size traits. Initially, three SNPs, namely G100597A (SNP1), C105331A (SNP2), and G105521A (SNP3) and eight distinct haplotypes were identified. In a total of 12 SNP-SNP combinations, SNP2-SNP3 had a strong linkage in Qinchuan cattle. These four cattle populations belong to intermediate genetic diversity at three SNP loci except Shuxuan cattle population in SNP3. At SNP1, genotype AA was associated with an increased body size. For SNP2, the heterozygous genotype individuals had a greater rump length than those of two other homozygotic genotypes. At SNP3, individuals with GG genotype had smaller rump length and hip width. A total of seven haplotype combinations were detected in Qinchuan cattle population and association analysis results showed individuals with Haplotype combination 4/2 (AAA/CAA) had greater rump length than those with Hap3/1 and Hap3/3 (P < 0.05). These results strongly suggest that bovine BMPER gene may be used as a genetic marker for cattle breeding.
Assuntos
Proteínas de Transporte/genética , Estudos de Associação Genética/veterinária , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Animais , Tamanho Corporal/genética , Cruzamento , Bovinos , Feminino , Haplótipos , FenótipoRESUMO
Smoothened (Smo)-mediated Hedgehog (Hh) signaling pathway governs the patterning, morphogenesis and growth of many different regions within animal body plans. This study evaluated the effects of genetic variations of the bovine SMO gene on economically important body size traits in Chinese Qinchuan cattle. Altogether, eight single nucleotide polymorphisms (SNPs: 1-8) were identified and genotyped via direct sequencing covering most of the coding region and 3'UTR of the bovine SMO gene. Both the p.698Ser.>Ser. synonymous mutation resulted from SNP1 and the p.700Ser.>Pro. non-synonymous mutation caused by SNP2 mapped to the intracellular C-terminal tail of bovine Smo protein; the other six SNPs were non-coding variants located in the 3'UTR. The linkage disequilibrium was analyzed, and five haplotypes were discovered in 520 Qinchuan cattle. Association analyses showed that SNP2, SNP3/5, SNP4 and SNP6/7 were significantly associated with some body size traits (p < 0.05) except SNP1/8 (p > 0.05). Meanwhile, cattle with wild-type combined haplotype Hap1/Hap1 had significantly (p < 0.05) greater body length than those with Hap2/Hap2. Our results indicate that variations in the SMO gene could affect body size traits of Qinchuan cattle, and the wild-type haplotype Hap1 together with the wild-type alleles of these detected SNPs in the SMO gene could be used to breed cattle with superior body size traits. Therefore, our results could be helpful for marker-assisted selection in beef cattle breeding programs.