Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence sugge...Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.展开更多
Shannan Prefecture of Tibet is the central producing region of Tibetan chicken, and Tibetan chicken feeding has become one of the characteristic industries of animal husbandry in local agricultural and pastoral area, ...Shannan Prefecture of Tibet is the central producing region of Tibetan chicken, and Tibetan chicken feeding has become one of the characteristic industries of animal husbandry in local agricultural and pastoral area, and it is an important source of food and income for the locals. However, because of extensive feed- ing managemem, low level of intensification, blind hybrid of exotic varieties and despising selective breeding, the number of pedigree Tibetan chickens have reduced year by year and the performance of Tibetan chicken herd varied greatly, premium specificity could not be effectively utihzed. By investigating the present situation of Tibetan chicken feeding, analyzing the specificity of Tibetan chicken germplasm resources, the scientific conservation breeding was started to make full use of the advantage of keeping Tibetan chickens on the plateau.展开更多
[ Objective] In order to study incubation conditions of Tibetan chickens in low altitude areas. [ Method] Eggs of Tibetan chicken were transported to low altitude areas in highland areas for artificial hatching. [ Res...[ Objective] In order to study incubation conditions of Tibetan chickens in low altitude areas. [ Method] Eggs of Tibetan chicken were transported to low altitude areas in highland areas for artificial hatching. [ Results] The results showed that the average hatching rate of fertilized eggs was 85.33% ; the average healthy chick rate was 91.77 % ; the average primary body mass was 31.2l g. Hatching rate of eggs in group 2 was the highest, which reached 90.52%, the aver- age egg mass was 43.25 g and the average egg shape index was 1.32. Hatching rate of eggs in group 2 was 13.11% and 2.47% higher than that in group 1 and group 3 respectively, which was 5.19% higher than the average value. Hatching rate and healthy chick rate of eggs in group 2 also showed the same trend. [ Conclusion] High hatching effect could be obtained under the better hatching condition in low altitude areas in highland areas.展开更多
The relevance of genetic mechanism to the phenotype of hypoxic adaptation remains elusive.Tibetan chickens typically used to investigate the mechanism for the adaptation of hypoxia and the recognition of hypoxia-relat...The relevance of genetic mechanism to the phenotype of hypoxic adaptation remains elusive.Tibetan chickens typically used to investigate the mechanism for the adaptation of hypoxia and the recognition of hypoxia-related piRNA remains an open issue.The purpose of this study was to illustrate whether the piRNAs were related to hypoxic adaptation.First of all,the differentially expressed piRNAs(DEpiRNAs)were identified through RNA sequencing between the Tibetan chickens and Daheng broilers.Subsequently,the target genes of DEpiRNAs were predicted and annotated by software.The network was constructed by Cytoscape.In our study,a total of 277 DEpiRNAs(33 down-regulated,244 up-regulated)were identified in the Tibetan chickens compared with the Daheng broilers.All of the 277 DEpiRNAs predicted 36658 targeted genes.Gene Ontology(GO)analysis showed that the target genes were significantly enriched in the biological process correlated with proliferation and apoptosis of cells,including cell cycle,mitochondrial outer membrane permeabilization,and positive regulation of stress-activated mitogen-activated protein kinase cascade.Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis implicated that the DEpiRNAs were mainly involved in immune and metabolism,including natural killer cell-mediated cytotoxicity,toll-like receptor signaling pathway and fatty acid metabolism.Furthermore,a predicted network with four piRNAs acted on 11 pathways via interacting with 22 target genes,in which piR-gga-1368839 regulated metabolic pathways by acting on DHCR24.In conclusion,we determined the DEpiRNAs in the Tibetan chickens and found that these piRNAs were associated with metabolism,which may be favorable for researching the biological adaptation to hypoxic stress.展开更多
Oxygen concentration is essential for appropriate metabolism.Hypoxia can exert a significant impact on physiological alteration of the cell and organism.Tibetan Chicken(Gallus gallus) is a Chinese indigenous breed inh...Oxygen concentration is essential for appropriate metabolism.Hypoxia can exert a significant impact on physiological alteration of the cell and organism.Tibetan Chicken(Gallus gallus) is a Chinese indigenous breed inhabiting in Tibetan areas,which is also a chicken breed living at high altitude for the longest time in the world.It has developed an adaptive mechanism to hypoxia,which is demonstrated by that Tibetan Chicken has much higher hatchability than low-land chicken breeds in high-altitude areas of Tibet.In the present study,Tibetan Chicken fertilized full sib eggs were incubated up to Hamburger-Hamilton stage 43 under 13% and 21% oxygen concentration,respectively.Shouguang Chicken and Dwarf Recessive White Chicken were used as control groups.The hearts in all of the 3 chicken breeds under hypoxic and normoxic conditions were isolated and hybridized to Genechip Chicken Genome Array to study molecular mechanisms underlying the adaptation to high altitude of Tibetan Chicken.As a result,50 transcripts highly expressed in hypoxia are screened out.Among up-regulated genes,some are involved in the gene ontology(GO) such as cell growth,cell difference,muscle contraction and signal transduction.However,the expression levels of 21 transcripts are lower in hypoxia than those in normoxia.Some down-regulated genes take part in cell communication,ion transport,protein amino acid phosphorylation and signal transduction.Interestingly,gene enrichment analyses of these differential gene expressions are mainly associated with immune system response and ion channel activity in response to stimulus.Moreover,the transcriptional expression profiles analyzed by hierarchical clustering and CPP-SOM software in all of the 3 different chicken breeds revealed that Tibetan Chicken is much closely related to Shouguang Chicken rather than Dwarf Recessive White Chicken.In addition,12 transcripts of Tibetan Chicken breed-specific expressed genes were identified,which seem to result in a more effective and efficient induction of energy demand and signal transduction of transcription and suppression of abnormal development in response to hypoxia.These findings will be beneficial in clarifying the adaptive molecular mechanism of Tibetan Chicken as well as providing new insight into cardiovascular disease at high altitude medicine.展开更多
Tibetan chicken lives in high-altitude area and has adapted well to hypoxia genetically. Shouguang chicken and Silky chicken are both lowland chicken breeds. In the present study, the complete mito-chondrial genome se...Tibetan chicken lives in high-altitude area and has adapted well to hypoxia genetically. Shouguang chicken and Silky chicken are both lowland chicken breeds. In the present study, the complete mito-chondrial genome sequences of the three chicken breeds were all sequenced. The results showed that the mitochondrial DNAs (mtDNAs) of Shouguang chicken and Silky chicken consist of 16784 bp and 16785 bp respectively, and Tibetan chicken mitochondrial genome varies from 16784 bp to 16786 bp. After sequence analysis, 120 mutations, including 4 single nucleotide polymorphisms (SNPs) in tRNA genes, 9 SNPs and 1 insertion in rRNA genes, 38 SNPs and 1 deletion in D-LOOP, 66 SNPs in pro-tein-coding genes, were found. This work will provide clues for the future study on the association between mitochondrial genes and the adaptation to hypoxia.Tibetan chicken, lowland chicken, mitochondrial genome, hypoxia.展开更多
基金supported by the National Natural Science Foundation of China(31972532)the China Agricultural Research System(CARS-40-K05)the Innovation Base Cu。
文摘Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.
文摘Shannan Prefecture of Tibet is the central producing region of Tibetan chicken, and Tibetan chicken feeding has become one of the characteristic industries of animal husbandry in local agricultural and pastoral area, and it is an important source of food and income for the locals. However, because of extensive feed- ing managemem, low level of intensification, blind hybrid of exotic varieties and despising selective breeding, the number of pedigree Tibetan chickens have reduced year by year and the performance of Tibetan chicken herd varied greatly, premium specificity could not be effectively utihzed. By investigating the present situation of Tibetan chicken feeding, analyzing the specificity of Tibetan chicken germplasm resources, the scientific conservation breeding was started to make full use of the advantage of keeping Tibetan chickens on the plateau.
基金Supported by Taizhou Science and Technology Support Project of Jiangsu Province(No.TN201326)
文摘[ Objective] In order to study incubation conditions of Tibetan chickens in low altitude areas. [ Method] Eggs of Tibetan chicken were transported to low altitude areas in highland areas for artificial hatching. [ Results] The results showed that the average hatching rate of fertilized eggs was 85.33% ; the average healthy chick rate was 91.77 % ; the average primary body mass was 31.2l g. Hatching rate of eggs in group 2 was the highest, which reached 90.52%, the aver- age egg mass was 43.25 g and the average egg shape index was 1.32. Hatching rate of eggs in group 2 was 13.11% and 2.47% higher than that in group 1 and group 3 respectively, which was 5.19% higher than the average value. Hatching rate and healthy chick rate of eggs in group 2 also showed the same trend. [ Conclusion] High hatching effect could be obtained under the better hatching condition in low altitude areas in highland areas.
基金Supported by Science and Technology Support Planning Project of Sichuan Province(2021YFYZ00312020YFN0146+1 种基金SASA2022CZYX002)National Modern Agricultural Technology System Construction of China(CARS-41-G04)。
文摘The relevance of genetic mechanism to the phenotype of hypoxic adaptation remains elusive.Tibetan chickens typically used to investigate the mechanism for the adaptation of hypoxia and the recognition of hypoxia-related piRNA remains an open issue.The purpose of this study was to illustrate whether the piRNAs were related to hypoxic adaptation.First of all,the differentially expressed piRNAs(DEpiRNAs)were identified through RNA sequencing between the Tibetan chickens and Daheng broilers.Subsequently,the target genes of DEpiRNAs were predicted and annotated by software.The network was constructed by Cytoscape.In our study,a total of 277 DEpiRNAs(33 down-regulated,244 up-regulated)were identified in the Tibetan chickens compared with the Daheng broilers.All of the 277 DEpiRNAs predicted 36658 targeted genes.Gene Ontology(GO)analysis showed that the target genes were significantly enriched in the biological process correlated with proliferation and apoptosis of cells,including cell cycle,mitochondrial outer membrane permeabilization,and positive regulation of stress-activated mitogen-activated protein kinase cascade.Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis implicated that the DEpiRNAs were mainly involved in immune and metabolism,including natural killer cell-mediated cytotoxicity,toll-like receptor signaling pathway and fatty acid metabolism.Furthermore,a predicted network with four piRNAs acted on 11 pathways via interacting with 22 target genes,in which piR-gga-1368839 regulated metabolic pathways by acting on DHCR24.In conclusion,we determined the DEpiRNAs in the Tibetan chickens and found that these piRNAs were associated with metabolism,which may be favorable for researching the biological adaptation to hypoxic stress.
基金Supported by National Key Basic Research and Development Program of China (Grant No.2006CB102101)the Project of National Fundamental Platform for Scientific Work (Grant No.2005DKA21100-02)
文摘Oxygen concentration is essential for appropriate metabolism.Hypoxia can exert a significant impact on physiological alteration of the cell and organism.Tibetan Chicken(Gallus gallus) is a Chinese indigenous breed inhabiting in Tibetan areas,which is also a chicken breed living at high altitude for the longest time in the world.It has developed an adaptive mechanism to hypoxia,which is demonstrated by that Tibetan Chicken has much higher hatchability than low-land chicken breeds in high-altitude areas of Tibet.In the present study,Tibetan Chicken fertilized full sib eggs were incubated up to Hamburger-Hamilton stage 43 under 13% and 21% oxygen concentration,respectively.Shouguang Chicken and Dwarf Recessive White Chicken were used as control groups.The hearts in all of the 3 chicken breeds under hypoxic and normoxic conditions were isolated and hybridized to Genechip Chicken Genome Array to study molecular mechanisms underlying the adaptation to high altitude of Tibetan Chicken.As a result,50 transcripts highly expressed in hypoxia are screened out.Among up-regulated genes,some are involved in the gene ontology(GO) such as cell growth,cell difference,muscle contraction and signal transduction.However,the expression levels of 21 transcripts are lower in hypoxia than those in normoxia.Some down-regulated genes take part in cell communication,ion transport,protein amino acid phosphorylation and signal transduction.Interestingly,gene enrichment analyses of these differential gene expressions are mainly associated with immune system response and ion channel activity in response to stimulus.Moreover,the transcriptional expression profiles analyzed by hierarchical clustering and CPP-SOM software in all of the 3 different chicken breeds revealed that Tibetan Chicken is much closely related to Shouguang Chicken rather than Dwarf Recessive White Chicken.In addition,12 transcripts of Tibetan Chicken breed-specific expressed genes were identified,which seem to result in a more effective and efficient induction of energy demand and signal transduction of transcription and suppression of abnormal development in response to hypoxia.These findings will be beneficial in clarifying the adaptive molecular mechanism of Tibetan Chicken as well as providing new insight into cardiovascular disease at high altitude medicine.
基金Supported by the National 973 Projects of China (Grant No. 2006CB102101)Special Fund for the scientific Research of Doctoral Station in the Higher Colleges (Grant No. 20050019021)
文摘Tibetan chicken lives in high-altitude area and has adapted well to hypoxia genetically. Shouguang chicken and Silky chicken are both lowland chicken breeds. In the present study, the complete mito-chondrial genome sequences of the three chicken breeds were all sequenced. The results showed that the mitochondrial DNAs (mtDNAs) of Shouguang chicken and Silky chicken consist of 16784 bp and 16785 bp respectively, and Tibetan chicken mitochondrial genome varies from 16784 bp to 16786 bp. After sequence analysis, 120 mutations, including 4 single nucleotide polymorphisms (SNPs) in tRNA genes, 9 SNPs and 1 insertion in rRNA genes, 38 SNPs and 1 deletion in D-LOOP, 66 SNPs in pro-tein-coding genes, were found. This work will provide clues for the future study on the association between mitochondrial genes and the adaptation to hypoxia.Tibetan chicken, lowland chicken, mitochondrial genome, hypoxia.
